Switch build from setuptools to Poetry and move tests path

.devcontainer/postCreateCommand.sh

@@ -1,5 +1,5 @@
 #! /usr/bin/env bash
-
-python -m pip install -r requirements-dev.txt
-python -m pip install -e .
-pre-commit install --install-hooks
+python -m pip install poetry
+poetry config virtualenvs.in-project true --local
+poetry install --all-extras
+poetry run pre-commit install --install-hooks

.github/ISSUE_TEMPLATE/documentation_request.yml

@@ -10,7 +10,7 @@ body:
       label: File location of the documentation
       description: >
         Please provide the source of the documentation that this issue is referencing.
-      placeholder: Example - https://github.com/cytomining/pycytominer/edit/master/docs/index.rst
+      placeholder: Example - https://github.com/cytomining/pycytominer/edit/main/docs/index.rst
     validations:
       require: true
   - type: textarea

.github/workflows/codecov.yml

@@ -2,25 +2,62 @@ name: Code coverage
 
 on:
   push:
-    branches: [master]
+    branches:
+      - main
+      # Temporary inclusion of master branch during default branch name transition
+      - master
   pull_request:
-    branches: [master]
+    branches:
+      - main
+      # Temporary inclusion of master branch during default branch name transition
+      - master
 
 jobs:
   run:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@master
+      - uses: actions/checkout@v3
       - name: Setup Python
-        uses: actions/setup-python@master
+        uses: actions/setup-python@v4
         with:
-          python-version: 3.9
-      - name: Generate coverage report
-        run: |
-          pip install pytest
-          pip install pytest-cov
-          pip install .[collate,cell_locations]
-          pytest --cov=./ --cov-report=xml
+          python-version: 3.11
+      #----------------------------------------------
+      #  -----  install & configure poetry  -----
+      #----------------------------------------------
+      - name: Install Poetry
+        uses: snok/install-poetry@v1
+        with:
+          virtualenvs-create: true
+          virtualenvs-in-project: true
+      #----------------------------------------------
+      #       load cached venv if cache exists
+      #----------------------------------------------
+      - name: Load cached venv
+        id: cached-poetry-dependencies
+        uses: actions/cache@v3
+        with:
+          path: .venv
+          key: venv-${{ runner.os }}-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/poetry.lock') }}
+      #----------------------------------------------
+      # install dependencies if cache does not exist
+      #----------------------------------------------
+      - name: Install dependencies
+        if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
+        run: poetry install --no-interaction --no-root
+      #----------------------------------------------
+      # install your root project, if required
+      #----------------------------------------------
+      - name: Install library
+        run: poetry install --no-interaction
+      #----------------------------------------------
+      #    run test suite and output coverage file
+      #----------------------------------------------
+      - name: Test with pytest
+        run: poetry run pytest --cov=./ --cov-report=xml
+      #----------------------------------------------
+      #             upload coverage stats
+      # (requires CODECOV_TOKEN in repository secrets)
+      #----------------------------------------------
       - name: Upload coverage to Codecov
         uses: codecov/codecov-action@v1
         with:

.github/workflows/pre-commit-ci.yml

@@ -2,14 +2,16 @@ name: pre-commit-ci
 on:
   pull_request:
     branches:
+      - main
+      # Temporary inclusion of master branch during default branch name transition
       - master
 jobs:
   pre-commit-ci:
     name: Run pre-commit checks on changed files
     runs-on: ubuntu-latest
     steps:
       - name: Checkout repo with all branches and tags
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           fetch-depth: 0
       - name: Setup python 3.9

.github/workflows/publish-to-pypi.yml

@@ -4,35 +4,17 @@ on: [release]
 jobs:
   build-n-publish:
     name: Build and publish Python 🐍 distributions 📦 to PyPI and TestPyPI
-    runs-on: ubuntu-18.04
-    strategy:
-      matrix:
-        python-version: [3.8]
-
+    runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@master
-
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v1
-        with:
-          python-version: ${{ matrix.python-version }}
-
-      - name: Install pypa/build
-        run: python -m pip install setuptools build wheel --user
-
-      - name: Build a binary wheel
-        run: python setup.py sdist bdist_wheel
-
+      - uses: actions/checkout@v3
       - name: Publish any distribution 📦 to Test PyPI
-        uses: pypa/gh-action-pypi-publish@master
+        uses: JRubics/poetry-publish@v1.17
         with:
-          password: ${{ secrets.TEST_PYPI_API_TOKEN }}
+          pypi_token: ${{ secrets.TEST_PYPI_API_TOKEN }}
           repository_url: https://test.pypi.org/legacy/
-          skip_existing: true
-
+          ignore_dev_requirements: "yes"
       - name: Publish tagged distribution 📦 to PyPI
+        uses: JRubics/poetry-publish@v1.17
         if: startsWith(github.ref, 'refs/tags')
-        uses: pypa/gh-action-pypi-publish@master
         with:
-          password: ${{ secrets.PYPI_API_TOKEN }}
-          skip_existing: true
+          pypi_token: ${{ secrets.PYPI_API_TOKEN }}

.github/workflows/pytest.yml

@@ -0,0 +1,69 @@
+# This workflow will install Python dependencies, run tests and black with a single version of Python
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Python build
+
+on:
+  push:
+    branches:
+      - main
+      # Temporary inclusion of master branch during default branch name transition
+      - master
+  pull_request:
+    branches:
+      - main
+      # Temporary inclusion of master branch during default branch name transition
+      - master
+
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        os: [ubuntu-latest, macos-latest]
+    env:
+      OS: ${{ matrix.os }}
+      # This is needed to avoid a warning from SQLAlchemy
+      # https://sqlalche.me/e/b8d9
+      # We can remove this once we upgrade to SQLAlchemy >= 2.0
+      SQLALCHEMY_SILENCE_UBER_WARNING: "1"
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+      #----------------------------------------------
+      #  -----  install & configure poetry  -----
+      #----------------------------------------------
+      - name: Install Poetry
+        run: |
+          python -m pip install poetry
+          poetry config virtualenvs.in-project true --local
+      #----------------------------------------------
+      #       load cached venv if cache exists
+      #----------------------------------------------
+      - name: Load cached venv
+        id: cached-poetry-dependencies
+        uses: actions/cache@v3
+        with:
+          path: .venv
+          key: venv-${{ runner.os }}-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/poetry.lock') }}
+      #----------------------------------------------
+      # install dependencies if cache does not exist
+      #----------------------------------------------
+      - name: Install dependencies
+        if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
+        run: poetry install --no-interaction --no-root  --all-extras
+      #----------------------------------------------
+      # install pycytominer
+      #----------------------------------------------
+      - name: Install library
+        run: poetry install --no-interaction --only-root
+      #----------------------------------------------
+      #    run test suite and output coverage file
+      #----------------------------------------------
+      - name: Test with pytest
+        run: |
+          poetry run pytest