pyIsoPEP 0.1.0__tar.gz

pyisopep-0.1.0/.github/workflows/PyPIpublish.yml

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+name: Publish pyIsotonicPEP Python Package
+
+on:
+  workflow_dispatch:
+  push:
+    branches: [ main ]
+    paths:
+      - '.github/workflows/PyPIpublish.yml'
+      - 'pyIsoPEP/__init__.py'
+      - 'pyIsoPEP/main.py'
+      - 'pyIsoPEP/IsotonicPEP.py'
+      - 'pyproject.toml'
+  release:
+    types: [published]
+
+permissions:
+  contents: read
+  packages: write
+  # id-token: write
+
+jobs:
+  publish:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.x"
+
+      - name: Build release distributions
+        run: |
+          python -m pip install --upgrade pip build hatchling
+          python -m build
+
+      - name: Build distributions
+        run: |
+          python -m build --sdist --wheel
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          packages-dir: dist/
+          password: ${{ secrets.PYPI_API_TOKEN }}

pyisopep-0.1.0/.github/workflows/pyisopep.yaml

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+name: Build and Push pyIsotonicPEP Image
+
+permissions:
+  contents: read
+  packages: write
+
+on:
+  workflow_dispatch:
+  push:
+    branches: [ main ]
+    paths:
+      - '.github/workflows/pyisopep.yaml'
+      - 'pyIsoPEP/*'
+      - 'example/*'
+
+jobs:
+  build_and_push_image:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Setup QEMU
+        uses: docker/setup-qemu-action@v3
+
+      - name: Setup Buildx
+        id: buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: Set up Python 3.13
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.13'
+
+      - name: Docker login
+        uses: docker/login-action@v3
+        with:
+          registry: ghcr.io
+          username: ${{ github.repository_owner }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+  
+      - name: Generate metadata
+        id: meta
+        uses: docker/metadata-action@v5
+        with:
+          images: ghcr.io/${{ github.repository_owner }}/pyIsotonicPEP
+          flavor: |
+            latest=auto
+          tags: |
+            type=ref,event=branch
+            type=semver,pattern={{version}}
+            type=sha,format=long
+          labels: |
+            org.opencontainers.image.title=pyIsotonicPEP
+            org.opencontainers.image.description="Image for estimating Posterior Error Probabilities (PEPs) for identifications using isotonic regression in shotgun proteomics."
+            org.opencontainers.image.url=${{ github.event.repository.html_url }}
+            org.opencontainers.image.source=${{ github.event.repository.html_url }}
+  
+      - name: Build and push pyIsotonicPEP image
+        uses: docker/build-push-action@v6
+        with:
+          context: .
+          file: ./pyIsoPEP/Dockerfile
+          push: true
+          platforms: linux/amd64
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}

pyisopep-0.1.0/.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/
+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/
+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/
+
+data/*.mzML
+data/*.pin
+data/*.txt
+output/*
+output_latest
+figs/*.png
+*simplified*
+pyiso_test/*
+figs/ispline/*
+figs/pyiso_test_onecrux/*
+figs/pyiso_test/*
+datasets/*/*
+!datasets/*/*.sh
+pyiso_test_onecrux/*
+pyiso_scripts/*onecrux*
+pyiso_scripts/*podman*
+pyiso_scripts/repeat_main.sh
+pyiso_scripts/run_all.sh
+pyIsoPEP/*maj*
+percolator_PEP_issues/*
+example/results/*