CI with GitHub Actions

.coveragerc

@@ -0,0 +1,30 @@
+# .coveragerc to control coverage.py
+[run]
+branch = True
+source = spreg
+
+[report]
+# Regexes for lines to exclude from consideration
+exclude_lines =
+    # Have to re-enable the standard pragma
+    pragma: no cover
+
+    # Don't complain about missing debug-only code:
+    def __repr__
+    if self\.debug
+
+    # Don't complain if tests don't hit defensive assertion code:
+    raise AssertionError
+    raise NotImplementedError
+
+    # Don't complain if non-runnable code isn't run:
+    if 0:
+    if __name__ == .__main__.:
+
+ignore_errors = True
+omit =
+    */tests/*
+    *__init__.py
+
+[html]
+directory = coverage_html_report

.github/workflows/build_docs.yml

@@ -12,7 +12,7 @@
      strategy:
        matrix:
          os: ['ubuntu-latest']
-         environment-file: [ci/37-GIT-PLUS.yaml]
+         environment-file: [ci/38-GIT-PLUS.yaml]
          experimental: [false]
      defaults:
        run:

.github/workflows/unittests.yml

@@ -0,0 +1,68 @@
+ on:
+   push:
+     branches:
+     - '*'
+   pull_request:
+     branches:
+     - '*'
+   schedule:
+     - cron: '59 23 * * *'
+
+ jobs:
+   unittests:
+     name: conda (${{ matrix.os }}, ${{ matrix.environment-file }})
+     runs-on: ${{ matrix.os }}
+     timeout-minutes: 30
+     strategy:
+       matrix:
+         os: [macos-latest, ubuntu-latest]
+         ############################################ replace above with this chunk when Windows testing gets worked out
+         #os: [macos-latest, ubuntu-latest, windows-latest]
+         ############################################
+         environment-file: [ci/36-GIT.yaml, ci/36-PYPI.yaml, ci/36-GIT-PLUS.yaml, ci/36-PYPI-PLUS.yaml, ci/37-GIT.yaml, ci/37-PYPI.yaml, ci/37-GIT-PLUS.yaml, ci/37-PYPI-PLUS.yaml, ci/38-GIT.yaml, ci/38-PYPI.yaml, ci/38-GIT-PLUS.yaml, ci/38-PYPI-PLUS.yaml]
+         ############################################ replace above with this chunk when Python 3.9 dependecies get worked out
+         #environment-file: [ci/36-GIT.yaml, ci/36-PYPI.yaml, ci/36-GIT-PLUS.yaml, ci/36-PYPI-PLUS.yaml, ci/37-GIT.yaml, ci/37-PYPI.yaml, ci/37-GIT-PLUS.yaml, ci/37-PYPI-PLUS.yaml, ci/38-GIT.yaml, ci/38-PYPI.yaml, ci/38-GIT-PLUS.yaml, ci/38-PYPI-PLUS.yaml, ci/39-GIT.yaml, ci/39-PYPI.yaml, ci/39-GIT-PLUS.yaml, ci/39-PYPI-PLUS.yaml]
+         ############################################
+         ############################################ uncomment this chunk when Windows testing gets worked out
+         #exclude:
+         #  - environment-file: ci/36-PYPI-PLUS.yaml
+         #    os: windows-latest
+         #  - environment-file: ci/36-GIT-PLUS.yaml
+         #    os: windows-latest
+         ############################################
+     defaults:
+       run:
+         shell: bash -l {0}
+     steps:
+       - uses: actions/checkout@v2
+       - uses: actions/cache@v2
+         env:
+           CACHE_NUMBER: 0
+         with:
+           path: ~/conda_pkgs_dir
+           key: ${{ matrix.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles(matrix.environment-file) }}
+       - uses: conda-incubator/setup-miniconda@v2
+         with:
+            miniconda-version: 'latest'
+            mamba-version: '*'
+            channels: conda-forge
+            channel-priority: true
+            auto-update-conda: false
+            auto-activate-base: false
+            environment-file: ${{ matrix.environment-file }}
+            activate-environment: test
+            use-only-tar-bz2: true
+       - run: mamba info --all
+       - run: mamba list
+       - run: conda config --show-sources
+       - run: conda config --show
+       - run: pytest -v spreg --cov=spreg --cov-config=.coveragerc --cov-report=xml
+       ############################################## replace above with this chunk when docstring testing gets worked out
+       #- run: pytest -v spreg --cov=spreg --doctest-modules --cov-config=.coveragerc --cov-report=xml
+       ##############################################
+       - name: codecov (${{ matrix.os }}, ${{ matrix.environment-file }})
+         uses: codecov/codecov-action@v1
+         with:
+           token: ${{ secrets.CODECOV_TOKEN }}
+           file: ./coverage.xml
+           name: spreg-codecov

README.md

@@ -1,7 +1,7 @@
 # spreg
 
-[![Build Status](https://travis-ci.com/pysal/spreg.svg?branch=master)](https://travis-ci.com/pysal/spreg)
-[![Coverage Status](https://coveralls.io/repos/github/pysal/spreg/badge.svg?branch=master)](https://coveralls.io/github/pysal/spreg?branch=master&service=github)
+[![unittests](https://github.com/pysal/spreg/workflows/.github/workflows/unittests.yml/badge.svg)](https://github.com/pysal/spreg/actions?query=workflow%3A.github%2Fworkflows%2Funittests.yml)
+[![codecov](https://codecov.io/gh/pysal/spreg/branch/master/graph/badge.svg?token=9VrJpIYIl3)](https://codecov.io/gh/pysal/spreg)
 ![PyPI - Python Version](https://img.shields.io/pypi/pyversions/spreg)
 ![PyPI](https://img.shields.io/pypi/v/spreg)
 ![Conda (channel only)](https://img.shields.io/conda/vn/conda-forge/spreg)

ci/36-GIT-PLUS.yaml

@@ -0,0 +1,29 @@
+name: test
+channels:
+  - conda-forge
+dependencies:
+  - python=3.6
+  # required
+  - numpy>=1.3
+  - pandas>=1.0
+  - scipy>=0.11
+  # testing/formatting
+  - codecov
+  - pytest
+  - pytest-cov
+  # optional
+  - bokeh>=0.11.1
+  - folium>=0.2.1
+  - geopandas>=0.2
+  - geojson>=1.3.2
+  - matplotlib>=1.5.1
+  - mplleaflet>=0.0.5
+  - numba
+  - numexpr
+  - scikit-learn>=0.17.1
+  - seaborn>=0.7.0
+  - statsmodels>=0.6.1
+  # required
+  - pip
+  - pip:
+    - git+https://github.com/pysal/libpysal.git@master

ci/36-GIT.yaml

@@ -0,0 +1,17 @@
+name: test
+channels:
+  - conda-forge
+dependencies:
+  - python=3.6
+  # required
+  - numpy>=1.3
+  - pandas>=1.0
+  - scipy>=0.11
+  # testing/formatting
+  - codecov
+  - pytest
+  - pytest-cov
+  # required
+  - pip
+  - pip:
+    - git+https://github.com/pysal/libpysal.git@master

ci/36-PYPI-PLUS.yaml

@@ -0,0 +1,26 @@
+name: test
+channels:
+  - conda-forge
+dependencies:
+  - python=3.6
+  # required
+  - libpysal
+  - numpy>=1.3
+  - pandas>=1.0
+  - scipy>=0.11
+  # testing/formatting
+  - codecov
+  - pytest
+  - pytest-cov
+  # optional
+  - bokeh>=0.11.1
+  - folium>=0.2.1
+  - geopandas>=0.2
+  - geojson>=1.3.2
+  - matplotlib>=1.5.1
+  - mplleaflet>=0.0.5
+  - numba
+  - numexpr
+  - scikit-learn>=0.17.1
+  - seaborn>=0.7.0
+  - statsmodels>=0.6.1

ci/36-PYPI.yaml

@@ -0,0 +1,14 @@
+name: test
+channels:
+  - conda-forge
+dependencies:
+  - python=3.6
+  # required
+  - libpysal
+  - numpy>=1.3
+  - pandas>=1.0
+  - scipy>=0.11
+  # testing/formatting
+  - codecov
+  - pytest
+  - pytest-cov

ci/37-GIT-PLUS.yaml

@@ -23,12 +23,6 @@ dependencies:
   - scikit-learn>=0.17.1
   - seaborn>=0.7.0
   - statsmodels>=0.6.1
-  # for docs build action (this env only)
-  - nbsphinx
-  - numpydoc
-  - sphinx>=1.4.3
-  - sphinxcontrib-bibtex<2.0.0
-  - sphinx_bootstrap_theme
   # required
   - pip
   - pip:

ci/37-GIT.yaml

@@ -0,0 +1,17 @@
+name: test
+channels:
+  - conda-forge
+dependencies:
+  - python=3.7
+  # required
+  - numpy>=1.3
+  - pandas>=1.0
+  - scipy>=0.11
+  # testing/formatting
+  - codecov
+  - pytest
+  - pytest-cov
+  # required
+  - pip
+  - pip:
+    - git+https://github.com/pysal/libpysal.git@master

ci/37-PYPI-PLUS.yaml

@@ -0,0 +1,26 @@
+name: test
+channels:
+  - conda-forge
+dependencies:
+  - python=3.7
+  # required
+  - libpysal
+  - numpy>=1.3
+  - pandas>=1.0
+  - scipy>=0.11
+  # testing/formatting
+  - codecov
+  - pytest
+  - pytest-cov
+  # optional
+  - bokeh>=0.11.1
+  - folium>=0.2.1
+  - geopandas>=0.2
+  - geojson>=1.3.2
+  - matplotlib>=1.5.1
+  - mplleaflet>=0.0.5
+  - numba
+  - numexpr
+  - scikit-learn>=0.17.1
+  - seaborn>=0.7.0
+  - statsmodels>=0.6.1

ci/37-PYPI.yaml

@@ -0,0 +1,14 @@
+name: test
+channels:
+  - conda-forge
+dependencies:
+  - python=3.7
+  # required
+  - libpysal
+  - numpy>=1.3
+  - pandas>=1.0
+  - scipy>=0.11
+  # testing/formatting
+  - codecov
+  - pytest
+  - pytest-cov

ci/38-GIT-PLUS.yaml

@@ -0,0 +1,35 @@
+name: test
+channels:
+  - conda-forge
+dependencies:
+  - python=3.8
+  # required
+  - numpy>=1.3
+  - pandas>=1.0
+  - scipy>=0.11
+  # testing/formatting
+  - codecov
+  - pytest
+  - pytest-cov
+  # optional
+  - bokeh>=0.11.1
+  - folium>=0.2.1
+  - geopandas>=0.2
+  - geojson>=1.3.2
+  - matplotlib>=1.5.1
+  - mplleaflet>=0.0.5
+  - numba
+  - numexpr
+  - scikit-learn>=0.17.1
+  - seaborn>=0.7.0
+  - statsmodels>=0.6.1
+  # for docs build action (this env only)
+  - nbsphinx
+  - numpydoc
+  - sphinx>=1.4.3
+  - sphinxcontrib-bibtex<2.0.0
+  - sphinx_bootstrap_theme
+  # required
+  - pip
+  - pip:
+    - git+https://github.com/pysal/libpysal.git@master