Initial commit

.github/ISSUE_TEMPLATE/bug_report.md

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+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+### Describe the bug
+A clear and concise description of what the bug is.
+
+### To Reproduce
+Code snippet or clear steps to reproduce the behaviour.
+
+### Expected behavior
+A clear and concise description of what you expected to happen.
+
+### Screenshots
+If applicable, add screenshots to help explain your problem.
+
+### Version
+ - Version info such as v0.1.0
+
+### Additional context
+Add any other context about the problem here.

.github/ISSUE_TEMPLATE/config.yml

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+blank_issues_enabled: false

.github/ISSUE_TEMPLATE/feature_request.md

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+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+### Is your feature request related to a problem? Please describe.
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+### Describe the solution you'd like
+A clear and concise description of what you want to happen.
+
+### Describe alternatives you've considered
+A clear and concise description of any alternative solutions or features you've considered.
+
+### Additional context
+Add any other context or screenshots about the feature request here.

.github/pull_request_template.md

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+# PR Type
+[Feature | Fix | Documentation | Refactor | Other]
+
+# Short Description
+Add a short description of what is in this PR.
+
+# Tests Added
+Describe the tests that have been added to ensure the codes correctness, if applicable.

.github/workflows/code_checks.yml

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+name: code checks
+
+on:
+  push:
+    branches:
+      - main
+    paths:
+      - .pre-commit-config.yaml
+      - .github/workflows/code_checks.yml
+      - '**.py'
+      - poetry.lock
+      - pyproject.toml
+      - '**.ipynb'
+  pull_request:
+    branches:
+      - main
+    paths:
+      - .pre-commit-config.yaml
+      - .github/workflows/code_checks.yml
+      - '**.py'
+      - poetry.lock
+      - pyproject.toml
+      - '**.ipynb'
+
+jobs:
+  run-code-check:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/[email protected]
+      - name: Install and configure Poetry
+        uses: snok/install-poetry@v1
+        with:
+          virtualenvs-create: true
+          virtualenvs-in-project: true
+      - uses: actions/[email protected]
+        with:
+          python-version: '3.9'
+          cache: 'poetry'
+      - name: Install dependencies and check code
+        run: |
+          poetry env use '3.9'
+          source .venv/bin/activate
+          poetry install --with test --all-extras
+          pre-commit run --all-files
+      - name: pip-audit (gh-action-pip-audit)
+        uses: pypa/[email protected]
+        with:
+          virtual-environment: .venv/
+          ignore-vulns: GHSA-cqh9-jfqr-h9jj

.github/workflows/integration_tests.yml

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+name: integration tests
+
+on:
+  push:
+    branches:
+      - main
+    paths:
+      - .pre-commit-config.yaml
+      - .github/workflows/code_checks.yml
+      - .github/workflows/integration_tests.yml
+      - '**.py'
+      - '**.ipynb'
+      - poetry.lock
+      - pyproject.toml
+      - '**.rst'
+      - '**.md'
+  pull_request:
+    branches:
+      - main
+    paths:
+      - .pre-commit-config.yaml
+      - .github/workflows/code_checks.yml
+      - .github/workflows/integration_tests.yml
+      - '**.py'
+      - '**.ipynb'
+      - poetry.lock
+      - pyproject.toml
+      - '**.rst'
+      - '**.md'
+
+jobs:
+  integration-tests:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/[email protected]
+      - name: Install poetry
+        run: python3 -m pip install --upgrade pip && python3 -m pip install poetry
+      - uses: actions/[email protected]
+        with:
+          python-version: '3.9'
+      - name: Install dependencies and check code
+        run: |
+          poetry env use '3.9'
+          source $(poetry env info --path)/bin/activate
+          poetry install --with test
+          pytest -m integration_test

.github/workflows/publish.yml

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+name: publish package
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  deploy:
+    name: Upload release to PyPI
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/mmlearn
+    permissions:
+      id-token: write  # IMPORTANT: this permission is mandatory for trusted publishing
+    steps:
+      - name: Install apt dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install libcurl4-openssl-dev libssl-dev
+      - uses: actions/[email protected]
+      - name: Install poetry
+        run: python3 -m pip install --upgrade pip && python3 -m pip install poetry
+      - uses: actions/[email protected]
+        with:
+          python-version: '3.9'
+      - name: Build package
+        run: poetry build
+      - name: Publish package
+        uses: pypa/gh-action-pypi-publish@release/v1

.gitignore

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+# 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/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# 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/
+
+# Translations
+*.mo
+*.pot
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.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
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__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/
+
+# pycharm
+.idea/
+
+# vscode
+.vscode/
+
+# wandb
+wandb/
+
+# hydra
+outputs/
+
+# slurm
+*slurm-*

.pre-commit-config.yaml

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+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.6.0  # Use the ref you want to point at
+    hooks:
+      - id: trailing-whitespace
+      - id: check-ast
+      - id: check-builtin-literals
+      - id: check-docstring-first
+      - id: check-executables-have-shebangs
+      - id: debug-statements
+      - id: end-of-file-fixer
+      - id: mixed-line-ending
+        args: [--fix=lf]
+      - id: detect-private-key
+      - id: check-yaml
+      - id: check-toml
+
+  - repo: https://github.com/python-poetry/poetry
+    rev: 1.8.3
+    hooks:
+      - id: poetry-check
+        args: [--lock]
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.5.7
+    hooks:
+      - id: ruff
+        args: [--fix, --exit-non-zero-on-fix]
+        types_or: [ python, pyi, jupyter ]
+      - id: ruff-format
+        types_or: [ python, pyi, jupyter ]
+
+  - repo: https://github.com/crate-ci/typos
+    rev: v1.23.6
+    hooks:
+      - id: typos
+        args: []
+
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.11.1
+    hooks:
+      - id: mypy
+        entry: python3 -m mypy --show-error-codes --pretty --config-file pyproject.toml
+        types: [python]
+        exclude: "tests"
+
+  - repo: https://github.com/nbQA-dev/nbQA
+    rev: 1.8.7
+    hooks:
+      - id: nbqa-ruff
+        args: [--fix, --exit-non-zero-on-fix]
+
+  - repo: local
+    hooks:
+    - id: pytest
+      name: pytest
+      language: system
+      entry: python3 -m pytest -m "not integration_test"
+      pass_filenames: false
+      always_run: true