cryodrgn 0.20.0__tar.gz

cryodrgn-0.20.0/.flake8

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+[flake8]
+extend-ignore = E203,E501
+max-complexity = 99
+max-line-length = 88

cryodrgn-0.20.0/.github/CODEOWNERS

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+* 	@michal-g @zhonge

cryodrgn-0.20.0/.github/ISSUE_TEMPLATE/bug_report.md

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+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+What is the command you used?
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Additional context**
+Add any other context about the problem here.

cryodrgn-0.20.0/.github/workflows/beta_release.yml

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+name: Beta Release
+
+on:
+  push:
+    tags:
+      - '[0-9]+\.[0-9]+\.[0-9]+-*'
+
+jobs:
+  beta-release:
+
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Upgrade setuptools/build
+        run: |
+          pip3 install wheel --upgrade
+          pip3 install setuptools --upgrade
+
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.9'
+
+      - name: Release to TestPyPI
+        env:
+          TWINE_USERNAME: __token__
+          TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN }}
+
+        run: |
+          python -m pip install --upgrade build
+          python -m build .
+          python -m pip install --upgrade twine
+          twine upload --repository testpypi dist/*

cryodrgn-0.20.0/.github/workflows/docs.yml

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+name: Docs
+
+on:
+  push:
+    branches: [ main ]
+
+jobs:
+
+  build_docs:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.9'
+
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Install Python dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install sphinx myst-parser sphinx-rtd-theme /home/runner/work/cryodrgn/cryodrgn/
+
+      - name: Setup Envvars
+        run: |
+            if [[ $GITHUB_REF = "refs/tags/"* ]] ; then echo "CRYODRGN_VERSION=${GITHUB_REF/refs\/tags\//}" ; else echo "CRYODRGN_VERSION=" ; fi >> $GITHUB_ENV
+
+      - name: Build docs
+        run: |
+          # Unless we add a .nojekyll to the base of the deployment folder, the underscores in foldernames
+          # like _static/ etc. pose problems on GH Pages.
+          cd docs && make html && touch _build/html/.nojekyll
+
+      - name: Deploy
+        uses: JamesIves/github-pages-deploy-action@v4
+        with:
+          folder: docs/_build/html
+          branch: gh-pages

cryodrgn-0.20.0/.github/workflows/release.yml

@@ -0,0 +1,36 @@
+name: Release
+
+on:
+  push:
+    tags:
+      - '[0-9]+.[0-9]+.[0-9]+'
+      - '!*-[a-z]+[0-9]+'
+
+jobs:
+  release:
+
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Upgrade setuptools/build
+        run: |
+          pip3 install wheel --upgrade
+          pip3 install setuptools --upgrade
+
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.9'
+
+      - name: Release to pypi
+        env:
+          TWINE_USERNAME: __token__
+          TWINE_PASSWORD: ${{ secrets.PYPI_MAIN_TOKEN }}
+
+        run: |
+          python -m pip install --upgrade build
+          python -m build .
+          python -m pip install --upgrade twine
+          twine upload dist/*

cryodrgn-0.20.0/.github/workflows/style.yml

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+name: Code Linting
+
+on:
+  push:
+    branches: [ main, develop ]
+    tags:
+      - '[0-9]+\.[0-9]+\.[0-9]+'
+      - '[0-9]+\.[0-9]+\.[0-9]+-*'
+  pull_request:
+    branches: [ main, develop ]
+
+jobs:
+  run_tests:
+
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.10'
+
+      - name: Install cryoDRGN with dev dependencies
+        run: |
+          python3 -m pip install .[dev]
+
+      - name: Run pre-commit checks
+        run: |
+          pre-commit run --all-files --show-diff-on-failure
+
+      - name: Run Pyright
+        run: |
+          pyright --version
+          #pyright

cryodrgn-0.20.0/.github/workflows/tests.yml

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+name: CI Testing
+
+on:
+  push:
+    branches: [ main, develop ]
+    tags:
+      - '[0-9]+\.[0-9]+\.[0-9]+'
+      - '[0-9]+\.[0-9]+\.[0-9]+-*'
+  pull_request:
+    branches: [ main, develop ]
+
+jobs:
+  run_tests:
+
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+        python: ['3.9', '3.10']
+      fail-fast: false
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python }}
+
+      - name: Install cryoDRGN with pytest dependencies
+        run: |
+          python3 -m pip install pytest-xdist
+          python3 -m pip install .
+
+      - name: Pytest
+        run: |
+          pytest -v -n auto --dist=loadscope

cryodrgn-0.20.0/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+.DS_Store
+env/
+build/
+develop-eggs/
+docs/generated/
+dist/
+downloads/
+eggs/
+.eggs/
+.idea/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# 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/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+
+testing/output
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+cryodrgn/_version.py
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# dotenv
+.env
+
+# virtualenv
+.venv
+venv/
+ENV/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/

cryodrgn-0.20.0/.pre-commit-config.yaml

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+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+
+exclude: '.cs$|.star$'
+
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v3.2.0
+    hooks:
+    -   id: trailing-whitespace
+    -   id: end-of-file-fixer
+
+-   repo: https://github.com/pycqa/flake8
+    rev: '4.0.1'
+    hooks:
+    -   id: flake8
+
+-   repo: https://github.com/psf/black
+    rev: 22.10.0
+    hooks:
+      - id: black
+        language_version: python3
+
+-   repo: https://github.com/MarcoGorelli/absolufy-imports
+    rev: v0.3.1
+    hooks:
+    -   id: absolufy-imports