ci: add pre-commit, linters configs, github workflows, .gitignore

.github/workflows/pre-commit.yml

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+name: pre-commit
+
+on:
+  pull_request:
+  push:
+    branches:
+      - main
+jobs:
+  pre-commit:
+    name: pre-commit
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+          clean: false
+          ref: ${{ github.head_ref }}
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.8'
+          cache: 'pip'
+      # N.B. we don't need all the dependencies to run the code for just pre-commit
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r requirements-dev.txt
+
+      - name: Cache pre-commit envs
+        uses: actions/cache@v2
+        with:
+          path: ~/.cache/pre-commit
+          key: ${{ runner.os }}-pre-commit-${{ hashFiles('**/requirements-dev.txt') }}-${{ hashFiles('**/.pre-commit-config.yaml') }}
+          restore-keys: |
+            ${{ runner.os }}-pre-commit-${{ hashFiles('**/requirements-dev.txt') }}-
+            ${{ runner.os }}-pre-commit-
+
+      - name: Run pre-commit
+        env:
+          REF_BEFORE: ${{ github.event_name == 'pull_request' && github.base_ref || github.event.before }}
+          REF_AFTER: ${{ github.event_name == 'pull_request' && github.head_ref || github.event.after }}
+        run: |
+          # make sure dropped commits are fetched
+          git fetch origin $REF_BEFORE:$REF_BEFORE
+          # if it's a push, check since the common ancestor of the before/after (for forced pushes)
+          if [[ "${{ github.event_name }}" == "push" ]]; then
+            export REF_BEFORE=$(git merge-base $REF_BEFORE $REF_AFTER)
+          fi
+          # make sure gitlint knows which commits to lint
+          export GITLINT_COMMITS=$REF_BEFORE..$REF_AFTER
+          # run pre-commit
+          pre-commit run --from-ref $REF_BEFORE --to-ref $REF_AFTER

.gitignore

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+# OS files
+Thumbs.db
+ehthumbs.db
+Desktop.ini
+$RECYCLE.BIN/
+*.msm
+*.msp
+*.lnk
+.DS_Store
+.AppleDouble
+.LSOverride
+.DocumentRevisions-V100
+.fseventsd
+.Spotlight-V100
+.TemporaryItems
+.Trashes
+.VolumeIcon.icns
+.AppleDB
+.AppleDesktop
+Network Trash Folder
+Temporary Items
+.apdisk
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+logs
+
+# 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
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+.idea/
+
+# Added by paper-dragonfly
+/media/
+/models/

.gitlint

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+[general]
+ignore=body-max-line-length, body-is-missing, contrib-disallow-cleanup-commits
+contrib=contrib-title-conventional-commits
+ignore-merge-commits=false
+regex-style-search=True
+
+[title-max-length]
+line-length=70
+
+[body-min-length]
+min-length=5
+
+[contrib-title-conventional-commits]
+types = fix,feat,chore,docs,style,refactor,ref,perf,test,revert,ci,build

.pre-commit-config.yaml

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+default_language_version:
+  python: python3.8
+exclude: ^(build|dist|.*\.egg(-info)?|\.github)
+
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
+    hooks:
+      - id: check-added-large-files
+      - id: check-ast
+      - id: check-case-conflict
+      - id: trailing-whitespace
+        exclude: (\.md|\.rst|splash.py)$
+      - id: end-of-file-fixer
+      - id: check-yaml
+      - id: check-merge-conflict
+      - id: check-symlinks
+      - id: check-xml
+      - id: check-executables-have-shebangs
+      - id: check-shebang-scripts-are-executable
+        exclude: (\.jinjia2?|\.j2)$
+      - id: debug-statements
+      - id: destroyed-symlinks
+      - id: detect-private-key
+        exclude: ^(modules)
+      - id: end-of-file-fixer
+      - id: fix-byte-order-marker
+      - id: fix-encoding-pragma
+        args: [ "--remove" ]
+      - id: mixed-line-ending
+        args: [ "--fix=lf" ]
+      - id: name-tests-test
+        args: [ "--pytest-test-first" ]
+      - id: requirements-txt-fixer
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.1.14
+    hooks:
+      - id: ruff-format
+      - id: ruff
+        name: ruff-required
+        args:
+          - --ignore=FIX,ERA,D,PLR6301,PLR2004,RUF100
+          - --fix
+          - --exit-non-zero-on-fix
+      - id: ruff
+        name: ruff-optional
+        verbose: true
+        args:
+          - --select=FIX,ERA,D,PLR6301,PLR2004
+          - --ignore=D105,D107,D203,D205,D212,RUF100
+          - --no-fix
+          - --exit-zero
+      # this one is needed to properly apply noqa removal when all rules are selected, N.B. will exit 0
+      - id: ruff
+        name: ruff-cleanups
+        args:
+          - --fix
+          - --silent
+          - --exit-zero
+
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.8.0
+    hooks:
+      - id: mypy
+        exclude: ^tests/
+        args:
+          - --install-types
+          - --non-interactive
+        additional_dependencies:
+          - numpy
+
+  - repo: https://github.com/Lucas-C/pre-commit-hooks-safety
+    rev: v1.3.2
+    hooks:
+      - id: python-safety-dependencies-check
+        files: requirements.*\.txt
+
+  - repo: https://github.com/jorisroovers/gitlint
+    rev: v0.19.1
+    hooks:
+    - id: gitlint
+    - id: gitlint-ci