ci: migrate to GH Actions

.github/workflows/check.yml

@@ -0,0 +1,42 @@
+name: Checks
+
+on:
+  push:
+  pull_request:
+  schedule:
+  - cron: "0 0 1 * *"
+
+jobs:
+  build:
+
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        python-version: ['3.7', '3.8']
+        os: [macos-latest, ubuntu-latest]
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        # prerequisites
+        python -m pip install --upgrade pip wheel
+        python -m pip install codecov coverage flake8 pytest
+        # install dependencies
+        pip install -e .[CLI]
+        # show installed packages
+        pip freeze
+    - name: Test with pytest
+      run: |
+        coverage run --source=nanite setup.py test
+    - name: Lint with flake8
+      run: |
+        flake8 .
+    - name: Submit code coverage
+      run: |
+        coverage report -m
+        codecov

.github/workflows/deploy_pypi.yml

@@ -0,0 +1,33 @@
+name: Release to PyPI
+
+on:  
+  push:
+    tags:
+      - '*'
+
+jobs:
+  deploy:
+
+    runs-on: macos-latest
+    strategy:
+      matrix:
+        python-version: ['3.7', '3.8', '3.9']
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install setuptools wheel twine
+        pip install -e .
+    - name: Build and publish
+      env:
+        TWINE_USERNAME: ci_afm
+        TWINE_PASSWORD: ${{ secrets.PYPI_PWD }}
+      run: |
+        python setup.py sdist bdist_wheel
+        twine upload --skip-existing dist/*

CHANGELOG

@@ -1,3 +1,5 @@
+1.7.1
+ - build: migrate to GitHub Actions
 1.7.0
  - enh: simplified writing new model functions by introducing default
    modeling and residual wrappers

docs/conf.py

@@ -18,6 +18,7 @@
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 
 # Get version number from nanite._version file
+import matplotlib
 import mock
 import os.path as op
 import sys
@@ -26,7 +27,6 @@
 # include extensions
 sys.path.append(op.abspath('extensions'))
 
-import matplotlib
 matplotlib.use("agg")
 
 for mod in ["tkinter",
@@ -72,6 +72,9 @@
               'github_changelog',
               ]
 
+# specify bibtex files (required for sphinxcontrib.bibtex>=2.0)
+bibtex_bibfiles = ['nanite.bib']
+
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
 
@@ -95,11 +98,11 @@
 # built documents.
 #
 # The short X.Y version.
-# 
+#
 # The full version, including alpha/beta/rc tags.
 # This gets 'version'
 exec(open(op.join(pdir, "nanite/_version.py")).read())
-release = version #@UndefinedVariable
+release = version  # noqa: F821
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
 #
@@ -136,7 +139,7 @@
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-#html_static_path = ['data']
+# html_static_path = ['data']
 
 
 # -- Options for HTMLHelp output ------------------------------------------
@@ -196,12 +199,11 @@
 ]
 
 
-
-
 # Example configuration for intersphinx: refer to the Python standard library.
-intersphinx_mapping = {"python": ('https://docs.python.org/', None),
-                       "numpy": ('http://docs.scipy.org/doc/numpy', None),
-                       "scipy": ('https://docs.scipy.org/doc/scipy/reference/', None),
-                       "sklearn": ('https://scikit-learn.org/stable/', None),
-                       "afmformats": ('https://afmformats.readthedocs.io/en/stable', None),
+intersphinx_mapping = {
+    "python": ('https://docs.python.org/', None),
+    "numpy": ('http://docs.scipy.org/doc/numpy', None),
+    "scipy": ('https://docs.scipy.org/doc/scipy/reference/', None),
+    "sklearn": ('https://scikit-learn.org/stable/', None),
+    "afmformats": ('https://afmformats.readthedocs.io/en/stable', None),
                        }

docs/requirements.txt

@@ -4,5 +4,5 @@ matplotlib
 # Remove sphinx from requirements b/c it lead to issues
 # on rtd and it's a dependency of the rtd theme anyway.
 # sphinx>=1.6.4,<2
-sphinxcontrib.bibtex
-sphinx_rtd_theme
+sphinxcontrib.bibtex>=2.0
+sphinx_rtd_theme

docs/sec_z_bib.rst

@@ -2,4 +2,4 @@
 Bilbliography
 =============
 
-.. bibliography:: nanite.bib
+.. bibliography::