netzoopy-sponge 0.0__tar.gz

netzoopy_sponge-0.0/.dockerignore

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+# Include any files or directories that you don't want to be copied to your
+# container here (e.g., local build artifacts, temporary files, etc.).
+#
+# For more help, visit the .dockerignore file reference guide at
+# https://docs.docker.com/go/build-context-dockerignore/
+
+**/.DS_Store
+**/__pycache__
+**/.venv
+**/.classpath
+**/.dockerignore
+**/.env
+**/.git
+**/.gitignore
+**/.project
+**/.settings
+**/.toolstarget
+**/.vs
+**/.vscode
+**/*.*proj.user
+**/*.dbmdl
+**/*.jfm
+**/bin
+**/charts
+**/docker-compose*
+**/compose.y*ml
+**/Dockerfile*
+**/node_modules
+**/npm-debug.log
+**/obj
+**/secrets.dev.yaml
+**/values.dev.yaml
+README.md

netzoopy_sponge-0.0/.github/workflows/publish_package.yaml

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+name: SPONGE GHCR package
+
+on:
+  workflow_run:
+    workflows:
+    - SPONGE PyPI upload
+    types:
+    - completed
+
+env:
+  IMAGE_NAME: netzoopy_sponge
+  VERSION_FILE: version.txt
+
+jobs:
+  push:
+    name: Push package to GHCR
+
+    runs-on: ubuntu-latest
+
+    if: ${{ github.event.workflow_run.conclusion == 'success' }}
+
+    permissions:
+      actions: read
+      contents: read
+      packages: write
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+
+    - name: Build image
+      run: docker build . --file Dockerfile --tag $IMAGE_NAME --label "runnumber=${GITHUB_RUN_ID}"
+
+    - name: Check basic functionality
+      run: docker run $IMAGE_NAME --help
+
+    - name: Download the artifact with the version
+      uses: dawidd6/action-download-artifact@v9
+      with:
+        name: version
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        workflow: test_testpypi_install.yaml
+        workflow_conclusion: success
+
+    - name: Check the downloaded file
+      run: |
+        ls -lah
+        cat $VERSION_FILE
+
+    - name: Log in to registry
+      run: echo "${{ secrets.GITHUB_TOKEN }}" | docker login ghcr.io -u ${{ github.actor }} --password-stdin
+
+    - name: Push images
+      run: |
+        IMAGE_ID=ghcr.io/${{ github.repository_owner }}/$IMAGE_NAME
+
+        # This changes all uppercase characters to lowercase
+        IMAGE_ID=$(echo $IMAGE_ID | tr '[A-Z]' '[a-z]')
+
+        VERSION=$(cat $VERSION_FILE)
+
+        # This strips the "v" prefix from the tag name
+        [[ $VERSION =~ v[0-9]+.[0-9]+.[0-9]+ ]] && VERSION=$(echo $VERSION | sed -e 's/^v//')
+
+        # Show the derived image ID and version
+        echo IMAGE_ID=$IMAGE_ID
+        echo VERSION=$VERSION
+
+        # Push the with the version tag
+        docker tag $IMAGE_NAME $IMAGE_ID:$VERSION
+        docker push $IMAGE_ID:$VERSION
+
+        # Push with the latest tag
+        docker tag $IMAGE_NAME $IMAGE_ID:latest
+        docker push $IMAGE_ID:latest

netzoopy_sponge-0.0/.github/workflows/publish_pypi.yaml

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+name: SPONGE PyPI upload
+
+on:
+  workflow_run:
+    workflows:
+    - SPONGE TestPyPI installation test
+    types:
+    - completed
+
+jobs:
+  pypi-publish:
+    name: Publish release to PyPI
+
+    runs-on: ubuntu-latest
+
+    if: ${{ github.event.workflow_run.conclusion == 'success' }}
+
+    environment:
+      name: pypi
+      url: https://pypi.org/p/netzoopy-sponge
+
+    permissions:
+      id-token: write
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: '3.10'
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install build setuptools wheel
+
+    - name: Build package
+      run: |
+        python -m build
+
+    - name: Publish package distributions to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1

netzoopy_sponge-0.0/.github/workflows/publish_testpypi.yaml

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+name: SPONGE TestPyPI upload
+
+on:
+  release:
+    types:
+    - released
+
+jobs:
+  testpypi-publish:
+    name: Publish release to TestPyPI
+
+    runs-on: ubuntu-latest
+
+    environment:
+      name: pypi
+      url: https://test.pypi.org/p/netzoopy-sponge
+
+    permissions:
+      id-token: write
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: '3.10'
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install build setuptools wheel
+
+    - name: Build package
+      run: |
+        python -m build
+
+    - name: Publish package distributions to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        repository-url: https://test.pypi.org/legacy/

netzoopy_sponge-0.0/.github/workflows/test.yaml

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+name: SPONGE tests
+
+on:
+  push:
+    branches:
+    - main
+    - devel
+  pull_request:
+    branches:
+    - main
+    - devel
+  workflow_dispatch:
+
+jobs:
+  os-python-compatibility:
+    name: Test SPONGE on multiple OS and Python versions
+
+    strategy:
+      matrix:
+        os: [ 'ubuntu-latest', 'macos-latest' ]
+        python: [ '3.9', '3.10', '3.11', '3.12' ]
+
+    runs-on: ${{ matrix.os }}
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+
+    - name: Setup Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python }}
+
+    - name: Check Python version
+      run: |
+        which python3
+        python3 --version
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install pytest
+        pip install -r requirements.txt
+        pip install -e .
+
+    - name: Run the tests
+      run: pytest tests -m 'not slow'

netzoopy_sponge-0.0/.github/workflows/test_testpypi_install.yaml

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+name: SPONGE TestPyPI installation test
+
+on:
+  workflow_run:
+    workflows:
+    - SPONGE TestPyPI upload
+    types:
+    - completed
+  
+jobs:
+  test-install:
+    name: Test installation of SPONGE from TestPyPI
+
+    runs-on: ubuntu-latest
+
+    if: ${{ github.event.workflow_run.conclusion == 'success' }}
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: '3.10'
+
+    - name: Update pip
+      run: |
+        python -m pip install --upgrade pip
+
+    - name: Install dependencies
+      run: |
+        pip install -r requirements.txt
+
+    - name: Install from TestPyPI
+      run: |
+        pip install --index-url https://test.pypi.org/simple/ netzoopy-sponge
+
+    - name: Test basic functionality
+      run: |
+        netzoopy-sponge --help
+
+    - name: Save release version
+      run: |
+        echo ${{ github.event.workflow_run.head_branch }} >> version.txt
+    
+    - name: Upload artifact with the version
+      uses: actions/upload-artifact@v4
+      with:
+        name: version
+        path: ./version.txt
+        retention-days: 1

netzoopy_sponge-0.0/Dockerfile

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+# Copyright (C) 2025 Ladislav Hovan <ladislav.hovan@ncmbm.uio.no>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+#
+# This library is free software: you can redistribute it and/or
+# modify it under the terms of the GNU Public License as published
+# by the Free Software Foundation; either version 3 of the License,
+# or (at your option) any later version.
+#
+# This library is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+# Library General Public License for more details.
+#
+# You should have received a copy of the GNU Public License along
+# with this library. If not, see <https://www.gnu.org/licenses/>.
+
+ARG PYTHON_VERSION=3.12
+FROM python:${PYTHON_VERSION}-slim
+
+# Keeps Python from buffering stdout and stderr to avoid situations where
+# the application crashes without emitting any logs due to buffering
+ENV PYTHONUNBUFFERED=1
+
+# Keeps Python from writing .pyc files
+ENV PYTHONDONTWRITEBYTECODE=1
+
+# Create a non-privileged user that the app will run under
+# See https://docs.docker.com/go/dockerfile-user-best-practices/
+ARG UID=10001
+RUN adduser \
+    --disabled-password \
+    --gecos "" \
+    --uid "${UID}" \
+    --shell "/bin/bash" \
+    appuser
+
+# Install SPONGE
+RUN python -m pip install --no-cache-dir netzoopy-sponge
+
+# Create the working directory
+WORKDIR /app
+RUN chown appuser /app
+
+# Switch to the non-privileged user to run the application
+USER appuser
+
+# Create an entry point
+ENTRYPOINT ["netzoopy-sponge"]
+CMD []
+
+# Labels
+LABEL org.opencontainers.image.source=https://github.com/kuijjerlab/sponge
+LABEL org.opencontainers.image.description="Container image of SPONGE"
+LABEL org.opencontainers.image.licenses=GPL-3.0-or-later