Merge branch 'NREL:main' into main

malcolm-dsider · Nov 2, 2023 · b93a923 · b93a923
2 parents 2803b6b + 12562a0
commit b93a923
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Showing 237 changed files with 2,211 additions and 19,220 deletions.
diff --git a/.bumpversion.cfg b/.bumpversion.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 3.1.2
+current_version = 3.2.0
 commit = True
 tag = True
 
@@ -15,6 +15,10 @@ replace = /v{new_version}.svg
 search = /v{current_version}...main
 replace = /v{new_version}...main
 
+[bumpversion:file:docs/conf.py]
+search = version = release = '{current_version}'
+replace = version = release = '{new_version}'
+
 [bumpversion:file:src/geophires_x/__init__.py]
 search = __version__ = '{current_version}'
 replace = __version__ = '{new_version}'

diff --git a/.cookiecutterrc b/.cookiecutterrc
@@ -28,18 +28,18 @@ default_context:
     command_line_interface_bin_name: "geophires-x"
     coveralls: "no"
     distribution_name: "geophires-x"
-    email: "[email protected]"
+    email: "[email protected]"
     formatter_quote_style: "single"
     full_name: "NREL"
     github_actions: "yes"
     github_actions_osx: "yes"
     github_actions_windows: "no"
     license: "MIT license"
     package_name: "geophires_x"
-    pre_commit: "no"
+    pre_commit: "yes"
     project_name: "geophires-x"
     project_short_description: "GEOPHIRES-X python package"
-    pypi_badge: "yes"
+    pypi_badge: "no"
     pypi_disable_upload: "yes"
     release_date: "today"
     repo_hosting: "github.com"
@@ -49,12 +49,12 @@ default_context:
     repo_username: "NREL"
     scrutinizer: "no"
     setup_py_uses_setuptools_scm: "no"
-    sphinx_docs: "no"
+    sphinx_docs: "yes"
     sphinx_docs_hosting: "https://python-geophires-x.readthedocs.io/"
     sphinx_doctest: "no"
-    sphinx_theme: "sphinx-rtd-theme"
+    sphinx_theme: "sphinx-py3doc-enhanced-theme"
     test_matrix_separate_coverage: "no"
-    version: 3.1.2
+    version: "3.2.0"
     version_manager: "bump2version"
     website: "https://github.com/NREL"
     year_from: "2023"

diff --git a/.github/workflows/github-actions.yml b/.github/workflows/github-actions.yml
@@ -1,5 +1,12 @@
 name: build
 on: [push, pull_request]
+
+# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
 jobs:
   test:
     name: ${{ matrix.name }}
@@ -14,18 +21,11 @@ jobs:
             toxpython: 'python3.11'
             tox_env: 'check'
             os: 'ubuntu-latest'
-#          - name: 'py37 (ubuntu)'
-#            python: '3.7'
-#            toxpython: 'python3.7'
-#            python_arch: 'x64'
-#            tox_env: 'py37'
-#            os: 'ubuntu-latest'
-#          - name: 'py37 (macos)'
-#            python: '3.7'
-#            toxpython: 'python3.7'
-#            python_arch: 'x64'
-#            tox_env: 'py37'
-#            os: 'macos-latest'
+          - name: 'docs'
+            python: '3.11'
+            toxpython: 'python3.11'
+            tox_env: 'docs'
+            os: 'ubuntu-latest'
           - name: 'py38 (ubuntu)'
             python: '3.8'
             toxpython: 'python3.8'
@@ -74,18 +74,13 @@ jobs:
             python_arch: 'x64'
             tox_env: 'py311'
             os: 'macos-latest'
-#          - name: 'pypy37 (ubuntu)'
-#            python: 'pypy-3.7'
-#            toxpython: 'pypy3.7'
-#            python_arch: 'x64'
-#            tox_env: 'pypy37'
-#            os: 'ubuntu-latest'
-#          - name: 'pypy37 (macos)'
-#            python: 'pypy-3.7'
-#            toxpython: 'pypy3.7'
-#            python_arch: 'x64'
-#            tox_env: 'pypy37'
-#            os: 'macos-latest'
+          - name: 'py311 (windows)'
+            python: '3.11'
+            toxpython: 'python3.11'
+            python_arch: 'x64'
+            tox_env: 'py311'
+            os: 'windows-latest'
+
 #          - name: 'pypy38 (ubuntu)'
 #            python: 'pypy-3.8'
 #            toxpython: 'pypy3.8'
@@ -110,6 +105,7 @@ jobs:
 #            python_arch: 'x64'
 #            tox_env: 'pypy39'
 #            os: 'macos-latest'
+
     steps:
     - uses: actions/checkout@v3
       with:
@@ -120,6 +116,7 @@ jobs:
         architecture: ${{ matrix.python_arch }}
     - name: install dependencies
       run: |
+        python -mpip install --upgrade pip
         python -mpip install --progress-bar=off -r ci/requirements.txt
         virtualenv --version
         pip --version
@@ -130,3 +127,48 @@ jobs:
         TOXPYTHON: '${{ matrix.toxpython }}'
       run: >
         tox -e ${{ matrix.tox_env }} -v
+
+  deploy_docs:
+    name: Deploy docs to GitHub Pages
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    needs: test
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+      with:
+        fetch-depth: 0
+    - uses: actions/setup-python@v4
+      with:
+        python-version: '3.11'
+        architecture: 'x64'
+    - name: install dependencies
+      run: |
+        python -mpip install --upgrade pip
+        python -mpip install --progress-bar=off -r ci/requirements.txt
+        virtualenv --version
+        pip --version
+        tox --version
+        pip list --format=freeze
+
+    - name: generate docs
+      env:
+        TOXPYTHON: '3.11'
+      run: |
+        tox -e docs -v
+        ls -l dist/docs
+        cp -r dist/docs _site/
+
+    - name: fix permissions # https://github.com/actions/upload-pages-artifact#file-permissions
+      run: |
+        chmod -c -R +rX "_site/" | while read line; do
+          echo "::warning title=Invalid file permissions automatically fixed::$line"
+        done
+
+    - name: upload artifact
+      uses: actions/upload-pages-artifact@v2
+
+    - name: deploy to GitHub Pages
+      id: deployment
+      uses: actions/deploy-pages@v2
diff --git a/.gitignore b/.gitignore
@@ -69,8 +69,13 @@ nosetests.xml
 output/*.html
 output/*/index.html
 
-# Sphinx
+# Sphinx/docs
 docs/_build
+docs/reference/geophires-request.json
+docs/reference/parameters.rst
+docs/geophires-request.json
+docs/parameters.rst
+_site/
 
 # Mypy Cache
 .mypy_cache/
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -6,16 +6,16 @@ exclude: '^(\.tox|ci/templates|\.bumpversion\.cfg|src/geophires_x)(/|$)'
 # Note the order is intentional to avoid multiple passes of the hooks
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.0.277
+    rev: v0.1.3
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix, --show-fixes]
   - repo: https://github.com/psf/black
-    rev: 23.7.0
+    rev: 23.10.1
     hooks:
       - id: black
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.5.0
     hooks:
       - id: trailing-whitespace
       - id: end-of-file-fixer

diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -0,0 +1,14 @@
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+version: 2
+sphinx:
+  configuration: docs/conf.py
+formats: all
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3"
+python:
+  install:
+    - requirements: docs/requirements.txt
+    - method: pip
+      path: .
diff --git a/AUTHORS.rst b/AUTHORS.rst
@@ -2,4 +2,7 @@
 Authors
 =======
 
-* softwareengineerprogrammer - https://github.com/softwareengineerprogrammer
+* Koenraad Beckers - https://github.com/kfbeckers
+* Malcolm Ross - https://github.com/malcolm-dsider
+* Jonathan Pezzino - https://github.com/softwareengineerprogrammer
+* Kevin McCabe (GEOPHIRES v2.0) - [email protected]
diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -2,7 +2,22 @@
 Changelog
 =========
 
-0.0.0 (2023-07-12)
-------------------
+GEOPHIRES-X (3.0) (2023)
+------------------------
 
-* First release on PyPI.
+- Ported from `malcolm-dsider/GEOPHIRES-X <https://github.com/malcolm-dsider/GEOPHIRES-X>`_ and `softwareengineerprogrammer/python-geophires-x <https://github.com/softwareengineerprogrammer/python-geophires-x>`_ using `ionelmc/cookiecutter-pylibrary <https://github.com/ionelmc/cookiecutter-pylibrary/>`_.
+- https://github.com/NREL/python-geophires-x
+- Releases now marked with tags/version metadata generated with ``bumpversion``
+
+2.0 (2019)
+----------
+
+* `GEOPHIRES v2.0 </References/Beckers%202019%20GEOPHIRES%20v2.pdf>`__
+* https://github.com/NREL/GEOPHIRES-v2
+* https://www.nrel.gov/docs/fy18osti/70856.pdf
+
+
+1.0 (2013)
+------------
+
+* `GEOPHIRES v1 </References/Beckers%202013%20GEOPHIRES%20v1.pdf>`_