code cleanup

.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: [ubuntu-latest, windows-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 .
+        # show installed packages
+        pip freeze
+    - name: Test with pytest
+      run: |
+        coverage run --source=qpsphere -m pytest tests
+    - name: Lint with flake8
+      run: |
+        flake8 .
+    - name: Submit code coverage
+      run: |
+        coverage report -m
+        codecov

.github/workflows/deploy_pypi.yml

@@ -0,0 +1,44 @@
+name: Release to PyPI
+
+on:  
+  push:
+    tags:
+      - '*'
+
+jobs:
+  deploy:
+
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, windows-latest]
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.8
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install setuptools wheel twine
+        pip install -e .
+    - name: Build and publish (Linux)
+      if: runner.os == 'Linux'
+      env:
+        TWINE_USERNAME: ci_qpi
+        TWINE_PASSWORD: ${{ secrets.PYPI_PWD }}
+      run: |
+        # give the wheel a specific platform name for linux
+        python setup.py bdist_wheel --plat-name manylinux1_x86_64
+        python setup.py sdist
+        twine upload --skip-existing dist/*
+    - name: Build and publish (Windows)
+      if: runner.os == 'Windows'
+      env:
+        TWINE_USERNAME: ci_qpi
+        TWINE_PASSWORD: ${{ secrets.PYPI_PWD }}
+      run: |
+        # platform name for Windows
+        python setup.py bdist_wheel --plat-name win_amd64
+        twine upload --skip-existing dist/*

.gitignore

@@ -109,3 +109,4 @@ _version_save.py
 qpsphere/resources/*.bin
 qpsphere/resources/*.exe
 qpsphere/resources/*.dll
+.idea

.readthedocs.yml

@@ -1,5 +1,10 @@
+version: 2
 formats:
  - pdf
-requirements_file: docs/requirements.txt
 python:
-   version: 3
+  version: 3.8
+  install:
+    - requirements: docs/requirements.txt
+    - method: pip
+      path: .
+  system_packages: false

CHANGELOG

@@ -1,3 +1,7 @@
+0.5.8
+ - build: migrate to GitHub Actions
+ - tests: setup.py test is deprecated
+ - docs: refurbish docs
 0.5.7
  - setup: bump qpimage from 0.4.0 to 0.6.1
 0.5.6

README.rst

@@ -1,10 +1,11 @@
 qpsphere
 ========
 
-|PyPI Version| |Tests Status Linux| |Tests Status Win| |Coverage Status| |Docs Status|
+|PyPI Version| |Tests Status| |Coverage Status| |Docs Status|
 
 
-**qpsphere** is a Python3 library for analyzing spherical objects in quantitative phase imaging.
+**qpsphere** is a Python3 library for analyzing spherical objects in
+quantitative phase imaging.
 
 
 Documentation
@@ -28,7 +29,8 @@ Testing
 ::
 
     pip install -e .
-    python setup.py test
+    pip install pytest
+    pytest tests
 
 
 Releases to PyPI
@@ -47,10 +49,8 @@ command line argument must be set.
 
 .. |PyPI Version| image:: https://img.shields.io/pypi/v/qpsphere.svg
    :target: https://pypi.python.org/pypi/qpsphere
-.. |Tests Status Linux| image:: https://img.shields.io/travis/RI-imaging/qpsphere.svg?label=tests_linux
-   :target: https://travis-ci.com/RI-imaging/qpsphere
-.. |Tests Status Win| image:: https://img.shields.io/appveyor/ci/paulmueller/qpsphere/master.svg?label=tests_win
-   :target: https://ci.appveyor.com/project/paulmueller/qpsphere
+.. |Tests Status| image:: https://img.shields.io/github/workflow/status/RI-Imaging/qpsphere/Checks
+   :target: https://github.com/RI-Imaging/qpsphere/actions?query=workflow%3AChecks
 .. |Coverage Status| image:: https://img.shields.io/codecov/c/github/RI-imaging/qpsphere/master.svg
    :target: https://codecov.io/gh/RI-imaging/qpsphere
 .. |Docs Status| image:: https://readthedocs.org/projects/qpsphere/badge/?version=latest

docs/conf.py

@@ -22,10 +22,12 @@
 # sys.path.insert(0, os.path.abspath('.'))
 
 # Get version number from qpsphere._version file
-import mock
 import os
 import os.path as op
 import sys
+
+import qpsphere
+
 # include parent directory
 pdir = op.dirname(op.dirname(op.abspath(__file__)))
 sys.path.insert(0, pdir)
@@ -40,21 +42,9 @@
 # Used for linking to libraries in the qpimage universe
 rtd_link = "stable" if rtd_version != "latest" else "latest"
 
-
-# Mock all dependencies
-install_requires = ["lmfit", "matplotlib", "matplotlib.pylab",
-                    "nrefocus", "numpy", "scipy", "h5py",
-                    "scipy.interpolate", "scipy.special",
-                    "skimage", "skimage.restoration",
-                    "qpimage"]
-
-for mod_name in install_requires:
-    sys.modules[mod_name] = mock.Mock()
-
 # http://www.sphinx-doc.org/en/stable/ext/autodoc.html#confval-autodoc_member_order
 # Order class attributes and functions in separate blocks
 autodoc_member_order = 'bysource'
-autodoc_mock_imports = install_requires
 autoclass_content = 'both'
 
 # Display link to GitHub repo instead of doc on rtfd
@@ -81,6 +71,9 @@
               'fancy_include',
               ]
 
+# specify bibtex files (required for sphinxcontrib.bibtex>=2.0)
+bibtex_bibfiles = ['qpsphere.bib']
+
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
 
@@ -103,11 +96,11 @@
 # built documents.
 #
 # The short X.Y version.
-# 
+#
 # The full version, including alpha/beta/rc tags.
 # This gets 'version'
-exec(open(op.join(pdir, "qpsphere/_version.py")).read())
-release = version #@UndefinedVariable
+version = qpsphere.__version__
+release = version
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
 #
@@ -134,17 +127,6 @@
 #
 html_theme = 'default'
 
-# Theme options are theme-specific and customize the look and feel of a theme
-# further.  For a list of options available for each theme, see the
-# documentation.
-#
-# html_theme_options = {}
-
-# 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 = ['_static']
-
 
 # -- Options for HTMLHelp output ------------------------------------------
 
@@ -203,14 +185,13 @@
 ]
 
 
-
-
 # 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),
-                       "skimage": ('http://scikit-image.org/docs/stable/', None),
-                       "lmfit": ('http://lmfit.github.io/lmfit-py/', None),
-                       "qpimage": ('http://qpimage.readthedocs.io/en/'+rtd_link, None),
-                       "qpformat": ('http://qpformat.readthedocs.io/en/'+rtd_link, 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),
+    "skimage": ('http://scikit-image.org/docs/stable/', None),
+    "lmfit": ('http://lmfit.github.io/lmfit-py/', None),
+    "qpimage": ('http://qpimage.readthedocs.io/en/'+rtd_link, None),
+    "qpformat": ('http://qpformat.readthedocs.io/en/'+rtd_link, None),
+    }

docs/sec_z_bib.rst

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

qpsphere/models/mod_mie_avg.py

@@ -137,7 +137,7 @@ def mie_avg(radius=5e-6, sphere_index=1.339, medium_index=1.333,
         d=-((radius+focus) / pixel_size) * interpolate,
         nm=medium_index,
         res=wavelength / pixel_size * interpolate
-        )
+    )
 
     # Phase (2PI offset corrected) and amplitude
     ampli, phase = field2ap_corr(refoc_field2d)

setup.cfg

@@ -1,6 +1,3 @@
-[aliases]
-test = pytest
-
 [metadata]
 license_file = LICENSE