CodeEntropy 1.0.6__tar.gz → 1.1.0__tar.gz

{codeentropy-1.0.6 → codeentropy-1.1.0}/.github/CONTRIBUTING.md

@@ -10,7 +10,7 @@ This guide explains how to set up your environment, make changes, and submit the
 
 ## Getting Started
 
-Before contributing, please review the [Developer Guide](https://codeentropy.readthedocs.io/en/latest/developer_guide.html).  
+Before contributing, please review the [Developer Guide](https://codeentropy.readthedocs.io/en/latest/developer_guide.html).
 It covers CodeEntropy’s architecture, setup instructions, and contribution workflow.
 
 If you’re new to the project, we also recommend:
@@ -23,19 +23,19 @@ If you’re new to the project, we also recommend:
 
 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.  
+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.)  
+   - 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  
+   - 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.  
+   - 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.
 
@@ -45,12 +45,12 @@ We aim to provide constructive feedback quickly and appreciate your patience dur
 
 Found a bug or have a feature request?
 
-1. **Open a new issue** on GitHub.  
-2. Provide a **clear and descriptive title**.  
+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  
+   - 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 CodeEntropy stable and robust.
 

codeentropy-1.1.0/.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,70 @@
+---
+name: Bug report
+about: Create a report to help us improve CodeEntropy
+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:
+- CodeEntropy 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. -->

codeentropy-1.1.0/.github/ISSUE_TEMPLATE/config.yml

@@ -0,0 +1,22 @@
+blank_issues_enabled: false
+issue_templates:
+  - name: "Bug Report"
+    description: "Report a bug in CodeEntropy."
+    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"

codeentropy-1.1.0/.github/ISSUE_TEMPLATE/documentation.md

@@ -0,0 +1,19 @@
+---
+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. -->

codeentropy-1.1.0/.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,28 @@
+---
+name: Feature request
+about: Suggest an idea for CodeEntropy
+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 -->

codeentropy-1.1.0/.github/ISSUE_TEMPLATE/general_report.md

@@ -0,0 +1,13 @@
+---
+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. -->

{codeentropy-1.0.6 → codeentropy-1.1.0}/.github/PULL_REQUEST_TEMPLATE.md

@@ -5,16 +5,16 @@
 <!-- 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. -->
--  
+-

{codeentropy-1.0.6 → codeentropy-1.1.0}/.github/renovate.json

@@ -1,21 +1,21 @@
 {
   "extends": [
     "config:best-practices",
-    ":pinAllExceptPeerDependencies",
     ":dependencyDashboard",
     "group:monorepos",
     "group:recommended"
   ],
-  "rangeStrategy": "pin",
-  "schedule": ["* 8 * * 1-5"],
-  "labels": ["dependencies"],
-  "lockFileMaintenance": {
+  "enabledManagers": ["pep621"],
+  "pep621": {
     "enabled": true
   },
+  "rangeStrategy": "replace",
+  "schedule": ["* 8 * * 1-5"],
+  "labels": ["dependencies"],
   "packageRules": [
     {
       "matchUpdateTypes": ["minor", "patch"],
       "automerge": false
     }
   ]
-}
+}

codeentropy-1.1.0/.github/workflows/daily.yaml

@@ -0,0 +1,38 @@
+name: Daily Unit Tests
+
+on:
+  schedule:
+    - cron: '0 8 * * 1-5'
+  workflow_dispatch:
+
+concurrency:
+  group: daily-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  unit:
+    name: Unit (${{ matrix.os }}, ${{ matrix.python-version }})
+    runs-on: ${{ matrix.os }}
+    timeout-minutes: 30
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-24.04, macos-15, windows-2025]
+        python-version: ["3.12", "3.13", "3.14"]
+    steps:
+      - name: Checkout
+        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: pip
+
+      - name: Install (testing)
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install -e .[testing]
+
+      - name: Pytest (unit) • ${{ matrix.os }} • py${{ matrix.python-version }}
+        run: python -m pytest tests/unit -q

codeentropy-1.1.0/.github/workflows/pr.yaml

@@ -0,0 +1,175 @@
+name: Pull Request CI
+
+on:
+  pull_request:
+
+concurrency:
+  group: pr-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  unit:
+    name: Unit
+    runs-on: ${{ matrix.os }}
+    timeout-minutes: 25
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-24.04, macos-15, windows-2025]
+        python-version: ["3.12", "3.13", "3.14"]
+    steps:
+      - name: Checkout
+        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: pip
+
+      - name: Install testing dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install -e .[testing]
+
+      - name: Pytest (unit) • ${{ matrix.os }}, ${{ matrix.python-version }}
+        run: python -m pytest tests/unit -q
+
+  regression-quick:
+    name: Regression (quick)
+    needs: unit
+    runs-on: ubuntu-24.04
+    timeout-minutes: 35
+    steps:
+      - name: Checkout
+        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6
+
+      - name: Set up Python 3.14
+        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0
+        with:
+          python-version: "3.14"
+          cache: pip
+
+      - name: Cache testdata
+        uses: actions/cache@v4
+        with:
+          path: .testdata
+          key: codeentropy-testdata-v1-${{ runner.os }}-py3.14
+
+      - name: Install (testing)
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install -e .[testing]
+
+      - name: Pytest (regression quick)
+        run: python -m pytest tests/regression -q
+
+      - name: Upload artifacts (failure)
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: quick-regression-failure
+          path: |
+            .testdata/**
+            tests/regression/**/.pytest_cache/**
+            /tmp/pytest-of-*/pytest-*/**/config.yaml
+            /tmp/pytest-of-*/pytest-*/**/codeentropy_stdout.txt
+            /tmp/pytest-of-*/pytest-*/**/codeentropy_stderr.txt
+            /tmp/pytest-of-*/pytest-*/**/codeentropy_output.json
+
+  docs:
+    name: Docs
+    needs: unit
+    runs-on: ubuntu-24.04
+    timeout-minutes: 25
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8
+
+      - name: Set up Python 3.14
+        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405
+        with:
+          python-version: "3.14"
+          cache: pip
+
+      - name: Install
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install -e .[docs]
+
+      - name: Build docs
+        run: |
+          make -C docs clean
+          make -C docs html SPHINXOPTS="-W --keep-going"
+
+      - name: Upload docs artifact
+        if: always()
+        uses: actions/upload-artifact@v4
+        with:
+          name: docs-html
+          path: docs/_build/html
+
+  pre-commit:
+    name: Pre-commit
+    runs-on: ubuntu-24.04
+    timeout-minutes: 15
+    steps:
+      - name: Checkout
+        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6
+
+      - name: Set up Python 3.14
+        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0
+        with:
+          python-version: "3.14"
+          cache: pip
+
+      - name: Install (pre-commit)
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install -e .[pre-commit]
+
+      - name: Run pre-commit
+        shell: bash
+        run: |
+          pre-commit install
+          pre-commit run --all-files || {
+            git status --short
+            git diff
+            exit 1
+          }
+
+  coverage:
+    name: Coverage
+    needs: unit
+    runs-on: ubuntu-24.04
+    timeout-minutes: 30
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8
+
+      - name: Set up Python 3.14
+        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405
+        with:
+          python-version: "3.14"
+          cache: pip
+
+      - name: Install (testing)
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install -e .[testing]
+
+      - name: Run unit test suite with coverage
+        run: |
+          pytest tests/unit \
+            --cov CodeEntropy \
+            --cov-report term-missing \
+            --cov-report xml \
+            -q
+
+      - name: Upload to Coveralls
+        uses: coverallsapp/github-action@5cbfd81b66ca5d10c19b062c04de0199c215fb6e
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          file: coverage.xml
+          fail-on-error: false

{codeentropy-1.0.6 → codeentropy-1.1.0}/.github/workflows/release.yaml

@@ -1,4 +1,4 @@
-name: release
+name: Release CodeEntropy
 
 on:
   workflow_dispatch:
@@ -18,10 +18,10 @@ jobs:
     steps:
     - name: Checkout repository
       id: repo
-      uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6
+      uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6
 
     - name: Set up Python
-      uses: actions/setup-python@83679a892e2d95755f2dac6acb0bfd1e9ac5d548 # v6.1.0
+      uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0
       with:
         python-version: 3.14.0
 
@@ -46,7 +46,7 @@ jobs:
     steps:
 
       - name: checkout
-        uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6
+        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6
 
       - name: Change version in repo and CITATION.cff
         run: |
@@ -61,7 +61,7 @@ jobs:
 
       - name: send PR
         id: pr_id
-        uses: peter-evans/create-pull-request@84ae59a2cdc2258d6fa0732dd66352dddae2a412 # v7.0.9
+        uses: peter-evans/create-pull-request@c0f553fe549906ede9cf27b5156039d195d2ece0 # v8.1.0
         with:
           commit-message: Update version to ${{ github.event.inputs.version }}
           branch: version-update
@@ -95,7 +95,7 @@ jobs:
     runs-on: ubuntu-24.04
     steps:
       - name: Checkout repository
-        uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6
+        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6
         with:
           ref: main
 
@@ -113,7 +113,7 @@ jobs:
     steps:
 
       - name: create release
-        uses: softprops/action-gh-release@5be0e66d93ac7ed76da52eca8bb058f665c3a5fe # v2.4.2
+        uses: softprops/action-gh-release@a06a81a03ee405af7f2048a818ed3f03bbf83c7b # v2.5.0
         with:
           name: v${{ github.event.inputs.version }}
           generate_release_notes: true
@@ -126,12 +126,12 @@ jobs:
     steps:
 
     - name: checkout
-      uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6
+      uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6
       with:
         ref: main
 
     - name: Set up Python
-      uses: actions/setup-python@83679a892e2d95755f2dac6acb0bfd1e9ac5d548 # v6.1.0
+      uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0
       with:
         python-version: 3.14.0
 
@@ -146,4 +146,46 @@ jobs:
       env:
         FLIT_USERNAME: __token__
         FLIT_PASSWORD:  ${{ secrets.PYPI_API_TOKEN }}
- 
+
+  conda:
+    name: publish conda to anaconda.org
+    needs: [tag, release]
+    runs-on: ubuntu-24.04
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          ref: main
+
+      - name: Set version in conda recipe
+        run: |
+          sed -i -E "s/^{% set version = \".*\" %}$/{% set version = \"${{ github.event.inputs.version }}\" %}/" conda-recipe/meta.yaml
+
+      - name: Setup Conda
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          miniforge-variant: Miniforge3
+          python-version: "3.12"
+          auto-activate-base: false
+
+      - name: Install build tools
+        shell: bash -l {0}
+        run: |
+          conda install -y conda-build anaconda-client
+          conda config --add channels conda-forge
+          conda config --set channel_priority strict
+          conda config --set anaconda_upload no
+
+      - name: Build package
+        shell: bash -l {0}
+        run: |
+          conda build conda-recipe
+
+      - name: Upload to Anaconda
+        shell: bash -l {0}
+        env:
+          ANACONDA_API_TOKEN: ${{ secrets.ANACONDA_TOKEN }}
+        run: |
+          PKG_PATH=$(conda build conda-recipe --output)
+          anaconda -t "$ANACONDA_API_TOKEN" upload "$PKG_PATH" --user CCPBioSim --force

codeentropy-1.1.0/.github/workflows/update-copyright-years-in-license-file.yaml

@@ -0,0 +1,17 @@
+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 }}

codeentropy-1.1.0/.github/workflows/weekly-docs.yaml

@@ -0,0 +1,49 @@
+name: Weekly Docs Build
+
+on:
+  schedule:
+    - cron: '0 8 * * 1'
+  workflow_dispatch:
+
+concurrency:
+  group: weekly-docs-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  docs:
+    name: Docs build (${{ matrix.os }}, python ${{ matrix.python-version }})
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-24.04, windows-2025, macos-15]
+        python-version: ["3.12", "3.13", "3.14"]
+    timeout-minutes: 30
+
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: pip
+
+      - name: Install python dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install -e .[docs]
+
+      - name: Build docs (warnings as errors)
+        run: |
+          make -C docs clean
+          make -C docs html SPHINXOPTS="-W --keep-going"
+
+      - name: Upload docs artifacts on failure
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: docs-${{ matrix.os }}-py${{ matrix.python-version }}-failure
+          path: |
+            docs/_build/**