PythiaLabelGenerator 1.0.0__tar.gz

pythialabelgenerator-1.0.0/.github/actions/setup-iqtree/action.yml

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+name: Setup IQ-TREE
+runs:
+  using: composite
+  steps:
+    - name: Download IQ-TREE MacOS
+      if: runner.os == 'macOS'
+      run: |
+        wget https://github.com/iqtree/iqtree2/releases/download/v2.4.0/iqtree-2.4.0-macOS.zip
+        unzip iqtree-*.zip && mv iqtree-*/* .
+      shell: bash
+    - name: Download IQ-TREE Linux
+      if: runner.os == 'Linux'
+      run: |
+        wget https://github.com/iqtree/iqtree2/releases/download/v2.4.0/iqtree-2.4.0-Linux-intel.tar.gz
+        tar xvf iqtree-*.tar.gz && mv iqtree-*/* .
+      shell: bash
+    - name: Unzip IQ-TREE and set Env variable
+      run: echo iqtree2=$(pwd)/bin/iqtree2 >> $GITHUB_ENV
+      shell: bash
+    - name: Check IQ-TREE installation
+      run: $iqtree2 -v
+      shell: bash

pythialabelgenerator-1.0.0/.github/actions/setup-raxmlng/action.yml

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+name: Setup RAxML-NG
+runs:
+  using: composite
+  steps:
+    - name: Download RAxML-NG MacOS
+      if: runner.os == 'macOS'
+      run: wget https://github.com/amkozlov/raxml-ng/releases/download/1.2.2/raxml-ng_v1.2.2_macos.zip
+      shell: bash
+    - name: Download RAxML-NG Linux
+      if: runner.os == 'Linux'
+      run: wget https://github.com/amkozlov/raxml-ng/releases/download/1.2.2/raxml-ng_v1.2.2_linux_x86_64.zip
+      shell: bash
+    - name: Unzip RAxML-NG and set Env variable
+      run: |
+        unzip raxml-ng_*.zip
+        echo raxmlng=$(pwd)/raxml-ng >> $GITHUB_ENV
+      shell: bash
+    - name: Check RAxML-NG installation
+      run: $raxmlng -v
+      shell: bash

pythialabelgenerator-1.0.0/.github/actions/test-label-cli/action.yml

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+name: Test Label CLI
+inputs:
+  msa-file:
+    description: MSA file to test Label CLI with
+    default: examples/example.phy
+runs:
+  using: composite
+  steps:
+    - name: Run Label CLI with an exemplary MSA to make sure everything is working
+      run: |
+        label -m ${{ inputs.msa-file }} -r ${{ env.raxmlng }} -i ${{ env.iqtree2 }} --ntrees 4
+      shell: bash -el {0}

pythialabelgenerator-1.0.0/.github/workflows/test-label-generator.yml

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+name: Build and test LabelGenerator
+run-name: Build and run the tests of the LabelGenerator python library.
+on:
+  push:
+    paths-ignore:
+      - 'docs/**'
+jobs:
+  Run-Label-Generator-Tests:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+        python-version: ["3.9", "3.12"]
+    steps:
+      - name: Check out repository code
+        uses: actions/checkout@v3
+      - name: Setup Conda
+        uses: mamba-org/setup-micromamba@v2
+        with:
+          environment-file: etc/environment.yml
+          cache-environment: true
+          create-args:
+            python=${{ matrix.python-version }}
+          generate-run-shell: false
+          post-cleanup: none
+      - name: Setup RAxML-NG and RAxML-NG env variable
+        uses: ./.github/actions/setup-raxmlng
+      - name: Setup IQ-TREE and IQ-TREE env variable
+        uses: ./.github/actions/setup-iqtree
+      - name: Install LabelGenerator and setup requirements
+        run: |
+          pip install -e . --no-deps
+          rm tests/test_config.py
+          echo "RAXMLNG_COMMAND = '${{ env.raxmlng }}'" >> tests/test_config.py
+          echo "IQTREE_COMMAND = '${{ env.iqtree2 }}'" >> tests/test_config.py
+          cat tests/test_config.py
+        shell: bash -el {0}
+#      - name: Setup tmate session
+#        uses: mxschmitt/action-tmate@v3
+      - name: Run LabelGenerator tests
+        run: |
+          PYTHONPATH=. pytest -svx
+        shell: bash -el {0}
+
+  Install-using-conda:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+        python-version: ["3.9", "3.12"]
+    steps:
+      - name: Check out repository code
+        uses: actions/checkout@v3
+      - name: Setup Conda
+        uses: mamba-org/setup-micromamba@v2
+        with:
+          environment-file: etc/environment.yml
+          cache-environment: true
+          create-args:
+            python=${{ matrix.python-version }}
+          generate-run-shell: false
+          post-cleanup: none
+      - name: Install LabelGenerator  # Install LabelGenerator manually to get the correct branch
+        run: |
+          pip install -e . --no-deps
+        shell: bash -el {0}
+      - name: Setup RAxML-NG and RAxML-NG env variable
+        uses: ./.github/actions/setup-raxmlng
+      - name: Setup IQ-TREE and IQ-TREE env variable
+        uses: ./.github/actions/setup-iqtree
+      - name: Test installation by running the CLI
+        uses: ./.github/actions/test-label-cli

pythialabelgenerator-1.0.0/.gitignore

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+**/*.reduced.*
+**/*.log
+**/*.csv
+
+*.raxml.*
+!tests/**/*.raxml.*
+
+*.iqtree.*
+!tests/**/*.iqtree.log
+!tests/**/*.iqtree.iqtree
+
+*.reduced.phy
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+.DS_Store
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+.idea/
+site/

pythialabelgenerator-1.0.0/.pre-commit-config.yaml

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+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v2.3.0
+    hooks:
+    -   id: check-yaml
+    -   id: end-of-file-fixer
+    -   id: trailing-whitespace
+    -   id: detect-private-key
+-   repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.9.7
+    hooks:
+    # Run the linter.
+    -   id: ruff
+        args: [--fix, --exit-non-zero-on-fix]
+    # Run the formatter.
+    -   id: ruff-format