mxlpy 0.8.0__tar.gz

mxlpy-0.8.0/.flake8

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+[flake8]
+max-line-length = 100
+max-complexity = 18
+select = B,C,E,F,W,T4,B9
+ignore = C901, E203, E266, E402, E501, E741, E722, F401, F403, W503, W605, W291
+
+# C901: too complex
+# E203: whitespace before ':'
+# E741: ambiguous variable name
+# W503: line break before binary operator

mxlpy-0.8.0/.gitattributes

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+# proper line endings
+* text=auto eol=lf
+*.{cmd,[cC][mM][dD]} text eol=crlf
+*.{bat,[bB][aA][tT]} text eol=crlf# GitHub syntax highlighting
+pixi.lock linguist-language=YAML linguist-generated=true

mxlpy-0.8.0/.gitchangelog.rc

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+# -*- coding: utf-8; mode: python -*-
+
+ignore_regexps = [
+    r'^dev:\s*(chg|fix|new)\s*:',
+    # r'^bot:\s*(chg|fix|new)\s*:',
+]
+
+section_regexps = [
+    ('New',     [r'^((dev|usr|bot)\s*:\s*new\s*:\s*)([^\n]*)$']),
+    ('Changes', [r'^((dev|usr|bot)\s*:\s*chg\s*:\s*)([^\n]*)$']),
+    ('Fix',     [r'^((dev|usr|bot)\s*:\s*fix\s*:\s*)([^\n]*)$']),
+]
+
+
+body_process = ReSub(r'((^|\n)[A-Z]\w+(-\w+)*: .*(\n\s+.*)*)+$', r'') | strip
+
+subject_process = (
+    strip 
+    | ReSub(r'^((dev|usr|bot)\s*:\s*)(chg|fix|new)\s*:\s*([^\n@]*)(@[a-z]+\s+)*$', r'\4')
+)
+
+tag_filter_regexp = r'^[0-9]+\.[0-9]+(\.[0-9]+)?$'
+
+unreleased_version_label = "(unreleased)"
+
+output_engine = rest_py
+include_merge = True
+
+revs = []

mxlpy-0.8.0/.github/ISSUE_TEMPLATE/bug_report.md

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+---
+name: "\U0001F41B Bug report"
+about: "Create a report to help us improve"
+title: ''
+labels: bug
+assignees: ''
+---
+
+## Bug report
+
+<!-- Before creating a bug report, check if there is already an open issue about the bug -->
+
+**Describe the bug**
+
+<!-- A clear and concise description of what the bug is. -->
+
+**To Reproduce**
+
+<!-- Steps to reproduce the behavior: -->
+
+**Expected behavior**
+
+<!-- A clear and concise description of what you expected to happen. -->
+
+**Screenshots**
+
+<!-- If applicable, add screenshots to help explain your problem. -->
+
+**Desktop (please complete the following information):**
+
+- OS, version:
+- Environment:
+
+**Additional context**
+
+<!-- Add any other context about the problem or helpful links here. -->

mxlpy-0.8.0/.github/ISSUE_TEMPLATE/discussion

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+---
+name: "\U0001F5E8 Discussion"
+about: "Create a discussion"
+title: ''
+labels: bug
+assignees: ''
+---
+
+## Discussion

mxlpy-0.8.0/.github/ISSUE_TEMPLATE/feature_request.md

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+---
+name: "\U0001F680 Feature Request"
+about: "I have a suggestion (and may want to implement it \U0001F642)!"
+title: ''
+labels: 'enhancement'
+assignees: ''
+
+---
+
+## Feature Request
+
+<!-- Only create a feature request after discussing on mxlpy discussion forum. A feature report should only be filled for concise, concrete deliverables. Simple suggestions or general features, like "implementing structural identifiability method" should be addressed on the discussion forum and no feature request should be created. Before creating a feature request, check if there is already an open issue about the feature.-->
+
+**Is your feature request related to a problem/ another issue? Please describe.**
+- [ ] Yes: _Please provide a clear and concise description of what the problem is or to what other issue the feature request is linked. If possible use follow [Github's guidance on linking issues to pull requests](https://docs.github.com/en/issues/tracking-your-work-with-issues/linking-a-pull-request-to-an-issue) to link issues
+- [ ] No: _Why do you consider this feature to be necessary?
+
+**Describe the the feature**
+A clear and concise description of what you want to happen and to be included. Add any considered drawbacks.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Teachability, Documentation, Adoption, Migration Strategy**
+If you can, explain how users will be able to use this and possibly write out a draft for the docs.

mxlpy-0.8.0/.github/workflows/docs.yml

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+name: documentation
+
+on:
+  release:
+    types: [published]
+
+permissions:
+  contents: write
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Configure Git Credentials
+        run: |
+          git config user.name github-actions[bot]
+          git config user.email 41898282+github-actions[bot]@users.noreply.github.com
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v4
+
+      - name: Set up Python
+        run: uv python install
+
+      - run: echo "cache_id=$(date --utc '+%V')" >> $GITHUB_ENV
+      - uses: actions/cache@v4
+        with:
+          key: mkdocs-material-${{ env.cache_id }}
+          path: .cache
+          restore-keys: |
+            mkdocs-material-
+      - run: uv sync --extra dev --extra torch
+      - run: uv run python -c "import toml;print('VERSION={}'.format(toml.load(open('pyproject.toml'))['project']['version']))" >> $GITHUB_ENV"
+      - run: mike deploy --push $(VERSION)

mxlpy-0.8.0/.github/workflows/python-publish.yml

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+name: Upload Python Package
+
+on:
+  release:
+    types: [published]
+
+permissions:
+  contents: read
+
+jobs:
+  release-build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v4
+
+      - name: Set up Python
+        run: uv python install
+
+      - name: Build release distribution
+        run: uv build
+
+      - name: Upload distributions
+        uses: actions/upload-artifact@v4
+        with:
+          name: release-dists
+          path: dist/
+
+  pypi-publish:
+    runs-on: ubuntu-latest
+    needs:
+      - release-build
+    permissions:
+      id-token: write
+
+    environment:
+      name: pypi
+
+    steps:
+      - name: Retrieve release distributions
+        uses: actions/download-artifact@v4
+        with:
+          name: release-dists
+          path: dist/
+
+      - name: Publish release distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          packages-dir: dist/

mxlpy-0.8.0/.github/workflows/tests.yml

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+name: ci
+
+on:
+  push:
+    branches:
+      - main
+
+permissions:
+  contents: write
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v4
+
+      - name: Set up environment
+        run: uv sync --extra dev --extra torch
+
+      - name: Run tests
+        run: uv run pytest --disable-warnings --cov --cov-report json tests/
+
+      - name: Get coverage value
+        run: python -c "import json; print('COVERAGE={}'.format(json.load(open('coverage.json'))['totals']['percent_covered_display']))" >> $GITHUB_ENV
+
+      - name: Coverage badge
+        uses: schneegans/dynamic-badges-action@v1.7.0
+        with:
+          auth: ${{ secrets.GIST_SECRET }}
+          gistID: 98ab3ce1db511de42f9871e91d85e4cd
+          filename: coverage.json
+          label: Coverage
+          message: ${{ env.COVERAGE }}
+          valColorRange: ${{ env.COVERAGE }}
+          maxColorRange: 100
+          minColorRange: 0

mxlpy-0.8.0/.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/
+*.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/
+coverage.json
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+.pytest_cache/
+.ruff_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# 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
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+
+# vscode
+.vscode/
+
+# temporary files and folders
+*temp*
+tmp
+# pixi environments
+.pixi
+*.egg-info
+
+# copilot
+.github/copilot-instructions.md

mxlpy-0.8.0/.pre-commit-config.yaml

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+repos:
+  - repo: https://github.com/hakancelikdev/unexport
+    rev: 0.4.0
+    hooks:
+      - id: unexport
+        exclude: "tests|__init__.py"
+        args: [--refactor]
+
+  - repo: local
+    hooks:
+      - id: jupyter-nb-clear-output
+        name: jupyter-nb-clear-output
+        files: \.ipynb$
+        stages: [pre-commit]
+        language: system
+        entry: uvx --from nbconvert jupyter-nbconvert --ClearOutputPreprocessor.enabled=True --inplace
+
+  - repo: https://github.com/aio-libs/sort-all
+    rev: v1.3.0
+    hooks:
+      - id: sort-all
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.11.6
+    hooks:
+      - id: ruff-format

mxlpy-0.8.0/CONTRIBUTING.md

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+All contributions, bug reports, bug fixes, documentation improvements, enhancements and ideas are welcome.
+In order to contribute:
+
+1. [Fork the project](https://github.com/Computational-Biology-Aachen/mxlpy)
+2. Improve or extend the project
+3. Create unit tests for your added / improved features in the respective [test directory](https://github.com/Computational-Biology-Aachen/mxlpy/tree/main/tests). The old test suite mostly uses the standard [unittest](https://docs.python.org/3/library/unittest.html) library, however new tests are written with [pytest](https://docs.pytest.org/en/latest/). If you are not familiar with pytest you can still use the unittest interface, as pytest supports both test styles.
+4. Create a [pull request](https://docs.github.com/de/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/creating-a-pull-request)
+
+Your work will then be reviewed as soon as possible (suggestions about some changes, improvements or alternatives may be given).
+
+## Coding standards
+
+In order for your improvements to be accepted, please make sure that you added tests in the respective subfolder of the [test directory](https://github.com/Computational-Biology-Aachen/mxlpy/tree/main/tests).
+We also ask you to write proper documentation in the [NumPy / SciPy style](https://docs.scipy.org/doc/numpy/docs/howto_document.html) and
+that you name your functions according to [pep8](http://pep8.org/). Further, please use the supplied [pre-commit](https://pre-commit.com/) hook, to make sure that your code passes our guidelines.
+
+Thank you for participating!