masster 0.5.25__tar.gz → 0.5.27__tar.gz

{masster-0.5.25 → masster-0.5.27}/PKG-INFO

@@ -1,10 +1,11 @@
 Metadata-Version: 2.4
 Name: masster
-Version: 0.5.25
+Version: 0.5.27
 Summary: Mass spectrometry data analysis package
 Project-URL: homepage, https://github.com/zamboni-lab/masster
 Project-URL: repository, https://github.com/zamboni-lab/masster
 Project-URL: documentation, https://github.com/zamboni-lab/masster#readme
+Project-URL: Third-Party Licenses, https://github.com/zamboni-lab/masster/blob/main/THIRD_PARTY_NOTICES.md
 Author: Zamboni Lab
 License:                     GNU AFFERO GENERAL PUBLIC LICENSE
                                Version 3, 19 November 2007
@@ -851,5 +852,10 @@ python -c "from masster import Wizard; wiz = Wizard(source='D:/Data/studies/my_s
 ## License
 GNU Affero General Public License v3
 
+See the [LICENSE](LICENSE) file for details.
+
+### Third-Party Licenses
+This project uses several third-party libraries, including pyOpenMS which is licensed under the BSD 3-Clause License. For complete information about third-party dependencies and their licenses, see [THIRD_PARTY_NOTICES.md](THIRD_PARTY_NOTICES.md).
+
 ## Citation
 If you use Masster in your research, please cite this repository.

{masster-0.5.25 → masster-0.5.27}/README.md

@@ -124,5 +124,10 @@ python -c "from masster import Wizard; wiz = Wizard(source='D:/Data/studies/my_s
 ## License
 GNU Affero General Public License v3
 
+See the [LICENSE](LICENSE) file for details.
+
+### Third-Party Licenses
+This project uses several third-party libraries, including pyOpenMS which is licensed under the BSD 3-Clause License. For complete information about third-party dependencies and their licenses, see [THIRD_PARTY_NOTICES.md](THIRD_PARTY_NOTICES.md).
+
 ## Citation
 If you use Masster in your research, please cite this repository.

masster-0.5.27/THIRD_PARTY_NOTICES.md

@@ -0,0 +1,64 @@
+# Third-Party Licenses and Notices
+
+This project uses third-party libraries and components that are distributed under their own licenses. Below is a list of these dependencies and their respective license information.
+
+---
+
+## pyOpenMS
+
+**License:** BSD 3-Clause License  
+**Copyright:** OpenMS Team  
+**Source:** https://github.com/OpenMS/OpenMS
+
+pyOpenMS is a Python wrapper for OpenMS, a library for mass spectrometry data analysis.
+
+### BSD 3-Clause License
+
+```
+Copyright (c) 2002-2025, The OpenMS Team
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice,
+   this list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+```
+
+---
+
+## Other Dependencies
+
+This project also depends on the following open-source libraries. Please refer to their respective repositories for detailed license information:
+
+- **NumPy** - BSD License
+- **Pandas** - BSD License
+- **SciPy** - BSD License
+- **Matplotlib** - PSF-based License
+- **h5py** - BSD License
+- **Bokeh** - BSD License
+- **Panel** - BSD License
+- **Polars** - MIT License
+- **scikit-learn** - BSD License
+- **and others** - See pyproject.toml for complete dependency list
+
+For the most up-to-date license information for these dependencies, please refer to their official repositories and documentation.

{masster-0.5.25 → masster-0.5.27}/pyproject.toml

@@ -1,7 +1,7 @@
 
 [project]
 name = "masster"
-version = "0.5.25"
+version = "0.5.27"
 description = "Mass spectrometry data analysis package"
 authors = [
     { name = "Zamboni Lab" }
@@ -25,6 +25,7 @@ classifiers = [
 urls.homepage = "https://github.com/zamboni-lab/masster"
 urls.repository = "https://github.com/zamboni-lab/masster"
 urls.documentation = "https://github.com/zamboni-lab/masster#readme"
+urls."Third-Party Licenses" = "https://github.com/zamboni-lab/masster/blob/main/THIRD_PARTY_NOTICES.md"
 dependencies = [
     "alpharaw>=0.4.8",
     "bokeh>=3.7.3",
@@ -83,6 +84,23 @@ masster-version = "masster._version:main"
 requires = ["hatchling>=1.18.0"]
 build-backend = "hatchling.build"
 
+# Hatchling configuration - include additional files in distribution
+[tool.hatch.build.targets.sdist]
+include = [
+    "/src",
+    "/tests",
+    "/LICENSE",
+    "/README.md",
+    "/THIRD_PARTY_NOTICES.md",
+    "/pyproject.toml",
+]
+
+[tool.hatch.build.targets.wheel]
+packages = ["src/masster"]
+include = [
+    "/THIRD_PARTY_NOTICES.md",
+]
+
 # Testing configuration
 [tool.pytest.ini_options]
 testpaths = ["tests"]
@@ -132,18 +150,18 @@ exclude_lines = [
 line-length = 88
 target-version = ['py311']
 include = '\.pyi?$'
-extend-exclude = '''
-/(
-  # directories
-  \.eggs
-  | \.git
-  | \.hg
-  | \.mypy_cache
-  | \.tox
-  | \.venv
-  | build
-  | dist
-)/
+extend-exclude = '''
+/(
+  # directories
+  \.eggs
+  | \.git
+  | \.hg
+  | \.mypy_cache
+  | \.tox
+  | \.venv
+  | build
+  | dist
+)/
 '''
 
 # MyPy configuration

masster-0.5.25/.github/workflows/publish.yml

@@ -1,174 +0,0 @@
-name: Create release and Publish to PyPI
-
-on:
-  workflow_dispatch:
-    inputs:
-      version:
-        description: 'Version to release (e.g., v1.0.0)'
-        required: true
-        type: string
-      test_pypi:
-        description: 'Publish to Test PyPI instead of PyPI'
-        required: false
-        default: false
-        type: boolean
-
-jobs:
-  create-release:
-    runs-on: ubuntu-latest
-    steps:
-    - uses: actions/checkout@v4
-      with:
-        fetch-depth: 0
-
-    - name: Set up Python
-      uses: actions/setup-python@v5
-      with:
-        python-version: "3.11"
-
-    - name: Update version in pyproject.toml
-      run: |
-        # Remove 'v' prefix if present
-        VERSION="${{ github.event.inputs.version }}"
-        VERSION=${VERSION#v}
-        
-        # Update version in pyproject.toml
-        sed -i "s/^version = \".*\"/version = \"$VERSION\"/" pyproject.toml
-        
-        # Verify the change
-        echo "Updated pyproject.toml version:"
-        grep "^version = " pyproject.toml
-
-    - name: Update version in _version.py
-      run: |
-        # Remove 'v' prefix if present
-        VERSION="${{ github.event.inputs.version }}"
-        VERSION=${VERSION#v}
-        
-        # Update version in _version.py
-        sed -i "s/__version__ = \".*\"/__version__ = \"$VERSION\"/" src/masster/_version.py
-        
-        # Verify the change
-        echo "Updated _version.py:"
-        grep "__version__ = " src/masster/_version.py
-
-    - name: Commit version updates
-      run: |
-        git config --local user.email "action@github.com"
-        git config --local user.name "GitHub Action"
-        git add pyproject.toml src/masster/_version.py
-        git commit -m "Update version to ${{ github.event.inputs.version }}" || echo "No changes to commit"
-        git push
-
-    - name: Create Release
-      id: create-release
-      uses: softprops/action-gh-release@v1
-      with:
-        tag_name: ${{ github.event.inputs.version }}
-        name: Release ${{ github.event.inputs.version }}
-        draft: false
-        prerelease: false
-        generate_release_notes: true
-      env:
-        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-
-  build:
-    needs: create-release
-    runs-on: ubuntu-latest
-    steps:
-    - uses: actions/checkout@v4
-      with:
-        fetch-depth: 0
-
-    - name: Pull latest changes
-      run: git pull origin ${{ github.ref_name }}
-
-    - name: Verify version synchronization
-      run: |
-        echo "Checking version synchronization..."
-        PYPROJECT_VERSION=$(grep "^version = " pyproject.toml | sed 's/version = "\(.*\)"/\1/')
-        VERSION_PY=$(grep "__version__ = " src/masster/_version.py | sed 's/__version__ = "\(.*\)"/\1/')
-        INPUT_VERSION="${{ github.event.inputs.version }}"
-        INPUT_VERSION=${INPUT_VERSION#v}
-        
-        echo "Input version: $INPUT_VERSION"
-        echo "pyproject.toml version: $PYPROJECT_VERSION"
-        echo "_version.py version: $VERSION_PY"
-        
-        if [ "$PYPROJECT_VERSION" != "$INPUT_VERSION" ] || [ "$VERSION_PY" != "$INPUT_VERSION" ]; then
-          echo "Version mismatch detected!"
-          exit 1
-        fi
-        echo "All versions synchronized correctly!"
-
-    - name: Set up Python
-      uses: actions/setup-python@v5
-      with:
-        python-version: "3.11"
-
-    - name: Install UV
-      uses: astral-sh/setup-uv@v3
-
-    - name: Install dependencies
-      run: |
-        uv sync --all-extras --dev
-
-    - name: Run tests
-      run: |
-        uv run pytest tests/ -v
-
-    - name: Build package
-      run: |
-        uv build
-
-    - name: Check package
-      run: |
-        uv run twine check dist/*
-
-    - name: Upload build artifacts
-      uses: actions/upload-artifact@v4
-      with:
-        name: dist
-        path: dist/
-
-  publish-test-pypi:
-    needs: build
-    runs-on: ubuntu-latest
-    if: github.event.inputs.test_pypi == 'true'
-    environment:
-      name: testpypi
-      url: https://test.pypi.org/p/masster
-    permissions:
-      id-token: write
-
-    steps:
-    - name: Download build artifacts
-      uses: actions/download-artifact@v4
-      with:
-        name: dist
-        path: dist/
-
-    - name: Publish to Test PyPI
-      uses: pypa/gh-action-pypi-publish@release/v1
-      with:
-        repository-url: https://test.pypi.org/legacy/
-
-  publish-pypi:
-    needs: build
-    runs-on: ubuntu-latest
-    if: github.event.inputs.test_pypi != 'true'
-    environment:
-      name: pypi
-      url: https://pypi.org/p/masster
-    permissions:
-      id-token: write
-
-    steps:
-    - name: Download build artifacts
-      uses: actions/download-artifact@v4
-      with:
-        name: dist
-        path: dist/
-
-    - name: Publish to PyPI
-      uses: pypa/gh-action-pypi-publish@release/v1

masster-0.5.25/.github/workflows/security.yml

@@ -1,88 +0,0 @@
-name: Security Scan
-
-on:
-  workflow_dispatch:
-    inputs:
-      scan_type:
-        description: 'Type of security scan to run'
-        required: false
-        default: 'all'
-        type: choice
-        options:
-          - all
-          - safety-only
-          - bandit-only
-      upload_reports:
-        description: 'Upload security reports as artifacts'
-        required: false
-        default: true
-        type: boolean
-  schedule:
-    - cron: '0 3 * * 1'  # Weekly on Monday at 3 AM UTC
-
-jobs:
-  security:
-    runs-on: ubuntu-latest
-    steps:
-    - uses: actions/checkout@v4
-
-    - name: Set up Python
-      uses: actions/setup-python@v5
-      with:
-        python-version: "3.11"
-
-    - name: Install UV
-      uses: astral-sh/setup-uv@v3
-
-    - name: Install dependencies
-      run: |
-        uv sync --all-extras --dev
-
-    - name: Run safety check
-      if: github.event_name == 'schedule' || github.event.inputs.scan_type == 'all' || github.event.inputs.scan_type == 'safety-only'
-      run: |
-        echo "Running Safety security scan..."
-        uv run safety check --json --output safety-report.json || true
-        echo "Safety scan completed. Check safety-report.json for results."
-
-    - name: Run bandit security check
-      if: github.event_name == 'schedule' || github.event.inputs.scan_type == 'all' || github.event.inputs.scan_type == 'bandit-only'
-      run: |
-        echo "Running Bandit security scan..."
-        uv run bandit -r src/masster -f json -o bandit-report.json || true
-        echo "Bandit scan completed. Check bandit-report.json for results."
-
-    - name: Display scan summary
-      run: |
-        echo "=== Security Scan Summary ==="
-        if [ "${{ github.event_name }}" = "schedule" ]; then
-          echo "Scan type: all (scheduled run)"
-        else
-          echo "Scan type: ${{ github.event.inputs.scan_type || 'all' }}"
-        fi
-        
-        if [[ ("${{ github.event_name }}" == "schedule") || ("${{ github.event.inputs.scan_type }}" == "all" || "${{ github.event.inputs.scan_type }}" == "safety-only") ]] && [ -f safety-report.json ]; then
-          echo "Safety report generated: safety-report.json"
-          # Show summary if available
-          if command -v jq &> /dev/null && [ -s safety-report.json ]; then
-            echo "Safety vulnerabilities found: $(jq '.vulnerabilities | length' safety-report.json 2>/dev/null || echo 'Unable to parse')"
-          fi
-        fi
-        
-        if [[ ("${{ github.event_name }}" == "schedule") || ("${{ github.event.inputs.scan_type }}" == "all" || "${{ github.event.inputs.scan_type }}" == "bandit-only") ]] && [ -f bandit-report.json ]; then
-          echo "Bandit report generated: bandit-report.json"
-          # Show summary if available
-          if command -v jq &> /dev/null && [ -s bandit-report.json ]; then
-            echo "Bandit issues found: $(jq '.results | length' bandit-report.json 2>/dev/null || echo 'Unable to parse')"
-          fi
-        fi
-
-    - name: Upload security reports
-      if: github.event_name == 'schedule' || github.event.inputs.upload_reports == 'true'
-      uses: actions/upload-artifact@v4
-      with:
-        name: security-reports-${{ github.run_number }}
-        path: |
-          safety-report.json
-          bandit-report.json
-        retention-days: 30

masster-0.5.25/.github/workflows/test.yml

@@ -1,164 +0,0 @@
-name: Test Suite
-
-on:
-  workflow_dispatch:
-    inputs:
-      run_all_tests:
-        description: 'Run tests on all OS and Python versions'
-        required: false
-        default: true
-        type: boolean
-      target_os:
-        description: 'Target OS for testing (if not running all)'
-        required: false
-        default: 'ubuntu-latest'
-        type: choice
-        options:
-          - ubuntu-latest
-          - windows-latest
-          - macos-latest
-      python_version:
-        description: 'Python version for testing (if not running all)'
-        required: false
-        default: '3.11'
-        type: choice
-        options:
-          - '3.11'
-          - '3.12'
-          - '3.13'
-  schedule:
-    - cron: '0 2 * * 1'  # Weekly on Monday at 2 AM UTC
-
-jobs:
-  test-all:
-    if: github.event_name == 'schedule' || github.event.inputs.run_all_tests == 'true'
-    runs-on: ${{ matrix.os }}
-    strategy:
-      fail-fast: false
-      matrix:
-        os: [ubuntu-latest, windows-latest, macos-latest]
-        python-version: ["3.11", "3.12", "3.13"]
-        exclude:
-          # Exclude macOS with Python 3.11 and 3.12 to reduce CI costs
-          - os: macos-latest
-            python-version: "3.11"
-          - os: macos-latest
-            python-version: "3.12"
-          # Exclude Windows with Python 3.12 to reduce CI costs
-          - os: windows-latest
-            python-version: "3.12"
-
-    steps:
-    - uses: actions/checkout@v4
-
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v5
-      with:
-        python-version: ${{ matrix.python-version }}
-
-    - name: Install UV
-      uses: astral-sh/setup-uv@v3
-      with:
-        enable-cache: true
-        cache-dependency-glob: "uv.lock"
-
-    - name: Install dependencies
-      run: |
-        uv sync --all-extras --dev
-
-    - name: Lint with flake8
-      run: |
-        uv run flake8 src/masster tests --count --select=E9,F63,F7,F82 --show-source --statistics
-        uv run flake8 src/masster tests --count --exit-zero --max-complexity=10 --max-line-length=88 --statistics
-
-    - name: Type check with mypy
-      run: |
-        uv run mypy src/masster --ignore-missing-imports --no-strict-optional
-
-    - name: Test with pytest
-      run: |
-        uv run pytest tests/ -v --cov=masster --cov-report=xml --cov-report=term-missing
-
-    - name: Upload coverage to Codecov
-      if: matrix.os == 'ubuntu-latest' && matrix.python-version == '3.11'
-      uses: codecov/codecov-action@v3
-      with:
-        file: ./coverage.xml
-        flags: unittests
-        name: codecov-umbrella
-
-  test-selective:
-    if: github.event_name == 'workflow_dispatch' && github.event.inputs.run_all_tests != 'true'
-    runs-on: ${{ github.event.inputs.target_os || 'ubuntu-latest' }}
-
-    steps:
-    - uses: actions/checkout@v4
-
-    - name: Set up Python ${{ github.event.inputs.python_version || '3.11' }}
-      uses: actions/setup-python@v5
-      with:
-        python-version: ${{ github.event.inputs.python_version || '3.11' }}
-
-    - name: Install UV
-      uses: astral-sh/setup-uv@v3
-      with:
-        enable-cache: true
-        cache-dependency-glob: "uv.lock"
-
-    - name: Install dependencies
-      run: |
-        uv sync --all-extras --dev
-
-    - name: Lint with flake8
-      run: |
-        uv run flake8 src/masster tests --count --select=E9,F63,F7,F82 --show-source --statistics
-        uv run flake8 src/masster tests --count --exit-zero --max-complexity=10 --max-line-length=88 --statistics
-
-    - name: Type check with mypy
-      run: |
-        uv run mypy src/masster --ignore-missing-imports --no-strict-optional
-
-    - name: Test with pytest
-      run: |
-        uv run pytest tests/ -v --cov=masster --cov-report=xml --cov-report=term-missing
-
-    - name: Upload coverage to Codecov
-      if: github.event.inputs.target_os == 'ubuntu-latest' && github.event.inputs.python_version == '3.11'
-      uses: codecov/codecov-action@v3
-      with:
-        file: ./coverage.xml
-        flags: unittests
-        name: codecov-umbrella
-
-  build:
-    needs: [test-all, test-selective]
-    if: always() && (needs.test-all.result == 'success' || needs.test-selective.result == 'success')
-    runs-on: ubuntu-latest
-    steps:
-    - uses: actions/checkout@v4
-
-    - name: Set up Python
-      uses: actions/setup-python@v5
-      with:
-        python-version: "3.11"
-
-    - name: Install UV
-      uses: astral-sh/setup-uv@v3
-
-    - name: Install dependencies
-      run: |
-        uv sync --all-extras --dev
-
-    - name: Build package
-      run: |
-        uv build
-
-    - name: Check package
-      run: |
-        uv run twine check dist/*
-
-    - name: Upload build artifacts
-      uses: actions/upload-artifact@v4
-      with:
-        name: dist
-        path: dist/

masster-0.5.25/.pre-commit-config.yaml

@@ -1,96 +0,0 @@
----
-repos:
-  - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v5.0.0
-    hooks:
-      - id: check-added-large-files
-      - id: check-ast
-      - id: check-builtin-literals
-      - id: check-case-conflict
-      - id: check-docstring-first
-      - id: check-executables-have-shebangs
-      - id: check-illegal-windows-names
-      - id: check-merge-conflict
-      - id: check-symlinks
-      - id: check-shebang-scripts-are-executable
-      - id: check-symlinks
-      - id: check-toml
-      - id: check-xml
-      - id: check-yaml
-      - id: check-json
-        exclude: ^.devcontainer/devcontainer.json
-      - id: pretty-format-json
-        exclude: ^.devcontainer/devcontainer.json
-        args:
-          - --autofix
-      - id: debug-statements
-      - id: end-of-file-fixer
-      - id: mixed-line-ending
-      - id: pretty-format-json
-      - id: trailing-whitespace
-  # - repo: https://github.com/openstack/bashate
-  #   rev: 2.1.1
-  #   hooks:
-  #     - id: bashate
-  - repo: https://github.com/fpgmaas/deptry
-    rev: 0.23.1
-    hooks:
-      - id: deptry
-        language: python
-        additional_dependencies: [deptry]
-  - repo: https://github.com/python-jsonschema/check-jsonschema
-    rev: 0.33.2
-    hooks:
-      - id: check-github-workflows
-      - id: check-taskfile
-  # - repo: https://github.com/mrtazz/checkmake.git
-  #   rev: 0.2.2
-  #   hooks:
-  #     - id: checkmake
-  # - repo: https://github.com/hukkin/mdformat
-  #   rev: 0.7.22
-  #   hooks:
-  #     - id: mdformat
-  # - repo: https://github.com/markdownlint/markdownlint
-  #   rev: v0.12.0
-  #   hooks:
-  #     - id: markdownlint
-  # - repo: https://github.com/shssoichiro/oxipng
-  #   rev: v9.1.5
-  #   hooks:
-  #     - id: oxipng
-  - repo: https://github.com/asottile/pyupgrade
-    rev: v3.20.0
-    hooks:
-      - id: pyupgrade
-  - repo: https://github.com/asottile/add-trailing-comma
-    rev: v3.2.0
-    hooks:
-      - id: add-trailing-comma
-  - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.12.7
-    hooks:
-      - id: ruff-check
-        args:
-          - --fix
-      - id: ruff-format
-  - repo: https://github.com/crate-ci/typos
-    rev: v1.34.0
-    hooks:
-      - id: typos
-  # - repo: https://github.com/shellcheck-py/shellcheck-py
-  #   rev: v0.10.0.1
-  #   hooks:
-  #     - id: shellcheck
-  # - repo: https://github.com/sqlfluff/sqlfluff
-  #   rev: 3.4.2
-  #   hooks:
-  #     - id: sqlfluff-fix
-  #     - id: sqlfluff-lint
-  - repo: local
-    hooks:
-      - id: ty-check
-        name: ty-check
-        language: python
-        entry: ty check
-        additional_dependencies: [ty]