From 83f1a486f82a54e97bf3ba01f011d171c353d13a Mon Sep 17 00:00:00 2001 From: Shyue Ping Ong Date: Tue, 1 Aug 2023 14:09:49 -0700 Subject: [PATCH] Update docs. --- .github/workflows/test.yml | 4 + README.rst => README.md | 13 +- docs/.nojekyll | 0 docs/Gemfile | 35 + docs/Gemfile.lock | 266 + {docs_rst => docs}/Makefile | 0 docs/_config.yml | 21 + docs/_includes/footer_custom.html | 1 + docs/_includes/nav_footer_custom.html | 1 + docs/_modules/index.html | 102 - docs/_modules/monty/bisect.html | 141 - docs/_modules/monty/collections.html | 299 - docs/_modules/monty/design_patterns.html | 204 - docs/_modules/monty/dev.html | 326 - docs/_modules/monty/fnmatch.html | 140 - docs/_modules/monty/fractions.html | 145 - docs/_modules/monty/functools.html | 501 - docs/_modules/monty/inspect.html | 181 - docs/_modules/monty/io.html | 344 - docs/_modules/monty/itertools.html | 174 - docs/_modules/monty/json.html | 698 - docs/_modules/monty/logging.html | 161 - docs/_modules/monty/math.html | 114 - docs/_modules/monty/msgpack.html | 102 - docs/_modules/monty/multiprocessing.html | 117 - docs/_modules/monty/operator.html | 112 - docs/_modules/monty/os.html | 134 - docs/_modules/monty/os/path.html | 206 - docs/_modules/monty/pprint.html | 206 - docs/_modules/monty/re.html | 128 - docs/_modules/monty/serialization.html | 204 - docs/_modules/monty/shutil.html | 227 - docs/_modules/monty/string.html | 220 - docs/_modules/monty/subprocess.html | 181 - docs/_modules/monty/tempfile.html | 205 - docs/_modules/monty/termcolor.html | 285 - .../_sphinx_javascript_frameworks_compat.js | 134 - docs/_static/ajax-loader.gif | Bin 673 -> 0 bytes docs/_static/basic.css | 903 -- docs/_static/comment-bright.png | Bin 756 -> 0 bytes docs/_static/comment-close.png | Bin 829 -> 0 bytes docs/_static/comment.png | Bin 641 -> 0 bytes docs/_static/doctools.js | 156 - docs/_static/documentation_options.js | 14 - docs/_static/down-pressed.png | Bin 222 -> 0 bytes docs/_static/down.png | Bin 202 -> 0 bytes docs/_static/file.png | Bin 286 -> 0 bytes docs/_static/flasky.css | 445 - docs/_static/jquery-3.1.0.js | 10074 -------------- docs/_static/jquery-3.2.1.js | 10253 --------------- docs/_static/jquery-3.4.1.js | 10598 --------------- docs/_static/jquery-3.5.1.js | 10872 --------------- docs/_static/jquery-3.6.0.js | 10881 ---------------- docs/_static/jquery.js | 2 - docs/_static/language_data.js | 199 - docs/_static/minus.png | Bin 90 -> 0 bytes docs/_static/plus.png | Bin 90 -> 0 bytes docs/_static/pygments.css | 74 - docs/_static/searchtools.js | 566 - docs/_static/small_flask.css | 90 - docs/_static/sphinx_highlight.js | 144 - docs/_static/underscore-1.12.0.js | 2027 --- docs/_static/underscore-1.13.1.js | 2042 --- docs/_static/underscore-1.3.1.js | 999 -- docs/_static/underscore.js | 6 - docs/_static/up-pressed.png | Bin 214 -> 0 bytes docs/_static/up.png | Bin 203 -> 0 bytes docs/_static/websupport.js | 808 -- docs/_themes/README.html | 108 - docs/changelog.html | 714 - docs_rst/changelog.rst => docs/changelog.md | 265 +- docs/conf.py | 60 + docs/genindex.html | 760 -- docs/index.html | 489 - docs/index.md | 35 + {docs_rst => docs}/make.bat | 0 docs/modules.html | 327 - docs/monty.bisect.html | 149 - docs/monty.bisect.md | 34 + docs/monty.collections.html | 313 - docs/monty.collections.md | 197 + docs/monty.design_patterns.html | 169 - docs/monty.design_patterns.md | 59 + docs/monty.dev.html | 201 - docs/monty.dev.md | 102 + docs/monty.fnmatch.html | 153 - docs/monty.fnmatch.md | 48 + docs/monty.fractions.html | 158 - docs/monty.fractions.md | 61 + docs/monty.functools.html | 270 - docs/monty.functools.md | 159 + docs/monty.html | 356 - docs/monty.inspect.html | 157 - docs/monty.inspect.md | 49 + docs/monty.io.html | 248 - docs/monty.io.md | 147 + docs/monty.itertools.html | 180 - docs/monty.itertools.md | 77 + docs/monty.json.html | 375 - docs/monty.json.md | 270 + docs/monty.logging.html | 138 - docs/monty.logging.md | 33 + docs/monty.math.html | 145 - docs/monty.math.md | 48 + docs/monty.md | 441 + docs/monty.msgpack.html | 127 - docs/monty.msgpack.md | 21 + docs/monty.multiprocessing.html | 131 - docs/monty.multiprocessing.md | 38 + docs/monty.operator.html | 121 - docs/monty.operator.md | 18 + docs/monty.os.html | 165 - docs/monty.os.md | 51 + docs/monty.os.path.html | 172 - docs/monty.os.path.md | 82 + docs/monty.pprint.html | 207 - docs/monty.pprint.md | 110 + docs/monty.re.html | 146 - docs/monty.re.md | 55 + docs/monty.serialization.html | 166 - docs/monty.serialization.md | 77 + docs/monty.shutil.html | 229 - docs/monty.shutil.md | 121 + docs/monty.string.html | 248 - docs/monty.string.md | 154 + docs/monty.subprocess.html | 171 - docs/monty.subprocess.md | 58 + docs/monty.tempfile.html | 181 - docs/monty.tempfile.md | 97 + docs/monty.termcolor.html | 150 - docs/monty.termcolor.md | 58 + docs/objects.inv | Bin 1915 -> 0 bytes docs/py-modindex.html | 226 - docs/search.html | 100 - docs/searchindex.js | 1 - docs_rst/_templates/layout.html | 10 - docs_rst/_themes/LICENSE | 45 - docs_rst/_themes/README.rst | 25 - docs_rst/_themes/flask_theme_support.py | 87 - docs_rst/_themes/kr/layout.html | 16 - docs_rst/_themes/kr/relations.html | 19 - docs_rst/_themes/kr/static/flasky.css_t | 445 - docs_rst/_themes/kr/static/small_flask.css | 90 - docs_rst/_themes/kr/theme.conf | 7 - docs_rst/_themes/kr_small/layout.html | 22 - docs_rst/_themes/kr_small/static/flasky.css_t | 287 - docs_rst/_themes/kr_small/theme.conf | 10 - docs_rst/conf.py | 296 - docs_rst/index.rst | 144 - docs_rst/modules.rst | 7 - docs_rst/monty.bisect.rst | 7 - docs_rst/monty.collections.rst | 7 - docs_rst/monty.design_patterns.rst | 7 - docs_rst/monty.dev.rst | 7 - docs_rst/monty.fnmatch.rst | 7 - docs_rst/monty.fractions.rst | 7 - docs_rst/monty.functools.rst | 7 - docs_rst/monty.inspect.rst | 7 - docs_rst/monty.io.rst | 7 - docs_rst/monty.itertools.rst | 7 - docs_rst/monty.json.rst | 7 - docs_rst/monty.logging.rst | 7 - docs_rst/monty.math.rst | 7 - docs_rst/monty.msgpack.rst | 7 - docs_rst/monty.multiprocessing.rst | 7 - docs_rst/monty.operator.rst | 7 - docs_rst/monty.os.path.rst | 7 - docs_rst/monty.os.rst | 18 - docs_rst/monty.pprint.rst | 7 - docs_rst/monty.re.rst | 7 - docs_rst/monty.rst | 49 - docs_rst/monty.serialization.rst | 7 - docs_rst/monty.shutil.rst | 7 - docs_rst/monty.string.rst | 7 - docs_rst/monty.subprocess.rst | 7 - docs_rst/monty.tempfile.rst | 7 - docs_rst/monty.termcolor.rst | 7 - tasks.py | 72 +- 178 files changed, 3220 insertions(+), 77065 deletions(-) rename README.rst => README.md (55%) delete mode 100644 docs/.nojekyll create mode 100644 docs/Gemfile create mode 100644 docs/Gemfile.lock rename {docs_rst => docs}/Makefile (100%) create mode 100644 docs/_config.yml create mode 100644 docs/_includes/footer_custom.html create mode 100644 docs/_includes/nav_footer_custom.html delete mode 100644 docs/_modules/index.html delete mode 100644 docs/_modules/monty/bisect.html delete 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100644 docs_rst/monty.msgpack.rst delete mode 100644 docs_rst/monty.multiprocessing.rst delete mode 100644 docs_rst/monty.operator.rst delete mode 100644 docs_rst/monty.os.path.rst delete mode 100644 docs_rst/monty.os.rst delete mode 100644 docs_rst/monty.pprint.rst delete mode 100644 docs_rst/monty.re.rst delete mode 100644 docs_rst/monty.rst delete mode 100644 docs_rst/monty.serialization.rst delete mode 100644 docs_rst/monty.shutil.rst delete mode 100644 docs_rst/monty.string.rst delete mode 100644 docs_rst/monty.subprocess.rst delete mode 100644 docs_rst/monty.tempfile.rst delete mode 100644 docs_rst/monty.termcolor.rst diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 52460d47c..95aff67b3 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -27,3 +27,7 @@ jobs: - name: pytest run: | pytest --cov=monty --cov-report html:coverage_reports monty tests + - name: Upload coverage reports to Codecov + uses: codecov/codecov-action@v3 + env: + CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} \ No newline at end of file diff --git a/README.rst b/README.md similarity index 55% rename from README.rst rename to README.md index 988a1f8b0..52cf835f2 100644 --- a/README.rst +++ b/README.md @@ -1,9 +1,10 @@ -Monty: Python Made Even Easier -============================== +[![GitHub license](https://img.shields.io/github/license/materialsvirtuallab/monty)](https://github.com/materialsvirtuallab/monty/blob/main/LICENSE) +[![Linting](https://github.com/materialsvirtuallab/monty/workflows/Linting/badge.svg)](https://github.com/materialsvirtuallab/monty/workflows/Linting/badge.svg) +[![Testing](https://github.com/materialsvirtuallab/monty/workflows/Testing/badge.svg)](https://github.com/materialsvirtuallab/monty/workflows/Testing/badge.svg) +[![Downloads](https://pepy.tech/badge/monty)](https://pepy.tech/project/monty) +[![codecov](https://codecov.io/gh/materialsvirtuallab/monty/branch/main/graph/badge.svg?token=3V3O79GODQ)](https://codecov.io/gh/materialsvirtuallab/monty) -.. image:: https://travis-ci.org/materialsvirtuallab/monty.png?branch=master -.. image:: https://coveralls.io/repos/github/materialsvirtuallab/monty/badge.svg?branch=master -.. image:: https://anaconda.org/conda-forge/monty/badges/downloads.svg +# Monty: Python Made Even Easier Monty is the missing complement to Python. Monty implements supplementary useful functions for Python that are not part of the standard library. @@ -25,4 +26,4 @@ be a resource to collect the best solutions. Monty supports Python 3.x. -Please visit the `official docs `_ for more information. +Please visit the [official docs](https://materialsvirtuallab.github.io/monty) for more information. diff --git a/docs/.nojekyll b/docs/.nojekyll deleted file mode 100644 index e69de29bb..000000000 diff --git a/docs/Gemfile b/docs/Gemfile new file mode 100644 index 000000000..68a681b41 --- /dev/null +++ b/docs/Gemfile @@ -0,0 +1,35 @@ +source "https://rubygems.org" +# Hello! This is where you manage which Jekyll version is used to run. +# When you want to use a different version, change it below, save the +# file and run `bundle install`. Run Jekyll with `bundle exec`, like so: +# +# bundle exec jekyll serve +# +# This will help ensure the proper Jekyll version is running. +# Happy Jekylling! +# gem "jekyll", "~> 4.3.2" +# This is the default theme for new Jekyll sites. You may change this to anything you like. +gem "minima", "~> 2.5" +# If you want to use GitHub Pages, remove the "gem "jekyll"" above and +# uncomment the line below. To upgrade, run `bundle update github-pages`. +gem "github-pages", group: :jekyll_plugins +# If you have any plugins, put them here! +group :jekyll_plugins do + gem "jekyll-feed", "~> 0.12" +end + +# Windows and JRuby does not include zoneinfo files, so bundle the tzinfo-data gem +# and associated library. +platforms :mingw, :x64_mingw, :mswin, :jruby do + gem "tzinfo", ">= 1", "< 3" + gem "tzinfo-data" +end + +# Performance-booster for watching directories on Windows +gem "wdm", "~> 0.1.1", :platforms => [:mingw, :x64_mingw, :mswin] + +# Lock `http_parser.rb` gem to `v0.6.x` on JRuby builds since newer versions of the gem +# do not have a Java counterpart. +gem "http_parser.rb", "~> 0.6.0", :platforms => [:jruby] + +gem "webrick", "~> 1.8" diff --git a/docs/Gemfile.lock b/docs/Gemfile.lock new file mode 100644 index 000000000..2763cfeb1 --- /dev/null +++ b/docs/Gemfile.lock @@ -0,0 +1,266 @@ +GEM + remote: https://rubygems.org/ + specs: + activesupport (7.0.6) + concurrent-ruby (~> 1.0, >= 1.0.2) + i18n (>= 1.6, < 2) + minitest (>= 5.1) + tzinfo (~> 2.0) + addressable (2.8.4) + public_suffix (>= 2.0.2, < 6.0) + coffee-script (2.4.1) + coffee-script-source + execjs + coffee-script-source (1.11.1) + colorator (1.1.0) + commonmarker (0.23.10) + concurrent-ruby (1.2.2) + dnsruby (1.70.0) + simpleidn (~> 0.2.1) + em-websocket (0.5.3) + eventmachine (>= 0.12.9) + http_parser.rb (~> 0) + ethon (0.16.0) + ffi (>= 1.15.0) + eventmachine (1.2.7) + execjs (2.8.1) + faraday (2.7.10) + faraday-net_http (>= 2.0, < 3.1) + ruby2_keywords (>= 0.0.4) + faraday-net_http (3.0.2) + ffi (1.15.5) + forwardable-extended (2.6.0) + gemoji (3.0.1) + github-pages (228) + github-pages-health-check (= 1.17.9) + jekyll (= 3.9.3) + jekyll-avatar (= 0.7.0) + jekyll-coffeescript (= 1.1.1) + jekyll-commonmark-ghpages (= 0.4.0) + jekyll-default-layout (= 0.1.4) + jekyll-feed (= 0.15.1) + jekyll-gist (= 1.5.0) + jekyll-github-metadata (= 2.13.0) + jekyll-include-cache (= 0.2.1) + jekyll-mentions (= 1.6.0) + jekyll-optional-front-matter (= 0.3.2) + jekyll-paginate (= 1.1.0) + jekyll-readme-index (= 0.3.0) + jekyll-redirect-from (= 0.16.0) + jekyll-relative-links (= 0.6.1) + jekyll-remote-theme (= 0.4.3) + jekyll-sass-converter (= 1.5.2) + jekyll-seo-tag (= 2.8.0) + jekyll-sitemap (= 1.4.0) + jekyll-swiss (= 1.0.0) + jekyll-theme-architect (= 0.2.0) + jekyll-theme-cayman (= 0.2.0) + jekyll-theme-dinky (= 0.2.0) + jekyll-theme-hacker (= 0.2.0) + jekyll-theme-leap-day (= 0.2.0) + jekyll-theme-merlot (= 0.2.0) + jekyll-theme-midnight (= 0.2.0) + jekyll-theme-minimal (= 0.2.0) + jekyll-theme-modernist (= 0.2.0) + jekyll-theme-primer (= 0.6.0) + jekyll-theme-slate (= 0.2.0) + jekyll-theme-tactile (= 0.2.0) + jekyll-theme-time-machine (= 0.2.0) + jekyll-titles-from-headings (= 0.5.3) + jemoji (= 0.12.0) + kramdown (= 2.3.2) + kramdown-parser-gfm (= 1.1.0) + liquid (= 4.0.4) + mercenary (~> 0.3) + minima (= 2.5.1) + nokogiri (>= 1.13.6, < 2.0) + rouge (= 3.26.0) + terminal-table (~> 1.4) + github-pages-health-check (1.17.9) + addressable (~> 2.3) + dnsruby (~> 1.60) + octokit (~> 4.0) + public_suffix (>= 3.0, < 5.0) + typhoeus (~> 1.3) + html-pipeline (2.14.3) + activesupport (>= 2) + nokogiri (>= 1.4) + http_parser.rb (0.8.0) + i18n (1.14.1) + concurrent-ruby (~> 1.0) + jekyll (3.9.3) + addressable (~> 2.4) + colorator (~> 1.0) + em-websocket (~> 0.5) + i18n (>= 0.7, < 2) + jekyll-sass-converter (~> 1.0) + jekyll-watch (~> 2.0) + kramdown (>= 1.17, < 3) + liquid (~> 4.0) + mercenary (~> 0.3.3) + pathutil (~> 0.9) + rouge (>= 1.7, < 4) + safe_yaml (~> 1.0) + jekyll-avatar (0.7.0) + jekyll (>= 3.0, < 5.0) + jekyll-coffeescript (1.1.1) + coffee-script (~> 2.2) + coffee-script-source (~> 1.11.1) + jekyll-commonmark (1.4.0) + commonmarker (~> 0.22) + jekyll-commonmark-ghpages (0.4.0) + commonmarker (~> 0.23.7) + jekyll (~> 3.9.0) + jekyll-commonmark (~> 1.4.0) + rouge (>= 2.0, < 5.0) + jekyll-default-layout (0.1.4) + jekyll (~> 3.0) + jekyll-feed (0.15.1) + jekyll (>= 3.7, 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(>= 3.3, < 5.0) + jekyll-watch (2.2.1) + listen (~> 3.0) + jemoji (0.12.0) + gemoji (~> 3.0) + html-pipeline (~> 2.2) + jekyll (>= 3.0, < 5.0) + kramdown (2.3.2) + rexml + kramdown-parser-gfm (1.1.0) + kramdown (~> 2.0) + liquid (4.0.4) + listen (3.8.0) + rb-fsevent (~> 0.10, >= 0.10.3) + rb-inotify (~> 0.9, >= 0.9.10) + mercenary (0.3.6) + minima (2.5.1) + jekyll (>= 3.5, < 5.0) + jekyll-feed (~> 0.9) + jekyll-seo-tag (~> 2.1) + minitest (5.16.3) + nokogiri (1.15.3-arm64-darwin) + racc (~> 1.4) + octokit (4.25.1) + faraday (>= 1, < 3) + sawyer (~> 0.9) + pathutil (0.16.2) + forwardable-extended (~> 2.6) + public_suffix (4.0.7) + racc (1.6.2) + rb-fsevent (0.11.2) + rb-inotify (0.10.1) + ffi (~> 1.0) + rexml (3.2.5) + rouge (3.26.0) + ruby2_keywords (0.0.5) + rubyzip (2.3.2) + safe_yaml (1.0.5) + sass (3.7.4) + sass-listen (~> 4.0.0) + sass-listen (4.0.0) + rb-fsevent (~> 0.9, >= 0.9.4) + rb-inotify (~> 0.9, >= 0.9.7) + sawyer (0.9.2) + addressable (>= 2.3.5) + faraday (>= 0.17.3, < 3) + simpleidn (0.2.1) + unf (~> 0.1.4) + terminal-table (1.8.0) + unicode-display_width (~> 1.1, >= 1.1.1) + typhoeus (1.4.0) + ethon (>= 0.9.0) + tzinfo (2.0.6) + concurrent-ruby (~> 1.0) + unf (0.1.4) + unf_ext + unf_ext (0.0.8.2) + unicode-display_width (1.8.0) + webrick (1.8.1) + +PLATFORMS + arm64-darwin-22 + +DEPENDENCIES + github-pages + http_parser.rb (~> 0.6.0) + jekyll-feed (~> 0.12) + minima (~> 2.5) + tzinfo (>= 1, < 3) + tzinfo-data + wdm (~> 0.1.1) + webrick (~> 1.8) + +BUNDLED WITH + 2.4.17 diff --git a/docs_rst/Makefile b/docs/Makefile similarity index 100% rename from docs_rst/Makefile rename to docs/Makefile diff --git a/docs/_config.yml b/docs/_config.yml new file mode 100644 index 000000000..581d848ab --- /dev/null +++ b/docs/_config.yml @@ -0,0 +1,21 @@ +title: monty +email: ongsp@ucsd.edu +description: >- # this means to ignore newlines until "baseurl:" + A graph deep learning library for materials science. +# twitter_username: jekyllrb +github_username: materialsvirtuallab + +# Build settings +remote_theme: just-the-docs/just-the-docs +plugins: + - jekyll-feed + +# favicon_ico: "/assets/favicon.ico" + +nav_external_links: + - title: "monty on GitHub" + url: "https://github.com/materialsvirtuallab/monty" + +aux_links: + "Materials Virtual Lab": + - "https://materialsvirtuallab.org" \ No newline at end of file diff --git a/docs/_includes/footer_custom.html b/docs/_includes/footer_custom.html new file mode 100644 index 000000000..773d554f1 --- /dev/null +++ b/docs/_includes/footer_custom.html @@ -0,0 +1 @@ +© Copyright 2022, Materials Virtual Lab \ No newline at end of file diff --git a/docs/_includes/nav_footer_custom.html b/docs/_includes/nav_footer_custom.html new file mode 100644 index 000000000..177a82bc4 --- /dev/null +++ b/docs/_includes/nav_footer_custom.html @@ -0,0 +1 @@ +© Copyright 2022, Materials Virtual Lab \ No newline at end of file diff --git a/docs/_modules/index.html b/docs/_modules/index.html deleted file mode 100644 index e8a69b7b1..000000000 --- a/docs/_modules/index.html +++ /dev/null @@ -1,102 +0,0 @@ - - - - - - - Overview: module code — monty 2023.5.8 documentation - - - - - - - - - - - - - - - - - -
-
-
-
- -

All modules for which code is available

- - -
-
-
-
- -
-
- -
- © Copyright 2014, Shyue Ping Ong. -
- - - - \ No newline at end of file diff --git a/docs/_modules/monty/bisect.html b/docs/_modules/monty/bisect.html deleted file mode 100644 index 41e2e3ab9..000000000 --- a/docs/_modules/monty/bisect.html +++ /dev/null @@ -1,141 +0,0 @@ - - - - - - - monty.bisect — monty 2023.5.8 documentation - - - - - - - - - - - - - - - - - -
-
-
-
- -

Source code for monty.bisect

-"""
-Additional bisect functions. Taken from
-https://docs.python.org/2/library/bisect.html
-The above bisect() functions are useful for finding insertion points but can be
-tricky or awkward to use for common searching tasks.
-The functions show how to transform them into the standard lookups for sorted
-lists.
-"""
-
-import bisect as bs
-
-__author__ = "Matteo Giantomassi"
-__copyright__ = "Copyright 2013, The Materials Virtual Lab"
-__version__ = "0.1"
-__maintainer__ = "Matteo Giantomass"
-__email__ = "gmatteo@gmail.com"
-__date__ = "11/09/14"
-
-
-
[docs]def index(a, x, atol=None):
-    """Locate the leftmost value exactly equal to x."""
-    i = bs.bisect_left(a, x)
-    if i != len(a):
-        if atol is None:
-            if a[i] == x:
-                return i
-        else:
-            if abs(a[i] - x) < atol:
-                return i
-    raise ValueError

-
-
-
[docs]def find_lt(a, x):
-    """Find rightmost value less than x."""
-    i = bs.bisect_left(a, x)
-    if i:
-        return i - 1
-    raise ValueError

-
-
-
[docs]def find_le(a, x):
-    """Find rightmost value less than or equal to x."""
-    i = bs.bisect_right(a, x)
-    if i:
-        return i - 1
-    raise ValueError

-
-
-
[docs]def find_gt(a, x):
-    """Find leftmost value greater than x."""
-    i = bs.bisect_right(a, x)
-    if i != len(a):
-        return i
-    raise ValueError

-
-
-
[docs]def find_ge(a, x):
-    """Find leftmost item greater than or equal to x."""
-    i = bs.bisect_left(a, x)
-    if i != len(a):
-        return i
-    raise ValueError

-
- -
-
-
-
- -
-
- -
- © Copyright 2014, Shyue Ping Ong. -
- - - - \ No newline at end of file diff --git a/docs/_modules/monty/collections.html b/docs/_modules/monty/collections.html deleted file mode 100644 index daae99fc6..000000000 --- a/docs/_modules/monty/collections.html +++ /dev/null @@ -1,299 +0,0 @@ - - - - - - - monty.collections — monty 2023.5.8 documentation - - - - - - - - - - - - - - - - - -
-
-
-
- -

Source code for monty.collections

-"""
-Useful collection classes, e.g., tree, frozendict, etc.
-"""
-
-import collections
-
-
-
[docs]def tree():
-    """
-    A tree object, which is effectively a recursive defaultdict that
-    adds tree as members.
-
-    Usage:
-        x = tree()
-        x['a']['b']['c'] = 1
-
-    Returns:
-        A tree.
-    """
-    return collections.defaultdict(tree)

-
-
-
[docs]class frozendict(dict):
-    """
-    A dictionary that does not permit changes. The naming
-    violates PEP8 to be consistent with standard Python's "frozenset" naming.
-    """
-
-    def __init__(self, *args, **kwargs):
-        """
-        :param args: Passthrough arguments for standard dict.
-        :param kwargs: Passthrough keyword arguments for standard dict.
-        """
-        dict.__init__(self, *args, **kwargs)
-
-    def __setitem__(self, key, val):
-        raise KeyError(f"Cannot overwrite existing key: {str(key)}")
-
-
[docs]    def update(self, *args, **kwargs):
-        """
-        :param args: Passthrough arguments for standard dict.
-        :param kwargs: Passthrough keyword arguments for standard dict.
-        """
-        raise KeyError(f"Cannot update a {self.__class__.__name__}")

-
-
-
[docs]class Namespace(dict):
-    """A dictionary that does not permit to redefine its keys."""
-
-    def __init__(self, *args, **kwargs):
-        """
-        :param args: Passthrough arguments for standard dict.
-        :param kwargs: Passthrough keyword arguments for standard dict.
-        """
-        self.update(*args, **kwargs)
-
-    def __setitem__(self, key, val):
-        if key in self:
-            raise KeyError(f"Cannot overwrite existent key: {str(key)}")
-
-        dict.__setitem__(self, key, val)
-
-
[docs]    def update(self, *args, **kwargs):
-        """
-        :param args: Passthrough arguments for standard dict.
-        :param kwargs: Passthrough keyword arguments for standard dict.
-        """
-        for k, v in dict(*args, **kwargs).items():
-            self[k] = v

-
-
-
[docs]class AttrDict(dict):
-    """
-    Allows to access dict keys as obj.foo in addition
-    to the traditional way obj['foo']"
-
-    Example:
-        >>> d = AttrDict(foo=1, bar=2)
-        >>> assert d["foo"] == d.foo
-        >>> d.bar = "hello"
-        >>> assert d.bar == "hello"
-    """
-
-    def __init__(self, *args, **kwargs):
-        """
-        :param args: Passthrough arguments for standard dict.
-        :param kwargs: Passthrough keyword arguments for standard dict.
-        """
-        super().__init__(*args, **kwargs)
-        self.__dict__ = self
-
-
[docs]    def copy(self):
-        """
-        :return: Copy of AttrDict
-        """
-        newd = super().copy()
-        return self.__class__(**newd)

-
-
-
[docs]class FrozenAttrDict(frozendict):
-    """
-    A dictionary that:
-        * does not permit changes.
-        * Allows to access dict keys as obj.foo in addition
-          to the traditional way obj['foo']
-    """
-
-    def __init__(self, *args, **kwargs):
-        """
-        :param args: Passthrough arguments for standard dict.
-        :param kwargs: Passthrough keyword arguments for standard dict.
-        """
-        super().__init__(*args, **kwargs)
-
-    def __getattribute__(self, name):
-        try:
-            return super().__getattribute__(name)
-        except AttributeError:
-            try:
-                return self[name]
-            except KeyError as exc:
-                raise AttributeError(str(exc))
-
-    def __setattr__(self, name, value):
-        raise KeyError(f"You cannot modify attribute {name} of {self.__class__.__name__}")

-
-
-
[docs]class MongoDict:
-    """
-    This dict-like object allows one to access the entries in a nested dict as
-    attributes.
-    Entries (attributes) cannot be modified. It also provides Ipython tab
-    completion hence this object is particularly useful if you need to analyze
-    a nested dict interactively (e.g. documents extracted from a MongoDB
-    database).
-
-    >>> m = MongoDict({'a': {'b': 1}, 'x': 2})
-    >>> assert m.a.b == 1 and m.x == 2
-    >>> assert "a" in m and "b" in m.a
-    >>> m["a"]
-    {'b': 1}
-
-    .. note::
-
-        Cannot inherit from ABC collections.Mapping because otherwise
-        dict.keys and dict.items will pollute the namespace.
-        e.g MongoDict({"keys": 1}).keys would be the ABC dict method.
-    """
-
-    def __init__(self, *args, **kwargs):
-        """
-        :param args: Passthrough arguments for standard dict.
-        :param kwargs: Passthrough keyword arguments for standard dict.
-        """
-        self.__dict__["_mongo_dict_"] = dict(*args, **kwargs)
-
-    def __repr__(self):
-        return str(self)
-
-    def __str__(self):
-        return str(self._mongo_dict_)
-
-    def __setattr__(self, name, value):
-        raise NotImplementedError(f"You cannot modify attribute {name} of {self.__class__.__name__}")
-
-    def __getattribute__(self, name):
-        try:
-            return super().__getattribute__(name)
-        except AttributeError:
-            # raise
-            try:
-                a = self._mongo_dict_[name]
-                if isinstance(a, collections.abc.Mapping):
-                    a = self.__class__(a)
-                return a
-            except Exception as exc:
-                raise AttributeError(str(exc))
-
-    def __getitem__(self, slice_):
-        return self._mongo_dict_.__getitem__(slice_)
-
-    def __iter__(self):
-        return iter(self._mongo_dict_)
-
-    def __len__(self):
-        return len(self._mongo_dict_)
-
-    def __dir__(self):
-        """
-        For Ipython tab completion.
-        See http://ipython.org/ipython-doc/dev/config/integrating.html
-        """
-        return sorted(list(k for k in self._mongo_dict_ if not callable(k)))

-
-
-
[docs]def dict2namedtuple(*args, **kwargs):
-    """
-    Helper function to create a :class:`namedtuple` from a dictionary.
-
-    Example:
-
-        >>> t = dict2namedtuple(foo=1, bar="hello")
-        >>> assert t.foo == 1 and t.bar == "hello"
-
-        >>> t = dict2namedtuple([("foo", 1), ("bar", "hello")])
-        >>> assert t[0] == t.foo and t[1] == t.bar
-
-    .. warning::
-
-        - The order of the items in the namedtuple is not deterministic if
-          kwargs are used.
-          namedtuples, however, should always be accessed by attribute hence
-          this behaviour should not represent a serious problem.
-
-        - Don't use this function in code in which memory and performance are
-          crucial since a dict is needed to instantiate the tuple!
-    """
-    d = collections.OrderedDict(*args)
-    d.update(**kwargs)
-    return collections.namedtuple(typename="dict2namedtuple", field_names=list(d.keys()))(**d)

-
- -
-
-
-
- -
-
- -
- © Copyright 2014, Shyue Ping Ong. -
- - - - \ No newline at end of file diff --git a/docs/_modules/monty/design_patterns.html b/docs/_modules/monty/design_patterns.html deleted file mode 100644 index 009797f77..000000000 --- a/docs/_modules/monty/design_patterns.html +++ /dev/null @@ -1,204 +0,0 @@ - - - - - - - monty.design_patterns — monty 2023.5.8 documentation - - - - - - - - - - - - - - - - - -
-
-
-
- -

Source code for monty.design_patterns

-"""
-Some common design patterns such as singleton and cached classes.
-"""
-
-from __future__ import annotations
-
-import os
-from functools import wraps
-from typing import Hashable, TypeVar
-
-
-
[docs]def singleton(cls):
-    """
-    This decorator can be used to create a singleton out of a class.
-
-    Usage::
-
-        @singleton
-        class MySingleton():
-
-            def __init__():
-                pass
-    """
-
-    instances = {}
-
-    def getinstance():
-        if cls not in instances:
-            instances[cls] = cls()
-        return instances[cls]
-
-    return getinstance

-
-
-# https://github.com/microsoft/pylance-release/issues/3478
-Klass = TypeVar("Klass")
-
-
-
[docs]def cached_class(klass: type[Klass]) -> type[Klass]:
-    """
-    Decorator to cache class instances by constructor arguments.
-    This results in a class that behaves like a singleton for each
-    set of constructor arguments, ensuring efficiency.
-
-    Note that this should be used for *immutable classes only*.  Having
-    a cached mutable class makes very little sense.  For efficiency,
-    avoid using this decorator for situations where there are many
-    constructor arguments permutations.
-
-    The keywords argument dictionary is converted to a tuple because
-    dicts are mutable; keywords themselves are strings and
-    so are always hashable, but if any arguments (keyword
-    or positional) are non-hashable, that set of arguments
-    is not cached.
-    """
-    cache: dict[tuple[Hashable, ...], type[Klass]] = {}
-
-    @wraps(klass, assigned=("__name__", "__module__"), updated=())
-    class _decorated(klass):  # type: ignore
-        # The wraps decorator can't do this because __doc__
-        # isn't writable once the class is created
-        __doc__ = klass.__doc__
-
-        def __new__(cls, *args, **kwargs):
-            """
-            Pass through...
-            :param args:
-            :param kwargs:
-            :return:
-            """
-            key = (cls,) + args + tuple(kwargs.items())
-            try:
-                inst = cache.get(key, None)
-            except TypeError:
-                # Can't cache this set of arguments
-                inst = key = None
-            if inst is None:
-                # Technically this is cheating, but it works,
-                # and takes care of initializing the instance
-                # (so we can override __init__ below safely);
-                # calling up to klass.__new__ would be the
-                # "official" way to create the instance, but
-                # that raises DeprecationWarning if there are
-                # args or kwargs and klass does not override
-                # __new__ (which most classes don't), because
-                # object.__new__ takes no parameters (and in
-                # Python 3 the warning will become an error)
-                inst = klass(*args, **kwargs)
-                # This makes isinstance and issubclass work
-                # properly
-                inst.__class__ = cls
-                if key is not None:
-                    cache[key] = inst
-            return inst
-
-        def __init__(self, *args, **kwargs):
-            # This will be called every time __new__ is
-            # called, so we skip initializing here and do
-            # it only when the instance is created above
-            pass
-
-    return _decorated

-
-
-
[docs]class NullFile:
-    """A file object that is associated to /dev/null."""
-
-    def __new__(cls):
-        """
-        Pass through
-        """
-        return open(os.devnull, "w")  # pylint: disable=R1732
-
-    def __init__(self):
-        """no-op"""

-
-
-
[docs]class NullStream:
-    """A fake stream with a no-op write."""
-
-
[docs]    def write(self, *args):  # pylint: disable=E0211
-        """
-        Does nothing...
-        :param args:
-        """

-
- -
-
-
-
- -
-
- -
- © Copyright 2014, Shyue Ping Ong. -
- - - - \ No newline at end of file diff --git a/docs/_modules/monty/dev.html b/docs/_modules/monty/dev.html deleted file mode 100644 index f6bc5569c..000000000 --- a/docs/_modules/monty/dev.html +++ /dev/null @@ -1,326 +0,0 @@ - - - - - - - monty.dev — monty 2023.5.8 documentation - - - - - - - - - - - - - - - - - -
-
-
-
- -

Source code for monty.dev

-"""
-This module implements several useful functions and decorators that can be
-particularly useful for developers. E.g., deprecating methods / classes, etc.
-"""
-
-import functools
-import inspect
-import logging
-import multiprocessing
-import os
-import re
-import subprocess
-import sys
-import warnings
-
-logger = logging.getLogger(__name__)
-
-
-
[docs]def deprecated(replacement=None, message=None, category=FutureWarning):
-    """
-    Decorator to mark classes or functions as deprecated,
-    with a possible replacement.
-
-    Args:
-        replacement (callable): A replacement class or method.
-        message (str): A warning message to be displayed.
-        category (Warning): Choose the category of the warning to issue. Defaults
-            to FutureWarning. Another choice can be DeprecationWarning. NOte that
-            FutureWarning is meant for end users and is always shown unless silenced.
-            DeprecationWarning is meant for developers and is never shown unless
-            python is run in developmental mode or the filter is changed. Make
-            the choice accordingly.
-
-    Returns:
-        Original function, but with a warning to use the updated class.
-    """
-
-    def craft_message(old, replacement, message):
-        msg = f"{old.__name__} is deprecated"
-        if replacement is not None:
-            if isinstance(replacement, property):
-                r = replacement.fget
-            elif isinstance(replacement, (classmethod, staticmethod)):
-                r = replacement.__func__
-            else:
-                r = replacement
-            msg += f"; use {r.__name__} in {r.__module__} instead."
-        if message is not None:
-            msg += "\n" + message
-        return msg
-
-    def deprecated_decorator(old):
-        if inspect.isclass(old):
-
-            class _DecoratedClass(old):
-                def __init__(self, *args, **kwargs):
-                    msg = craft_message(old, replacement, message)
-                    warnings.warn(msg, category=category, stacklevel=2)
-                    super().__init__(*args, **kwargs)
-
-            return _DecoratedClass
-        else:
-
-            def wrapped(*args, **kwargs):
-                msg = craft_message(old, replacement, message)
-                warnings.warn(msg, category=category, stacklevel=2)
-                return old(*args, **kwargs)
-
-            return wrapped
-
-    return deprecated_decorator

-
-
-
[docs]class requires:
-    """
-    Decorator to mark classes or functions as requiring a specified condition
-    to be true. This can be used to present useful error messages for
-    optional dependencies. For example, decorating the following code will
-    check if scipy is present and if not, a runtime error will be raised if
-    someone attempts to call the use_scipy function::
-
-        try:
-            import scipy
-        except ImportError:
-            scipy = None
-
-        @requires(scipy is not None, "scipy is not present.")
-        def use_scipy():
-            print(scipy.majver)
-
-    Args:
-        condition: Condition necessary to use the class or function.
-        message: A message to be displayed if the condition is not True.
-    """
-
-    def __init__(self, condition, message):
-        """
-        :param condition: A expression returning a bool.
-        :param message: Message to display if condition is False.
-        """
-        self.condition = condition
-        self.message = message
-
-    def __call__(self, _callable):
-        """
-        :param _callable: Callable function.
-        """
-
-        @functools.wraps(_callable)
-        def decorated(*args, **kwargs):
-            if not self.condition:
-                raise RuntimeError(self.message)
-            return _callable(*args, **kwargs)
-
-        return decorated

-
-
-
[docs]def get_ncpus():
-    """
-    .. note::
-
-        If you are using Python >= 2.7, multiprocessing.cpu_count() already
-        provides the number of CPUs. In fact, this is the first method tried.
-        The purpose of this function is to cater to old Python versions that
-        still exist on many Linux style clusters.
-
-    Number of virtual or physical CPUs on this system, i.e.
-    user/real as output by time(1) when called with an optimally scaling
-    userspace-only program. Return -1 if ncpus cannot be detected. Taken from:
-    http://stackoverflow.com/questions/1006289/how-to-find-out-the-number-of-
-    cpus-in-python
-    """
-    # Python 2.6+
-    # May raise NonImplementedError
-    try:
-        return multiprocessing.cpu_count()
-    except (ImportError, NotImplementedError):
-        pass
-
-    # POSIX
-    try:
-        res = int(os.sysconf("SC_NPROCESSORS_ONLN"))
-        if res > 0:
-            return res
-    except (AttributeError, ValueError):
-        pass
-
-    # Windows
-    try:
-        res = int(os.environ["NUMBER_OF_PROCESSORS"])
-        if res > 0:
-            return res
-    except (KeyError, ValueError):
-        pass
-
-    # jython
-    try:
-        from java.lang import Runtime  # pylint: disable=import-outside-toplevel
-
-        runtime = Runtime.getRuntime()
-        res = runtime.availableProcessors()
-        if res > 0:
-            return res
-    except ImportError:
-        pass
-
-    # BSD
-    try:
-        with subprocess.Popen(["sysctl", "-n", "hw.ncpu"], stdout=subprocess.PIPE) as sysctl:
-            scstdout = sysctl.communicate()[0]
-            res = int(scstdout)
-            if res > 0:
-                return res
-    except (OSError, ValueError):
-        pass
-
-    # Linux
-    try:
-        res = open("/proc/cpuinfo").read().count("processor\t:")  # pylint: disable=R1732
-        if res > 0:
-            return res
-    except OSError:
-        pass
-
-    # Solaris
-    try:
-        pseudo_devices = os.listdir("/devices/pseudo/")
-        expr = re.compile("^cpuid@[0-9]+$")
-        res = 0
-        for pd in pseudo_devices:
-            if expr.match(pd) is not None:
-                res += 1
-        if res > 0:
-            return res
-    except OSError:
-        pass
-
-    # Other UNIXes (heuristic)
-    try:
-        try:
-            with open("/var/run/dmesg.boot") as f:
-                dmesg = f.read()
-        except OSError:
-            with subprocess.Popen(["dmesg"], stdout=subprocess.PIPE) as dmesg_process:
-                dmesg = dmesg_process.communicate()[0]
-
-        res = 0
-        while "\ncpu" + str(res) + ":" in dmesg:
-            res += 1
-
-        if res > 0:
-            return res
-    except OSError:
-        pass
-
-    logger.warning("Cannot determine number of CPUs on this system!")
-    return -1

-
-
-
[docs]def install_excepthook(hook_type="color", **kwargs):
-    """
-    This function replaces the original python traceback with an improved
-    version from Ipython. Use `color` for colourful traceback formatting,
-    `verbose` for Ka-Ping Yee's "cgitb.py" version kwargs are the keyword
-    arguments passed to the constructor. See IPython.core.ultratb.py for more
-    info.
-
-    Return:
-        0 if hook is installed successfully.
-    """
-    try:
-        from IPython.core import ultratb  # pylint: disable=import-outside-toplevel
-    except ImportError:
-        warnings.warn("Cannot install excepthook, IPyhon.core.ultratb not available")
-        return 1
-
-    # Select the hook.
-    hook = dict(
-        color=ultratb.ColorTB,
-        verbose=ultratb.VerboseTB,
-    ).get(hook_type.lower(), None)
-
-    if hook is None:
-        return 2
-
-    sys.excepthook = hook(**kwargs)
-    return 0

-
- -
-
-
-
- -
-
- -
- © Copyright 2014, Shyue Ping Ong. -
- - - - \ No newline at end of file diff --git a/docs/_modules/monty/fnmatch.html b/docs/_modules/monty/fnmatch.html deleted file mode 100644 index 7c0d68c91..000000000 --- a/docs/_modules/monty/fnmatch.html +++ /dev/null @@ -1,140 +0,0 @@ - - - - - - - monty.fnmatch — monty 2023.5.8 documentation - - - - - - - - - - - - - - - - - -
-
-
-
- -

Source code for monty.fnmatch

-"""
-This module provides support for Unix shell-style wildcards
-"""
-
-import fnmatch
-
-from monty.string import list_strings
-
-
-
[docs]class WildCard:
-    """
-    This object provides an easy-to-use interface for filename matching with
-    shell patterns (fnmatch).
-
-    >>> w = WildCard("*.nc|*.pdf")
-    >>> w.filter(["foo.nc", "bar.pdf", "hello.txt"])
-    ['foo.nc', 'bar.pdf']
-
-    >>> w.filter("foo.nc")
-    ['foo.nc']
-    """
-
-    def __init__(self, wildcard, sep="|"):
-        """
-        Initializes a WildCard.
-
-        Args:
-            wildcard (str): String of tokens separated by sep. Each token
-                represents a pattern.
-            sep (str): Separator for shell patterns.
-        """
-        self.pats = ["*"]
-        if wildcard:
-            self.pats = wildcard.split(sep)
-
-    def __str__(self):
-        return f"<{self.__class__.__name__}, patterns = {self.pats}>"
-
-
[docs]    def filter(self, names):
-        """
-        Returns a list with the names matching the pattern.
-        """
-        names = list_strings(names)
-
-        fnames = []
-        for f in names:
-            for pat in self.pats:
-                if fnmatch.fnmatch(f, pat):
-                    fnames.append(f)
-
-        return fnames

-
-
[docs]    def match(self, name):
-        """
-        Returns True if name matches one of the patterns.
-        """
-        for pat in self.pats:
-            if fnmatch.fnmatch(name, pat):
-                return True
-
-        return False

-
- -
-
-
-
- -
-
- -
- © Copyright 2014, Shyue Ping Ong. -
- - - - \ No newline at end of file diff --git a/docs/_modules/monty/fractions.html b/docs/_modules/monty/fractions.html deleted file mode 100644 index c396ec386..000000000 --- a/docs/_modules/monty/fractions.html +++ /dev/null @@ -1,145 +0,0 @@ - - - - - - - monty.fractions — monty 2023.5.8 documentation - - - - - - - - - - - - - - - - - -
-
-
-
- -

Source code for monty.fractions

-"""
-Math functions.
-"""
-
-import math
-
-
-
[docs]def gcd(*numbers):
-    r"""
-    Returns the greatest common divisor for a sequence of numbers.
-
-    Args:
-        *numbers: Sequence of numbers.
-
-    Returns:
-        (int) Greatest common divisor of numbers.
-    """
-    n = numbers[0]
-    for i in numbers:
-        n = math.gcd(n, i)
-    return n

-
-
-
[docs]def lcm(*numbers):
-    r"""
-    Return lowest common multiple of a sequence of numbers.
-
-    Args:
-        *numbers: Sequence of numbers.
-
-    Returns:
-        (int) Lowest common multiple of numbers.
-    """
-    n = 1
-    for i in numbers:
-        n = (i * n) // gcd(i, n)
-    return n

-
-
-
[docs]def gcd_float(numbers, tol=1e-8):
-    """
-    Returns the greatest common divisor for a sequence of numbers.
-    Uses a numerical tolerance, so can be used on floats
-
-    Args:
-        numbers: Sequence of numbers.
-        tol: Numerical tolerance
-
-    Returns:
-        (int) Greatest common divisor of numbers.
-    """
-
-    def pair_gcd_tol(a, b):
-        """Calculate the Greatest Common Divisor of a and b.
-
-        Unless b==0, the result will have the same sign as b (so that when
-        b is divided by it, the result comes out positive).
-        """
-        while b > tol:
-            a, b = b, a % b
-        return a
-
-    n = numbers[0]
-    for i in numbers:
-        n = pair_gcd_tol(n, i)
-    return n

-
- -
-
-
-
- -
-
- -
- © Copyright 2014, Shyue Ping Ong. -
- - - - \ No newline at end of file diff --git a/docs/_modules/monty/functools.html b/docs/_modules/monty/functools.html deleted file mode 100644 index 329b1efb5..000000000 --- a/docs/_modules/monty/functools.html +++ /dev/null @@ -1,501 +0,0 @@ - - - - - - - monty.functools — monty 2023.5.8 documentation - - - - - - - - - - - - - - - - - -
-
-
-
- -

Source code for monty.functools

-"""
-functools, especially backported from Python 3.
-"""
-
-import cProfile
-import pstats
-import signal
-import sys
-import tempfile
-from collections import namedtuple
-from functools import partial, update_wrapper, wraps
-from threading import RLock
-
-_CacheInfo = namedtuple("_CacheInfo", ["hits", "misses", "maxsize", "currsize"])
-
-
-class _HashedSeq(list):  # pylint: disable=C0205
-    """
-    This class guarantees that hash() will be called no more than once
-    per element.  This is important because the lru_cache() will hash
-    the key multiple times on a cache miss.
-    """
-
-    __slots__ = "hashvalue"
-
-    def __init__(self, tup, hashfunc=hash):
-        """
-        :param tup: Tuple.
-        :param hashfunc: Hash function.
-        """
-        self[:] = tup
-        self.hashvalue = hashfunc(tup)
-
-    def __hash__(self):
-        return self.hashvalue
-
-
-def _make_key(args, kwds, typed, kwd_mark=(object(),), fasttypes={int, str, frozenset, type(None)}):
-    """
-    Make a cache key from optionally typed positional and keyword arguments
-
-    The key is constructed in a way that is flat as possible rather than
-    as a nested structure that would take more memory.
-
-    If there is only a single argument and its data type is known to cache
-    its hash value, then that argument is returned without a wrapper.  This
-    saves space and improves lookup speed.
-
-    """
-    key = args
-    if kwds:
-        sorted_items = sorted(kwds.items())
-        key += kwd_mark
-        for item in sorted_items:
-            key += item
-    if typed:
-        key += tuple(type(v) for v in args)
-        if kwds:
-            key += tuple(type(v) for k, v in sorted_items)
-    elif len(key) == 1 and isinstance(key[0], fasttypes):
-        return key[0]
-    return _HashedSeq(key)
-
-
-
[docs]def lru_cache(maxsize=128, typed=False):
-    """
-    Least-recently-used cache decorator, which is a backport of the same
-    function in Python >= 3.2.
-
-    If *maxsize* is set to None, the LRU features are disabled and the cache
-    can grow without bound.
-
-    If *typed* is True, arguments of different types will be cached separately.
-    For example, f(3.0) and f(3) will be treated as distinct calls with
-    distinct results.
-
-    Arguments to the cached function must be hashable.
-
-    View the cache statistics named tuple (hits, misses, maxsize, currsize)
-    with f.cache_info().  Clear the cache and statistics with f.cache_clear().
-    Access the underlying function with f.__wrapped__.
-
-    See:  http://en.wikipedia.org/wiki/Cache_algorithms#Least_Recently_Used
-    """
-
-    # Users should only access the lru_cache through its public API:
-    #       cache_info, cache_clear, and f.__wrapped__
-    # The internals of the lru_cache are encapsulated for thread safety and
-    # to allow the implementation to change (including a possible C version).
-
-    # Early detection of an erroneous call to @lru_cache without any arguments
-    # resulting in the inner function being passed to maxsize instead of an
-    # integer or None.
-    if maxsize is not None and not isinstance(maxsize, int):
-        raise TypeError("Expected maxsize to be an integer or None")
-
-    # Constants shared by all lru cache instances:
-    sentinel = object()  # unique object used to signal cache misses
-    make_key = _make_key  # build a key from the function arguments
-    PREV, NEXT, KEY, RESULT = 0, 1, 2, 3  # names for the link fields
-
-    def decorating_function(user_function):
-        cache = {}
-        hits = [0]
-        misses = [0]
-        full = [False]
-        cache_get = cache.get  # bound method to lookup a key or return None
-        lock = RLock()  # because linkedlist updates aren't threadsafe
-        root = []  # root of the circular doubly linked list
-        root[:] = [root, root, None, None]  # initialize by pointing to self
-        r = [root]
-
-        if maxsize == 0:
-
-            def wrapper(*args, **kwds):
-                # No caching - just a statistics update after a successful call
-                result = user_function(*args, **kwds)
-                misses[0] += 1
-                return result
-
-        elif maxsize is None:
-
-            def wrapper(*args, **kwds):
-                # Simple caching without ordering or size limit
-                key = make_key(args, kwds, typed)
-                result = cache_get(key, sentinel)
-                if result is not sentinel:
-                    hits[0] += 1
-                    return result
-                result = user_function(*args, **kwds)
-                cache[key] = result
-                misses[0] += 1
-                return result
-
-        else:
-
-            def wrapper(*args, **kwds):
-                # Size limited caching that tracks accesses by recency
-                key = make_key(args, kwds, typed)
-                with lock:
-                    link = cache_get(key)
-                    if link is not None:
-                        # Move the link to the front of the circular queue
-                        link_prev, link_next, _key, result = link
-                        link_prev[NEXT] = link_next
-                        link_next[PREV] = link_prev
-                        last = r[0][PREV]
-                        last[NEXT] = r[0][PREV] = link
-                        link[PREV] = last
-                        link[NEXT] = r[0]
-                        hits[0] += 1
-                        return result
-                result = user_function(*args, **kwds)
-                with lock:
-                    if key in cache:
-                        # Getting here means that this same key was added to
-                        # cache while the lock was released.  Since the link
-                        # update is already done, we need only return the
-                        # computed result and update the count of misses.
-                        pass
-                    elif full[0]:
-                        # Use the old root to store the new key and result.
-                        oldroot = r[0]
-                        oldroot[KEY] = key
-                        oldroot[RESULT] = result
-                        # Empty the oldest link and make it the new root.
-                        # Keep a reference to the old key and old result to
-                        # prevent their ref counts from going to zero during
-                        # update. That will prevent arbitrary object
-                        # clean-up code (i.e. __del__) from running while we're
-                        # still adjusting the links.
-                        r[0] = oldroot[NEXT]
-                        oldkey = r[0][KEY]
-                        r[0][KEY] = r[0][RESULT] = None
-                        # Now update the cache dictionary.
-                        del cache[oldkey]
-                        # Save the potentially reentrant cache[key] assignment
-                        # for last, after the root and links have been put in
-                        # a consistent state.
-                        cache[key] = oldroot
-                    else:
-                        # Put result in a new link at the front of the queue.
-                        last = r[0][PREV]
-                        link = [last, r[0], key, result]
-                        last[NEXT] = r[0][PREV] = cache[key] = link
-                        full[0] = len(cache) >= maxsize
-                    misses[0] += 1
-                return result
-
-        def cache_info():
-            """Report cache statistics"""
-            with lock:
-                return _CacheInfo(hits[0], misses[0], maxsize, len(cache))
-
-        def cache_clear():
-            """Clear the cache and cache statistics"""
-            with lock:
-                cache.clear()
-                root[:] = [root, root, None, None]
-                r[0] = root
-                hits[0] = 0
-                misses[0] = 0
-                full[0] = False
-
-        wrapper.cache_info = cache_info
-        wrapper.cache_clear = cache_clear
-        return update_wrapper(wrapper, user_function)
-
-    return decorating_function

-
-
-
[docs]class lazy_property:
-    """
-    lazy_property descriptor
-
-    Used as a decorator to create lazy attributes. Lazy attributes
-    are evaluated on first use.
-    """
-
-    def __init__(self, func):
-        """
-        :param func: Function to decorate.
-        """
-        self.__func = func
-        wraps(self.__func)(self)
-
-    def __get__(self, inst, inst_cls):
-        if inst is None:
-            return self
-
-        if not hasattr(inst, "__dict__"):
-            raise AttributeError(f"'{inst_cls.__name__}' object has no attribute '__dict__'")
-
-        name = self.__name__  # pylint: disable=E1101
-        if name.startswith("__") and not name.endswith("__"):
-            name = f"_{inst_cls.__name__}{name}"
-
-        value = self.__func(inst)
-        inst.__dict__[name] = value
-        return value
-
-
[docs]    @classmethod
-    def invalidate(cls, inst, name):
-        """Invalidate a lazy attribute.
-
-        This obviously violates the lazy contract. A subclass of lazy
-        may however have a contract where invalidation is appropriate.
-        """
-        inst_cls = inst.__class__
-
-        if not hasattr(inst, "__dict__"):
-            raise AttributeError(f"'{inst_cls.__name__}' object has no attribute '__dict__'")
-
-        if name.startswith("__") and not name.endswith("__"):
-            name = f"_{inst_cls.__name__}{name}"
-
-        if not isinstance(getattr(inst_cls, name), cls):
-            raise AttributeError(f"'{inst_cls.__name__}.{name}' is not a {cls.__name__} attribute")
-
-        if name in inst.__dict__:
-            del inst.__dict__[name]

-
-
-
[docs]def return_if_raise(exception_tuple, retval_if_exc, disabled=False):
-    """
-    Decorator for functions, methods or properties. Execute the callable in a
-    try block, and return retval_if_exc if one of the exceptions listed in
-    exception_tuple is raised (se also ``return_node_if_raise``).
-
-    Setting disabled to True disables the try except block (useful for
-    debugging purposes). One can use this decorator to define properties.
-
-    Example::
-
-        @return_if_raise(ValueError, None)
-        def return_none_if_value_error(self):
-            pass
-
-        @return_if_raise((ValueError, KeyError), "hello")
-        def another_method(self):
-            pass
-
-        @property
-        @return_if_raise(AttributeError, None)
-        def name(self):
-            "Name of the object, None if not set."
-            return self._name
-
-    """
-    # we need a tuple of exceptions.
-    if isinstance(exception_tuple, list):
-        exception_tuple = tuple(exception_tuple)
-    elif not isinstance(exception_tuple, tuple):
-        exception_tuple = (exception_tuple,)
-    else:
-        raise TypeError(f"Wrong exception_tuple {type(exception_tuple)}")
-
-    def decorator(func):
-        @wraps(func)
-        def wrapper(*args, **kwargs):
-            if disabled:
-                return func(*args, **kwargs)
-            try:
-                return func(*args, **kwargs)
-            except exception_tuple:  # pylint: disable=E0712
-                return retval_if_exc
-
-        return wrapper
-
-    return decorator

-
-
-# One could use None as default value in return_if_raise but this one is
-# explicit and  more readable
-return_none_if_raise = partial(return_if_raise, retval_if_exc=None)
-"""
-This decorator returns None if one of the exceptions is raised.
-
-    @return_none_if_raise(ValueError)
-    def method(self):
-"""
-
-
-
[docs]class timeout:
-    """
-    Timeout function. Use to limit matching to a certain time limit. Note that
-    this works only on Unix-based systems as it uses signal. Usage:
-
-    try:
-        with timeout(3):
-            do_stuff()
-    except TimeoutError:
-        do_something_else()
-    """
-
-    def __init__(self, seconds=1, error_message="Timeout"):
-        """
-        Args:
-            seconds (int): Allowed time for function in seconds.
-            error_message (str): An error message.
-
-        """
-        self.seconds = seconds
-        self.error_message = error_message
-
-
[docs]    def handle_timeout(self, signum, frame):
-        """
-        :param signum: Return signal from call.
-        :param frame:
-        """
-        raise TimeoutError(self.error_message)

-
-    def __enter__(self):
-        signal.signal(signal.SIGALRM, self.handle_timeout)
-        signal.alarm(self.seconds)
-
-    def __exit__(self, type, value, traceback):
-        signal.alarm(0)

-
-
-
[docs]class TimeoutError(Exception):
-    """
-    Exception class for timeouts.
-    """
-
-    def __init__(self, message):
-        """
-        :param message: Error message
-        """
-        self.message = message

-
-
-
[docs]def prof_main(main):
-    """
-    Decorator for profiling main programs.
-
-    Profiling is activated by prepending the command line options
-    supported by the original main program with the keyword `prof`.
-    Example:
-
-        $ script.py arg --foo=1
-
-    becomes
-
-        $ script.py prof arg --foo=1
-
-    The decorated main accepts two new arguments:
-
-        prof_file: Name of the output file with profiling data
-            If not given, a temporary file is created.
-        sortby: Profiling data are sorted according to this value.
-            default is "time". See sort_stats.
-    """
-
-    @wraps(main)
-    def wrapper(*args, **kwargs):
-        try:
-            do_prof = sys.argv[1] == "prof"
-            if do_prof:
-                sys.argv.pop(1)
-        except Exception:
-            do_prof = False
-
-        if not do_prof:
-            sys.exit(main())
-        else:
-            print("Entering profiling mode...")
-            prof_file = kwargs.get("prof_file", None)
-            if prof_file is None:
-                _, prof_file = tempfile.mkstemp()
-                print(f"Profiling data stored in {prof_file}")
-
-            sortby = kwargs.get("sortby", "time")
-            cProfile.runctx("main()", globals(), locals(), prof_file)
-            s = pstats.Stats(prof_file)
-            s.strip_dirs().sort_stats(sortby).print_stats()
-            if "retval" not in kwargs:
-                sys.exit(0)
-            else:
-                return kwargs["retval"]
-
-    return wrapper

-
- -
-
-
-
- -
-
- -
- © Copyright 2014, Shyue Ping Ong. -
- - - - \ No newline at end of file diff --git a/docs/_modules/monty/inspect.html b/docs/_modules/monty/inspect.html deleted file mode 100644 index 868d90986..000000000 --- a/docs/_modules/monty/inspect.html +++ /dev/null @@ -1,181 +0,0 @@ - - - - - - - monty.inspect — monty 2023.5.8 documentation - - - - - - - - - - - - - - - - - -
-
-
-
- -

Source code for monty.inspect

-"""
-Useful additional functions to help get information about live objects
-"""
-
-import inspect
-import os
-from functools import wraps
-from inspect import currentframe, getframeinfo, getfullargspec
-
-
-
[docs]def all_subclasses(cls):
-    """
-    Given a class `cls`, this recursive function returns a list with
-    all subclasses, subclasses of subclasses, and so on.
-    """
-    subclasses = cls.__subclasses__()
-    return subclasses + [g for s in subclasses for g in all_subclasses(s)]

-
-
-
[docs]def find_top_pyfile():
-    """
-    This function inspects the Cpython frame to find the path of the script.
-    """
-    frame = currentframe()
-    while True:
-        if frame.f_back is None:
-            finfo = getframeinfo(frame)
-            return os.path.abspath(finfo.filename)
-
-        frame = frame.f_back

-
-
-
[docs]def caller_name(skip=2):
-    """
-    Get a name of a caller in the format module.class.method
-
-    `skip` specifies how many levels of stack to skip while getting caller
-    name. skip=1 means "who calls me", skip=2 "who calls my caller" etc.
-
-    An empty string is returned if skipped levels exceed stack height
-
-    Taken from:
-
-        https://gist.github.com/techtonik/2151727
-
-    Public Domain, i.e. feel free to copy/paste
-    """
-    stack = inspect.stack()
-    start = 0 + skip
-    if len(stack) < start + 1:
-        return ""
-    parentframe = stack[start][0]
-
-    name = []
-    module = inspect.getmodule(parentframe)
-    # `modname` can be None when frame is executed directly in console
-    # TODO(techtonik): consider using __main__
-    if module:
-        name.append(module.__name__)
-    # detect classname
-    if "self" in parentframe.f_locals:
-        # I don't know any way to detect call from the object method
-        # XXX: there seems to be no way to detect static method call - it will
-        #      be just a function call
-        name.append(parentframe.f_locals["self"].__class__.__name__)
-    codename = parentframe.f_code.co_name
-    if codename != "<module>":  # top level usually
-        name.append(codename)  # function or a method
-    del parentframe
-    return ".".join(name)

-
-
-
[docs]def initializer(func):
-    """
-    Automatically assigns the parameters.
-    http://stackoverflow.com/questions/1389180/python-automatically-initialize
-    -instance-variables
-
-    >>> class process:
-    ...     @initializer
-    ...     def __init__(self, cmd, reachable=False, user='root'):
-    ...         pass
-    >>> p = process('halt', True)
-    >>> p.cmd, p.reachable, p.user
-    ('halt', True, 'root')
-    """
-    names, varargs, keywords, defaults = getfullargspec(func)  # type: ignore
-
-    @wraps(func)
-    def wrapper(self, *args, **kargs):
-        for name, arg in list(zip(names[1:], args)) + list(kargs.items()):
-            setattr(self, name, arg)
-
-        # Avoid TypeError: argument to reversed() must be a sequence
-        if defaults is not None:
-            for name, default in zip(reversed(names), reversed(defaults)):
-                if not hasattr(self, name):
-                    setattr(self, name, default)
-
-        return func(self, *args, **kargs)
-
-    return wrapper

-
- -
-
-
-
- -
-
- -
- © Copyright 2014, Shyue Ping Ong. -
- - - - \ No newline at end of file diff --git a/docs/_modules/monty/io.html b/docs/_modules/monty/io.html deleted file mode 100644 index c41b6b6cc..000000000 --- a/docs/_modules/monty/io.html +++ /dev/null @@ -1,344 +0,0 @@ - - - - - - - monty.io — monty 2023.5.8 documentation - - - - - - - - - - - - - - - - - -
-
-
-
- -

Source code for monty.io

-"""
-Augments Python's suite of IO functions with useful transparent support for
-compressed files.
-"""
-
-import bz2
-import errno
-import gzip
-import io
-import lzma
-import mmap
-import os
-import subprocess
-import time
-from pathlib import Path
-from typing import IO, Generator, Union
-
-
-
[docs]def zopen(filename: Union[str, Path], *args, **kwargs) -> IO:
-    r"""
-    This function wraps around the bz2, gzip, lzma, xz and standard python's open
-    function to deal intelligently with bzipped, gzipped or standard text
-    files.
-
-    Args:
-        filename (str/Path): filename or pathlib.Path.
-        *args: Standard args for python open(..). E.g., 'r' for read, 'w' for
-            write.
-        **kwargs: Standard kwargs for python open(..).
-
-    Returns:
-        File-like object. Supports with context.
-    """
-    if Path is not None and isinstance(filename, Path):
-        filename = str(filename)
-
-    name, ext = os.path.splitext(filename)
-    ext = ext.upper()
-    if ext == ".BZ2":
-        return bz2.open(filename, *args, **kwargs)
-    if ext in (".GZ", ".Z"):
-        return gzip.open(filename, *args, **kwargs)
-    if ext in (".XZ", ".LZMA"):
-        return lzma.open(filename, *args, **kwargs)
-    return open(filename, *args, **kwargs)  # pylint: disable=R1732

-
-
-
[docs]def reverse_readfile(filename: Union[str, Path]) -> Generator[str, str, None]:
-    """
-    A much faster reverse read of file by using Python's mmap to generate a
-    memory-mapped file. It is slower for very small files than
-    reverse_readline, but at least 2x faster for large files (the primary use
-    of such a method).
-
-    Args:
-        filename (str):
-            Name of file to read.
-
-    Yields:
-        Lines from the file in reverse order.
-    """
-    try:
-        with zopen(filename, "rb") as f:
-            if isinstance(f, (gzip.GzipFile, bz2.BZ2File)):
-                for line in reversed(f.readlines()):
-                    yield line.decode("utf-8").rstrip()
-            else:
-                fm = mmap.mmap(f.fileno(), 0, access=mmap.ACCESS_READ)
-                n = len(fm)
-                while n > 0:
-                    i = fm.rfind(b"\n", 0, n)
-                    yield fm[i + 1 : n].decode("utf-8").strip("\n")
-                    n = i
-    except ValueError:
-        return

-
-
-
[docs]def reverse_readline(m_file, blk_size=4096, max_mem=4000000) -> Generator[str, str, None]:
-    """
-    Generator method to read a file line-by-line, but backwards. This allows
-    one to efficiently get data at the end of a file.
-
-    Based on code by Peter Astrand <astrand@cendio.se>, using modifications by
-    Raymond Hettinger and Kevin German.
-    http://code.activestate.com/recipes/439045-read-a-text-file-backwards
-    -yet-another-implementat/
-
-    Reads file forwards and reverses in memory for files smaller than the
-    max_mem parameter, or for gzip files where reverse seeks are not supported.
-
-    Files larger than max_mem are dynamically read backwards.
-
-    Args:
-        m_file (File): File stream to read (backwards)
-        blk_size (int): The buffer size. Defaults to 4096.
-        max_mem (int): The maximum amount of memory to involve in this
-            operation. This is used to determine when to reverse a file
-            in-memory versus seeking portions of a file. For bz2 files,
-            this sets the maximum block size.
-
-    Returns:
-        Generator that returns lines from the file. Similar behavior to the
-        file.readline() method, except the lines are returned from the back
-        of the file.
-    """
-    # Check if the file stream is a bit stream or not
-    is_text = isinstance(m_file, io.TextIOWrapper)
-
-    try:
-        file_size = os.path.getsize(m_file.name)
-    except AttributeError:
-        # Bz2 files do not have name attribute. Just set file_size to above
-        # max_mem for now.
-        file_size = max_mem + 1
-
-    # If the file size is within our desired RAM use, just reverse it in memory
-    # GZip files must use this method because there is no way to negative seek
-    # For windows, we also read the whole file.
-    if file_size < max_mem or isinstance(m_file, gzip.GzipFile) or os.name == "nt":
-        for line in reversed(m_file.readlines()):
-            yield line.rstrip()
-    else:
-        if isinstance(m_file, bz2.BZ2File):
-            # for bz2 files, seeks are expensive. It is therefore in our best
-            # interest to maximize the blk_size within limits of desired RAM
-            # use.
-            blk_size = min(max_mem, file_size)
-
-        buf = ""
-        m_file.seek(0, 2)
-        if is_text:
-            lastchar = m_file.read(1)
-        else:
-            lastchar = m_file.read(1).decode("utf-8")
-
-        trailing_newline = lastchar == "\n"
-
-        while 1:
-            newline_pos = buf.rfind("\n")
-            pos = m_file.tell()
-            if newline_pos != -1:
-                # Found a newline
-                line = buf[newline_pos + 1 :]
-                buf = buf[:newline_pos]
-                if pos or newline_pos or trailing_newline:
-                    line += "\n"
-                yield line
-            elif pos:
-                # Need to fill buffer
-                toread = min(blk_size, pos)
-                m_file.seek(pos - toread, 0)
-                if is_text:
-                    buf = m_file.read(toread) + buf
-                else:
-                    buf = m_file.read(toread).decode("utf-8") + buf
-                m_file.seek(pos - toread, 0)
-                if pos == toread:
-                    buf = "\n" + buf
-            else:
-                # Start-of-file
-                return

-
-
-
[docs]class FileLockException(Exception):
-    """Exception raised by FileLock."""

-
-
-
[docs]class FileLock:
-    """
-    A file locking mechanism that has context-manager support so you can use
-    it in a with statement. This should be relatively cross-compatible as it
-    doesn't rely on msvcrt or fcntl for the locking.
-    Taken from http://www.evanfosmark.com/2009/01/cross-platform-file-locking
-    -support-in-python/
-    """
-
-    Error = FileLockException
-
-    def __init__(self, file_name, timeout=10, delay=0.05):
-        """
-        Prepare the file locker. Specify the file to lock and optionally
-        the maximum timeout and the delay between each attempt to lock.
-
-        Args:
-            file_name: Name of file to lock.
-            timeout: Maximum timeout for locking. Defaults to 10.
-            delay: Delay between each attempt to lock. Defaults to 0.05.
-        """
-        self.file_name = os.path.abspath(file_name)
-        self.lockfile = os.path.abspath(file_name) + ".lock"
-        self.timeout = float(timeout)
-        self.delay = float(delay)
-        self.is_locked = False
-
-        if self.delay > self.timeout or self.delay <= 0 or self.timeout <= 0:
-            raise ValueError("delay and timeout must be positive with delay " "<= timeout")
-
-
[docs]    def acquire(self):
-        """
-        Acquire the lock, if possible. If the lock is in use, it check again
-        every `delay` seconds. It does this until it either gets the lock or
-        exceeds `timeout` number of seconds, in which case it throws
-        an exception.
-        """
-        start_time = time.time()
-        while True:
-            try:
-                self.fd = os.open(self.lockfile, os.O_CREAT | os.O_EXCL | os.O_RDWR)
-                break
-            except (OSError,) as e:
-                if e.errno != errno.EEXIST:
-                    raise
-                if (time.time() - start_time) >= self.timeout:
-                    raise FileLockException(f"{self.lockfile}: Timeout occurred.")
-                time.sleep(self.delay)
-
-        self.is_locked = True

-
-
[docs]    def release(self):
-        """
-        Get rid of the lock by deleting the lockfile.
-        When working in a `with` statement, this gets automatically
-        called at the end.
-        """
-        if self.is_locked:
-            os.close(self.fd)
-            os.unlink(self.lockfile)
-            self.is_locked = False

-
-    def __enter__(self):
-        """
-        Activated when used in the with statement. Should automatically
-        acquire a lock to be used in the with block.
-        """
-        if not self.is_locked:
-            self.acquire()
-        return self
-
-    def __exit__(self, type_, value, traceback):
-        """
-        Activated at the end of the with statement. It automatically releases
-        the lock if it isn't locked.
-        """
-        if self.is_locked:
-            self.release()
-
-    def __del__(self):
-        """
-        Make sure that the FileLock instance doesn't leave a lockfile
-        lying around.
-        """
-        self.release()

-
-
-
[docs]def get_open_fds():
-    """
-    Return the number of open file descriptors for current process
-
-    .. warning: will only work on UNIX-like OS-es.
-    """
-    pid = os.getpid()
-    procs = subprocess.check_output(["lsof", "-w", "-Ff", "-p", str(pid)])
-    procs = procs.decode("utf-8")
-
-    return len([s for s in procs.split("\n") if s and s[0] == "f" and s[1:].isdigit()])

-
- -
-
-
-
- -
-
- -
- © Copyright 2014, Shyue Ping Ong. -
- - - - \ No newline at end of file diff --git a/docs/_modules/monty/itertools.html b/docs/_modules/monty/itertools.html deleted file mode 100644 index c4f46bc97..000000000 --- a/docs/_modules/monty/itertools.html +++ /dev/null @@ -1,174 +0,0 @@ - - - - - - - monty.itertools — monty 2023.5.8 documentation - - - - - - - - - - - - - - - - - -
-
-
-
- -

Source code for monty.itertools

-"""
-Additional tools for iteration.
-"""
-import itertools
-
-try:
-    import numpy as np
-except ImportError:
-    np = None  # type: ignore
-
-
-
[docs]def chunks(items, n):
-    """
-    Yield successive n-sized chunks from a list-like object.
-
-    >>> import pprint
-    >>> pprint.pprint(list(chunks(range(1, 25), 10)))
-    [(1, 2, 3, 4, 5, 6, 7, 8, 9, 10),
-     (11, 12, 13, 14, 15, 16, 17, 18, 19, 20),
-     (21, 22, 23, 24)]
-    """
-    it = iter(items)
-    chunk = tuple(itertools.islice(it, n))
-    while chunk:
-        yield chunk
-        chunk = tuple(itertools.islice(it, n))

-
-
-
[docs]def iterator_from_slice(s):
-    """
-    Constructs an iterator given a slice object s.
-
-    .. note::
-
-        The function returns an infinite iterator if s.stop is None
-    """
-    start = s.start if s.start is not None else 0
-    step = s.step if s.step is not None else 1
-
-    if s.stop is None:
-        # Infinite iterator.
-        return itertools.count(start=start, step=step)
-
-    # xrange-like iterator that supports float.
-    return iter(np.arange(start, s.stop, step))

-
-
-
[docs]def iuptri(items, diago=True, with_inds=False):
-    """
-    A generator that yields the upper triangle of the matrix (items x items)
-
-    Args:
-        items: Iterable object with elements [e0, e1, ...]
-        diago: False if diagonal matrix elements should be excluded
-        with_inds: If True, (i,j) (e_i, e_j) is returned else (e_i, e_j)
-
-    >>> for (ij, mate) in iuptri([0,1], with_inds=True):
-    ...     print("ij:", ij, "mate:", mate)
-    ij: (0, 0) mate: (0, 0)
-    ij: (0, 1) mate: (0, 1)
-    ij: (1, 1) mate: (1, 1)
-    """
-    for ii, item1 in enumerate(items):
-        for jj, item2 in enumerate(items):
-            do_yield = (jj >= ii) if diago else (jj > ii)
-            if do_yield:
-                if with_inds:
-                    yield (ii, jj), (item1, item2)
-                else:
-                    yield item1, item2

-
-
-
[docs]def ilotri(items, diago=True, with_inds=False):
-    """
-    A generator that yields the lower triangle of the matrix (items x items)
-
-    Args:
-        items: Iterable object with elements [e0, e1, ...]
-        diago: False if diagonal matrix elements should be excluded
-        with_inds: If True, (i,j) (e_i, e_j) is returned else (e_i, e_j)
-
-    >>> for (ij, mate) in ilotri([0,1], with_inds=True):
-    ...     print("ij:", ij, "mate:", mate)
-    ij: (0, 0) mate: (0, 0)
-    ij: (1, 0) mate: (1, 0)
-    ij: (1, 1) mate: (1, 1)
-    """
-    for ii, item1 in enumerate(items):
-        for jj, item2 in enumerate(items):
-            do_yield = (jj <= ii) if diago else (jj < ii)
-            if do_yield:
-                if with_inds:
-                    yield (ii, jj), (item1, item2)
-                else:
-                    yield item1, item2

-
- -
-
-
-
- -
-
- -
- © Copyright 2014, Shyue Ping Ong. -
- - - - \ No newline at end of file diff --git a/docs/_modules/monty/json.html b/docs/_modules/monty/json.html deleted file mode 100644 index 3e512d9d6..000000000 --- a/docs/_modules/monty/json.html +++ /dev/null @@ -1,698 +0,0 @@ - - - - - - - monty.json — monty 2023.5.8 documentation - - - - - - - - - - - - - - - - - -
-
-
-
- -

Source code for monty.json

-"""
-JSON serialization and deserialization utilities.
-"""
-
-import datetime
-import json
-import os
-import pathlib
-import types
-from collections import OrderedDict, defaultdict
-from enum import Enum
-from hashlib import sha1
-from importlib import import_module
-from inspect import getfullargspec
-from uuid import UUID
-
-try:
-    import numpy as np
-except ImportError:
-    np = None  # type: ignore
-
-try:
-    import pandas as pd
-except ImportError:
-    pd = None  # type: ignore
-
-try:
-    import pydantic
-except ImportError:
-    pydantic = None  # type: ignore
-
-try:
-    import bson
-except ImportError:
-    bson = None  # type: ignore
-
-try:
-    from ruamel.yaml import YAML
-except ImportError:
-    YAML = None  # type: ignore
-
-try:
-    import orjson
-except ImportError:
-    orjson = None  # type: ignore
-
-try:
-    import dataclasses
-except ImportError:
-    dataclasses = None  # type: ignore
-
-try:
-    import torch
-except ImportError:
-    torch = None  # type: ignore
-
-__version__ = "3.0.0"
-
-
-def _load_redirect(redirect_file):
-    try:
-        with open(redirect_file) as f:
-            yaml = YAML()
-            d = yaml.load(f)
-    except OSError:
-        # If we can't find the file
-        # Just use an empty redirect dict
-        return {}
-
-    # Convert the full paths to module/class
-    redirect_dict = defaultdict(dict)
-    for old_path, new_path in d.items():
-        old_class = old_path.split(".")[-1]
-        old_module = ".".join(old_path.split(".")[:-1])
-
-        new_class = new_path.split(".")[-1]
-        new_module = ".".join(new_path.split(".")[:-1])
-
-        redirect_dict[old_module][old_class] = {
-            "@module": new_module,
-            "@class": new_class,
-        }
-
-    return dict(redirect_dict)
-
-
-
[docs]class MSONable:
-    """
-    This is a mix-in base class specifying an API for msonable objects. MSON
-    is Monty JSON. Essentially, MSONable objects must implement an as_dict
-    method, which must return a json serializable dict and must also support
-    no arguments (though optional arguments to finetune the output is ok),
-    and a from_dict class method that regenerates the object from the dict
-    generated by the as_dict method. The as_dict method should contain the
-    "@module" and "@class" keys which will allow the MontyEncoder to
-    dynamically deserialize the class. E.g.::
-
-        d["@module"] = self.__class__.__module__
-        d["@class"] = self.__class__.__name__
-
-    A default implementation is provided in MSONable, which automatically
-    determines if the class already contains self.argname or self._argname
-    attributes for every arg. If so, these will be used for serialization in
-    the dict format. Similarly, the default from_dict will deserialization
-    classes of such form. An example is given below::
-
-        class MSONClass(MSONable):
-
-        def __init__(self, a, b, c, d=1, **kwargs):
-            self.a = a
-            self.b = b
-            self._c = c
-            self._d = d
-            self.kwargs = kwargs
-
-    For such classes, you merely need to inherit from MSONable and you do not
-    need to implement your own as_dict or from_dict protocol.
-
-    New to Monty V2.0.6....
-    Classes can be redirected to moved implementations by putting in the old
-    fully qualified path and new fully qualified path into .monty.yaml in the
-    home folder
-
-    Example:
-    old_module.old_class: new_module.new_class
-    """
-
-    REDIRECT = _load_redirect(os.path.join(os.path.expanduser("~"), ".monty.yaml"))
-
-
[docs]    def as_dict(self) -> dict:
-        """
-        A JSON serializable dict representation of an object.
-        """
-        d = {"@module": self.__class__.__module__, "@class": self.__class__.__name__}
-
-        try:
-            parent_module = self.__class__.__module__.split(".", maxsplit=1)[0]
-            module_version = import_module(parent_module).__version__  # type: ignore
-            d["@version"] = str(module_version)
-        except (AttributeError, ImportError):
-            d["@version"] = None  # type: ignore
-
-        spec = getfullargspec(self.__class__.__init__)
-        args = spec.args
-
-        def recursive_as_dict(obj):
-            if isinstance(obj, (list, tuple)):
-                return [recursive_as_dict(it) for it in obj]
-            if isinstance(obj, dict):
-                return {kk: recursive_as_dict(vv) for kk, vv in obj.items()}
-            if hasattr(obj, "as_dict"):
-                return obj.as_dict()
-            if dataclasses is not None and dataclasses.is_dataclass(obj):
-                d = dataclasses.asdict(obj)
-                d.update({"@module": obj.__class__.__module__, "@class": obj.__class__.__name__})
-                return d
-            return obj
-
-        for c in args:
-            if c != "self":
-                try:
-                    a = getattr(self, c)
-                except AttributeError:
-                    try:
-                        a = getattr(self, "_" + c)
-                    except AttributeError:
-                        raise NotImplementedError(
-                            "Unable to automatically determine as_dict "
-                            "format from class. MSONAble requires all "
-                            "args to be present as either self.argname or "
-                            "self._argname, and kwargs to be present under "
-                            "a self.kwargs variable to automatically "
-                            "determine the dict format. Alternatively, "
-                            "you can implement both as_dict and from_dict."
-                        )
-                d[c] = recursive_as_dict(a)
-        if hasattr(self, "kwargs"):
-            # type: ignore
-            d.update(**getattr(self, "kwargs"))  # pylint: disable=E1101
-        if spec.varargs is not None and getattr(self, spec.varargs, None) is not None:
-            d.update({spec.varargs: getattr(self, spec.varargs)})
-        if hasattr(self, "_kwargs"):
-            d.update(**getattr(self, "_kwargs"))  # pylint: disable=E1101
-        if isinstance(self, Enum):
-            d.update({"value": self.value})  # pylint: disable=E1101
-        return d

-
-
[docs]    @classmethod
-    def from_dict(cls, d):
-        """
-        :param d: Dict representation.
-        :return: MSONable class.
-        """
-        decoded = {k: MontyDecoder().process_decoded(v) for k, v in d.items() if not k.startswith("@")}
-        return cls(**decoded)

-
-
[docs]    def to_json(self) -> str:
-        """
-        Returns a json string representation of the MSONable object.
-        """
-        return json.dumps(self, cls=MontyEncoder)

-
-
[docs]    def unsafe_hash(self):
-        """
-        Returns an hash of the current object. This uses a generic but low
-        performance method of converting the object to a dictionary, flattening
-        any nested keys, and then performing a hash on the resulting object
-        """
-
-        def flatten(obj, separator="."):
-            # Flattens a dictionary
-
-            flat_dict = {}
-            for key, value in obj.items():
-                if isinstance(value, dict):
-                    flat_dict.update({separator.join([key, _key]): _value for _key, _value in flatten(value).items()})
-                elif isinstance(value, list):
-                    list_dict = {f"{key}{separator}{num}": item for num, item in enumerate(value)}
-                    flat_dict.update(flatten(list_dict))
-                else:
-                    flat_dict[key] = value
-
-            return flat_dict
-
-        ordered_keys = sorted(flatten(jsanitize(self.as_dict())).items(), key=lambda x: x[0])
-        ordered_keys = [item for item in ordered_keys if "@" not in item[0]]
-        return sha1(json.dumps(OrderedDict(ordered_keys)).encode("utf-8"))

-
-    @classmethod
-    def __get_validators__(cls):
-        """Return validators for use in pydantic"""
-        yield cls.validate_monty
-
-
[docs]    @classmethod
-    def validate_monty(cls, v):
-        """
-        pydantic Validator for MSONable pattern
-        """
-        if isinstance(v, cls):
-            return v
-        if isinstance(v, dict):
-            new_obj = MontyDecoder().process_decoded(v)
-            if isinstance(new_obj, cls):
-                return new_obj
-
-            new_obj = cls(**v)
-            return new_obj
-
-        raise ValueError(f"Must provide {cls.__name__}, the as_dict form, or the proper")

-
-    @classmethod
-    def __modify_schema__(cls, field_schema):
-        """JSON schema for MSONable pattern"""
-        field_schema.update(
-            {
-                "type": "object",
-                "properties": {
-                    "@class": {"enum": [cls.__name__], "type": "string"},
-                    "@module": {"enum": [cls.__module__], "type": "string"},
-                    "@version": {"type": "string"},
-                },
-                "required": ["@class", "@module"],
-            }
-        )

-
-
-
[docs]class MontyEncoder(json.JSONEncoder):
-    """
-    A Json Encoder which supports the MSONable API, plus adds support for
-    numpy arrays, datetime objects, bson ObjectIds (requires bson).
-    Usage::
-        # Add it as a *cls* keyword when using json.dump
-        json.dumps(object, cls=MontyEncoder)
-    """
-
-
[docs]    def default(self, o) -> dict:  # pylint: disable=E0202
-        """
-        Overriding default method for JSON encoding. This method does two
-        things: (a) If an object has a to_dict property, return the to_dict
-        output. (b) If the @module and @class keys are not in the to_dict,
-        add them to the output automatically. If the object has no to_dict
-        property, the default Python json encoder default method is called.
-        Args:
-            o: Python object.
-        Return:
-            Python dict representation.
-        """
-        if isinstance(o, datetime.datetime):
-            return {"@module": "datetime", "@class": "datetime", "string": str(o)}
-        if isinstance(o, UUID):
-            return {"@module": "uuid", "@class": "UUID", "string": str(o)}
-
-        if torch is not None and isinstance(o, torch.Tensor):
-            # Support for Pytorch Tensors.
-            d = {
-                "@module": "torch",
-                "@class": "Tensor",
-                "dtype": o.type(),
-            }
-            if "Complex" in o.type():
-                d["data"] = [o.real.tolist(), o.imag.tolist()]  # type: ignore
-            else:
-                d["data"] = o.numpy().tolist()
-            return d
-
-        if np is not None:
-            if isinstance(o, np.ndarray):
-                if str(o.dtype).startswith("complex"):
-                    return {
-                        "@module": "numpy",
-                        "@class": "array",
-                        "dtype": str(o.dtype),
-                        "data": [o.real.tolist(), o.imag.tolist()],
-                    }
-                return {
-                    "@module": "numpy",
-                    "@class": "array",
-                    "dtype": str(o.dtype),
-                    "data": o.tolist(),
-                }
-            if isinstance(o, np.generic):
-                return o.item()
-
-        if pd is not None:
-            if isinstance(o, pd.DataFrame):
-                return {
-                    "@module": "pandas",
-                    "@class": "DataFrame",
-                    "data": o.to_json(default_handler=MontyEncoder().encode),
-                }
-            if isinstance(o, pd.Series):
-                return {
-                    "@module": "pandas",
-                    "@class": "Series",
-                    "data": o.to_json(default_handler=MontyEncoder().encode),
-                }
-
-        if bson is not None:
-            if isinstance(o, bson.objectid.ObjectId):
-                return {"@module": "bson.objectid", "@class": "ObjectId", "oid": str(o)}
-
-        if callable(o) and not isinstance(o, MSONable):
-            return _serialize_callable(o)
-
-        try:
-            if pydantic is not None and isinstance(o, pydantic.BaseModel):
-                d = o.dict()
-            elif dataclasses is not None and (not issubclass(o.__class__, MSONable)) and dataclasses.is_dataclass(o):
-                # This handles dataclasses that are not subclasses of MSONAble.
-                d = dataclasses.asdict(o)
-            else:
-                d = o.as_dict()
-
-            if "@module" not in d:
-                d["@module"] = str(o.__class__.__module__)
-            if "@class" not in d:
-                d["@class"] = str(o.__class__.__name__)
-            if "@version" not in d:
-                try:
-                    parent_module = o.__class__.__module__.split(".")[0]
-                    module_version = import_module(parent_module).__version__  # type: ignore
-                    d["@version"] = str(module_version)
-                except (AttributeError, ImportError):
-                    d["@version"] = None  # type: ignore
-            return d
-        except AttributeError:
-            return json.JSONEncoder.default(self, o)

-
-
-
[docs]class MontyDecoder(json.JSONDecoder):
-    """
-    A Json Decoder which supports the MSONable API. By default, the
-    decoder attempts to find a module and name associated with a dict. If
-    found, the decoder will generate a Pymatgen as a priority.  If that fails,
-    the original decoded dictionary from the string is returned. Note that
-    nested lists and dicts containing pymatgen object will be decoded correctly
-    as well.
-
-    Usage:
-
-        # Add it as a *cls* keyword when using json.load
-        json.loads(json_string, cls=MontyDecoder)
-    """
-
-
[docs]    def process_decoded(self, d):
-        """
-        Recursive method to support decoding dicts and lists containing
-        pymatgen objects.
-        """
-        if isinstance(d, dict):
-            if "@module" in d and "@class" in d:
-                modname = d["@module"]
-                classname = d["@class"]
-                if classname in MSONable.REDIRECT.get(modname, {}):
-                    modname = MSONable.REDIRECT[modname][classname]["@module"]
-                    classname = MSONable.REDIRECT[modname][classname]["@class"]
-            elif "@module" in d and "@callable" in d:
-                modname = d["@module"]
-                objname = d["@callable"]
-                classname = None
-                if d.get("@bound", None) is not None:
-                    # if the function is bound to an instance or class, first
-                    # deserialize the bound object and then remove the object name
-                    # from the function name.
-                    obj = self.process_decoded(d["@bound"])
-                    objname = objname.split(".")[1:]
-                else:
-                    # if the function is not bound to an object, import the
-                    # function from the module name
-                    obj = __import__(modname, globals(), locals(), [objname], 0)
-                    objname = objname.split(".")
-                try:
-                    # the function could be nested. e.g., MyClass.NestedClass.function
-                    # so iteratively access the nesting
-                    for attr in objname:
-                        obj = getattr(obj, attr)
-
-                    return obj
-
-                except AttributeError:
-                    pass
-            else:
-                modname = None
-                classname = None
-
-            if classname:
-                if modname and modname not in ["bson.objectid", "numpy", "pandas", "torch"]:
-                    if modname == "datetime" and classname == "datetime":
-                        try:
-                            dt = datetime.datetime.strptime(d["string"], "%Y-%m-%d %H:%M:%S.%f")
-                        except ValueError:
-                            dt = datetime.datetime.strptime(d["string"], "%Y-%m-%d %H:%M:%S")
-                        return dt
-
-                    if modname == "uuid" and classname == "UUID":
-                        return UUID(d["string"])
-
-                    mod = __import__(modname, globals(), locals(), [classname], 0)
-                    if hasattr(mod, classname):
-                        cls_ = getattr(mod, classname)
-                        data = {k: v for k, v in d.items() if not k.startswith("@")}
-                        if hasattr(cls_, "from_dict"):
-                            return cls_.from_dict(data)
-                        if pydantic is not None and issubclass(cls_, pydantic.BaseModel):  # pylint: disable=E1101
-                            return cls_(**data)
-                        if (
-                            dataclasses is not None
-                            and (not issubclass(cls_, MSONable))
-                            and dataclasses.is_dataclass(cls_)
-                        ):
-                            d = {k: self.process_decoded(v) for k, v in data.items()}
-                            return cls_(**d)
-                elif torch is not None and modname == "torch" and classname == "Tensor":
-                    if "Complex" in d["dtype"]:
-                        return torch.tensor(  # pylint: disable=E1101
-                            [np.array(r) + np.array(i) * 1j for r, i in zip(*d["data"])],
-                        ).type(d["dtype"])
-                    return torch.tensor(d["data"]).type(d["dtype"])  # pylint: disable=E1101
-                elif np is not None and modname == "numpy" and classname == "array":
-                    if d["dtype"].startswith("complex"):
-                        return np.array(
-                            [np.array(r) + np.array(i) * 1j for r, i in zip(*d["data"])],
-                            dtype=d["dtype"],
-                        )
-                    return np.array(d["data"], dtype=d["dtype"])
-                elif pd is not None and modname == "pandas":
-                    if classname == "DataFrame":
-                        decoded_data = MontyDecoder().decode(d["data"])
-                        return pd.DataFrame(decoded_data)
-                    if classname == "Series":
-                        decoded_data = MontyDecoder().decode(d["data"])
-                        return pd.Series(decoded_data)
-                elif (bson is not None) and modname == "bson.objectid" and classname == "ObjectId":
-                    return bson.objectid.ObjectId(d["oid"])
-
-            return {self.process_decoded(k): self.process_decoded(v) for k, v in d.items()}
-
-        if isinstance(d, list):
-            return [self.process_decoded(x) for x in d]
-
-        return d

-
-
[docs]    def decode(self, s):
-        """
-        Overrides decode from JSONDecoder.
-
-        :param s: string
-        :return: Object.
-        """
-        if orjson is not None:
-            try:
-                d = orjson.loads(s)  # pylint: disable=E1101
-            except orjson.JSONDecodeError:  # pylint: disable=E1101
-                d = json.loads(s)
-        else:
-            d = json.loads(s)
-        return self.process_decoded(d)

-
-
-
[docs]class MSONError(Exception):
-    """
-    Exception class for serialization errors.
-    """

-
-
-
[docs]def jsanitize(obj, strict=False, allow_bson=False, enum_values=False, recursive_msonable=False):
-    """
-    This method cleans an input json-like object, either a list or a dict or
-    some sequence, nested or otherwise, by converting all non-string
-    dictionary keys (such as int and float) to strings, and also recursively
-    encodes all objects using Monty's as_dict() protocol.
-
-    Args:
-        obj: input json-like object.
-        strict (bool): This parameters sets the behavior when jsanitize
-            encounters an object it does not understand. If strict is True,
-            jsanitize will try to get the as_dict() attribute of the object. If
-            no such attribute is found, an attribute error will be thrown. If
-            strict is False, jsanitize will simply call str(object) to convert
-            the object to a string representation.
-        allow_bson (bool): This parameters sets the behavior when jsanitize
-            encounters a bson supported type such as objectid and datetime. If
-            True, such bson types will be ignored, allowing for proper
-            insertion into MongoDB databases.
-        enum_values (bool): Convert Enums to their values.
-        recursive_msonable (bool): If True, uses .as_dict() for MSONables regardless
-            of the value of strict.
-
-    Returns:
-        Sanitized dict that can be json serialized.
-    """
-    if isinstance(obj, Enum) and enum_values:
-        return obj.value
-
-    if allow_bson and (
-        isinstance(obj, (datetime.datetime, bytes)) or (bson is not None and isinstance(obj, bson.objectid.ObjectId))
-    ):
-        return obj
-    if isinstance(obj, (list, tuple)):
-        return [jsanitize(i, strict=strict, allow_bson=allow_bson, enum_values=enum_values) for i in obj]
-    if np is not None and isinstance(obj, np.ndarray):
-        return [jsanitize(i, strict=strict, allow_bson=allow_bson, enum_values=enum_values) for i in obj.tolist()]
-    if np is not None and isinstance(obj, np.generic):
-        return obj.item()
-    if pd is not None and isinstance(obj, (pd.Series, pd.DataFrame)):
-        return obj.to_dict()
-    if isinstance(obj, dict):
-        return {
-            str(k): jsanitize(
-                v,
-                strict=strict,
-                allow_bson=allow_bson,
-                enum_values=enum_values,
-                recursive_msonable=recursive_msonable,
-            )
-            for k, v in obj.items()
-        }
-    if isinstance(obj, (int, float)):
-        return obj
-    if obj is None:
-        return None
-    if isinstance(obj, pathlib.Path) or isinstance(obj, datetime.datetime):
-        return str(obj)
-
-    if callable(obj) and not isinstance(obj, MSONable):
-        try:
-            return _serialize_callable(obj)
-        except TypeError:
-            pass
-
-    if recursive_msonable and isinstance(obj, MSONable):
-        return obj.as_dict()
-
-    if not strict:
-        return str(obj)
-
-    if isinstance(obj, str):
-        return obj
-
-    if pydantic is not None and isinstance(obj, pydantic.BaseModel):  # pylint: disable=E1101
-        return jsanitize(
-            MontyEncoder().default(obj),
-            strict=strict,
-            allow_bson=allow_bson,
-            enum_values=enum_values,
-            recursive_msonable=recursive_msonable,
-        )
-
-    return jsanitize(
-        obj.as_dict(),
-        strict=strict,
-        allow_bson=allow_bson,
-        enum_values=enum_values,
-        recursive_msonable=recursive_msonable,
-    )

-
-
-def _serialize_callable(o):
-    if isinstance(o, types.BuiltinFunctionType):
-        # don't care about what builtin functions (sum, open, etc) are bound to
-        bound = None
-    else:
-        # bound methods (i.e., instance methods) have a __self__ attribute
-        # that points to the class/module/instance
-        bound = getattr(o, "__self__", None)
-
-    # we are only able to serialize bound methods if the object the method is
-    # bound to is itself serializable
-    if bound is not None:
-        try:
-            bound = MontyEncoder().default(bound)
-        except TypeError:
-            raise TypeError("Only bound methods of classes or MSONable instances are supported.")
-
-    return {
-        "@module": o.__module__,
-        "@callable": getattr(o, "__qualname__", o.__name__),
-        "@bound": bound,
-    }
-
- -
-
-
-
- -
-
- -
- © Copyright 2014, Shyue Ping Ong. -
- - - - \ No newline at end of file diff --git a/docs/_modules/monty/logging.html b/docs/_modules/monty/logging.html deleted file mode 100644 index 78cb0f90b..000000000 --- a/docs/_modules/monty/logging.html +++ /dev/null @@ -1,161 +0,0 @@ - - - - - - - monty.logging — monty 2023.5.8 documentation - - - - - - - - - - - - - - - - - -
-
-
-
- -

Source code for monty.logging

-#!/usr/bin/env python
-
-"""
-Logging tools
-"""
-
-import argparse
-import datetime
-import functools
-import logging
-
-logger = logging.getLogger(__name__)
-
-
-
[docs]def logged(level=logging.DEBUG):
-    """
-    Useful logging decorator. If a method is logged, the beginning and end of
-    the method call will be logged at a pre-specified level.
-
-    Args:
-        level: Level to log method at. Defaults to DEBUG.
-    """
-
-    def wrap(f):
-        _logger = logging.getLogger(f"{f.__module__}.{f.__name__}")
-
-        def wrapped_f(*args, **kwargs):
-            _logger.log(
-                level,
-                f"Called at {datetime.datetime.now()} with args = {args} and kwargs = {kwargs}",
-            )
-            data = f(*args, **kwargs)
-            _logger.log(
-                level,
-                f"Done at {datetime.datetime.now()} with args = {args} and kwargs = {kwargs}",
-            )
-            return data
-
-        return wrapped_f
-
-    return wrap

-
-
-
[docs]def enable_logging(main):
-    """
-    This decorator is used to decorate main functions.
-    It adds the initialization of the logger and an argument parser that allows
-    one to select the loglevel.
-    Useful if we are writing simple main functions that call libraries where
-    the logging module is used
-
-    Args:
-        main:
-            main function.
-    """
-
-    @functools.wraps(main)
-    def wrapper(*args, **kwargs):
-        parser = argparse.ArgumentParser()
-
-        parser.add_argument(
-            "--loglevel",
-            default="ERROR",
-            type=str,
-            help="Set the loglevel. Possible values: CRITICAL, ERROR (default)," "WARNING, INFO, DEBUG",
-        )
-
-        options = parser.parse_args()
-
-        # loglevel is bound to the string value obtained from the command line
-        # argument.
-        # Convert to upper case to allow the user to specify --loglevel=DEBUG
-        # or --loglevel=debug
-        numeric_level = getattr(logging, options.loglevel.upper(), None)
-        if not isinstance(numeric_level, int):
-            raise ValueError(f"Invalid log level: {options.loglevel}")
-        logging.basicConfig(level=numeric_level)
-
-        retcode = main(*args, **kwargs)
-        return retcode
-
-    return wrapper

-
- -
-
-
-
- -
-
- -
- © Copyright 2014, Shyue Ping Ong. -
- - - - \ No newline at end of file diff --git a/docs/_modules/monty/math.html b/docs/_modules/monty/math.html deleted file mode 100644 index 8d05d1aff..000000000 --- a/docs/_modules/monty/math.html +++ /dev/null @@ -1,114 +0,0 @@ - - - - - - - monty.math — monty 2023.5.8 documentation - - - - - - - - - - - - - - - - - -
-
-
-
- -

Source code for monty.math

-"""
-Addition math functions.
-"""
-
-import math
-
-
-
[docs]def nCr(n, r):
-    """
-    Calculates nCr.
-
-    Args:
-        n (int): total number of items.
-        r (int): items to choose
-
-    Returns:
-        nCr.
-    """
-    f = math.factorial
-    return int(f(n) / f(r) / f(n - r))

-
-
-
[docs]def nPr(n, r):
-    """
-    Calculates nPr.
-
-    Args:
-        n (int): total number of items.
-        r (int): items to permute
-
-    Returns:
-        nPr.
-    """
-    f = math.factorial
-    return int(f(n) / f(n - r))

-
- -
-
-
-
- -
-
- -
- © Copyright 2014, Shyue Ping Ong. -
- - - - \ No newline at end of file diff --git a/docs/_modules/monty/msgpack.html b/docs/_modules/monty/msgpack.html deleted file mode 100644 index 709cbbe21..000000000 --- a/docs/_modules/monty/msgpack.html +++ /dev/null @@ -1,102 +0,0 @@ - - - - - - - monty.msgpack — monty 2023.5.8 documentation - - - - - - - - - - - - - - - - - -
-
-
-
- -

Source code for monty.msgpack

-"""
-msgpack serialization and deserialization utilities. Right now, this is a stub
-using monty.json encoder and decoders. The naming is just for clearer usage with
-msgpack's default and object_hook naming.
-"""
-
-from monty.json import MontyDecoder, MontyEncoder
-
-
-
[docs]def default(obj):
-    """
-    For use with msgpack.packb(obj, default=default). Supports Monty's as_dict
-    protocol, numpy arrays and datetime.
-    """
-    return MontyEncoder().default(obj)

-
-
-
[docs]def object_hook(d):
-    """
-    For use with msgpack.unpackb(dict, object_hook=object_hook.).  Supports
-    Monty's as_dict protocol, numpy arrays and datetime.
-    """
-    return MontyDecoder().process_decoded(d)

-
- -
-
-
-
- -
-
- -
- © Copyright 2014, Shyue Ping Ong. -
- - - - \ No newline at end of file diff --git a/docs/_modules/monty/multiprocessing.html b/docs/_modules/monty/multiprocessing.html deleted file mode 100644 index d5a6ac2a9..000000000 --- a/docs/_modules/monty/multiprocessing.html +++ /dev/null @@ -1,117 +0,0 @@ - - - - - - - monty.multiprocessing — monty 2023.5.8 documentation - - - - - - - - - - - - - - - - - -
-
-
-
- -

Source code for monty.multiprocessing

-"""
-Multiprocessing utilities.
-"""
-
-from multiprocessing import Pool
-from typing import Callable, Iterable
-
-try:
-    from tqdm.autonotebook import tqdm
-except ImportError:
-    tqdm = None
-
-
-
[docs]def imap_tqdm(nprocs: int, func: Callable, iterable: Iterable, *args, **kwargs):
-    """
-    A wrapper around Pool.imap. Creates a Pool with nprocs and then runs a f
-    unction over an iterable with progress bar.
-
-    :param nprocs: Number of processes
-    :param func: Callable
-    :param iterable: Iterable of arguments.
-    :param args: Passthrough to Pool.imap
-    :param kwargs: Passthrough to Pool.imap
-    :return: Results of Pool.imap.
-    """
-    if tqdm is None:
-        raise ImportError("tqdm must be installed for this function.")
-    data = []
-    with Pool(nprocs) as pool:
-        try:
-            n = len(iterable)  # type: ignore
-        except TypeError:
-            n = None  # type: ignore
-        with tqdm(total=n) as pbar:
-            for i, d in enumerate(pool.imap(func, iterable, *args, **kwargs)):
-                pbar.update()
-                data.append(d)
-    return data

-
- -
-
-
-
- -
-
- -
- © Copyright 2014, Shyue Ping Ong. -
- - - - \ No newline at end of file diff --git a/docs/_modules/monty/operator.html b/docs/_modules/monty/operator.html deleted file mode 100644 index a8a2c90d9..000000000 --- a/docs/_modules/monty/operator.html +++ /dev/null @@ -1,112 +0,0 @@ - - - - - - - monty.operator — monty 2023.5.8 documentation - - - - - - - - - - - - - - - - - -
-
-
-
- -

Source code for monty.operator

-"""
-Useful additional functions for operators
-"""
-import operator
-
-
-
[docs]def operator_from_str(op):
-    """
-    Return the operator associated to the given string `op`.
-
-    raises:
-        `KeyError` if invalid string.
-    """
-    d = {
-        "==": operator.eq,
-        "!=": operator.ne,
-        ">": operator.gt,
-        ">=": operator.ge,
-        "<": operator.lt,
-        "<=": operator.le,
-        "+": operator.add,
-        "-": operator.sub,
-        "*": operator.mul,
-        "%": operator.mod,
-        "^": operator.xor,
-    }
-
-    try:
-        d["/"] = operator.truediv
-    except AttributeError:
-        pass
-
-    return d[op]

-
- -
-
-
-
- -
-
- -
- © Copyright 2014, Shyue Ping Ong. -
- - - - \ No newline at end of file diff --git a/docs/_modules/monty/os.html b/docs/_modules/monty/os.html deleted file mode 100644 index f38b2cee6..000000000 --- a/docs/_modules/monty/os.html +++ /dev/null @@ -1,134 +0,0 @@ - - - - - - - monty.os — monty 2023.5.8 documentation - - - - - - - - - - - - - - - - - -
-
-
-
- -

Source code for monty.os

-"""
-Os functions, e.g., cd, makedirs_p.
-"""
-
-import errno
-import os
-from contextlib import contextmanager
-
-__author__ = "Shyue Ping Ong"
-__copyright__ = "Copyright 2013, The Materials Project"
-__version__ = "0.1"
-__maintainer__ = "Shyue Ping Ong"
-__email__ = "ongsp@ucsd.edu"
-__date__ = "1/24/14"
-
-
-
[docs]@contextmanager
-def cd(path):
-    """
-    A Fabric-inspired cd context that temporarily changes directory for
-    performing some tasks, and returns to the original working directory
-    afterwards. E.g.,
-
-        with cd("/my/path/"):
-            do_something()
-
-    Args:
-        path: Path to cd to.
-    """
-    cwd = os.getcwd()
-    os.chdir(path)
-    try:
-        yield
-    finally:
-        os.chdir(cwd)

-
-
-
[docs]def makedirs_p(path, **kwargs):
-    """
-    Wrapper for os.makedirs that does not raise an exception if the directory
-    already exists, in the fashion of "mkdir -p" command. The check is
-    performed in a thread-safe way
-
-    Args:
-        path: path of the directory to create
-        kwargs: standard kwargs for os.makedirs
-    """
-
-    try:
-        os.makedirs(path, **kwargs)
-    except OSError as exc:
-        if exc.errno == errno.EEXIST and os.path.isdir(path):
-            pass
-        else:
-            raise

-
- -
-
-
-
- -
-
- -
- © Copyright 2014, Shyue Ping Ong. -
- - - - \ No newline at end of file diff --git a/docs/_modules/monty/os/path.html b/docs/_modules/monty/os/path.html deleted file mode 100644 index abcd9552f..000000000 --- a/docs/_modules/monty/os/path.html +++ /dev/null @@ -1,206 +0,0 @@ - - - - - - - monty.os.path — monty 2023.5.8 documentation - - - - - - - - - - - - - - - - - -
-
-
-
- -

Source code for monty.os.path

-"""
-Path based methods, e.g., which, zpath, etc.
-"""
-import os
-import shutil
-
-from monty.dev import deprecated
-from monty.fnmatch import WildCard
-from monty.string import list_strings
-
-
-@deprecated(shutil.which, message="shutil.which has been available since Python 3.3. This will be removed in v2023.")
-def which(cmd):
-    """
-    Returns full path to a executable.
-
-    Args:
-        cmd (str): Executable command to search for.
-
-    Returns:
-        (str) Full path to command. None if it is not found.
-
-    Example::
-
-        full_path_to_python = which("python")
-    """
-
-    def is_exe(fp):
-        return os.path.isfile(fp) and os.access(fp, os.X_OK)
-
-    fpath, fname = os.path.split(cmd)
-    if fpath:
-        if is_exe(cmd):
-            return cmd
-    else:
-        for path in os.environ["PATH"].split(os.pathsep):
-            exe_file = os.path.join(path, cmd)
-            if is_exe(exe_file):
-                return exe_file
-    return None
-
-
-
[docs]def zpath(filename):
-    """
-    Returns an existing (zipped or unzipped) file path given the unzipped
-    version. If no path exists, returns the filename unmodified.
-
-    Args:
-        filename: filename without zip extension
-
-    Returns:
-        filename with a zip extension (unless an unzipped version
-        exists). If filename is not found, the same filename is returned
-        unchanged.
-    """
-    for ext in ["", ".gz", ".GZ", ".bz2", ".BZ2", ".z", ".Z"]:
-        zfilename = f"{filename}{ext}"
-        if os.path.exists(zfilename):
-            return zfilename
-    return filename

-
-
-
[docs]def find_exts(top, exts, exclude_dirs=None, include_dirs=None, match_mode="basename"):
-    """
-    Find all files with the extension listed in `exts` that are located within
-    the directory tree rooted at `top` (including top itself, but excluding
-    '.' and '..')
-
-    Args:
-        top (str): Root directory
-        exts (str or list of strings): List of extensions.
-        exclude_dirs (str): Wildcards used to exclude particular directories.
-            Can be concatenated via `|`
-        include_dirs (str): Wildcards used to select particular directories.
-            `include_dirs` and `exclude_dirs` are mutually exclusive
-        match_mode (str): "basename" if  match should be done on the basename.
-            "abspath" for absolute path.
-
-    Returns:
-        (list of str): Absolute paths of the files.
-
-    Examples::
-
-        # Find all pdf and ps files starting from the current directory.
-        find_exts(".", ("pdf", "ps"))
-
-        # Find all pdf files, exclude hidden directories and dirs whose name
-        # starts with `_`
-        find_exts(".", "pdf", exclude_dirs="_*|.*")
-
-        # Find all ps files, in the directories whose basename starts with
-        # output.
-        find_exts(".", "ps", include_dirs="output*"))
-    """
-    exts = list_strings(exts)
-
-    # Handle file!
-    if os.path.isfile(top):
-        return [os.path.abspath(top)] if any(top.endswith(ext) for ext in exts) else []
-
-    # Build shell-style wildcards.
-    if exclude_dirs is not None:
-        exclude_dirs = WildCard(exclude_dirs)
-
-    if include_dirs is not None:
-        include_dirs = WildCard(include_dirs)
-
-    mangle = dict(basename=os.path.basename, abspath=os.path.abspath)[match_mode]
-
-    # Assume directory
-    paths = []
-    for dirpath, dirnames, filenames in os.walk(top):
-        dirpath = os.path.abspath(dirpath)
-
-        if exclude_dirs and exclude_dirs.match(mangle(dirpath)):
-            continue
-        if include_dirs and not include_dirs.match(mangle(dirpath)):
-            continue
-
-        for filename in filenames:
-            if any(filename.endswith(ext) for ext in exts):
-                paths.append(os.path.join(dirpath, filename))
-
-    return paths

-
- -
-
-
-
- -
-
- -
- © Copyright 2014, Shyue Ping Ong. -
- - - - \ No newline at end of file diff --git a/docs/_modules/monty/pprint.html b/docs/_modules/monty/pprint.html deleted file mode 100644 index 69defc30f..000000000 --- a/docs/_modules/monty/pprint.html +++ /dev/null @@ -1,206 +0,0 @@ - - - - - - - monty.pprint — monty 2023.5.8 documentation - - - - - - - - - - - - - - - - - -
-
-
-
- -

Source code for monty.pprint

-"""
-Pretty printing functions.
-"""
-
-import sys
-from io import StringIO
-from json import JSONEncoder, loads
-
-
-
[docs]def pprint_table(table, out=sys.stdout, rstrip=False):
-    """
-    Prints out a table of data, padded for alignment
-    Each row must have the same number of columns.
-
-    Args:
-        table: The table to print. A list of lists.
-        out: Output stream (file-like object)
-        rstrip: if True, trailing withespaces are removed from the entries.
-    """
-
-    def max_width_col(table, col_idx):
-        """
-        Get the maximum width of the given column index
-        """
-        return max(len(row[col_idx]) for row in table)
-
-    if rstrip:
-        for row_idx, row in enumerate(table):
-            table[row_idx] = [c.rstrip() for c in row]
-
-    col_paddings = []
-    ncols = len(table[0])
-    for i in range(ncols):
-        col_paddings.append(max_width_col(table, i))
-
-    for row in table:
-        # left col
-        out.write(row[0].ljust(col_paddings[0] + 1))
-        # rest of the cols
-        for i in range(1, len(row)):
-            col = row[i].rjust(col_paddings[i] + 2)
-            out.write(col)
-        out.write("\n")

-
-
-
[docs]def draw_tree(node, child_iter=lambda n: n.children, text_str=lambda n: str(n)):
-    """
-    Args:
-        node: the root of the tree to be drawn,
-        child_iter: function that when called with a node, returns an iterable
-            over all its children
-        text_str: turns a node into the text to be displayed in the tree.
-
-    The default implementations of these two arguments retrieve the children
-    by accessing node.children and simply use str(node) to convert a node to a
-    string. The resulting tree is drawn into a buffer and returned as a string.
-
-    Based on https://pypi.python.org/pypi/asciitree/
-    """
-    return _draw_tree(node, "", child_iter, text_str)

-
-
-def _draw_tree(node, prefix, child_iter, text_str):
-    buf = StringIO()
-
-    children = list(child_iter(node))
-
-    # check if root node
-    if prefix:
-        buf.write(prefix[:-3])
-        buf.write("  +--")
-    buf.write(text_str(node))
-    buf.write("\n")
-
-    for index, child in enumerate(children):
-        if index + 1 == len(children):
-            sub_prefix = prefix + "   "
-        else:
-            sub_prefix = prefix + "  |"
-
-        buf.write(_draw_tree(child, sub_prefix, child_iter, text_str))
-
-    return buf.getvalue()
-
-
-
[docs]class DisplayEcoder(JSONEncoder):
-    """
-    Help convert dicts and objects to a format that can be displayed in notebooks
-    """
-
-
[docs]    def default(self, o):
-        """
-        Try diffent ways of converting the present object for displaying
-        """
-        try:
-            return o.as_dict()
-        except Exception:
-            pass
-
-        try:
-            return o.__dict__
-        except Exception:
-            pass
-
-        try:
-            return str(o)
-        except Exception:
-            pass
-
-        return None

-
-
-
[docs]def pprint_json(data):
-    """
-    Display a tree-like object in a jupyter notebook.
-    Allows for collapsible interactive interaction with data.
-
-    Args:
-        data: a dictionary or object
-
-    Based on:
-    https://gist.github.com/jmmshn/d37d5a1be80a6da11f901675f195ca22
-
-    """
-    from IPython.display import JSON, display  # pylint: disable=C0415
-
-    display(JSON(loads(DisplayEcoder().encode(data))))

-
- -
-
-
-
- -
-
- -
- © Copyright 2014, Shyue Ping Ong. -
- - - - \ No newline at end of file diff --git a/docs/_modules/monty/re.html b/docs/_modules/monty/re.html deleted file mode 100644 index f3661b002..000000000 --- a/docs/_modules/monty/re.html +++ /dev/null @@ -1,128 +0,0 @@ - - - - - - - monty.re — monty 2023.5.8 documentation - - - - - - - - - - - - - - - - - -
-
-
-
- -

Source code for monty.re

-"""
-Helpful regex based functions. E.g., grepping.
-"""
-
-import collections
-import re
-
-from monty.io import reverse_readfile, zopen
-
-
-
[docs]def regrep(filename, patterns, reverse=False, terminate_on_match=False, postprocess=str):
-    r"""
-    A powerful regular expression version of grep.
-
-    Args:
-        filename (str): Filename to grep.
-        patterns (dict): A dict of patterns, e.g.,
-            {"energy": r"energy\\(sigma->0\\)\\s+=\\s+([\\d\\-\\.]+)"}.
-        reverse (bool): Read files in reverse. Defaults to false. Useful for
-            large files, especially when used with terminate_on_match.
-        terminate_on_match (bool): Whether to terminate when there is at
-            least one match in each key in pattern.
-        postprocess (callable): A post processing function to convert all
-            matches. Defaults to str, i.e., no change.
-
-    Returns:
-        A dict of the following form:
-            {key1: [[[matches...], lineno], [[matches...], lineno],
-                    [[matches...], lineno], ...],
-            key2: ...}
-        For reverse reads, the lineno is given as a -ve number. Please note
-        that 0-based indexing is used.
-    """
-    compiled = {k: re.compile(v) for k, v in patterns.items()}
-    matches = collections.defaultdict(list)
-    gen = reverse_readfile(filename) if reverse else zopen(filename, "rt")
-    for i, l in enumerate(gen):
-        for k, p in compiled.items():
-            m = p.search(l)
-            if m:
-                matches[k].append([[postprocess(g) for g in m.groups()], -i if reverse else i])
-        if terminate_on_match and all(len(matches.get(k, [])) for k in compiled.keys()):
-            break
-    try:
-        # Try to close open file handle. Pass if it is a generator.
-        gen.close()
-    except Exception:
-        pass
-    return matches

-
- -
-
-
-
- -
-
- -
- © Copyright 2014, Shyue Ping Ong. -
- - - - \ No newline at end of file diff --git a/docs/_modules/monty/serialization.html b/docs/_modules/monty/serialization.html deleted file mode 100644 index 48aa123dd..000000000 --- a/docs/_modules/monty/serialization.html +++ /dev/null @@ -1,204 +0,0 @@ - - - - - - - monty.serialization — monty 2023.5.8 documentation - - - - - - - - - - - - - - - - - -
-
-
-
- -

Source code for monty.serialization

-"""
-This module implements serialization support for common formats such as json
-and yaml.
-"""
-import json
-import os
-
-try:
-    from ruamel.yaml import YAML
-except ImportError:
-    YAML = None  # type: ignore
-
-from monty.io import zopen
-from monty.json import MontyDecoder, MontyEncoder
-from monty.msgpack import default, object_hook
-
-try:
-    import msgpack
-except ImportError:
-    msgpack = None
-
-
-
[docs]def loadfn(fn, *args, fmt=None, **kwargs):
-    r"""
-    Loads json/yaml/msgpack directly from a filename instead of a
-    File-like object. File may also be a BZ2 (".BZ2") or GZIP (".GZ", ".Z")
-    compressed file.
-    For YAML, ruamel.yaml must be installed. The file type is automatically
-    detected from the file extension (case insensitive).
-    YAML is assumed if the filename contains ".yaml" or ".yml".
-    Msgpack is assumed if the filename contains ".mpk".
-    JSON is otherwise assumed.
-
-    Args:
-        fn (str/Path): filename or pathlib.Path.
-        *args: Any of the args supported by json/yaml.load.
-        fmt (string): If specified, the fmt specified would be used instead
-            of autodetection from filename. Supported formats right now are
-            "json", "yaml" or "mpk".
-        **kwargs: Any of the kwargs supported by json/yaml.load.
-
-    Returns:
-        (object) Result of json/yaml/msgpack.load.
-    """
-
-    if fmt is None:
-        basename = os.path.basename(fn).lower()
-        if ".mpk" in basename:
-            fmt = "mpk"
-        elif any(ext in basename for ext in (".yaml", ".yml")):
-            fmt = "yaml"
-        else:
-            fmt = "json"
-
-    if fmt == "mpk":
-        if msgpack is None:
-            raise RuntimeError("Loading of message pack files is not possible as msgpack-python is not installed.")
-        if "object_hook" not in kwargs:
-            kwargs["object_hook"] = object_hook
-        with zopen(fn, "rb") as fp:
-            return msgpack.load(fp, *args, **kwargs)  # pylint: disable=E1101
-    else:
-        with zopen(fn, "rt") as fp:
-            if fmt == "yaml":
-                if YAML is None:
-                    raise RuntimeError("Loading of YAML files requires ruamel.yaml.")
-                yaml = YAML()
-                return yaml.load(fp, *args, **kwargs)
-            if fmt == "json":
-                if "cls" not in kwargs:
-                    kwargs["cls"] = MontyDecoder
-                return json.load(fp, *args, **kwargs)
-
-            raise TypeError(f"Invalid format: {fmt}")

-
-
-
[docs]def dumpfn(obj, fn, *args, fmt=None, **kwargs):
-    r"""
-    Dump to a json/yaml directly by filename instead of a
-    File-like object. File may also be a BZ2 (".BZ2") or GZIP (".GZ", ".Z")
-    compressed file.
-    For YAML, ruamel.yaml must be installed. The file type is automatically
-    detected from the file extension (case insensitive). YAML is assumed if the
-    filename contains ".yaml" or ".yml".
-    Msgpack is assumed if the filename contains ".mpk".
-    JSON is otherwise assumed.
-
-    Args:
-        obj (object): Object to dump.
-        fn (str/Path): filename or pathlib.Path.
-        *args: Any of the args supported by json/yaml.dump.
-        **kwargs: Any of the kwargs supported by json/yaml.dump.
-
-    Returns:
-        (object) Result of json.load.
-    """
-    if fmt is None:
-        basename = os.path.basename(fn).lower()
-        if ".mpk" in basename:
-            fmt = "mpk"
-        elif any(ext in basename for ext in (".yaml", ".yml")):
-            fmt = "yaml"
-        else:
-            fmt = "json"
-
-    if fmt == "mpk":
-        if msgpack is None:
-            raise RuntimeError("Loading of message pack files is not possible as msgpack-python is not installed.")
-        if "default" not in kwargs:
-            kwargs["default"] = default
-        with zopen(fn, "wb") as fp:
-            msgpack.dump(obj, fp, *args, **kwargs)  # pylint: disable=E1101
-    else:
-        with zopen(fn, "wt") as fp:
-            if fmt == "yaml":
-                if YAML is None:
-                    raise RuntimeError("Loading of YAML files requires ruamel.yaml.")
-                yaml = YAML()
-                yaml.dump(obj, fp, *args, **kwargs)
-            elif fmt == "json":
-                if "cls" not in kwargs:
-                    kwargs["cls"] = MontyEncoder
-                fp.write(json.dumps(obj, *args, **kwargs))
-            else:
-                raise TypeError(f"Invalid format: {fmt}")

-
- -
-
-
-
- -
-
- -
- © Copyright 2014, Shyue Ping Ong. -
- - - - \ No newline at end of file diff --git a/docs/_modules/monty/shutil.html b/docs/_modules/monty/shutil.html deleted file mode 100644 index 1ba6deae0..000000000 --- a/docs/_modules/monty/shutil.html +++ /dev/null @@ -1,227 +0,0 @@ - - - - - - - monty.shutil — monty 2023.5.8 documentation - - - - - - - - - - - - - - - - - -
-
-
-
- -

Source code for monty.shutil

-"""
-Copying and zipping utilities. Works on directories mostly.
-"""
-
-import os
-import shutil
-import warnings
-from gzip import GzipFile
-
-from .io import zopen
-
-
-
[docs]def copy_r(src, dst):
-    """
-    Implements a recursive copy function similar to Unix's "cp -r" command.
-    Surprisingly, python does not have a real equivalent. shutil.copytree
-    only works if the destination directory is not present.
-
-    Args:
-        src (str): Source folder to copy.
-        dst (str): Destination folder.
-    """
-
-    abssrc = os.path.abspath(src)
-    absdst = os.path.abspath(dst)
-    try:
-        os.makedirs(absdst)
-    except OSError:
-        # If absdst exists, an OSError is raised. We ignore this error.
-        pass
-    for f in os.listdir(abssrc):
-        fpath = os.path.join(abssrc, f)
-        if os.path.isfile(fpath):
-            shutil.copy(fpath, absdst)
-        elif not absdst.startswith(fpath):
-            copy_r(fpath, os.path.join(absdst, f))
-        else:
-            warnings.warn(f"Cannot copy {fpath} to itself")

-
-
-
[docs]def gzip_dir(path, compresslevel=6):
-    """
-    Gzips all files in a directory. Note that this is different from
-    shutil.make_archive, which creates a tar archive. The aim of this method
-    is to create gzipped files that can still be read using common Unix-style
-    commands like zless or zcat.
-
-    Args:
-        path (str): Path to directory.
-        compresslevel (int): Level of compression, 1-9. 9 is default for
-            GzipFile, 6 is default for gzip.
-    """
-    for root, _, files in os.walk(path):
-        for f in files:
-            full_f = os.path.abspath(os.path.join(root, f))
-            if not f.lower().endswith("gz") and not os.path.isdir(full_f):
-                with open(full_f, "rb") as f_in, GzipFile(f"{full_f}.gz", "wb", compresslevel=compresslevel) as f_out:
-                    shutil.copyfileobj(f_in, f_out)
-                shutil.copystat(full_f, f"{full_f}.gz")
-                os.remove(full_f)

-
-
-
[docs]def compress_file(filepath, compression="gz"):
-    """
-    Compresses a file with the correct extension. Functions like standard
-    Unix command line gzip and bzip2 in the sense that the original
-    uncompressed files are not retained.
-
-    Args:
-        filepath (str): Path to file.
-        compression (str): A compression mode. Valid options are "gz" or
-            "bz2". Defaults to "gz".
-    """
-    if compression not in ["gz", "bz2"]:
-        raise ValueError("Supported compression formats are 'gz' and 'bz2'.")
-    if not filepath.lower().endswith(f".{compression}"):
-        with open(filepath, "rb") as f_in, zopen(f"{filepath}.{compression}", "wb") as f_out:
-            f_out.writelines(f_in)
-        os.remove(filepath)

-
-
-
[docs]def compress_dir(path, compression="gz"):
-    """
-    Recursively compresses all files in a directory. Note that this
-    compresses all files singly, i.e., it does not create a tar archive. For
-    that, just use Python tarfile class.
-
-    Args:
-        path (str): Path to parent directory.
-        compression (str): A compression mode. Valid options are "gz" or
-            "bz2". Defaults to gz.
-    """
-    for parent, subdirs, files in os.walk(path):
-        for f in files:
-            compress_file(os.path.join(parent, f), compression=compression)

-
-
-
[docs]def decompress_file(filepath):
-    """
-    Decompresses a file with the correct extension. Automatically detects
-    gz, bz2 or z extension.
-
-    Args:
-        filepath (str): Path to file.
-        compression (str): A compression mode. Valid options are "gz" or
-            "bz2". Defaults to "gz".
-    """
-    toks = filepath.split(".")
-    file_ext = toks[-1].upper()
-    if file_ext in ["BZ2", "GZ", "Z"]:
-        with open(".".join(toks[0:-1]), "wb") as f_out, zopen(filepath, "rb") as f_in:
-            f_out.writelines(f_in)
-        os.remove(filepath)

-
-
-
[docs]def decompress_dir(path):
-    """
-    Recursively decompresses all files in a directory.
-
-    Args:
-        path (str): Path to parent directory.
-    """
-    for parent, subdirs, files in os.walk(path):
-        for f in files:
-            decompress_file(os.path.join(parent, f))

-
-
-
[docs]def remove(path, follow_symlink=False):
-    """
-    Implements a remove function that will delete files, folder trees and
-    symlink trees
-
-    1.) Remove a file
-    2.) Remove a symlink and follow into with a recursive rm if follow_symlink
-    3.) Remove directory with rmtree
-
-    Args:
-        path (str): path to remove
-        follow_symlink(bool): follow symlinks and removes whatever is in them
-    """
-    if os.path.isfile(path):
-        os.remove(path)
-    elif os.path.islink(path):
-        if follow_symlink:
-            remove(os.readlink(path))
-        os.unlink(path)
-    else:
-        shutil.rmtree(path)

-
- -
-
-
-
- -
-
- -
- © Copyright 2014, Shyue Ping Ong. -
- - - - \ No newline at end of file diff --git a/docs/_modules/monty/string.html b/docs/_modules/monty/string.html deleted file mode 100644 index 33a88f396..000000000 --- a/docs/_modules/monty/string.html +++ /dev/null @@ -1,220 +0,0 @@ - - - - - - - monty.string — monty 2023.5.8 documentation - - - - - - - - - - - - - - - - - -
-
-
-
- -

Source code for monty.string

-"""
-Useful additional string functions.
-"""
-
-import sys
-
-
-
[docs]def remove_non_ascii(s):
-    """
-    Remove non-ascii characters in a file. Needed when support for non-ASCII
-    is not available.
-
-    Args:
-        s (str): Input string
-
-    Returns:
-        String with all non-ascii characters removed.
-    """
-    return "".join(i for i in s if ord(i) < 128)

-
-
-
[docs]def unicode2str(s):
-    """
-    Forces a unicode to a string in Python 2, but transparently handles
-    Python 3.
-
-    Args:
-        s (str/unicode): Input string / unicode.
-
-    Returns:
-        str in Python 2. Unchanged otherwise.
-    """
-    return s.encode("utf-8") if sys.version_info.major < 3 else s

-
-
-
[docs]def is_string(s):
-    """True if s behaves like a string (duck typing test)."""
-    try:
-        s + " "
-        return True
-
-    except TypeError:
-        return False

-
-
-
[docs]def list_strings(arg):
-    """
-    Always return a list of strings, given a string or list of strings as
-    input.
-
-    :Examples:
-
-    >>> list_strings('A single string')
-    ['A single string']
-
-    >>> list_strings(['A single string in a list'])
-    ['A single string in a list']
-
-    >>> list_strings(['A','list','of','strings'])
-    ['A', 'list', 'of', 'strings']
-    """
-    if is_string(arg):
-        return [arg]
-
-    return arg

-
-
-
[docs]def marquee(text="", width=78, mark="*"):
-    """
-    Return the input string centered in a 'marquee'.
-
-    Args:
-        text (str): Input string
-        width (int): Width of final output string.
-        mark (str): Character used to fill string.
-
-    :Examples:
-
-    >>> marquee('A test', width=40)
-    '**************** A test ****************'
-
-    >>> marquee('A test', width=40, mark='-')
-    '---------------- A test ----------------'
-
-    marquee('A test',40, ' ')
-    '                 A test                 '
-    """
-    if not text:
-        return (mark * width)[:width]
-
-    nmark = (width - len(text) - 2) // len(mark) // 2
-    nmark = max(nmark, 0)
-
-    marks = mark * nmark
-    return f"{marks} {text} {marks}"

-
-
-
[docs]def boxed(msg, ch="=", pad=5):
-    """
-    Returns a string in a box
-
-    Args:
-        msg: Input string.
-        ch: Character used to form the box.
-        pad: Number of characters ch added before and after msg.
-
-    >>> print(boxed("hello", ch="*", pad=2))
-    ***********
-    ** hello **
-    ***********
-    """
-    if pad > 0:
-        msg = pad * ch + " " + msg.strip() + " " + pad * ch
-
-    return "\n".join(
-        [
-            len(msg) * ch,
-            msg,
-            len(msg) * ch,
-        ]
-    )

-
-
-
[docs]def make_banner(s, width=78, mark="*"):
-    """
-    :param s: String
-    :param width: Width of banner. Defaults to 78.
-    :param mark: The mark used to create the banner.
-    :return: Banner string.
-    """
-    banner = marquee(s, width=width, mark=mark)
-    return "\n" + len(banner) * mark + "\n" + banner + "\n" + len(banner) * mark

-
-
-
[docs]def indent(lines, amount, ch=" "):
-    """
-    Indent the lines in a string by padding each one with proper number of pad
-    characters
-    """
-    padding = amount * ch
-    return padding + ("\n" + padding).join(lines.split("\n"))

-
- -
-
-
-
- -
-
- -
- © Copyright 2014, Shyue Ping Ong. -
- - - - \ No newline at end of file diff --git a/docs/_modules/monty/subprocess.html b/docs/_modules/monty/subprocess.html deleted file mode 100644 index 6fe15b8f0..000000000 --- a/docs/_modules/monty/subprocess.html +++ /dev/null @@ -1,181 +0,0 @@ - - - - - - - monty.subprocess — monty 2023.5.8 documentation - - - - - - - - - - - - - - - - - -
-
-
-
- -

Source code for monty.subprocess

-"""
-Calling shell processes.
-"""
-import shlex
-import threading
-import traceback
-from subprocess import PIPE, Popen
-
-from .string import is_string
-
-__author__ = "Matteo Giantomass"
-__copyright__ = "Copyright 2014, The Materials Virtual Lab"
-__version__ = "0.1"
-__maintainer__ = "Matteo Giantomassi"
-__email__ = "gmatteo@gmail.com"
-__date__ = "10/26/14"
-
-
-
[docs]class Command:
-    """
-    Enables to run subprocess commands in a different thread with TIMEOUT
-    option.
-
-    Based on jcollado's solution:
-        http://stackoverflow.com/questions/1191374/subprocess-with-timeout/4825933#4825933
-    and
-        https://gist.github.com/kirpit/1306188
-
-    .. attribute:: retcode
-
-        Return code of the subprocess
-
-    .. attribute:: killed
-
-        True if subprocess has been killed due to the timeout
-
-    .. attribute:: output
-
-        stdout of the subprocess
-
-    .. attribute:: error
-
-        stderr of the subprocess
-
-    Example:
-        com = Command("sleep 1").run(timeout=2)
-        print(com.retcode, com.killed, com.output, com.output)
-    """
-
-    def __init__(self, command):
-        """
-        :param command: Command to execute
-        """
-        if is_string(command):
-            command = shlex.split(command)
-        self.command = command
-        self.process = None
-        self.retcode = None
-        self.output, self.error = "", ""
-        self.killed = False
-
-    def __str__(self):
-        return f"command: {self.command}, retcode: {self.retcode}"
-
-
[docs]    def run(self, timeout=None, **kwargs):
-        """
-        Run a command in a separated thread and wait timeout seconds.
-        kwargs are keyword arguments passed to Popen.
-
-        Return: self
-        """
-
-        def target(**kw):
-            try:
-                # print('Thread started')
-                with Popen(self.command, **kw) as self.process:
-                    self.output, self.error = self.process.communicate()
-                    self.retcode = self.process.returncode
-                # print('Thread stopped')
-            except Exception:
-                self.error = traceback.format_exc()
-                self.retcode = -1
-
-        # default stdout and stderr
-        if "stdout" not in kwargs:
-            kwargs["stdout"] = PIPE
-
-        if "stderr" not in kwargs:
-            kwargs["stderr"] = PIPE
-
-        # thread
-        thread = threading.Thread(target=target, kwargs=kwargs)
-        thread.start()
-        thread.join(timeout)
-
-        if thread.is_alive():
-            # print("Terminating process")
-            self.process.terminate()
-            self.killed = True
-            thread.join()
-
-        return self

-
- -
-
-
-
- -
-
- -
- © Copyright 2014, Shyue Ping Ong. -
- - - - \ No newline at end of file diff --git a/docs/_modules/monty/tempfile.html b/docs/_modules/monty/tempfile.html deleted file mode 100644 index 0081421cb..000000000 --- a/docs/_modules/monty/tempfile.html +++ /dev/null @@ -1,205 +0,0 @@ - - - - - - - monty.tempfile — monty 2023.5.8 documentation - - - - - - - - - - - - - - - - - -
-
-
-
- -

Source code for monty.tempfile

-"""
-Temporary directory and file creation utilities.
-"""
-
-import os
-import tempfile
-from pathlib import Path
-
-from monty.shutil import copy_r, gzip_dir, remove
-
-
-
[docs]class ScratchDir:
-    """
-    .. note::
-
-        With effect from Python 3.2, tempfile.TemporaryDirectory already
-        implements much of the functionality of ScratchDir. However, it does
-        not provide options for copying of files to and from (though it is
-        possible to do this with other methods provided by shutil).
-
-    Creates a "with" context manager that automatically handles creation of
-    temporary directories (utilizing Python's build in temp directory
-    functions) and cleanup when done. This improves on Python's built in
-    functions by allowing for truly temporary workspace that are deleted
-    when it is done. The way it works is as follows:
-
-    1. Create a temp dir in specified root path.
-    2. Optionally copy input files from current directory to temp dir.
-    3. Change to temp dir.
-    4. User performs specified operations.
-    5. Optionally copy generated output files back to original directory.
-    6. Change back to original directory.
-    7. Delete temp dir.
-    """
-
-    SCR_LINK = "scratch_link"
-
-    def __init__(
-        self,
-        rootpath,
-        create_symbolic_link=False,
-        copy_from_current_on_enter=False,
-        copy_to_current_on_exit=False,
-        gzip_on_exit=False,
-        delete_removed_files=True,
-    ):
-        """
-        Initializes scratch directory given a **root** path. There is no need
-        to try to create unique directory names. The code will generate a
-        temporary sub directory in the rootpath. The way to use this is using a
-        with context manager. Example::
-
-            with ScratchDir("/scratch"):
-                do_something()
-
-        If the root path does not exist or is None, this will function as a
-        simple pass through, i.e., nothing happens.
-
-        Args:
-            rootpath (str/Path): Path in which to create temp subdirectories.
-                If this is None, no temp directories will be created and
-                this will just be a simple pass through.
-            create_symbolic_link (bool): Whether to create a symbolic link in
-                the current working directory to the scratch directory
-                created.
-            copy_from_current_on_enter (bool): Whether to copy all files from
-                the current directory (recursively) to the temp dir at the
-                start, e.g., if input files are needed for performing some
-                actions. Defaults to False.
-            copy_to_current_on_exit (bool): Whether to copy files from the
-                scratch to the current directory (recursively) at the end. E
-                .g., if output files are generated during the operation.
-                Defaults to False.
-            gzip_on_exit (bool): Whether to gzip the files generated in the
-                ScratchDir before copying them back.
-                Defaults to False.
-            delete_removed_files (bool): Whether to delete files in the cwd
-                that are removed from the tmp dir.
-                Defaults to True
-        """
-        if Path is not None and isinstance(rootpath, Path):
-            rootpath = str(rootpath)
-
-        self.rootpath = os.path.abspath(rootpath) if rootpath is not None else None
-        self.cwd = os.getcwd()
-        self.create_symbolic_link = create_symbolic_link
-        self.start_copy = copy_from_current_on_enter
-        self.end_copy = copy_to_current_on_exit
-        self.gzip_on_exit = gzip_on_exit
-        self.delete_removed_files = delete_removed_files
-
-    def __enter__(self):
-        tempdir = self.cwd
-        if self.rootpath is not None and os.path.exists(self.rootpath):
-            tempdir = tempfile.mkdtemp(dir=self.rootpath)
-            self.tempdir = os.path.abspath(tempdir)
-            if self.start_copy:
-                copy_r(self.cwd, tempdir)
-            if self.create_symbolic_link:
-                os.symlink(tempdir, ScratchDir.SCR_LINK)
-            os.chdir(tempdir)
-        return tempdir
-
-    def __exit__(self, exc_type, exc_val, exc_tb):
-        if self.rootpath is not None and os.path.exists(self.rootpath):
-            if self.end_copy:
-                files = set(os.listdir(self.tempdir))
-                orig_files = set(os.listdir(self.cwd))
-
-                # gzip files
-                if self.gzip_on_exit:
-                    gzip_dir(self.tempdir)
-
-                # copy files over
-                copy_r(self.tempdir, self.cwd)
-
-                # Delete any files that are now gone
-                if self.delete_removed_files:
-                    for f in orig_files - files:
-                        fpath = os.path.join(self.cwd, f)
-                        remove(fpath)
-
-            os.chdir(self.cwd)
-            remove(self.tempdir)
-            if self.create_symbolic_link and os.path.islink(ScratchDir.SCR_LINK):
-                os.remove(ScratchDir.SCR_LINK)

-
- -
-
-
-
- -
-
- -
- © Copyright 2014, Shyue Ping Ong. -
- - - - \ No newline at end of file diff --git a/docs/_modules/monty/termcolor.html b/docs/_modules/monty/termcolor.html deleted file mode 100644 index 894143002..000000000 --- a/docs/_modules/monty/termcolor.html +++ /dev/null @@ -1,285 +0,0 @@ - - - - - - - monty.termcolor — monty 2023.5.8 documentation - - - - - - - - - - - - - - - - - -
-
-
-
- -

Source code for monty.termcolor

-"""
-Copyright (c) 2008-2011 Volvox Development Team
-
-# Permission is hereby granted, free of charge, to any person obtaining a copy
-# of this software and associated documentation files (the "Software"), to deal
-# in the Software without restriction, including without limitation the rights
-# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-# copies of the Software, and to permit persons to whom the Software is
-# furnished to do so, subject to the following conditions:
-#
-# The above copyright notice and this permission notice shall be included in
-# all copies or substantial portions of the Software.
-#
-# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
-# THE SOFTWARE.
-#
-# Author: Konstantin Lepa <konstantin.lepa@gmail.com>
-
-ANSII Color formatting for output in terminal.
-"""
-import os
-
-try:
-    import curses
-    import fcntl
-    import struct
-    import termios
-except Exception:
-    pass
-
-__all__ = ["colored", "cprint"]
-
-VERSION = (1, 1, 0)
-
-ATTRIBUTES = dict(bold=1, dark=2, underline=4, blink=5, reverse=7, concealed=8)
-
-HIGHLIGHTS = dict(
-    on_grey=40,
-    on_red=41,
-    on_green=42,
-    on_yellow=43,
-    on_blue=44,
-    on_magenta=45,
-    on_cyan=46,
-    on_white=47,
-)
-
-COLORS = dict(grey=30, red=31, green=32, yellow=33, blue=34, magenta=35, cyan=36, white=37)
-
-RESET = "\033[0m"
-
-__ISON = True
-
-
-def enable(true_false):
-    """Enable/Disable ANSII Color formatting"""
-    global __ISON
-    __ISON = true_false
-
-
-def ison():
-    """True if ANSII Color formatting is activated."""
-    return __ISON
-
-
-def stream_has_colours(stream):
-    """
-    True if stream supports colours. Python cookbook, #475186
-    """
-    if not hasattr(stream, "isatty"):
-        return False
-
-    if not stream.isatty():
-        return False  # auto color only on TTYs
-    try:
-        curses.setupterm()
-        return curses.tigetnum("colors") > 2
-    except Exception:
-        return False  # guess false in case of error
-
-
-
[docs]def colored(text, color=None, on_color=None, attrs=None):
-    """Colorize text.
-
-    Available text colors:
-        red, green, yellow, blue, magenta, cyan, white.
-
-    Available text highlights:
-        on_red, on_green, on_yellow, on_blue, on_magenta, on_cyan, on_white.
-
-    Available attributes:
-        bold, dark, underline, blink, reverse, concealed.
-
-    Example:
-        colored('Hello, World!', 'red', 'on_grey', ['blue', 'blink'])
-        colored('Hello, World!', 'green')
-    """
-
-    if __ISON and os.getenv("ANSI_COLORS_DISABLED") is None:
-        fmt_str = "\033[%dm%s"
-        if color is not None:
-            text = fmt_str % (COLORS[color], text)
-
-        if on_color is not None:
-            text = fmt_str % (HIGHLIGHTS[on_color], text)
-
-        if attrs is not None:
-            for attr in attrs:
-                text = fmt_str % (ATTRIBUTES[attr], text)
-
-        text += RESET
-    return text

-
-
-
[docs]def cprint(text, color=None, on_color=None, attrs=None, **kwargs):
-    """Print colorize text.
-
-    It accepts arguments of print function.
-    """
-    try:
-        print((colored(text, color, on_color, attrs)), **kwargs)
-    except TypeError:
-        # flush is not supported by py2.7
-        kwargs.pop("flush", None)
-        print((colored(text, color, on_color, attrs)), **kwargs)

-
-
-def colored_map(text, cmap):
-    """
-    Return colorized text. cmap is a dict mapping tokens to color options.
-
-    .. Example:
-
-        colored_key("foo bar", {bar: "green"})
-        colored_key("foo bar", {bar: {"color": "green", "on_color": "on_red"}})
-    """
-    if not __ISON:
-        return text
-    for key, v in cmap.items():
-        if isinstance(v, dict):
-            text = text.replace(key, colored(key, **v))
-        else:
-            text = text.replace(key, colored(key, color=v))
-    return text
-
-
-def cprint_map(text, cmap, **kwargs):
-    """
-    Print colorize text.
-    cmap is a dict mapping keys to color options.
-    kwargs are passed to print function
-
-    Example:
-        cprint_map("Hello world", {"Hello": "red"})
-    """
-    try:
-        print(colored_map(text, cmap), **kwargs)
-    except TypeError:
-        # flush is not supported by py2.7
-        kwargs.pop("flush", None)
-        print(colored_map(text, cmap), **kwargs)
-
-
-def get_terminal_size():
-    """
-    Return the size of the terminal as (nrow, ncols)
-
-    Based on:
-
-        http://stackoverflow.com/questions/566746/how-to-get-console-window-
-        width-in-python
-    """
-    try:
-        rc = os.popen("stty size", "r").read().split()
-        return int(rc[0]), int(rc[1])
-    except Exception:
-        pass
-
-    env = os.environ
-
-    def ioctl_GWINSZ(fd):
-        try:
-            rc = struct.unpack("hh", fcntl.ioctl(fd, termios.TIOCGWINSZ, "1234"))
-            return rc
-        except Exception:
-            return None
-
-    rc = ioctl_GWINSZ(0) or ioctl_GWINSZ(1) or ioctl_GWINSZ(2)
-
-    if not rc:
-        try:
-            fd = os.open(os.ctermid(), os.O_RDONLY)
-            rc = ioctl_GWINSZ(fd)
-            os.close(fd)
-        except Exception:
-            pass
-
-    if not rc:
-        rc = (env.get("LINES", 25), env.get("COLUMNS", 80))
-
-    return int(rc[0]), int(rc[1])
-
- -
-
-
-
- -
-
- -
- © Copyright 2014, Shyue Ping Ong. -
- - - - \ No newline at end of file diff --git a/docs/_static/_sphinx_javascript_frameworks_compat.js b/docs/_static/_sphinx_javascript_frameworks_compat.js deleted file mode 100644 index 8549469dc..000000000 --- a/docs/_static/_sphinx_javascript_frameworks_compat.js +++ /dev/null @@ -1,134 +0,0 @@ -/* - * _sphinx_javascript_frameworks_compat.js - * ~~~~~~~~~~ - * - * Compatability shim for jQuery and underscores.js. - * - * WILL BE REMOVED IN Sphinx 6.0 - * xref RemovedInSphinx60Warning - * - */ - -/** - * select a different prefix for underscore - */ -$u = _.noConflict(); - - -/** - * small helper function to urldecode strings - * - * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL - */ -jQuery.urldecode = function(x) { - if (!x) { - return x - } - return decodeURIComponent(x.replace(/\+/g, ' ')); -}; - -/** - * small helper function to urlencode strings - */ -jQuery.urlencode = encodeURIComponent; - -/** - * This function returns the parsed url parameters of the - * current request. Multiple values per key are supported, - * it will always return arrays of strings for the value parts. - */ -jQuery.getQueryParameters = function(s) { - if (typeof s === 'undefined') - s = document.location.search; - var parts = s.substr(s.indexOf('?') + 1).split('&'); - var result = {}; - for (var i = 0; i < parts.length; i++) { - var tmp = parts[i].split('=', 2); - var key = jQuery.urldecode(tmp[0]); - var value = jQuery.urldecode(tmp[1]); - if (key in result) - result[key].push(value); - else - result[key] = [value]; - } - return result; -}; - -/** - * highlight a given string on a jquery object by wrapping it in - * span elements with the given class name. - */ -jQuery.fn.highlightText = function(text, className) { - function highlight(node, addItems) { - if (node.nodeType === 3) { - var val = node.nodeValue; - var pos = val.toLowerCase().indexOf(text); - if (pos >= 0 && - !jQuery(node.parentNode).hasClass(className) && - !jQuery(node.parentNode).hasClass("nohighlight")) { - var span; - var isInSVG = jQuery(node).closest("body, svg, foreignObject").is("svg"); - if (isInSVG) { - span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); - } else { - span = document.createElement("span"); - span.className = className; - } - span.appendChild(document.createTextNode(val.substr(pos, text.length))); - node.parentNode.insertBefore(span, node.parentNode.insertBefore( - document.createTextNode(val.substr(pos + text.length)), - node.nextSibling)); - node.nodeValue = val.substr(0, pos); - if (isInSVG) { - var rect = document.createElementNS("http://www.w3.org/2000/svg", "rect"); - var bbox = node.parentElement.getBBox(); - rect.x.baseVal.value = bbox.x; - rect.y.baseVal.value = bbox.y; - rect.width.baseVal.value = bbox.width; - rect.height.baseVal.value = bbox.height; - rect.setAttribute('class', className); - addItems.push({ - "parent": node.parentNode, - "target": rect}); - } - } - } - else if (!jQuery(node).is("button, select, textarea")) { - jQuery.each(node.childNodes, function() { - highlight(this, addItems); - }); - } - } - var addItems = []; - var result = this.each(function() { - highlight(this, addItems); - }); - for (var i = 0; i < addItems.length; ++i) { - jQuery(addItems[i].parent).before(addItems[i].target); - } - return result; -}; - -/* - * backward compatibility for jQuery.browser - * This will be supported until firefox bug is fixed. - */ -if (!jQuery.browser) { - jQuery.uaMatch = function(ua) { - ua = ua.toLowerCase(); - - var match = /(chrome)[ \/]([\w.]+)/.exec(ua) || - /(webkit)[ \/]([\w.]+)/.exec(ua) || - /(opera)(?:.*version|)[ \/]([\w.]+)/.exec(ua) || - /(msie) ([\w.]+)/.exec(ua) || - ua.indexOf("compatible") < 0 && /(mozilla)(?:.*? rv:([\w.]+)|)/.exec(ua) || - []; - - return { - browser: match[ 1 ] || "", - version: match[ 2 ] || "0" - }; - }; - jQuery.browser = {}; - jQuery.browser[jQuery.uaMatch(navigator.userAgent).browser] = true; -} diff --git a/docs/_static/ajax-loader.gif b/docs/_static/ajax-loader.gif deleted file mode 100644 index 61faf8cab23993bd3e1560bff0668bd628642330..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 673 zcmZ?wbhEHb6krfw_{6~Q|Nno%(3)e{?)x>&1u}A`t?OF7Z|1gRivOgXi&7IyQd1Pl zGfOfQ60;I3a`F>X^fL3(@);C=vM_KlFfb_o=k{|A33hf2a5d61U}gjg=>Rd%XaNQW zW@Cw{|b%Y*pl8F?4B9 zlo4Fz*0kZGJabY|>}Okf0}CCg{u4`zEPY^pV?j2@h+|igy0+Kz6p;@SpM4s6)XEMg z#3Y4GX>Hjlml5ftdH$4x0JGdn8~MX(U~_^d!Hi)=HU{V%g+mi8#UGbE-*ao8f#h+S z2a0-5+vc7MU$e-NhmBjLIC1v|)9+Im8x1yacJ7{^tLX(ZhYi^rpmXm0`@ku9b53aN zEXH@Y3JaztblgpxbJt{AtE1ad1Ca>{v$rwwvK(>{m~Gf_=-Ro7Fk{#;i~+{{>QtvI yb2P8Zac~?~=sRA>$6{!(^3;ZP0TPFR(G_-UDU(8Jl0?(IXu$~#4A!880|o%~Al1tN diff --git a/docs/_static/basic.css b/docs/_static/basic.css deleted file mode 100644 index 7577acb1a..000000000 --- a/docs/_static/basic.css +++ /dev/null @@ -1,903 +0,0 @@ -/* - * basic.css - * ~~~~~~~~~ - * - * Sphinx stylesheet -- basic theme. - * - * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS. - * :license: BSD, see LICENSE for details. - * - */ - -/* -- main layout ----------------------------------------------------------- */ - -div.clearer { - clear: both; -} - -div.section::after { - display: block; - content: ''; - clear: left; -} - -/* -- relbar ---------------------------------------------------------------- */ - -div.related { - width: 100%; - font-size: 90%; -} - -div.related h3 { - display: none; -} - -div.related ul { - margin: 0; - padding: 0 0 0 10px; - list-style: none; -} - -div.related li { - display: inline; -} - -div.related li.right { - float: right; - margin-right: 5px; -} - -/* -- sidebar --------------------------------------------------------------- */ - -div.sphinxsidebarwrapper { - padding: 10px 5px 0 10px; -} - -div.sphinxsidebar { - float: left; - width: 230px; - margin-left: -100%; - font-size: 90%; - word-wrap: break-word; - overflow-wrap : break-word; -} - -div.sphinxsidebar ul { - list-style: none; -} - -div.sphinxsidebar ul ul, -div.sphinxsidebar ul.want-points { - margin-left: 20px; - list-style: square; -} - -div.sphinxsidebar ul ul { - margin-top: 0; - margin-bottom: 0; -} - -div.sphinxsidebar form { - margin-top: 10px; -} - -div.sphinxsidebar input { - border: 1px solid #98dbcc; - font-family: sans-serif; - font-size: 1em; -} - -div.sphinxsidebar #searchbox form.search { - overflow: hidden; -} - -div.sphinxsidebar #searchbox input[type="text"] { - float: left; - width: 80%; - padding: 0.25em; - box-sizing: border-box; -} - -div.sphinxsidebar #searchbox input[type="submit"] { - float: left; - width: 20%; - border-left: none; - padding: 0.25em; - box-sizing: border-box; -} - - -img { - border: 0; - max-width: 100%; -} - -/* -- search page ----------------------------------------------------------- */ - -ul.search { - margin: 10px 0 0 20px; - padding: 0; -} - -ul.search li { - padding: 5px 0 5px 20px; - background-image: url(file.png); - background-repeat: no-repeat; - background-position: 0 7px; -} - -ul.search li a { - font-weight: bold; -} - -ul.search li p.context { - color: #888; - margin: 2px 0 0 30px; - text-align: left; -} - -ul.keywordmatches li.goodmatch a { - font-weight: bold; -} - -/* -- index page ------------------------------------------------------------ */ - -table.contentstable { - width: 90%; - margin-left: auto; - margin-right: auto; -} - -table.contentstable p.biglink { - line-height: 150%; -} - -a.biglink { - font-size: 1.3em; -} - -span.linkdescr { - font-style: italic; - padding-top: 5px; - font-size: 90%; -} - -/* -- general index --------------------------------------------------------- */ - -table.indextable { - width: 100%; -} - -table.indextable td { - text-align: left; - vertical-align: top; -} - -table.indextable ul { - margin-top: 0; - margin-bottom: 0; - list-style-type: none; -} - -table.indextable > tbody > tr > td > ul { - padding-left: 0em; -} - -table.indextable tr.pcap { - height: 10px; -} - -table.indextable tr.cap { - margin-top: 10px; - background-color: #f2f2f2; -} - -img.toggler { - margin-right: 3px; - margin-top: 3px; - cursor: pointer; -} - -div.modindex-jumpbox { - border-top: 1px solid #ddd; - border-bottom: 1px solid #ddd; - margin: 1em 0 1em 0; - padding: 0.4em; -} - -div.genindex-jumpbox { - border-top: 1px solid #ddd; - border-bottom: 1px solid #ddd; - margin: 1em 0 1em 0; - padding: 0.4em; -} - -/* -- domain module index --------------------------------------------------- */ - -table.modindextable td { - padding: 2px; - border-collapse: collapse; -} - -/* -- general body styles --------------------------------------------------- */ - -div.body { - min-width: 360px; - max-width: 800px; -} - -div.body p, div.body dd, div.body li, div.body blockquote { - -moz-hyphens: auto; - -ms-hyphens: auto; - -webkit-hyphens: auto; - hyphens: auto; -} - -a.headerlink { - visibility: hidden; -} - -h1:hover > a.headerlink, -h2:hover > a.headerlink, -h3:hover > a.headerlink, -h4:hover > a.headerlink, -h5:hover > a.headerlink, -h6:hover > a.headerlink, -dt:hover > a.headerlink, -caption:hover > a.headerlink, -p.caption:hover > a.headerlink, -div.code-block-caption:hover > a.headerlink { - visibility: visible; -} - -div.body p.caption { - text-align: inherit; -} - -div.body td { - text-align: left; -} - -.first { - margin-top: 0 !important; -} - -p.rubric { - margin-top: 30px; - font-weight: bold; -} - -img.align-left, figure.align-left, .figure.align-left, object.align-left { - clear: left; - float: left; - margin-right: 1em; -} - -img.align-right, figure.align-right, .figure.align-right, object.align-right { - clear: right; - float: right; - margin-left: 1em; -} - -img.align-center, figure.align-center, .figure.align-center, object.align-center { - display: block; - margin-left: auto; - margin-right: auto; -} - -img.align-default, figure.align-default, .figure.align-default { - display: block; - margin-left: auto; - margin-right: auto; -} - -.align-left { - text-align: left; -} - -.align-center { - text-align: center; -} - -.align-default { - text-align: center; -} - -.align-right { - text-align: right; -} - -/* -- sidebars -------------------------------------------------------------- */ - -div.sidebar, -aside.sidebar { - margin: 0 0 0.5em 1em; - border: 1px solid #ddb; - padding: 7px; - background-color: #ffe; - width: 40%; - float: right; - clear: right; - overflow-x: auto; -} - -p.sidebar-title { - font-weight: bold; -} - -nav.contents, -aside.topic, -div.admonition, div.topic, blockquote { - clear: left; -} - -/* -- topics ---------------------------------------------------------------- */ - -nav.contents, -aside.topic, -div.topic { - border: 1px solid #ccc; - padding: 7px; - margin: 10px 0 10px 0; -} - -p.topic-title { - font-size: 1.1em; - font-weight: bold; - margin-top: 10px; -} - -/* -- admonitions ----------------------------------------------------------- */ - -div.admonition { - margin-top: 10px; - margin-bottom: 10px; - padding: 7px; -} - -div.admonition dt { - font-weight: bold; -} - -p.admonition-title { - margin: 0px 10px 5px 0px; - font-weight: bold; -} - -div.body p.centered { - text-align: center; - margin-top: 25px; -} - -/* -- content of sidebars/topics/admonitions -------------------------------- */ - -div.sidebar > :last-child, -aside.sidebar > :last-child, -nav.contents > :last-child, -aside.topic > :last-child, -div.topic > :last-child, -div.admonition > :last-child { - margin-bottom: 0; -} - -div.sidebar::after, -aside.sidebar::after, -nav.contents::after, -aside.topic::after, -div.topic::after, -div.admonition::after, -blockquote::after { - display: block; - content: ''; - clear: both; -} - -/* -- tables ---------------------------------------------------------------- */ - -table.docutils { - margin-top: 10px; - margin-bottom: 10px; - border: 0; - border-collapse: collapse; -} - -table.align-center { - margin-left: auto; - margin-right: auto; -} - -table.align-default { - margin-left: auto; - margin-right: auto; -} - -table caption span.caption-number { - font-style: italic; -} - -table caption span.caption-text { -} - -table.docutils td, table.docutils th { - padding: 1px 8px 1px 5px; - border-top: 0; - border-left: 0; - border-right: 0; - border-bottom: 1px solid #aaa; -} - -th { - text-align: left; - padding-right: 5px; -} - -table.citation { - border-left: solid 1px gray; - margin-left: 1px; -} - -table.citation td { - border-bottom: none; -} - -th > :first-child, -td > :first-child { - margin-top: 0px; -} - -th > :last-child, -td > :last-child { - margin-bottom: 0px; -} - -/* -- figures --------------------------------------------------------------- */ - -div.figure, figure { - margin: 0.5em; - padding: 0.5em; -} - -div.figure p.caption, figcaption { - padding: 0.3em; -} - -div.figure p.caption span.caption-number, -figcaption span.caption-number { - font-style: italic; -} - -div.figure p.caption span.caption-text, -figcaption span.caption-text { -} - -/* -- field list styles ----------------------------------------------------- */ - -table.field-list td, table.field-list th { - border: 0 !important; -} - -.field-list ul { - margin: 0; - padding-left: 1em; -} - -.field-list p { - margin: 0; -} - -.field-name { - -moz-hyphens: manual; - -ms-hyphens: manual; - -webkit-hyphens: manual; - hyphens: manual; -} - -/* -- hlist styles ---------------------------------------------------------- */ - -table.hlist { - margin: 1em 0; -} - -table.hlist td { - vertical-align: top; -} - -/* -- object description styles --------------------------------------------- */ - -.sig { - font-family: 'Consolas', 'Menlo', 'DejaVu Sans Mono', 'Bitstream Vera Sans Mono', monospace; -} - -.sig-name, code.descname { - background-color: transparent; - font-weight: bold; -} - -.sig-name { - font-size: 1.1em; -} - -code.descname { - font-size: 1.2em; -} - -.sig-prename, code.descclassname { - background-color: transparent; -} - -.optional { - font-size: 1.3em; -} - -.sig-paren { - font-size: larger; -} - -.sig-param.n { - font-style: italic; -} - -/* C++ specific styling */ - -.sig-inline.c-texpr, -.sig-inline.cpp-texpr { - font-family: unset; -} - -.sig.c .k, .sig.c .kt, -.sig.cpp .k, .sig.cpp .kt { - color: #0033B3; -} - -.sig.c .m, -.sig.cpp .m { - color: #1750EB; -} - -.sig.c .s, .sig.c .sc, -.sig.cpp .s, .sig.cpp .sc { - color: #067D17; -} - - -/* -- other body styles ----------------------------------------------------- */ - -ol.arabic { - list-style: decimal; -} - -ol.loweralpha { - list-style: lower-alpha; -} - -ol.upperalpha { - list-style: upper-alpha; -} - -ol.lowerroman { - list-style: lower-roman; -} - -ol.upperroman { - list-style: upper-roman; -} - -:not(li) > ol > li:first-child > :first-child, -:not(li) > ul > li:first-child > :first-child { - margin-top: 0px; -} - -:not(li) > ol > li:last-child > :last-child, -:not(li) > ul > li:last-child > :last-child { - margin-bottom: 0px; -} - -ol.simple ol p, -ol.simple ul p, -ul.simple ol p, -ul.simple ul p { - margin-top: 0; -} - -ol.simple > li:not(:first-child) > p, -ul.simple > li:not(:first-child) > p { - margin-top: 0; -} - -ol.simple p, -ul.simple p { - margin-bottom: 0; -} - -aside.footnote > span, -div.citation > span { - float: left; -} -aside.footnote > span:last-of-type, -div.citation > span:last-of-type { - padding-right: 0.5em; -} -aside.footnote > p { - margin-left: 2em; -} -div.citation > p { - margin-left: 4em; -} -aside.footnote > p:last-of-type, -div.citation > p:last-of-type { - margin-bottom: 0em; -} -aside.footnote > p:last-of-type:after, -div.citation > p:last-of-type:after { - content: ""; - clear: both; -} - -dl.field-list { - display: grid; - grid-template-columns: fit-content(30%) auto; -} - -dl.field-list > dt { - font-weight: bold; - word-break: break-word; - padding-left: 0.5em; 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- event.preventDefault(); - } - break; - case "ArrowRight": - if (!DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS) break; - - const nextLink = document.querySelector('link[rel="next"]'); - if (nextLink && nextLink.href) { - window.location.href = nextLink.href; - event.preventDefault(); - } - break; - } - } - - // some keyboard layouts may need Shift to get / - switch (event.key) { - case "/": - if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) break; - Documentation.focusSearchBar(); - event.preventDefault(); - } - }); - }, -}; - -// quick alias for translations -const _ = Documentation.gettext; - -_ready(Documentation.init); diff --git a/docs/_static/documentation_options.js b/docs/_static/documentation_options.js deleted file mode 100644 index 40ea65095..000000000 --- a/docs/_static/documentation_options.js +++ /dev/null @@ -1,14 +0,0 @@ -var DOCUMENTATION_OPTIONS = { - URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'), - VERSION: '2023.5.8', - LANGUAGE: 'en', - COLLAPSE_INDEX: false, - BUILDER: 'html', - FILE_SUFFIX: '.html', - LINK_SUFFIX: '.html', - HAS_SOURCE: true, - SOURCELINK_SUFFIX: '.txt', - NAVIGATION_WITH_KEYS: false, - SHOW_SEARCH_SUMMARY: true, - ENABLE_SEARCH_SHORTCUTS: true, -}; 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- } - - div.document { - width: 100%; - - } - - div.documentwrapper { - margin-left: 0; - margin-top: 0; - margin-right: 0; - margin-bottom: 0; - } - - div.bodywrapper { - margin-top: 0; - margin-right: 0; - margin-bottom: 0; - margin-left: 0; - } - - ul { - margin-left: 0; - } - - .document { - width: auto; - } - - .footer { - width: auto; - } - - .bodywrapper { - margin: 0; - } - - .footer { - width: auto; - } - - .github { - display: none; - } - -} - -/* misc. */ - -.revsys-inline { - display: none!important; -} \ No newline at end of file diff --git a/docs/_static/jquery-3.1.0.js b/docs/_static/jquery-3.1.0.js deleted file mode 100644 index f2fc27478..000000000 --- a/docs/_static/jquery-3.1.0.js +++ /dev/null @@ -1,10074 +0,0 @@ -/*eslint-disable no-unused-vars*/ -/*! - * jQuery JavaScript Library v3.1.0 - * https://jquery.com/ - * - * Includes Sizzle.js - * https://sizzlejs.com/ - * - * Copyright jQuery Foundation and other contributors - * Released under the MIT license - * https://jquery.org/license - * - * Date: 2016-07-07T21:44Z - */ -( function( global, factory ) { - - "use strict"; - - if ( typeof module === "object" && typeof module.exports === "object" ) { - - // For CommonJS and CommonJS-like environments where a proper `window` - // is present, execute the factory and get jQuery. - // For environments that do not have a `window` with a `document` - // (such as Node.js), expose a factory as module.exports. - // This accentuates the need for the creation of a real `window`. - // e.g. var jQuery = require("jquery")(window); - // See ticket #14549 for more info. - module.exports = global.document ? - factory( global, true ) : - function( w ) { - if ( !w.document ) { - throw new Error( "jQuery requires a window with a document" ); - } - return factory( w ); - }; - } else { - factory( global ); - } - -// Pass this if window is not defined yet -} )( typeof window !== "undefined" ? window : this, function( window, noGlobal ) { - -// Edge <= 12 - 13+, Firefox <=18 - 45+, IE 10 - 11, Safari 5.1 - 9+, iOS 6 - 9.1 -// throw exceptions when non-strict code (e.g., ASP.NET 4.5) accesses strict mode -// arguments.callee.caller (trac-13335). But as of jQuery 3.0 (2016), strict mode should be common -// enough that all such attempts are guarded in a try block. -"use strict"; - -var arr = []; - -var document = window.document; - -var getProto = Object.getPrototypeOf; - -var slice = arr.slice; - -var concat = arr.concat; - -var push = arr.push; - -var indexOf = arr.indexOf; - -var class2type = {}; - -var toString = class2type.toString; - -var hasOwn = class2type.hasOwnProperty; - -var fnToString = hasOwn.toString; - -var ObjectFunctionString = fnToString.call( Object ); - -var support = {}; - - - - function DOMEval( code, doc ) { - doc = doc || document; - - var script = doc.createElement( "script" ); - - script.text = code; - doc.head.appendChild( script ).parentNode.removeChild( script ); - } -/* global Symbol */ -// Defining this global in .eslintrc would create a danger of using the global -// unguarded in another place, it seems safer to define global only for this module - - - -var - version = "3.1.0", - - // Define a local copy of jQuery - jQuery = function( selector, context ) { - - // The jQuery object is actually just the init constructor 'enhanced' - // Need init if jQuery is called (just allow error to be thrown if not included) - return new jQuery.fn.init( selector, context ); - }, - - // Support: Android <=4.0 only - // Make sure we trim BOM and NBSP - rtrim = /^[\s\uFEFF\xA0]+|[\s\uFEFF\xA0]+$/g, - - // Matches dashed string for camelizing - rmsPrefix = /^-ms-/, - rdashAlpha = /-([a-z])/g, - - // Used by jQuery.camelCase as callback to replace() - fcamelCase = function( all, letter ) { - return letter.toUpperCase(); - }; - -jQuery.fn = jQuery.prototype = { - - // The current version of jQuery being used - jquery: version, - - constructor: jQuery, - - // The default length of a jQuery object is 0 - length: 0, - - toArray: function() { - return slice.call( this ); - }, - - // Get the Nth element in the matched element set OR - // Get the whole matched element set as a clean array - get: function( num ) { - return num != null ? - - // Return just the one element from the set - ( num < 0 ? this[ num + this.length ] : this[ num ] ) : - - // Return all the elements in a clean array - slice.call( this ); - }, - - // Take an array of elements and push it onto the stack - // (returning the new matched element set) - pushStack: function( elems ) { - - // Build a new jQuery matched element set - var ret = jQuery.merge( this.constructor(), elems ); - - // Add the old object onto the stack (as a reference) - ret.prevObject = this; - - // Return the newly-formed element set - return ret; - }, - - // Execute a callback for every element in the matched set. - each: function( callback ) { - return jQuery.each( this, callback ); - }, - - map: function( callback ) { - return this.pushStack( jQuery.map( this, function( elem, i ) { - return callback.call( elem, i, elem ); - } ) ); - }, - - slice: function() { - return this.pushStack( slice.apply( this, arguments ) ); - }, - - first: function() { - return this.eq( 0 ); - }, - - last: function() { - return this.eq( -1 ); - }, - - eq: function( i ) { - var len = this.length, - j = +i + ( i < 0 ? len : 0 ); - return this.pushStack( j >= 0 && j < len ? [ this[ j ] ] : [] ); - }, - - end: function() { - return this.prevObject || this.constructor(); - }, - - // For internal use only. - // Behaves like an Array's method, not like a jQuery method. - push: push, - sort: arr.sort, - splice: arr.splice -}; - -jQuery.extend = jQuery.fn.extend = function() { - var options, name, src, copy, copyIsArray, clone, - target = arguments[ 0 ] || {}, - i = 1, - length = arguments.length, - deep = false; - - // Handle a deep copy situation - if ( typeof target === "boolean" ) { - deep = target; - - // Skip the boolean and the target - target = arguments[ i ] || {}; - i++; - } - - // Handle case when target is a string or something (possible in deep copy) - if ( typeof target !== "object" && !jQuery.isFunction( target ) ) { - target = {}; - } - - // Extend jQuery itself if only one argument is passed - if ( i === length ) { - target = this; - i--; - } - - for ( ; i < length; i++ ) { - - // Only deal with non-null/undefined values - if ( ( options = arguments[ i ] ) != null ) { - - // Extend the base object - for ( name in options ) { - src = target[ name ]; - copy = options[ name ]; - - // Prevent never-ending loop - if ( target === copy ) { - continue; - } - - // Recurse if we're merging plain objects or arrays - if ( deep && copy && ( jQuery.isPlainObject( copy ) || - ( copyIsArray = jQuery.isArray( copy ) ) ) ) { - - if ( copyIsArray ) { - copyIsArray = false; - clone = src && jQuery.isArray( src ) ? src : []; - - } else { - clone = src && jQuery.isPlainObject( src ) ? src : {}; - } - - // Never move original objects, clone them - target[ name ] = jQuery.extend( deep, clone, copy ); - - // Don't bring in undefined values - } else if ( copy !== undefined ) { - target[ name ] = copy; - } - } - } - } - - // Return the modified object - return target; -}; - -jQuery.extend( { - - // Unique for each copy of jQuery on the page - expando: "jQuery" + ( version + Math.random() ).replace( /\D/g, "" ), - - // Assume jQuery is ready without the ready module - isReady: true, - - error: function( msg ) { - throw new Error( msg ); - }, - - noop: function() {}, - - isFunction: function( obj ) { - return jQuery.type( obj ) === "function"; - }, - - isArray: Array.isArray, - - isWindow: function( obj ) { - return obj != null && obj === obj.window; - }, - - isNumeric: function( obj ) { - - // As of jQuery 3.0, isNumeric is limited to - // strings and numbers (primitives or objects) - // that can be coerced to finite numbers (gh-2662) - var type = jQuery.type( obj ); - return ( type === "number" || type === "string" ) && - - // parseFloat NaNs numeric-cast false positives ("") - // ...but misinterprets leading-number strings, particularly hex literals ("0x...") - // subtraction forces infinities to NaN - !isNaN( obj - parseFloat( obj ) ); - }, - - isPlainObject: function( obj ) { - var proto, Ctor; - - // Detect obvious negatives - // Use toString instead of jQuery.type to catch host objects - if ( !obj || toString.call( obj ) !== "[object Object]" ) { - return false; - } - - proto = getProto( obj ); - - // Objects with no prototype (e.g., `Object.create( null )`) are plain - if ( !proto ) { - return true; - } - - // Objects with prototype are plain iff they were constructed by a global Object function - Ctor = hasOwn.call( proto, "constructor" ) && proto.constructor; - return typeof Ctor === "function" && fnToString.call( Ctor ) === ObjectFunctionString; - }, - - isEmptyObject: function( obj ) { - - /* eslint-disable no-unused-vars */ - // See https://github.com/eslint/eslint/issues/6125 - var name; - - for ( name in obj ) { - return false; - } - return true; - }, - - type: function( obj ) { - if ( obj == null ) { - return obj + ""; - } - - // Support: Android <=2.3 only (functionish RegExp) - return typeof obj === "object" || typeof obj === "function" ? - class2type[ toString.call( obj ) ] || "object" : - typeof obj; - }, - - // Evaluates a script in a global context - globalEval: function( code ) { - DOMEval( code ); - }, - - // Convert dashed to camelCase; used by the css and data modules - // Support: IE <=9 - 11, Edge 12 - 13 - // Microsoft forgot to hump their vendor prefix (#9572) - camelCase: function( string ) { - return string.replace( rmsPrefix, "ms-" ).replace( rdashAlpha, fcamelCase ); - }, - - nodeName: function( elem, name ) { - return elem.nodeName && elem.nodeName.toLowerCase() === name.toLowerCase(); - }, - - each: function( obj, callback ) { - var length, i = 0; - - if ( isArrayLike( obj ) ) { - length = obj.length; - for ( ; i < length; i++ ) { - if ( callback.call( obj[ i ], i, obj[ i ] ) === false ) { - break; - } - } - } else { - for ( i in obj ) { - if ( callback.call( obj[ i ], i, obj[ i ] ) === false ) { - break; - } - } - } - - return obj; - }, - - // Support: Android <=4.0 only - trim: function( text ) { - return text == null ? - "" : - ( text + "" ).replace( rtrim, "" ); - }, - - // results is for internal usage only - makeArray: function( arr, results ) { - var ret = results || []; - - if ( arr != null ) { - if ( isArrayLike( Object( arr ) ) ) { - jQuery.merge( ret, - typeof arr === "string" ? - [ arr ] : arr - ); - } else { - push.call( ret, arr ); - } - } - - return ret; - }, - - inArray: function( elem, arr, i ) { - return arr == null ? -1 : indexOf.call( arr, elem, i ); - }, - - // Support: Android <=4.0 only, PhantomJS 1 only - // push.apply(_, arraylike) throws on ancient WebKit - merge: function( first, second ) { - var len = +second.length, - j = 0, - i = first.length; - - for ( ; j < len; j++ ) { - first[ i++ ] = second[ j ]; - } - - first.length = i; - - return first; - }, - - grep: function( elems, callback, invert ) { - var callbackInverse, - matches = [], - i = 0, - length = elems.length, - callbackExpect = !invert; - - // Go through the array, only saving the items - // that pass the validator function - for ( ; i < length; i++ ) { - callbackInverse = !callback( elems[ i ], i ); - if ( callbackInverse !== callbackExpect ) { - matches.push( elems[ i ] ); - } - } - - return matches; - }, - - // arg is for internal usage only - map: function( elems, callback, arg ) { - var length, value, - i = 0, - ret = []; - - // Go through the array, translating each of the items to their new values - if ( isArrayLike( elems ) ) { - length = elems.length; - for ( ; i < length; i++ ) { - value = callback( elems[ i ], i, arg ); - - if ( value != null ) { - ret.push( value ); - } - } - - // Go through every key on the object, - } else { - for ( i in elems ) { - value = callback( elems[ i ], i, arg ); - - if ( value != null ) { - ret.push( value ); - } - } - } - - // Flatten any nested arrays - return concat.apply( [], ret ); - }, - - // A global GUID counter for objects - guid: 1, - - // Bind a function to a context, optionally partially applying any - // arguments. - proxy: function( fn, context ) { - var tmp, args, proxy; - - if ( typeof context === "string" ) { - tmp = fn[ context ]; - context = fn; - fn = tmp; - } - - // Quick check to determine if target is callable, in the spec - // this throws a TypeError, but we will just return undefined. - if ( !jQuery.isFunction( fn ) ) { - return undefined; - } - - // Simulated bind - args = slice.call( arguments, 2 ); - proxy = function() { - return fn.apply( context || this, args.concat( slice.call( arguments ) ) ); - }; - - // Set the guid of unique handler to the same of original handler, so it can be removed - proxy.guid = fn.guid = fn.guid || jQuery.guid++; - - return proxy; - }, - - now: Date.now, - - // jQuery.support is not used in Core but other projects attach their - // properties to it so it needs to exist. - support: support -} ); - -if ( typeof Symbol === "function" ) { - jQuery.fn[ Symbol.iterator ] = arr[ Symbol.iterator ]; -} - -// Populate the class2type map -jQuery.each( "Boolean Number String Function Array Date RegExp Object Error Symbol".split( " " ), -function( i, name ) { - class2type[ "[object " + name + "]" ] = name.toLowerCase(); -} ); - -function isArrayLike( obj ) { - - // Support: real iOS 8.2 only (not reproducible in simulator) - // `in` check used to prevent JIT error (gh-2145) - // hasOwn isn't used here due to false negatives - // regarding Nodelist length in IE - var length = !!obj && "length" in obj && obj.length, - type = jQuery.type( obj ); - - if ( type === "function" || jQuery.isWindow( obj ) ) { - return false; - } - - return type === "array" || length === 0 || - typeof length === "number" && length > 0 && ( length - 1 ) in obj; -} -var Sizzle = -/*! - * Sizzle CSS Selector Engine v2.3.0 - * https://sizzlejs.com/ - * - * Copyright jQuery Foundation and other contributors - * Released under the MIT license - * http://jquery.org/license - * - * Date: 2016-01-04 - */ -(function( window ) { - -var i, - support, - Expr, - getText, - isXML, - tokenize, - compile, - select, - outermostContext, - sortInput, - hasDuplicate, - - // Local document vars - setDocument, - document, - docElem, - documentIsHTML, - rbuggyQSA, - rbuggyMatches, - matches, - contains, - - // Instance-specific data - expando = "sizzle" + 1 * new Date(), - preferredDoc = window.document, - dirruns = 0, - done = 0, - classCache = createCache(), - tokenCache = createCache(), - compilerCache = createCache(), - sortOrder = function( a, b ) { - if ( a === b ) { - hasDuplicate = true; - } - return 0; - }, - - // Instance methods - hasOwn = ({}).hasOwnProperty, - arr = [], - pop = arr.pop, - push_native = arr.push, - push = arr.push, - slice = arr.slice, - // Use a stripped-down indexOf as it's faster than native - // https://jsperf.com/thor-indexof-vs-for/5 - indexOf = function( list, elem ) { - var i = 0, - len = list.length; - for ( ; i < len; i++ ) { - if ( list[i] === elem ) { - return i; - } - } - return -1; - }, - - booleans = "checked|selected|async|autofocus|autoplay|controls|defer|disabled|hidden|ismap|loop|multiple|open|readonly|required|scoped", - - // Regular expressions - - // http://www.w3.org/TR/css3-selectors/#whitespace - whitespace = "[\\x20\\t\\r\\n\\f]", - - // http://www.w3.org/TR/CSS21/syndata.html#value-def-identifier - identifier = "(?:\\\\.|[\\w-]|[^\0-\\xa0])+", - - // Attribute selectors: http://www.w3.org/TR/selectors/#attribute-selectors - attributes = "\\[" + whitespace + "*(" + identifier + ")(?:" + whitespace + - // Operator (capture 2) - "*([*^$|!~]?=)" + whitespace + - // "Attribute values must be CSS identifiers [capture 5] or strings [capture 3 or capture 4]" - "*(?:'((?:\\\\.|[^\\\\'])*)'|\"((?:\\\\.|[^\\\\\"])*)\"|(" + identifier + "))|)" + whitespace + - "*\\]", - - pseudos = ":(" + identifier + ")(?:\\((" + - // To reduce the number of selectors needing tokenize in the preFilter, prefer arguments: - // 1. quoted (capture 3; capture 4 or capture 5) - "('((?:\\\\.|[^\\\\'])*)'|\"((?:\\\\.|[^\\\\\"])*)\")|" + - // 2. simple (capture 6) - "((?:\\\\.|[^\\\\()[\\]]|" + attributes + ")*)|" + - // 3. anything else (capture 2) - ".*" + - ")\\)|)", - - // Leading and non-escaped trailing whitespace, capturing some non-whitespace characters preceding the latter - rwhitespace = new RegExp( whitespace + "+", "g" ), - rtrim = new RegExp( "^" + whitespace + "+|((?:^|[^\\\\])(?:\\\\.)*)" + whitespace + "+$", "g" ), - - rcomma = new RegExp( "^" + whitespace + "*," + whitespace + "*" ), - rcombinators = new RegExp( "^" + whitespace + "*([>+~]|" + whitespace + ")" + whitespace + "*" ), - - rattributeQuotes = new RegExp( "=" + whitespace + "*([^\\]'\"]*?)" + whitespace + "*\\]", "g" ), - - rpseudo = new RegExp( pseudos ), - ridentifier = new RegExp( "^" + identifier + "$" ), - - matchExpr = { - "ID": new RegExp( "^#(" + identifier + ")" ), - "CLASS": new RegExp( "^\\.(" + identifier + ")" ), - "TAG": new RegExp( "^(" + identifier + "|[*])" ), - "ATTR": new RegExp( "^" + attributes ), - "PSEUDO": new RegExp( "^" + pseudos ), - "CHILD": new RegExp( "^:(only|first|last|nth|nth-last)-(child|of-type)(?:\\(" + whitespace + - "*(even|odd|(([+-]|)(\\d*)n|)" + whitespace + "*(?:([+-]|)" + whitespace + - "*(\\d+)|))" + whitespace + "*\\)|)", "i" ), - "bool": new RegExp( "^(?:" + booleans + ")$", "i" ), - // For use in libraries implementing .is() - // We use this for POS matching in `select` - "needsContext": new RegExp( "^" + whitespace + "*[>+~]|:(even|odd|eq|gt|lt|nth|first|last)(?:\\(" + - whitespace + "*((?:-\\d)?\\d*)" + whitespace + "*\\)|)(?=[^-]|$)", "i" ) - }, - - rinputs = /^(?:input|select|textarea|button)$/i, - rheader = /^h\d$/i, - - rnative = /^[^{]+\{\s*\[native \w/, - - // Easily-parseable/retrievable ID or TAG or CLASS selectors - rquickExpr = /^(?:#([\w-]+)|(\w+)|\.([\w-]+))$/, - - rsibling = /[+~]/, - - // CSS escapes - // http://www.w3.org/TR/CSS21/syndata.html#escaped-characters - runescape = new RegExp( "\\\\([\\da-f]{1,6}" + whitespace + "?|(" + whitespace + ")|.)", "ig" ), - funescape = function( _, escaped, escapedWhitespace ) { - var high = "0x" + escaped - 0x10000; - // NaN means non-codepoint - // Support: Firefox<24 - // Workaround erroneous numeric interpretation of +"0x" - return high !== high || escapedWhitespace ? - escaped : - high < 0 ? - // BMP codepoint - String.fromCharCode( high + 0x10000 ) : - // Supplemental Plane codepoint (surrogate pair) - String.fromCharCode( high >> 10 | 0xD800, high & 0x3FF | 0xDC00 ); - }, - - // CSS string/identifier serialization - // https://drafts.csswg.org/cssom/#common-serializing-idioms - rcssescape = /([\0-\x1f\x7f]|^-?\d)|^-$|[^\x80-\uFFFF\w-]/g, - fcssescape = function( ch, asCodePoint ) { - if ( asCodePoint ) { - - // U+0000 NULL becomes U+FFFD REPLACEMENT CHARACTER - if ( ch === "\0" ) { - return "\uFFFD"; - } - - // Control characters and (dependent upon position) numbers get escaped as code points - return ch.slice( 0, -1 ) + "\\" + ch.charCodeAt( ch.length - 1 ).toString( 16 ) + " "; - } - - // Other potentially-special ASCII characters get backslash-escaped - return "\\" + ch; - }, - - // Used for iframes - // See setDocument() - // Removing the function wrapper causes a "Permission Denied" - // error in IE - unloadHandler = function() { - setDocument(); - }, - - disabledAncestor = addCombinator( - function( elem ) { - return elem.disabled === true; - }, - { dir: "parentNode", next: "legend" } - ); - -// Optimize for push.apply( _, NodeList ) -try { - push.apply( - (arr = slice.call( preferredDoc.childNodes )), - preferredDoc.childNodes - ); - // Support: Android<4.0 - // Detect silently failing push.apply - arr[ preferredDoc.childNodes.length ].nodeType; -} catch ( e ) { - push = { apply: arr.length ? - - // Leverage slice if possible - function( target, els ) { - push_native.apply( target, slice.call(els) ); - } : - - // Support: IE<9 - // Otherwise append directly - function( target, els ) { - var j = target.length, - i = 0; - // Can't trust NodeList.length - while ( (target[j++] = els[i++]) ) {} - target.length = j - 1; - } - }; -} - -function Sizzle( selector, context, results, seed ) { - var m, i, elem, nid, match, groups, newSelector, - newContext = context && context.ownerDocument, - - // nodeType defaults to 9, since context defaults to document - nodeType = context ? context.nodeType : 9; - - results = results || []; - - // Return early from calls with invalid selector or context - if ( typeof selector !== "string" || !selector || - nodeType !== 1 && nodeType !== 9 && nodeType !== 11 ) { - - return results; - } - - // Try to shortcut find operations (as opposed to filters) in HTML documents - if ( !seed ) { - - if ( ( context ? context.ownerDocument || context : preferredDoc ) !== document ) { - setDocument( context ); - } - context = context || document; - - if ( documentIsHTML ) { - - // If the selector is sufficiently simple, try using a "get*By*" DOM method - // (excepting DocumentFragment context, where the methods don't exist) - if ( nodeType !== 11 && (match = rquickExpr.exec( selector )) ) { - - // ID selector - if ( (m = match[1]) ) { - - // Document context - if ( nodeType === 9 ) { - if ( (elem = context.getElementById( m )) ) { - - // Support: IE, Opera, Webkit - // TODO: identify versions - // getElementById can match elements by name instead of ID - if ( elem.id === m ) { - results.push( elem ); - return results; - } - } else { - return results; - } - - // Element context - } else { - - // Support: IE, Opera, Webkit - // TODO: identify versions - // getElementById can match elements by name instead of ID - if ( newContext && (elem = newContext.getElementById( m )) && - contains( context, elem ) && - elem.id === m ) { - - results.push( elem ); - return results; - } - } - - // Type selector - } else if ( match[2] ) { - push.apply( results, context.getElementsByTagName( selector ) ); - return results; - - // Class selector - } else if ( (m = match[3]) && support.getElementsByClassName && - context.getElementsByClassName ) { - - push.apply( results, context.getElementsByClassName( m ) ); - return results; - } - } - - // Take advantage of querySelectorAll - if ( support.qsa && - !compilerCache[ selector + " " ] && - (!rbuggyQSA || !rbuggyQSA.test( selector )) ) { - - if ( nodeType !== 1 ) { - newContext = context; - newSelector = selector; - - // qSA looks outside Element context, which is not what we want - // Thanks to Andrew Dupont for this workaround technique - // Support: IE <=8 - // Exclude object elements - } else if ( context.nodeName.toLowerCase() !== "object" ) { - - // Capture the context ID, setting it first if necessary - if ( (nid = context.getAttribute( "id" )) ) { - nid = nid.replace( rcssescape, fcssescape ); - } else { - context.setAttribute( "id", (nid = expando) ); - } - - // Prefix every selector in the list - groups = tokenize( selector ); - i = groups.length; - while ( i-- ) { - groups[i] = "#" + nid + " " + toSelector( groups[i] ); - } - newSelector = groups.join( "," ); - - // Expand context for sibling selectors - newContext = rsibling.test( selector ) && testContext( context.parentNode ) || - context; - } - - if ( newSelector ) { - try { - push.apply( results, - newContext.querySelectorAll( newSelector ) - ); - return results; - } catch ( qsaError ) { - } finally { - if ( nid === expando ) { - context.removeAttribute( "id" ); - } - } - } - } - } - } - - // All others - return select( selector.replace( rtrim, "$1" ), context, results, seed ); -} - -/** - * Create key-value caches of limited size - * @returns {function(string, object)} Returns the Object data after storing it on itself with - * property name the (space-suffixed) string and (if the cache is larger than Expr.cacheLength) - * deleting the oldest entry - */ -function createCache() { - var keys = []; - - function cache( key, value ) { - // Use (key + " ") to avoid collision with native prototype properties (see Issue #157) - if ( keys.push( key + " " ) > Expr.cacheLength ) { - // Only keep the most recent entries - delete cache[ keys.shift() ]; - } - return (cache[ key + " " ] = value); - } - return cache; -} - -/** - * Mark a function for special use by Sizzle - * @param {Function} fn The function to mark - */ -function markFunction( fn ) { - fn[ expando ] = true; - return fn; -} - -/** - * Support testing using an element - * @param {Function} fn Passed the created element and returns a boolean result - */ -function assert( fn ) { - var el = document.createElement("fieldset"); - - try { - return !!fn( el ); - } catch (e) { - return false; - } finally { - // Remove from its parent by default - if ( el.parentNode ) { - el.parentNode.removeChild( el ); - } - // release memory in IE - el = null; - } -} - -/** - * Adds the same handler for all of the specified attrs - * @param {String} attrs Pipe-separated list of attributes - * @param {Function} handler The method that will be applied - */ -function addHandle( attrs, handler ) { - var arr = attrs.split("|"), - i = arr.length; - - while ( i-- ) { - Expr.attrHandle[ arr[i] ] = handler; - } -} - -/** - * Checks document order of two siblings - * @param {Element} a - * @param {Element} b - * @returns {Number} Returns less than 0 if a precedes b, greater than 0 if a follows b - */ -function siblingCheck( a, b ) { - var cur = b && a, - diff = cur && a.nodeType === 1 && b.nodeType === 1 && - a.sourceIndex - b.sourceIndex; - - // Use IE sourceIndex if available on both nodes - if ( diff ) { - return diff; - } - - // Check if b follows a - if ( cur ) { - while ( (cur = cur.nextSibling) ) { - if ( cur === b ) { - return -1; - } - } - } - - return a ? 1 : -1; -} - -/** - * Returns a function to use in pseudos for input types - * @param {String} type - */ -function createInputPseudo( type ) { - return function( elem ) { - var name = elem.nodeName.toLowerCase(); - return name === "input" && elem.type === type; - }; -} - -/** - * Returns a function to use in pseudos for buttons - * @param {String} type - */ -function createButtonPseudo( type ) { - return function( elem ) { - var name = elem.nodeName.toLowerCase(); - return (name === "input" || name === "button") && elem.type === type; - }; -} - -/** - * Returns a function to use in pseudos for :enabled/:disabled - * @param {Boolean} disabled true for :disabled; false for :enabled - */ -function createDisabledPseudo( disabled ) { - // Known :disabled false positives: - // IE: *[disabled]:not(button, input, select, textarea, optgroup, option, menuitem, fieldset) - // not IE: fieldset[disabled] > legend:nth-of-type(n+2) :can-disable - return function( elem ) { - - // Check form elements and option elements for explicit disabling - return "label" in elem && elem.disabled === disabled || - "form" in elem && elem.disabled === disabled || - - // Check non-disabled form elements for fieldset[disabled] ancestors - "form" in elem && elem.disabled === false && ( - // Support: IE6-11+ - // Ancestry is covered for us - elem.isDisabled === disabled || - - // Otherwise, assume any non-