merge develop into main

.github/workflows/citation-update.yml

@@ -0,0 +1,36 @@
+name: Update CITATION.cff on Release
+on:
+  release:
+    types: [published]
+
+jobs:
+  update_citation:
+    runs-on: ubuntu-latest
+    steps:
+    - name: Checkout code
+      uses: actions/checkout@v3
+
+    - name: Get Release Data
+      id: release_info
+      run: |
+        echo "RELEASE_TAG=$(echo ${GITHUB_REF#refs/tags/})" >> $GITHUB_ENV
+
+    - name: Fetch DOI from Zenodo
+      run: |
+        # Replace with actual API request or data fetch logic
+        # Example command to fetch the DOI for the latest release via Zenodo API
+        curl -s "https://zenodo.org/api/records?query=AdaptiveResonanceLib" | jq '.hits.hits[0].doi' > doi.txt
+
+    - name: Update CITATION.cff
+      run: |
+        DOI=$(cat doi.txt)
+        sed -i "s/doi: .*/doi: \"$DOI\"/" CITATION.cff
+        sed -i "s/version: .*/version: \"$RELEASE_TAG\"/" CITATION.cff
+
+    - name: Commit updated CITATION.cff
+      run: |
+        git config --global user.name "github-actions[bot]"
+        git config --global user.email "github-actions[bot]@users.noreply.github.com"
+        git add CITATION.cff
+        git commit -m "Update CITATION.cff with DOI and version for release $RELEASE_TAG"
+        git push origin main

.github/workflows/draft-pdf.yml

@@ -0,0 +1,24 @@
+name: Draft PDF
+on: [push]
+
+jobs:
+  paper:
+    runs-on: ubuntu-latest
+    name: Paper Draft
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Build draft PDF
+        uses: openjournals/openjournals-draft-action@master
+        with:
+          journal: joss
+          # This should be the path to the paper within your repo.
+          paper-path: paper.md
+      - name: Upload
+        uses: actions/upload-artifact@v4
+        with:
+          name: paper
+          # This is the output path where Pandoc will write the compiled
+          # PDF. Note, this should be the same directory as the input
+          # paper.md
+          path: paper.pdf

.github/workflows/pre_commit_checks.yml

@@ -0,0 +1,45 @@
+name: Pre-commit checks
+
+on:
+  pull_request:
+  push:
+    branches:
+      - develop
+      - main
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v3
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.9'  # Adjust this to your desired Python version
+
+      - name: Install Poetry
+        run: |
+          curl -sSL https://install.python-poetry.org | python3 -
+
+      - name: Install dependencies
+        run: |
+          poetry install --with dev
+
+      - name: Install pre-commit
+        run: |
+          poetry run pip install pre-commit
+
+      - name: Fetch the base branch
+        run: |
+          git fetch origin ${GITHUB_BASE_REF}:${GITHUB_BASE_REF}
+        env:
+          GITHUB_BASE_REF: ${{ github.event.pull_request.base.ref }}
+
+      - name: Run pre-commit on changed files
+        run: |
+          poetry run pre-commit run --from-ref origin/${GITHUB_BASE_REF} --to-ref HEAD
+        env:
+          GITHUB_BASE_REF: ${{ github.event.pull_request.base.ref }}

.github/workflows/pytest.yml

@@ -0,0 +1,37 @@
+name: Run Python Unit Tests
+
+on:
+  pull_request:
+    branches:
+      - main
+      - develop
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout code
+      uses: actions/checkout@v3
+
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.9'
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install poetry
+        poetry install --with dev  # Install dependencies from pyproject.toml, including dev dependencies
+
+    - name: Run tests
+      run: |
+        poetry run pytest unit_tests/ --maxfail=5 --disable-warnings -v --tb=short  # Add verbose and short traceback options
+
+    - name: Publish test results
+      if: failure()
+      uses: actions/upload-artifact@v3
+      with:
+        name: pytest-results
+        path: ./test-results/pytest-report.xml

.pre-commit-config.yaml

@@ -0,0 +1,47 @@
+# .pre-commit-config.yaml
+
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
+    hooks:
+      - id: check-yaml
+      - id: debug-statements
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+
+  - repo: local
+    hooks:
+      - id: docformatter
+        name: docformatter
+        entry: docformatter
+        language: python
+        types: [python]
+        additional_dependencies: [docformatter==1.7.5]
+        args:
+          - --black
+          - --style=numpy
+          - --blank
+          - --in-place
+
+  - repo: https://github.com/psf/black
+    rev: 23.9.1  # Use the latest stable version
+    hooks:
+      - id: black
+
+  - repo: https://github.com/PyCQA/flake8
+    rev: 6.1.0  # Use the latest stable version
+    hooks:
+      - id: flake8
+        args: [--max-line-length=88, '--ignore=D205,D400,D105,E731,W503,D401,E203,D209']
+        additional_dependencies: [flake8-docstrings]
+
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.5.1
+    hooks:
+      - id: mypy
+        args:
+          - --ignore-missing-imports
+          - --exclude=artlib/cvi/
+          - --follow-imports=silent
+
+exclude: ^(unit_tests/|scripts/|artlib/experimental/|examples/|docs/|artlib/cvi/)

CITATION.cff

@@ -0,0 +1,19 @@
+cff-version: 1.2.0
+message: "If you use this software, please cite it as below."
+title: "AdaptiveResonanceLib"
+version: "0.1.2"
+doi: "10.5281/zenodo.9999999"
+authors:
+  - family-names: "Melton"
+    given-names: "Niklas"
+    orcid: "https://orcid.org/0000-0001-9625-7086"
+date-released: 2024-10-03
+url: "https://github.com/NiklasMelton/AdaptiveResonanceLib"
+repository-code: "https://github.com/NiklasMelton/AdaptiveResonanceLib"
+license: "MIT"
+keywords:
+  - "adaptive resonance theory"
+  - "ART"
+  - "machine learning"
+  - "clustering"
+  - "neural networks"

CITATIONS.txt

@@ -366,4 +366,4 @@ Yava ̧s, M., & Alpaslan, F. N. (2012). Hierarchical behavior categorization usi
 
 Zadeh, L. A. (1965). Fuzzy sets. Information and Control, 8, 338 – 353. doi:10.1016/S0019-9958(65) 90241-X.
 
-Brito da Silva LE, Rayapati N, Wunsch DC. iCVI-ARTMAP: Using Incremental Cluster Validity Indices and Adaptive Resonance Theory Reset Mechanism to Accelerate Validation and Achieve Multiprototype Unsupervised Representations. IEEE Trans Neural Netw Learn Syst. 2023 Dec;34(12):9757-9770. doi: 10.1109/TNNLS.2022.3160381. Epub 2023 Nov 30. PMID: 35353707.
+Brito da Silva LE, Rayapati N, Wunsch DC. iCVI-ARTMAP: Using Incremental Cluster Validity Indices and Adaptive Resonance Theory Reset Mechanism to Accelerate Validation and Achieve Multiprototype Unsupervised Representations. IEEE Trans Neural Netw Learn Syst. 2023 Dec;34(12):9757-9770. doi: 10.1109/TNNLS.2022.3160381. Epub 2023 Nov 30. PMID: 35353707.

CONTRIBUTING.md

@@ -38,9 +38,9 @@ If you're ready to contribute, here's how you can do it:
 
 5. **Run the tests** to ensure your changes don't break existing functionality.
 
-6. **Update the documentation** if you're adding new features or changing existing behavior. 
+6. **Update the documentation** if you're adding new features or changing existing behavior.
 
-7. **Submit a pull request**. Include a clear description of the changes and reference any related issues. 
+7. **Submit a pull request**. Include a clear description of the changes and reference any related issues.
 
 ## Pull Request Process