release-2.2.0

Enhance Packaging, Testing, and Infrastructure with Modern Tools and Features

.editorconfig

@@ -9,4 +9,7 @@ indent_size = 4
 end_of_line = lf
 charset = utf-8
 trim_trailing_whitespace = true
-insert_final_newline = true
+insert_final_newline = true
+
+[*.yml]
+indent_size = 2

.github/CODEOWNERS

@@ -0,0 +1,4 @@
+# This file is used to automatically assign reviewers to PRs
+# For more information see: https://help.github.com/en/github/creating-cloning-and-archiving-repositories/about-code-owners
+
+* @jacksonpradolima

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -0,0 +1,64 @@
+name: Bug report
+description: Report an issue or bug with this library
+labels: ['bug']
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Thanks for taking the time to fill out this bug report!
+  - type: checkboxes
+    id: non_api
+    attributes:
+      label: Confirm this is an issue with the gsp-py library.
+      description: Issues relevant to other tools should be directed to their respective repositories.
+      options:
+        - label: This is an issue with the gsp-py library
+          required: true
+  - type: textarea
+    id: what-happened
+    attributes:
+      label: Describe the bug
+      description: A clear and concise description of what the bug is, and any additional context.
+      placeholder: Tell us what you see!
+    validations:
+      required: true
+  - type: textarea
+    id: repro-steps
+    attributes:
+      label: To Reproduce
+      description: Steps to reproduce the behavior.
+      placeholder: |
+        1. Fetch a '...'
+        2. Update the '....'
+        3. See error
+    validations:
+      required: true
+  - type: textarea
+    id: code-snippets
+    attributes:
+      label: Code snippets
+      description: If applicable, add code snippets to help explain your problem.
+      render: Python
+    validations:
+      required: false
+  - type: input
+    id: os
+    attributes:
+      label: OS
+      placeholder: macOS
+    validations:
+      required: true
+  - type: input
+    id: language-version
+    attributes:
+      label: Python version
+      placeholder: Python v3.11.4
+    validations:
+      required: true
+  - type: input
+    id: lib-version
+    attributes:
+      label: Library version
+      placeholder: gsp-py v1.0.0
+    validations:
+      required: true

.github/ISSUE_TEMPLATE/config.yml

@@ -0,0 +1,7 @@
+blank_issues_enabled: false
+contact_links:
+  - name: gsp-py Support
+    url: https://github.com/jacksonpradolima/gsp-py
+    about: |
+      Please only file issues here if they relate to actual bugs or feature requests for the gsp-py project.
+      For more general discussions or questions, open an issue and select the appropriate template.

.github/ISSUE_TEMPLATE/feature_request.yml

@@ -0,0 +1,28 @@
+name: Feature request
+description: Suggest an idea for this library
+labels: ['feature-request']
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Thanks for taking the time to fill out this feature request!
+  - type: checkboxes
+    id: non_api
+    attributes:
+      label: Confirm this is a feature request for the gsp-py library.
+      description: Feature requests relevant to other tools should be directed to the correct repository.
+      options:
+        - label: This is a feature request for the gsp-py library
+          required: true
+  - type: textarea
+    id: feature
+    attributes:
+      label: Describe the feature or improvement you're requesting
+      description: A clear and concise description of what you want to happen.
+    validations:
+      required: true
+  - type: textarea
+    id: context
+    attributes:
+      label: Additional context
+      description: Add any other context about the feature request here.

.github/workflows/code_quality.yml

@@ -0,0 +1,51 @@
+name: Code Quality
+
+on:
+  pull_request:
+    types: [ opened, synchronize, reopened, edited, ready_for_review ]
+
+jobs:
+  code-quality:
+    name: Code Quality Checks
+    runs-on: ubuntu-latest
+
+    steps:
+      # Step 1: Checkout the repository code
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      # Step 2: Install Rye (via Curl)
+      - name: Install Rye
+        uses: eifinger/setup-rye@v4
+        with:
+          version: '0.43.0'
+          enable-cache: 'true'
+
+      # Step 3: Sync dependencies
+      - name: Sync dependencies
+        run: rye sync
+
+      # Step 4: Get changed Python files
+      - name: Get Python changed files
+        id: changed-py-files
+        uses: tj-actions/changed-files@v45
+        with:
+          files: |
+            *.py
+            **/*.py
+
+      # Step 5: Run Ruff for only changed files
+      - name: Run Ruff (Lint)
+        if: steps.changed-py-files.outputs.any_changed == 'true'
+        run: |
+          echo "Running Ruff on changed files..."
+          echo "Changed files: ${{ steps.changed-py-files.outputs.all_changed_files }}"
+          rye run lint ${{ steps.changed-py-files.outputs.all_changed_files }}
+
+      # Step 6: Run Pyright for only changed files
+      - name: Run Pyright (Type Check)
+        if: steps.changed-py-files.outputs.any_changed == 'true'
+        run: |
+          echo "Running Pyright on changed files..."
+          echo "Changed files: ${{ steps.changed-py-files.outputs.all_changed_files }}"
+          rye run typecheck ${{ steps.changed-py-files.outputs.all_changed_files }}

.github/workflows/codecov.yml

@@ -19,7 +19,10 @@ jobs:
                     python-version: 3.11
 
             -   name: Install dependencies
-                run: pip install -r requirements-dev.txt
+                run: |
+                    pip install pytest==8.3.4 \
+                        pytest-benchmark==5.1.0 \
+                        pytest-cov==6.0.0
 
             -   name: Run tests
                 run: pytest --cov --cov-branch --junitxml=junit.xml -o junit_family=legacy

.github/workflows/publish.yml

@@ -10,22 +10,25 @@ jobs:
     runs-on: ubuntu-latest
     environment:
       name: pypi
-      url: https://pypi.org/p/gsppy
+      url: https://pypi.org/project/gsppy/
     permissions:
       id-token: write
     steps:
       - uses: actions/checkout@v4
+
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
           python-version: "3.x"
-      - name: Install dependencies
+
+      - name: Install build dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install setuptools wheel
+          pip install build
+
       - name: Build package
         run: |
-          python setup.py sdist bdist_wheel  # Could also be python -m build
+          python -m build
+
       - name: Publish package distributions to PyPI
         uses: pypa/gh-action-pypi-publish@v1.12.3
-

.python-version

@@ -1,6 +1,6 @@
-3.6.15
-3.7.12
 3.8.10
 3.9.16
 3.10.12
 3.11.4
+3.12.8
+3.13.1

CHANGELOG.md

@@ -1,5 +1,53 @@
 # Changelog
 
+## [v2.2.0] - 2024-12-27
+
+### **New Features**
+- Added a `.github/CODEOWNERS` file to automatically assign reviewers for pull requests.
+- Introduced new issue templates:
+  - `bug_report.yml` for structured bug reporting.
+  - `feature_request.yml` for feature suggestions.
+  - `config.yml` to disable blank issues and provide guidance for issue reporting.
+
+### **Infrastructure Improvements**
+- Added `SECURITY.md` to define the project's security policy, including supported versions and responsible disclosure practices.
+- Updated `.python-version` to include support for Python versions `3.12.8` and `3.13.1`.
+- **Migrated Dependency and Virtual Environment Management to Rye**:
+  - Introduced [Rye](https://github.com/mitsuhiko/rye) for managing Python dependencies and virtual environments.
+  - Deprecated the `requirements-dev.txt` file in favor of managing dependencies in `pyproject.toml`.
+  - Updated documentation to include instructions for using `rye sync` to set up the project environment.
+  - Updated CI workflows to install and use dependencies directly via Rye.
+
+### **CLI Enhancements**
+- Improved `gsppy/cli.py`:
+  - Enhanced logging setup with verbosity options (`--verbose`).
+  - Added type annotations for improved readability and maintainability.
+  - Refined error handling and user feedback for invalid inputs.
+
+### **Algorithm and Utility Enhancements**
+- Updated GSP implementation in `gsppy/gsp.py`:
+  - Added type annotations and clarified logic in methods.
+  - Improved `_worker_batch` and `_support` functions for better performance and readability.
+- Enhanced utility functions in `gsppy/utils.py`:
+  - Added stricter typing and validation in utilities like `is_subsequence_in_list`.
+
+### **Testing and Quality**
+- Reorganized tests:
+  - Moved test files from `gsppy/tests/` to `tests/` for a cleaner structure.
+  - Refactored test cases with type annotations and enhanced mock handling.
+- Introduced additional dev dependencies in `requirements-dev.txt`:
+  - `mypy`, `pyright`, and `ruff` for static analysis and linting.
+  - `cython` for performance optimization in future releases.
+- Added `mypy.ini` and updated `pyproject.toml` for stricter type-checking and configuration consistency.
+
+### **Build and Packaging**
+- Migrated to `pyproject.toml` for modern Python packaging:
+  - Removed `setup.py` and `setup.cfg`.
+  - Introduced `hatch` and `hatchling` for streamlined builds.
+- Updated GitHub Actions workflows:
+  - Fixed PyPI URL in `publish.yml`.
+  - Updated build steps to use `python -m build` for consistency.
+
 ## [v2.1.0] - 2024-12-26
 
 ### **Compatibility Updates**
@@ -98,7 +146,28 @@
 
 ## **Summary of Changes**
 
-### From v2.0 to v2.1.0
-- Enhanced compatibility with earlier Python versions (3.8+).
-- Improved testing and dependency management.
-- Updated workflows and documentation for broader support and clarity.
+### From v2.1.0 to v2.2.0
+- **New Features**:
+  - Added `.github/CODEOWNERS` and issue templates for better pull request and issue management.
+  - Introduced a `SECURITY.md` file to define project security policies.
+
+- **Infrastructure Improvements**:
+  - Added Python 3.12.8 and 3.13.1 compatibility in `.python-version`.
+  - Migrated to `pyproject.toml` for modern Python packaging, replacing `setup.py` and `setup.cfg`.
+  - Adopted **Rye** for dependency management and virtual environment setup:
+    - Deprecated `requirements-dev.txt` in favor of managing all dependencies in `pyproject.toml`.
+    - Updated workflows and documentation to reflect the use of `rye sync` for environment setu
+
+- **CLI Enhancements**:
+  - Improved logging, error handling, and added type annotations in the CLI.
+
+- **Algorithm & Utility Enhancements**:
+  - Refactored the GSP algorithm for better performance and clarity.
+  - Enhanced utility functions with stricter typing and validation.
+
+- **Testing & Quality**:
+  - Reorganized tests into a cleaner structure, added static analysis tools, and improved type-checking configurations.
+
+- **Build & Packaging**:
+  - Streamlined the build process with `hatch` and `hatchling`.
+  - Updated GitHub Actions workflows for improved consistency and functionality.

CITATION.cff

@@ -6,7 +6,7 @@ authors:
     given-names: "Jackson Antonio do"
     orcid: "https://orcid.org/10.5281/zenodo.3333987"
 year: 2024
-version: "2.1.0"
+version: "2.2.0"
 doi: "10.5281/zenodo.3333987"
 url: "https://github.com/jacksonpradolima/gsp-py"
 repository-code: "https://github.com/jacksonpradolima/gsp-py"