flexcode 0.1.5__tar.gz → 0.2.2__tar.gz

flexcode-0.2.2/.copier-answers.yml

@@ -0,0 +1,15 @@
+# Changes here will be overwritten by Copier
+_commit: v1.3.0
+_src_path: gh:lincc-frameworks/python-project-template
+author_email: annlee@andrew.cmu.edu
+author_name: Ann Lee
+create_example_module: false
+custom_install: true
+include_notebooks: true
+module_name: flexcode
+mypy_type_checking: none
+preferred_linter: black
+project_license: none
+project_name: flexcode
+use_gitlfs: none
+use_isort: true

flexcode-0.2.2/.github/workflows/linting.yml

@@ -0,0 +1,33 @@
+# This workflow will install Python dependencies, then perform static linting analysis.
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Lint
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python 3.10
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.10'
+    - name: Install dependencies
+      run: |
+        sudo apt-get update
+        python -m pip install --upgrade pip
+        pip install .
+        pip install .[dev]
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+    - name: Analyze code with linter
+
+      uses: psf/black@stable
+      with:
+        src: ./src
+

flexcode-0.2.2/.github/workflows/publish-to-pypi.yml

@@ -0,0 +1,39 @@
+# This workflow will upload a Python Package using Twine when a release is created
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python#publishing-to-package-registries
+
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+name: Upload Python Package
+
+on:
+  release:
+    types: [published]
+
+permissions:
+  contents: read
+
+jobs:
+  deploy:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.x'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install build
+    - name: Build package
+      run: python -m build
+    - name: Publish package
+      uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
+      with:
+        user: __token__
+        password: ${{ secrets.PYPI_API_TOKEN }}

flexcode-0.2.2/.github/workflows/smoke-test.yml

@@ -0,0 +1,33 @@
+# This workflow will run daily at 06:45.
+# It will install Python dependencies and run tests with a variety of Python versions.
+
+name: Unit test smoke test
+
+on:
+  schedule:
+    - cron: 45 6 * * *
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.10', '3.11', '3.12']
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        sudo apt-get update
+        python -m pip install --upgrade pip
+        pip install .
+        pip install .[dev]
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+    - name: Run unit tests with pytest
+      run: |
+        python -m pytest tests

flexcode-0.2.2/.github/workflows/testing-and-coverage.yml

@@ -0,0 +1,43 @@
+# This workflow will install Python dependencies, run tests and report code coverage with a variety of Python versions
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Unit test and code coverage
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.10', '3.11', '3.12']
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        sudo apt-get update
+        python -m pip install --upgrade pip
+        pip install .
+        pip install .[dev]
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+    - name: Run unit tests with pytest
+      run: |
+        python -m pytest tests --cov=flexcode --cov-report=xml
+    - name: Upload coverage report to codecov
+      uses: codecov/codecov-action@v3
+    - name: Install notebook requirements
+      run: |
+        sudo apt-get install pandoc
+    - name: Build docs
+      run: |
+        sphinx-build -T -E -b html -d docs/build/doctrees ./docs docs/build/html

flexcode-0.2.2/.gitignore

@@ -0,0 +1,140 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+_version.py
+
+# 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/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+_readthedocs/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.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
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__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/
+
+# vscode
+.vscode/
+
+# dask
+dask-worker-space/
+
+# tmp directory
+tmp/

flexcode-0.2.2/.pre-commit-config.yaml

@@ -0,0 +1,99 @@
+repos:
+
+    # Clear output from jupyter notebooks so that only the input cells are committed.
+  - repo: local
+    hooks:
+      - id: jupyter-nb-clear-output
+        name: jupyter-nb-clear-output
+        description: Clear output from Jupyter notebooks.
+        files: \.ipynb$
+        stages: [commit]
+        language: system
+        entry: jupyter nbconvert --ClearOutputPreprocessor.enabled=True --inplace
+
+    # Run unit tests, verify that they pass. Note that coverage is run against
+    # the ./src directory here because that is what will be committed. In the 
+    # github workflow script, the coverage is run against the installed package
+    # and uploaded to Codecov by calling pytest like so:
+    # `python -m pytest --cov=<package_name> --cov-report=xml`
+  - repo: local
+    hooks:
+      - id: pytest-check
+        name: pytest-check
+        description: Run unit tests with pytest.
+        entry: bash -c "if python -m pytest --co -qq; then python -m pytest --cov=./src --cov-report=html; fi"
+        language: system
+        pass_filenames: false
+        always_run: true
+
+    # prevents committing directly branches named 'main' and 'master'.
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+      - id: no-commit-to-branch
+        name: Don't commit to main or master branch
+        description: Prevent the user from committing directly to the primary branch.
+      - id: check-added-large-files
+        name: Check for large files
+        description: Prevent the user from committing very large files.
+        args: ['--maxkb=500']
+
+    # verify that pyproject.toml is well formed
+  - repo: https://github.com/abravalheri/validate-pyproject
+    rev: v0.12.1
+    hooks:
+      - id: validate-pyproject
+        name: Validate syntax of pyproject.toml
+        description: Verify that pyproject.toml adheres to the established schema.
+
+    # Automatically sort the imports used in .py files
+  - repo: https://github.com/pycqa/isort
+    rev: 5.12.0
+    hooks:
+      - id: isort
+        name: isort (python files in src/ and tests/)
+        description: Sort and organize imports in .py files.
+        types: [python]
+        files: ^(src|tests)/
+
+
+    # Analyze the code style and report code that doesn't adhere.
+  - repo: https://github.com/psf/black
+    rev: 23.1.0
+    hooks:
+      - id: black
+        types: [python]
+        files: ^(src|tests)/
+        # It is recommended to specify the latest version of Python
+        # supported by your project here, or alternatively use
+        # pre-commit's default_language_version, see
+        # https://pre-commit.com/#top_level-default_language_version
+        language_version: python3.10
+
+
+    # Make sure Sphinx can build the documentation while explicitly omitting 
+    # notebooks from the docs, so users don't have to wait through the execution 
+    # of each notebook or each commit. By default, these will be checked in the 
+    # GitHub workflows.
+  - repo: local
+    hooks:
+      - id: sphinx-build
+        name: Build documentation with Sphinx
+        entry: sphinx-build
+        language: system
+        always_run: true
+        exclude_types: [file, symlink]
+        args:
+          [
+            "-M", # Run sphinx in make mode, so we can use -D flag later
+                  # Note: -M requires next 3 args to be builder, source, output
+            "html", # Specify builder
+            "./docs", # Source directory of documents
+            "./docs/build/html", # Output directory for rendered documents
+            "-T", # Show full trace back on exception
+            "-E", # Don't use saved env; always read all files
+            "-d", # Flag for cached environment and doctrees
+            "./docs/build/doctrees", # Directory
+            "-D", # Flag to override settings in conf.py
+            "exclude_patterns=notebooks/*", # Exclude our notebooks from pre-commit
+          ]

flexcode-0.2.2/.readthedocs.yml

@@ -0,0 +1,22 @@
+# .readthedocs.yml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.10"
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+   configuration: docs/conf.py
+
+# Optionally declare the Python requirements required to build your docs
+python:
+   install:
+   - requirements: docs/requirements.txt
+   - method: pip
+     path: .

flexcode-0.2.2/.travis.yml

@@ -0,0 +1,15 @@
+sudo: false
+language: python
+python:
+- '2.7'
+- '3.6'
+install: pip install tox-travis
+script: tox
+deploy:
+  provider: pypi
+  on:
+    tags: true
+    condition: $TRAVIS_PYTHON_VERSION = "3.6"
+  user: tpospisi
+  password:
+    secure: oOtSw47ptRh+ELY0r3llOm2tjMy5iqhaxpnMEVgp48owe2MhvMxvvhtSxvFfRklzmFjB45hBVuERYjp1LXA9paC1rCEnigqgHisiyNHx7+QdQ4qGehv155pTDUOSXiPObiozEgE2rM6QXkwdAbAVvDt9f7YA0UjgQ+AQrDGBGuAWxqLi/aoCsqUcnwdkk64CNJq4J9W9S7KfJuUPcOVTorujA21p9/r8sOUUFDwkb7TmXOc+8LDDl6IEkgjhcckjOMGBW4Byh+bz6EfSbM1JkHdSlBLYFMdysO9WII3YhvMr4kGTEmBfeSI5p/J9lAtQAexiV2pWLobMFOZYt37LHDtMY7xaBR1bWPITkJevS26rFQ6WB+hypi1TDINB9apVXOzw/rPd8OvjKg4H6pNbCIGHL1NEwHxuvEIVFVxU/n9981CesC02NyC9PqIiL2ahihkk0f0j7b/an2tyundipgPPydg9Ut+GWVGG597Nban4awEy3zaCdGF8VCzaW76/neT0zrteOVKtpzSg/yJBq9/7Zqm4L7uCX5qGFIpguT4B4iab2GMPOZ5xSE5NqRjq2++3xr8aP86MSyJel4d1z/4C22FBmsugJb6QoiQD4VdvJVVDKxNqLC8zOAghZ4sIJ3/EgCDLSw5h+3iT/VcLiaQZLio+PqN/Zrx//LYFgDg=