biosim_extractor 0.0.4__tar.gz

biosim_extractor-0.0.4/.github/CONTRIBUTING.md

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+# Contributing to REPO-NAME
+
+Thank you for your interest in contributing to **REPO-NAME**!
+
+We’re excited to collaborate with developers, researchers, and community members to make REPO-NAME better for everyone.
+
+This guide explains how to set up your environment, make changes, and submit them for review. Whether you’re fixing a bug, improving documentation, or adding new features, every contribution makes a difference.
+
+---
+
+## Getting Started
+
+Before contributing, please review the [Developer Guide]().
+It covers REPO-NAME’s architecture, setup instructions, and contribution workflow.
+
+If you’re new to the project, we also recommend:
+- Reading the [README](../README.md) for an overview and installation details.
+- Checking open [issues]() labeled **good first issue** to find beginner-friendly tasks.
+
+---
+
+## Submitting a Pull Request (PR)
+
+When you’re ready to submit your work:
+
+1. **Push your branch** to GitHub.
+2. **Open a [pull request](https://help.github.com/articles/using-pull-requests/)** against the `main` branch.
+3. **Fill out the PR template**, including:
+   - A concise summary of what your PR does
+   - A list of all changes introduced
+   - Details on how these changes affect the repository (features, tests, documentation, etc.)
+4. **Verify before submission**:
+   - All tests pass
+   - Pre-commit checks succeed
+   - Documentation is updated where applicable
+5. **Review process**:
+   - Your PR will be reviewed by the core development team.
+   - At least **one approval** is required before merging.
+
+We aim to provide constructive feedback quickly and appreciate your patience during the review process.
+
+---
+
+## Reporting Issues
+
+Found a bug or have a feature request?
+
+1. **Open a new issue** on GitHub.
+2. Provide a **clear and descriptive title**.
+3. Include:
+   - Steps to reproduce the issue (if applicable)
+   - Expected vs. actual behavior
+   - Relevant logs, screenshots, or input files
+
+Well-documented issues help us address problems faster and keep REPO-NAME stable and robust.
+
+---
+
+## Additional Resources
+
+- [GitHub Docs](https://help.github.com/)
+
+---
+
+Thank you for helping improve **REPO-NAME**, your contributions make open source stronger!

biosim_extractor-0.0.4/.github/ISSUE_TEMPLATE/bug_report.md

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+---
+name: Bug report
+about: Create a report to help us improve
+title: '[Bug]: '
+labels: bug
+assignees: ''
+
+---
+
+# Bug Report
+<!-- A clear and concise description of the issue. -->
+
+---
+
+## To Reproduce
+<!-- Provide the YAML configuration and the exact CLI command that reproduces the issue. -->
+
+### YAML configuration
+<!-- Paste the YAML file or the smallest excerpt that reproduces the issue.
+Remove unrelated fields to make it minimal. -->
+```yaml
+# Paste the YAML snippet here
+```
+
+### CLI command used
+<!-- Write the exact command used, for example:   -->
+```bash
+# Paste the CLI command here
+```
+
+### Actual output
+<!-- Paste the output, logs, or error messages here -->
+```bash
+# Paste the output, logs, or error messages here
+```
+
+### Expected output
+<!-- Describe what you expected to see instead -->
+
+---
+
+## Environment and Versions
+
+- Operating System:
+- Package Version:
+- Python Version:
+- Package list:
+  - If using conda, run: `conda list > packages.txt` and paste the contents here.
+
+    ``` bash
+    # Paste packages.txt here
+    ```
+
+  - If using venv/pip, run: `pip list > packages.txt` and paste the contents here.
+
+    ``` bash
+    # Paste packages.txt here
+    ```
+
+---
+
+## Screenshots or Logs
+
+<!-- Attach any relevant screenshots, logs, or stack traces. -->
+
+---
+
+## Additional Context
+
+<!-- Include anything else that might help reproduce or understand the bug, such as changes from a previously working version. -->

biosim_extractor-0.0.4/.github/ISSUE_TEMPLATE/config.yml

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+blank_issues_enabled: false
+issue_templates:
+  - name: "Bug Report"
+    description: "Report a bug."
+    title: "[Bug]: "
+    labels: ["bug"]
+    body: "./ISSUE_TEMPLATE/bug_report.md"
+  - name: "Feature Request"
+    description: "Propose a new feature or improvement."
+    title: "[Feature]: "
+    labels: ["enhancement"]
+    body: "./ISSUE_TEMPLATE/feature_request.md"
+  - name: "Documentation"
+    description: "Suggest updates or additions to the documentation."
+    title: "[Docs]: "
+    labels: ["documentation"]
+    body: "./ISSUE_TEMPLATE/documentation.md"
+  - name: "General Report"
+    description: "Provide general feedback or inquiries."
+    title: "[General]: "
+    labels: ["general"]
+    body: "./ISSUE_TEMPLATE/general_report.md"

biosim_extractor-0.0.4/.github/ISSUE_TEMPLATE/documentation.md

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+---
+name: Documentation
+about: Suggest updates or additions to documentation
+title: "[Docs]: "
+labels: documentation
+assignees: ''
+---
+
+### Documentation Update
+<!-- What part of the documentation needs to be updated or added? -->
+
+### Why Is This Needed?
+<!-- Explain the importance of this update. -->
+
+### Suggested Changes
+<!-- Provide a detailed description of the changes. -->
+
+### Additional Context
+<!-- Include any related resources. -->

biosim_extractor-0.0.4/.github/ISSUE_TEMPLATE/feature_request.md

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+---
+name: Feature request
+about: Suggest an idea
+title: '[Feature]: '
+labels: 'enhancement'
+assignees: ''
+---
+
+# Feature Request
+
+## Problem / Motivation
+<!-- Describe the problem you want to solve or the motivation for this feature. -->
+
+## Proposed Solution
+<!-- Describe the feature you would like to see implemented. Include examples if applicable. -->
+
+## Alternatives Considered
+- <!-- Alternative 1 -->
+- <!-- Alternative 2 -->
+
+## Expected Impact
+<!-- How this feature would affect the codebase or workflow -->
+- <!-- Impact 1 -->
+- <!-- Impact 2 -->
+
+## Additional Context
+<!-- Add any other context, screenshots, or references for the feature request here. -->
+- <!-- Further context -->

biosim_extractor-0.0.4/.github/ISSUE_TEMPLATE/general_report.md

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+---
+name: General Report
+about: Provide general feedback or inquiries
+title: "[General]: "
+labels: general
+assignees: ''
+---
+
+### Feedback or Inquiry
+<!-- Provide your feedback or inquiry. -->
+
+### Additional Information
+<!-- Add any other relevant details here. -->

biosim_extractor-0.0.4/.github/pull_request_template.md

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+## Summary
+<!-- Provide a brief description of the PR's purpose here. -->
+
+## Changes
+<!-- List all the changes introduced in this PR. -->
+### Change 1 <!-- Rename Change 1 to reflect change title -->:
+- <!-- Bullet point the changes in update 1. -->
+-
+
+### Change 2 <!-- Rename Change 2 to reflect change title -->:
+- <!-- Bullet point the changes in update 2. -->
+-
+
+### Change 3 <!-- Rename Change 3 to reflect change title -->:
+- <!-- Bullet point the changes in update 3. -->
+-
+
+## Impact
+- <!-- Bullet point the expected impact this PR will have on the codebase. -->
+-

biosim_extractor-0.0.4/.github/renovate.json

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+{
+  "extends": [
+    "config:best-practices",
+    ":dependencyDashboard",
+    "group:monorepos",
+    "group:recommended"
+  ],
+  "enabledManagers": ["pep621"],
+  "pep621": {
+    "enabled": true
+  },
+  "rangeStrategy": "replace",
+  "schedule": ["* 8 * * 1-5"],
+  "labels": ["dependencies"],
+  "packageRules": [
+    {
+      "matchUpdateTypes": ["minor", "patch"],
+      "automerge": false
+    }
+  ]
+}

biosim_extractor-0.0.4/.github/workflows/biosim_extractor_project-ci.yaml

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+name: biosim-extractor CI
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+  schedule:
+    - cron: '0 8 * * 1-5'
+  workflow_dispatch:
+
+jobs:
+  tests:
+    name: Run tests
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-24.04, windows-2025, macos-15]
+        python-version: ["3.12", "3.13", "3.14"]
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@83679a892e2d95755f2dac6acb0bfd1e9ac5d548 # v6.1.0
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install biosim-extractor and its testing dependencies
+        run: pip install -e .[testing]
+
+      - name: Run test suite
+        run: pytest --cov biosim_extractor --cov-report term-missing --cov-append .
+
+      - name: Coveralls GitHub Action
+        uses: coverallsapp/github-action@5cbfd81b66ca5d10c19b062c04de0199c215fb6e # v2.3.7
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          parallel: true
+          fail-on-error: false
+
+  coveralls-finish:
+    name: Finish Coveralls
+    needs: tests
+    if: ${{ always() }}
+    runs-on: ubuntu-24.04
+    steps:
+    - name: Coveralls Finished
+      uses: coverallsapp/github-action@5cbfd81b66ca5d10c19b062c04de0199c215fb6e # v2.3.7
+      with:
+        github-token: ${{ secrets.GITHUB_TOKEN }}
+        parallel-finished: true
+        fail-on-error: false
+
+  docs:
+    runs-on: ubuntu-latest
+    timeout-minutes: 15
+    steps:
+      - uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6
+      - name: Set up Python 3.14
+        uses: actions/setup-python@83679a892e2d95755f2dac6acb0bfd1e9ac5d548 # v6.1.0
+        with:
+          python-version: 3.14.0
+      - name: Install python dependencies
+        run: |
+          pip install --upgrade pip
+          pip install -e .[docs]
+      - name: Build docs
+        run: cd docs && make
+
+  pre-commit:
+    runs-on: ubuntu-24.04
+    timeout-minutes: 15
+    steps:
+      - uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6
+      - name: Set up Python 3.14
+        uses: actions/setup-python@83679a892e2d95755f2dac6acb0bfd1e9ac5d548 # v6.1.0
+        with:
+          python-version: 3.14.0
+      - name: Install python dependencies
+        run: |
+          pip install --upgrade pip
+          pip install -e .[pre-commit]
+      - name: Run pre-commit
+        run: |
+          pre-commit install
+          pre-commit run --all-files || ( git status --short ; git diff ; exit 1 )

biosim_extractor-0.0.4/.github/workflows/release.yaml

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+name: release
+
+on:
+  workflow_dispatch:
+    inputs:
+      version:
+        required: true
+        default: 'x.y.z'
+
+permissions:
+  contents: write
+  pull-requests: write
+
+jobs:
+  checks:
+    name: Version check
+    runs-on: ubuntu-24.04
+    steps:
+    - name: Checkout repository
+      id: repo
+      uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6
+
+    - name: Set up Python
+      uses: actions/setup-python@83679a892e2d95755f2dac6acb0bfd1e9ac5d548 # v6.1.0
+      with:
+        python-version: 3.14.0
+
+    - name: Get latest release from pip
+      id: latestreleased
+      run: |
+        PREVIOUS_VERSION=$(python -m pip index versions biosim-extractor | grep "biosim-extractor" | cut -d "(" -f2 | cut -d ")" -f1)
+        echo "pip_tag=$PREVIOUS_VERSION" >> "$GITHUB_OUTPUT"
+        echo $PREVIOUS_VERSION
+
+    - name: version comparison
+      id: compare
+      run: |
+        pip3 install semver
+        output=$(pysemver compare ${{ steps.latestreleased.outputs.pip_tag }} ${{ github.event.inputs.version }})
+        if [ $output -ge 0 ]; then exit 1; fi
+
+  version:
+    name: prepare ${{ github.event.inputs.version }}
+    needs: checks
+    runs-on: ubuntu-24.04
+    steps:
+
+      - name: checkout
+        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6
+
+      - name: Change version in repo and CITATION.cff
+        run: |
+          # Update Python package version
+          sed -i "s/__version__ =.*/__version__ = \"${{ github.event.inputs.version }}\"/g" biosim_extractor/__init__.py
+
+          # Keep Sphinx release metadata in sync
+          sed -i -E "s/^(release = ).*/\1'${{ github.event.inputs.version }}'/" docs/source/conf.py
+
+          # Update CITATION.cff version and date-released
+          if [ -f CITATION.cff ]; then
+            sed -i -E "s/^(version:\s*).*/\1${{ github.event.inputs.version }}/" CITATION.cff
+            sed -i -E "s/^(date-released:\s*).*/\1'$(date -u +%F)'/" CITATION.cff
+          fi
+
+      - name: send PR
+        id: pr_id
+        uses: peter-evans/create-pull-request@98357b18bf14b5342f975ff684046ec3b2a07725 # v8.0.0
+        with:
+          commit-message: Update version to ${{ github.event.inputs.version }}
+          branch: version-update
+          title: "Update to version ${{ github.event.inputs.version }}"
+          body: |
+            Update version
+            - Update the __init__.py with new release
+            - Update CITATION.cff version & date-released
+            - Auto-generated by [CI]
+          committer: version-updater <vu.bot@users.noreply.github.com>
+          author: version-updater <vu.bot@users.noreply.github.com>
+          base: main
+          signoff: false
+          draft: false
+
+      - name: auto approve review
+        uses: hmarr/auto-approve-action@f0939ea97e9205ef24d872e76833fa908a770363 # v4.0.0
+        with:
+          pull-request-number: ${{ steps.pr_id.outputs.pull-request-number }}
+          review-message: "Auto approved version bump PR"
+          github-token: ${{ secrets.AUTO_PR_MERGE }}
+
+      - name: merge PR
+        run: gh pr merge --merge --delete-branch --auto "${{ steps.pr_id.outputs.pull-request-number }}"
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+  tag:
+    name: tag release
+    needs: version
+    runs-on: ubuntu-24.04
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6
+        with:
+          ref: main
+
+      - name: tag v${{ github.event.inputs.version }}
+        run: |
+          git config user.name github-actions
+          git config user.email github-actions@github.com
+          git tag ${{ github.event.inputs.version }}
+          git push origin tag ${{ github.event.inputs.version }}
+
+  release:
+    name: make github release
+    needs: tag
+    runs-on: ubuntu-24.04
+    steps:
+
+      - name: create release
+        uses: softprops/action-gh-release@a06a81a03ee405af7f2048a818ed3f03bbf83c7b # v2.5.0
+        with:
+          name: v${{ github.event.inputs.version }}
+          generate_release_notes: true
+          tag_name: ${{ github.event.inputs.version }}
+
+  pypi:
+    name: make pypi release
+    needs: [tag, release]
+    runs-on: ubuntu-24.04
+    steps:
+
+    - name: checkout
+      uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6
+      with:
+        ref: main
+
+    - name: Set up Python
+      uses: actions/setup-python@83679a892e2d95755f2dac6acb0bfd1e9ac5d548 # v6.1.0
+      with:
+        python-version: 3.14.0
+
+    - name: Install flit
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install flit~=3.9
+
+    - name: Build and publish
+      run: |
+        flit publish
+      env:
+        FLIT_USERNAME: __token__
+        FLIT_PASSWORD:  ${{ secrets.PYPI_API_TOKEN }}
+
+  conda:
+    name: publish conda to anaconda.org
+    needs: [tag, release]
+    runs-on: ubuntu-24.04
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          ref: main
+
+      - name: Set version in conda recipe
+        run: |
+          sed -i "s/^{% set version = \".*\" %}$/{% set version = \"${{ github.event.inputs.version }}\" %}/" conda-recipe/meta.yaml
+          grep '{% set version' conda-recipe/meta.yaml
+
+      - name: Setup Conda (conda-forge only)
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          miniforge-variant: Miniforge3
+          python-version: "3.12"
+          auto-activate: true
+          activate-environment: base
+          conda-remove-defaults: true
+          channels: conda-forge
+          channel-priority: strict
+
+      - name: Install build tools
+        shell: bash -l {0}
+        run: |
+          conda install -y conda-build anaconda-client
+          conda config --set anaconda_upload no
+          conda list conda-build
+          conda build --help
+
+      - name: Build package
+        shell: bash -l {0}
+        env:
+          PIP_NO_INDEX: "0"
+        run: |
+          PKG_PATH=$(conda build conda-recipe --output)
+          echo "PKG_PATH=$PKG_PATH" >> "$GITHUB_ENV"
+          conda build conda-recipe
+          test -f "$PKG_PATH"
+          echo "Built: $PKG_PATH"
+
+      - name: Upload to Anaconda
+        shell: bash -l {0}
+        env:
+          ANACONDA_API_TOKEN: ${{ secrets.ANACONDA_TOKEN }}
+        run: |
+          anaconda -t "$ANACONDA_API_TOKEN" upload "$PKG_PATH" --user CCPBioSim --force

biosim_extractor-0.0.4/.github/workflows/update-copyright-years-in-license-file.yaml

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+name: Update copyright year(s) in license file
+
+on:
+  schedule:
+    - cron: '0 3 1 1 *' # 03:00 AM on January 1
+  workflow_dispatch:
+
+jobs:
+    update-license-year:
+        runs-on: ubuntu-latest
+        steps:
+            - uses: actions/checkout@v6
+              with:
+                  fetch-depth: 0
+            - uses: FantasticFiasco/action-update-license-year@v3
+              with:
+                  token: ${{ secrets.GITHUB_TOKEN }}