Initial commit (#1)

.envs/testenv.yml

@@ -0,0 +1,27 @@
+---
+name: upper-envelope
+
+channels:
+  - conda-forge
+  - nodefaults
+
+dependencies:
+  - pip
+  - setuptools_scm
+  - toml
+
+  # Package dependencies
+  - jax
+  - numpy
+  - numba
+  - pandas
+  - pyyaml
+
+  # Testing infrastructure
+  - pytest
+  - pytest-cov
+  - pytest-xdist
+
+  # Install locally
+  - pip:
+      - -e ../

.github/workflows/main.yml

@@ -0,0 +1,48 @@
+---
+name: main
+# Automatically cancel a previous run.
+concurrency:
+  group: ${{ github.head_ref || github.run_id }}
+  cancel-in-progress: true
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - '*'
+jobs:
+  run-tests:
+    name: Run tests for ${{ matrix.os }} on ${{ matrix.python-version }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os:
+          - ubuntu-latest
+        python-version:
+          - '3.10'
+          - '3.11'
+    steps:
+      - uses: actions/checkout@v3
+      - name: create build environment
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          environment-file: ./.envs/testenv.yml
+          environment-name: upper-envelope
+          create-args: |
+            python=${{ matrix.python-version }}
+          init-shell: >-
+            bash
+            powershell
+          cache-environment: true
+      - name: run pytest
+        shell: bash -el {0}
+        run: |
+          micromamba activate upper-envelope
+          pytest --cov-report=xml --cov=./
+      - name: Upload coverage report.
+        if: runner.os == 'Linux' && matrix.python-version == '3.10'
+        uses: codecov/codecov-action@v3
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}

.gitignore

@@ -0,0 +1,142 @@
+# Files
+.pyc
+.txt
+.pdf
+.npy
+
+
+src/upper_envelope/_version.py
+
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+__pxcache__/
+*.py[cod]
+*$py.class
+
+# MacOS specific service store
+.DS_Store
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+_build/
+_generated/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+*build/
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+*.sublime-workspace
+*.sublime-project
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# VSCode project settings
+.vscode
+.idea
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+
+*notes/
+
+*.bak
+
+*.db
+
+.pytask.sqlite3
+
+*.~lock.*
+
+# Local envrc file
+*envrc
+
+
+# Debugging files should be ignored
+*.png

.pre-commit-config.yaml

@@ -0,0 +1,110 @@
+---
+repos:
+  - repo: meta
+    hooks:
+      - id: check-hooks-apply
+      - id: check-useless-excludes
+    # -   id: identity  # Prints all files passed to pre-commits. Debugging.
+  - repo: https://github.com/adrienverge/yamllint.git
+    rev: v1.32.0
+    hooks:
+      - id: yamllint
+  - repo: https://github.com/lyz-code/yamlfix
+    rev: 1.13.0
+    hooks:
+      - id: yamlfix
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+      - id: check-added-large-files
+        args:
+          - --maxkb=500
+      - id: check-case-conflict
+      - id: check-merge-conflict
+      - id: check-vcs-permalinks
+      - id: check-yaml
+      - id: debug-statements
+      - id: end-of-file-fixer
+      - id: fix-byte-order-marker
+      - id: mixed-line-ending
+      - id: no-commit-to-branch
+        args:
+          - --branch
+          - main
+      - id: trailing-whitespace
+  - repo: https://github.com/pre-commit/pygrep-hooks
+    rev: v1.10.0
+    hooks:
+      - id: python-check-blanket-noqa
+      - id: python-check-mock-methods
+      - id: python-no-eval
+      - id: python-no-log-warn
+      - id: python-use-type-annotations
+      - id: text-unicode-replacement-char
+  - repo: https://github.com/asottile/reorder-python-imports
+    rev: v3.10.0
+    hooks:
+      - id: reorder-python-imports
+        args:
+          - --py37-plus
+  - repo: https://github.com/asottile/setup-cfg-fmt
+    rev: v2.4.0
+    hooks:
+      - id: setup-cfg-fmt
+  - repo: https://github.com/psf/black
+    rev: 23.7.0
+    hooks:
+      - id: black
+        language_version: python3.10
+        exclude: tests/utils/fast_upper_envelope_org.py
+  - repo: https://github.com/charliermarsh/ruff-pre-commit
+    rev: v0.0.282
+    hooks:
+      - id: ruff
+        # exclude: |
+        #   (?x)^(
+        #     tests/|
+        #     docs/source/conf.py|
+        #   )$
+  - repo: https://github.com/PyCQA/docformatter
+    rev: v1.7.5
+    hooks:
+      - id: docformatter
+        args:
+          - --in-place
+          - --wrap-summaries
+          - '88'
+          - --wrap-descriptions
+          - '88'
+          - --blank
+        exclude: tests/utils/fast_upper_envelope_org.py
+  - repo: https://github.com/nbQA-dev/nbQA
+    rev: 1.7.0
+    hooks:
+      - id: nbqa-black
+      - id: nbqa-ruff
+  - repo: https://github.com/executablebooks/mdformat
+    rev: 0.7.16
+    hooks:
+      - id: mdformat
+        additional_dependencies:
+          - mdformat-gfm
+          - mdformat-black
+        args:
+          - --wrap
+          - '88'
+        files: (README\.md)
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.2.5
+    hooks:
+      - id: codespell
+        additional_dependencies:
+          - tomli
+# -   repo: https://github.com/mgedmin/check-manifest
+#     rev: "0.49"
+#     hooks:
+#     -   id: check-manifest
+#         args: [--no-build-isolation]
+#         additional_dependencies: [setuptools-scm, toml]
+ci:
+  autoupdate_schedule: monthly

.yamllint.yml

@@ -0,0 +1,36 @@
+---
+yaml-files:
+  - '*.yaml'
+  - '*.yml'
+  - .yamllint
+rules:
+  braces: enable
+  brackets: enable
+  colons: enable
+  commas: enable
+  comments:
+    level: warning
+  comments-indentation:
+    level: warning
+  document-end: disable
+  document-start:
+    level: warning
+  empty-lines: enable
+  empty-values: disable
+  float-values: disable
+  hyphens: enable
+  indentation: {spaces: 2}
+  key-duplicates: enable
+  key-ordering: disable
+  line-length:
+    max: 88
+    allow-non-breakable-words: true
+    allow-non-breakable-inline-mappings: false
+  new-line-at-end-of-file: enable
+  new-lines:
+    type: unix
+  octal-values: disable
+  quoted-strings: disable
+  trailing-spaces: enable
+  truthy:
+    level: warning

codecov.yml

@@ -0,0 +1,20 @@
+---
+codecov:
+  notify:
+    require_ci_to_pass: true
+coverage:
+  precision: 2
+  round: down
+  range: 60...100
+  status:
+    patch:
+      default:
+        target: 70%
+    project:
+      default:
+        target: 90%
+ignore:
+  - setup.py
+  - tests/*
+  - tests/**/*
+  - .tox/**/*