Merge pull request #50 from AllenCell/decoupling

Decoupling and remove dependency from datastep.

.github/dependabot.yml

@@ -0,0 +1,9 @@
+---
+# Set update schedule for GitHub Actions dependencies
+version: 2
+updates:
+
+  - package-ecosystem: "pip"
+    directory: "/"
+    schedule:
+      interval: "weekly"

.github/workflows/build-docs.yml

@@ -0,0 +1,33 @@
+name: Documentation
+
+on:
+  push:
+    branches:
+      - main
+
+jobs:
+  docs:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/[email protected]
+      with:
+        persist-credentials: false
+    - name: Set up Python
+      uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c
+      with:
+        python-version: 3.9
+    - name: Install Dependencies
+      run: |
+        pip install --upgrade pip
+        pip install .[dev]
+    - name: Generate Docs
+      run: |
+        make gen-docs
+        touch docs/_build/html/.nojekyll
+    - name: Publish Docs
+      uses: JamesIves/[email protected]
+      with:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        BASE_BRANCH: main # The branch the action should deploy from.
+        BRANCH: gh-pages # The branch the action should deploy to.
+        FOLDER: docs/_build/html/ # The folder the action should deploy.

.github/workflows/build-master.yml

@@ -1,54 +1,74 @@
 # name: Build Master
 
-# on:
-#   push:
-#     branches:
-#       - master
-#   schedule:
-#     # <minute [0,59]> <hour [0,23]> <day of the month [1,31]> <month of the year [1,12]> <day of the week [0,6]>
-#     # https://pubs.opengroup.org/onlinepubs/9699919799/utilities/crontab.html#tag_20_25_07
-#     # Run every Monday at 18:00:00 UTC (Monday at 10:00:00 PST)
-#     - cron: '0 18 * * 1'
+on:
+  push:
+    branches:
+      - master
 
-# jobs:
-#   test:
-#     runs-on: ${{ matrix.os }}
-#     strategy:
-#       matrix:
-#         python-version: [3.7, 3.8]
-#         os: [ubuntu-latest, macOS-latest]
+jobs:
+  test:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        python-version: ["3.9", "3.10", "3.11"]
+        os: [ubuntu-latest, windows-latest, macOS-latest]
 
-#     steps:
-#     - uses: actions/checkout@v1
-#     - name: Set up Python ${{ matrix.python-version }}
-#       uses: actions/setup-python@v1
-#       with:
-#         python-version: ${{ matrix.python-version }}
-#     - name: Install Dependencies
-#       run: |
-#         python -m pip install --upgrade pip
-#         pip install .[test]
-#     - name: Test with pytest
-#       run: |
-#         pytest --cov-report xml --cov=cvapipe_analysis cvapipe_analysis/tests/
-#         codecov -t ${{ secrets.CODECOV_TOKEN }}
+    steps:
+    - uses: actions/checkout@v1
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install Dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install .[test]
+    - name: Test with pytest
+      run: |
+        pytest --cov-report xml --cov=cvapipe_analysis cvapipe_analysis/tests/
+    - name: Upload codecov
+      uses: codecov/codecov-action@v1
 
 #   lint:
 #     runs-on: ubuntu-latest
 
-#     steps:
-#     - uses: actions/checkout@v1
-#     - name: Set up Python
-#       uses: actions/setup-python@v1
-#       with:
-#         python-version: 3.8
-#     - name: Install Dependencies
-#       run: |
-#         python -m pip install --upgrade pip
-#         pip install .[test]
-#     - name: Lint with flake8
-#       run: |
-#         flake8 cvapipe_analysis --count --verbose --show-source --statistics
-#     - name: Check with black
-#       run: |
-#         black --check cvapipe_analysis
+    steps:
+    - uses: actions/checkout@v1
+    - name: Set up Python
+      uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c
+      with:
+        python-version: 3.9
+    - name: Install Dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install .[test]
+    - name: Lint with flake8
+      run: |
+        flake8 cvapipe_analysis --count --verbose --show-source --statistics
+    - name: Check with black
+      run: |
+        black --check cvapipe_analysis
+
+  publish:
+    if: "contains(github.event.head_commit.message, 'Bump version')"
+    needs: [test, lint]
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v1
+    - name: Set up Python
+      uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c
+      with:
+        python-version: 3.9
+    - name: Install Dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install setuptools wheel
+    - name: Build Package
+      run: |
+        python setup.py sdist bdist_wheel
+    - name: Publish to PyPI
+      uses: pypa/gh-action-pypi-publish@master
+      with:
+        user: __token__
+        password: ${{ secrets.PYPI_TOKEN }}

.github/workflows/test-and-lint.yml

@@ -2,44 +2,46 @@
 
 # on: pull_request
 
-# jobs:
-#   test:
-#     runs-on: ${{ matrix.os }}
-#     strategy:
-#       matrix:
-#         python-version: [3.7, 3.8]
-#         os: [ubuntu-latest, macOS-latest]
+jobs:
+  test:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        python-version: ["3.9", "3.10", "3.11"]
+        os: [ubuntu-latest, windows-latest, macOS-latest]
 
-#     steps:
-#     - uses: actions/checkout@v1
-#     - name: Set up Python ${{ matrix.python-version }}
-#       uses: actions/setup-python@v1
-#       with:
-#         python-version: ${{ matrix.python-version }}
-#     - name: Install Dependencies
-#       run: |
-#         python -m pip install --upgrade pip
-#         pip install .[test]
-#     - name: Test with pytest
-#       run: |
-#         pytest cvapipe_analysis/tests/
+    steps:
+    - uses: actions/checkout@v1
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install Dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install .[test]
+    - name: Test with pytest
+      run: |
+        pytest cvapipe_analysis/tests/
+    - name: Upload codecov
+      uses: codecov/codecov-action@v1
 
 #   lint:
 #     runs-on: ubuntu-latest
 
-#     steps:
-#     - uses: actions/checkout@v1
-#     - name: Set up Python
-#       uses: actions/setup-python@v1
-#       with:
-#         python-version: 3.8
-#     - name: Install Dependencies
-#       run: |
-#         python -m pip install --upgrade pip
-#         pip install .[test]
-#     - name: Lint with flake8
-#       run: |
-#         flake8 cvapipe_analysis --count --verbose --show-source --statistics
-#     - name: Check with black
-#       run: |
-#         black --check cvapipe_analysis
+    steps:
+    - uses: actions/checkout@v1
+    - name: Set up Python
+      uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c
+      with:
+        python-version: 3.9
+    - name: Install Dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install .[test]
+    - name: Lint with flake8
+      run: |
+        flake8 cvapipe_analysis --count --verbose --show-source --statistics
+    - name: Check with black
+      run: |
+        black --check cvapipe_analysis

.gitignore

@@ -121,3 +121,9 @@ ENV/
 .mypy_cache/
 workflow_config.json
 .distribute/*
+
+# results
+*.png
+*.pdf
+*.vtk
+*.gif

README.md

@@ -2,6 +2,10 @@
 
 ## Analysis Pipeline for Cell Variance
 
+[![Build Status](https://github.com/AllenCell/cvapipe_analysis/workflows/Build%20Main/badge.svg)](https://github.com/AllenCell/cvapipe_analysis/actions)
+[![Documentation](https://github.com/AllenCell/cvapipe_analysis/workflows/Documentation/badge.svg)](https://AllenCell.github.io/cvapipe_analysis/)
+
+
 ![Shape modes](docs/logo.png)
 
 ---