CI migration and refresh (#41)

* CI migration and refresh

* update

* drop osx, add ci linting

Author: bjlittle

.cirrus.yml

@@ -0,0 +1,99 @@
+# Reference:
+#   - https://cirrus-ci.org/guide/writing-tasks/
+#   - https://cirrus-ci.org/guide/linux/
+#   - https://hub.docker.com/_/gcc/
+#   - https://hub.docker.com/_/python/
+
+#
+# Global defaults.
+#
+container:
+  image: python:3.8
+  cpu: 2
+  memory: 4G
+
+env:
+  # Maximum cache period (in weeks) before forcing a new cache upload.
+  CACHE_PERIOD: "2"
+  # Increment the build number to force new mambaforge cache upload.
+  MAMBA_CACHE_BUILD: "0"
+  # Increment the build number to force new stratify cache upload.
+  STRATIFY_CACHE_BUILD: "0"
+  # Base environment conda packages to be installed.
+  MAMBA_CACHE_PACKAGES: "conda-lock"
+  # Enable Cython code coverage.
+  CYTHON_COVERAGE: "1"
+  # Increment the build number to force new pip cache upload.
+  PIP_CACHE_BUILD: "0"
+
+
+#
+# Linting
+#
+lint_task:
+  auto_cancellation: true
+  name: "${CIRRUS_OS}: black, flake8 and isort"
+  pip_cache:
+    folder: ~/.cache/pip
+    fingerprint_script:
+      - echo "${CIRRUS_TASK_NAME}"
+      - echo "$(date +%Y).$(expr $(date +%U) / ${CACHE_PERIOD}):${PIP_CACHE_BUILD}"
+  lint_script:
+    - pip list
+    - python -m pip install --editable .[lint]
+    - pip list
+    - black .
+    - flake8 .
+    - isort .
+
+
+#
+# Testing (Linux)
+#
+linux_task:
+  auto_cancellation: true
+  matrix:
+    env:
+      PY_VER: "3.8"
+    env:
+      PY_VER: "3.9"
+      COVERAGE: "1"
+  name: "${CIRRUS_OS}: py${PY_VER}"
+  container:
+    image: gcc:latest 
+  env:
+    PATH: ${HOME}/mambaforge/bin:${PATH}
+  mamba_cache:
+    folder: ${HOME}/mambaforge
+    fingerprint_script:
+      - wget --quiet https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh -O mambaforge.sh
+      - echo "${CIRRUS_OS} $(sha256sum mambaforge.sh)"
+      - echo "${MAMBA_CACHE_PACKAGES}"
+      - echo "$(date +%Y).$(expr $(date +%U) / ${CACHE_PERIOD}):${MAMBA_CACHE_BUILD}"
+    populate_script:
+      - bash mambaforge.sh -b -p ${HOME}/mambaforge
+      - conda config --set always_yes yes --set changeps1 no
+      - conda config --set show_channel_urls True
+      - conda config --add channels conda-forge
+      - conda install --quiet --name base ${MAMBA_CACHE_PACKAGES}
+  check_script:
+    - conda info --all
+    - conda list --name base
+  stratify_cache:
+    folder: ${HOME}/mambaforge/envs/py${PY_VER}
+    fingerprint_script:
+      - echo "${CIRRUS_OS} py${PY_VER} tests"
+      - echo "$(date +%Y).$(expr $(date +%U) / ${CACHE_PERIOD}):${STRATIFY_CACHE_BUILD}"
+      - cat ${CIRRUS_WORKING_DIR}/requirements/py$(echo ${PY_VER} | tr -d ".").yml
+    populate_script:
+      - conda-lock --mamba --platform linux-64 --file ${CIRRUS_WORKING_DIR}/requirements/py$(echo ${PY_VER} | tr -d ".").yml
+      - mamba create --name py${PY_VER} --quiet --file conda-linux-64.lock
+      - cp conda-linux-64.lock ${HOME}/mambaforge/envs/py${PY_VER}
+  test_script:
+    - cat ${HOME}/mambaforge/envs/py${PY_VER}/conda-linux-64.lock >&2
+    - source ${HOME}/mambaforge/etc/profile.d/conda.sh >/dev/null 2>&1
+    - conda activate py${PY_VER} >/dev/null 2>&1
+    - python setup.py build_ext --inplace
+    - python -m pip install --no-deps --editable .
+    - if [ -n "${COVERAGE}" ]; then pytest --cov-report=xml --cov; else pytest; fi
+    - if [ -n "${COVERAGE}" ]; then codecov; fi

.coveragerc

@@ -0,0 +1,28 @@
+[flake8]
+
+# References:
+#   https://flake8.readthedocs.io/en/latest/user/configuration.html
+#   https://flake8.readthedocs.io/en/latest/user/error-codes.html
+#   https://pycodestyle.readthedocs.io/en/latest/intro.html#error-codes
+
+select = C,D,E,F,W,B,B950
+ignore =
+    # E203: whitespace before ':'
+    E203,
+    # E226: missing whitespace around arithmetic operator
+    E226,
+    # E231: missing whitespace after ',', ';', or ':'
+    E231,
+    # E402: module level imports on one line
+    E402,
+    # E501: line too long
+    E501,
+    # E731: do not assign a lambda expression, use a def
+    E731,
+    # W503: line break before binary operator
+    W503,
+    # W504: line break after binary operator
+    W504
+exclude = 
+    .eggs
+    build

.flake8

@@ -1,10 +1,136 @@
+# setuptools-scm
+_version.py
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
 *.so
-__pycache__
-*.egg-info
-build
-*.swp
-.ipynb_checkpoints
-*.pyc
 *.c
 
+# 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
+
+# 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/
+
+# 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/
+
+# PyCharm
+.idea

.gitignore

@@ -0,0 +1,40 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: 'v4.0.1'
+    hooks:
+        # Prevent giant files from being committed.
+    -   id: check-added-large-files
+        # Check whether files parse as valid Python.
+    -   id: check-ast
+        # Check for file name conflicts on case-insensitive filesytems.
+    -   id: check-case-conflict
+        # Check for files that contain merge conflict strings.
+    -   id: check-merge-conflict
+        # Check for debugger imports and py37+ `breakpoint()` calls in Python source.
+    -   id: debug-statements
+        # Don't commit to master branch.
+    -   id: no-commit-to-branch
+-   repo: https://github.com/psf/black
+    rev: '21.5b0'
+    hooks:
+    -   id: black
+        # Force black to run on whole repo, using settings from pyproject.toml
+        pass_filenames: false
+        args: [--config=./pyproject.toml, .]
+-   repo: https://github.com/PyCQA/flake8
+    rev: '3.9.2'
+    hooks:
+        # Run flake8.
+    -   id: flake8
+        args: [--config=./.flake8]
+-   repo: https://github.com/pycqa/isort
+    rev: 5.8.0
+    hooks:
+    -   id: isort
+        name: isort (python)
+        args: ["--profile", "black", "--filter-files"]
+    -   id: isort
+        name: isort (cython)
+        types: [cython]