Merge pull request #1 from ericpre/add_github_actions

Add GitHub actions

.github/workflows/docs.yml

@@ -0,0 +1,25 @@
+name: Docs
+
+on: [push, pull_request]
+
+jobs:
+  build_doc:
+    name: Build docs
+    runs-on: ubuntu-latest
+    env:
+      BUILD_DEPS: python3-dev build-essential graphviz
+      LATEX_DEPS: dvipng latexmk texlive-latex-recommended texlive-latex-extra texlive-fonts-recommended
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: ericpre/sphinx-action@latest_sphinx
+        with:
+          pre-build-command: "apt-get update -y && apt-get install -y ${{ env.BUILD_DEPS }} ${{ env.LATEX_DEPS }} && pip install .'[all, docs]'"
+          build-command: make html
+          docs-folder: docs/
+
+      - uses: actions/upload-artifact@v3
+        with:
+          path: ./docs/_build/html/
+          name: docs_build

.github/workflows/tests.yml

@@ -0,0 +1,77 @@
+name: Tests
+
+on: [push, pull_request]
+
+jobs:
+  run_test_site:
+    name: ${{ matrix.os }}-py${{ matrix.PYTHON_VERSION }}${{ matrix.LABEL }}
+    runs-on: ${{ matrix.os }}-latest
+    timeout-minutes: 30
+    env:
+      MPLBACKEND: agg
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu, windows, macos]
+        PYTHON_VERSION: ['3.8', '3.9']
+        PIP_SELECTOR: ['[all, tests]']
+        include:
+          # test oldest supported version of main dependencies on python 3.6
+          - os: ubuntu
+            PYTHON_VERSION: '3.7'
+            OLDEST_SUPPORTED_VERSION: true
+            DEPENDENCIES: matplotlib==3.1.3 numpy==1.17.1 scipy==1.1 imagecodecs==2020.1.31 tifffile==2020.2.16 dask==2.11.0 distributed==2.11.0 numba==0.52
+            PIP_SELECTOR: '[all, tests]'
+            LABEL: -oldest
+          # test minimum requirement
+          - os: ubuntu
+            PYTHON_VERSION: '3.8'
+            PIP_SELECTOR: '[tests]'
+            LABEL: -minimum
+          - os: ubuntu
+            PYTHON_VERSION: '3.7'
+            PIP_SELECTOR: '[all, tests]'
+          - os: ubuntu
+            PYTHON_VERSION: '3.10'
+            PIP_SELECTOR: '[all, tests]'
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: actions/setup-python@v3
+        name: Install Python
+        with:
+          python-version: ${{ matrix.PYTHON_VERSION }}
+
+      - name: Display version
+        run: |
+          python --version
+          pip --version
+
+      - name: Install oldest supported version
+        if: ${{ matrix.OLDEST_SUPPORTED_VERSION }}
+        run: |
+          pip install ${{ matrix.DEPENDENCIES }}
+
+      - name: Install
+        shell: bash
+        run: |
+          pip install --upgrade -e .'${{ matrix.PIP_SELECTOR }}'
+
+      - name: Install (HyperSpy dev)
+        # Need to install hyperspy dev until hyperspy 2.0 is released
+        shell: bash
+        run: |
+          pip install https://github.com/hyperspy/hyperspy/archive/refs/heads/RELEASE_next_major.zip
+
+      - name: Pip list
+        run: |
+          pip list
+
+      - name: Run test suite
+        run: |
+          pytest --pyargs rsciio --reruns 3 -n 2 --cov=. --cov-report=xml
+
+      - name: Upload coverage to Codecov
+        if: ${{ always() }}
+        uses: codecov/codecov-action@v2

.gitignore

@@ -1 +1,6 @@
-/docs/_build/*
+/docs/_build/*
+/build/*
+/RosettaSciIO.egg-info/*
+*__pycache__*
+*test_compilers.obj
+*pyd

.readthedocs.yaml

@@ -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 documentation in the docs/ directory with Sphinx
+sphinx:
+  configuration: docs/conf.py
+
+# Optionally build your docs in additional formats such as PDF and ePub
+formats:
+  - htmlzip
+
+python:
+   version: 3.10
+   install:
+      - method: pip
+        path: .
+        extra_requirements:
+           - docs

pyproject.toml

@@ -0,0 +1,12 @@
+[build-system]
+requires = ["setuptools>=49.0", "wheel", "cython", "pyyaml"]
+build-backend = "setuptools.build_meta:__legacy__"
+
+[tool.pytest.ini_options]
+# Note we may need to use `-n 2` argument for pytest-xdist on CI 
+# due to https://github.com/pytest-dev/pytest-xdist/issues/9.
+addopts = "-ra -n auto --dist loadfile"
+minversion = "6.0"
+testpaths = [
+    "rsciio/tests",
+]

setup.py

@@ -21,6 +21,8 @@
 import distutils.ccompiler
 from distutils.errors import CompileError, DistutilsPlatformError
 
+import itertools
+
 from rsciio.version import __version__
 
 setup_path = path.abspath(path.dirname(__file__))
@@ -139,6 +141,24 @@ def run(self):
         cythonize(extensions)
 
 
+extras_require = {
+    "mrcz": ["blosc>=1.5", 'mrcz>=0.3.6'],
+    "scalebar_export": ["matplotlib>=3.1.3"],
+    "tiff": ["tifffile>=2020.2.16", "imagecodecs>=2020.1.31"],
+    "tests": ["pytest>=3.6", "pytest-xdist", "pytest-rerunfailures", "pytest-cov"],  # for testing
+    "docs": ["pydata-sphinx-theme"],  # for building the docs
+}
+
+# Don't include "tests" and "docs" requirements since "all" is designed to be
+# used for user installation.
+runtime_extras_require = {x: extras_require[x] for x in extras_require.keys()
+                          if x not in ["tests", "coverage", "build-doc"]}
+extras_require["all"] = list(itertools.chain(*list(
+    runtime_extras_require.values())))
+
+extras_require["dev"] = list(itertools.chain(*list(extras_require.values())))
+
+
 # Arguments marked as "Required" below must be included for upload to PyPI.
 # Fields marked as "Optional" may be commented out.
 
@@ -268,14 +288,16 @@ def run(self):
     # For an analysis of "install_requires" vs pip's requirements files see:
     # https://packaging.python.org/en/latest/requirements.html
     install_requires=[
-        "scipy",
-        'numpy>=1.10, !=1.13.0',
-        'h5py',
-        'pint>=0.8',
-        'sparse',
+        'dask[array]>=2.11',
+        'h5py>=2.3',
         'imageio',
-        'dask[array]>=0.18',
+        'numba>=0.52',
+        'numpy>=1.17.1',
+        'pint>=0.8',
         'python-box>=6.0',
+        'pyyaml',
+        'sparse',
+        'scipy>=1.1',
     ],  # Optional
 
     # List additional groups of dependencies here (e.g. development
@@ -286,11 +308,7 @@ def run(self):
     #
     # Similar to `install_requires` above, these must be valid existing
     # projects.
-    extras_require={  # Optional
-        "mrcz": ["blosc>=1.5", 'mrcz>=0.3.6'],
-        "tests": ["pytest>=3.6", ],  # for testing
-        "docs": ["pydata-sphinx-theme"],  # for building the docs
-    },
+    extras_require=extras_require,
 
     # If there are data files included in your packages that need to be
     # installed, specify them here.