Merge branch 'main' into docs/add-docs-build-checks

.devcontainer/postCreateCommand.sh

@@ -3,5 +3,5 @@
 # re-included here for the benefit of manual dev environments.
 poetry self add "poetry-dynamic-versioning[plugin]"
 poetry config virtualenvs.in-project true --local
-poetry install --with dev --all-extras
+poetry install --with dev,docs --all-extras
 poetry run pre-commit install --install-hooks

.github/workflows/integration-test.yml

@@ -63,7 +63,7 @@ jobs:
       fail-fast: false
       matrix:
         os:
-          - macos-latest
+          - macos-13
           - ubuntu-latest
         python-version: ["3.8", "3.9", "3.10", "3.11"]
     runs-on: ${{ matrix.os }}
@@ -201,13 +201,14 @@ jobs:
       # Gather and prepare the dynamic version and other vars for use with work below.
       # For example, 1.1.0.post6.dev0+bc093ef becomes 1.1.0.post6.dev0_bc093ef
       - name: Gather dynamic version and set env var
+        if: (github.event_name == 'push'||  github.event_name == 'schedule') && github.ref == 'refs/heads/main'
         id: env-vars
         run: >-
-          echo "CLEAN_VERSION=$(echo ${{ env.sdist_filename }} | tr '+' '_' )" >> "$GITHUB_OUTPUT" &&
+          echo "CLEAN_VERSION=$(echo ${{ env.sdist_extracted_name }} | tr '+' '_' )" >> "$GITHUB_OUTPUT" &&
           echo "DATE_TAG=$(date +'%y%m%d')" >> "$GITHUB_OUTPUT"
       - name: Login to Docker Hub
         # only run this task if we have a pull request merged or the schedule triggers from main
-        if: (github.event.pull_request.merged ||  github.event_name == 'schedule') && github.ref == 'refs/heads/main'
+        if: (github.event_name == 'push'||  github.event_name == 'schedule') && github.ref == 'refs/heads/main'
         uses: docker/login-action@v3
         with:
           username: ${{ secrets.DOCKER_USER }}
@@ -220,26 +221,27 @@ jobs:
         with:
           context: "${{ env.sdist_extracted_name }}"
           push: true
-          file: ../build/docker/Dockerfile
+          file: ./build/docker/Dockerfile
           target: production
           tags: cytomining/pycytominer:${{ steps.env-vars.outputs.CLEAN_VERSION }}_${{ steps.env-vars.outputs.DATE_TAG }}
       # Docker image push based on GitHub pushes to main
       - name: Push-based docker image push
         # only run this task if we have a pull request which is merged
-        if: github.event.pull_request.merged && github.ref == 'refs/heads/main' && github.repository == 'cytomining/pycytominer'
+        if: github.event_name == 'push' && github.ref == 'refs/heads/main' && github.repository == 'cytomining/pycytominer'
         uses: docker/build-push-action@v5
         with:
           context: "${{ env.sdist_extracted_name }}"
           push: true
-          file: ../build/docker/Dockerfile
+          file: ./build/docker/Dockerfile
           target: production
           tags: cytomining/pycytominer:latest,cytomining/pycytominer:${{ steps.env-vars.outputs.CLEAN_VERSION }}
       # update docker hub description using readme on merge
-      - name: Docker Hub
+      - name: Update Docker Hub repository description from readme
         # only run this task if we have a pull request which is merged
-        if: github.event.pull_request.merged && github.ref == 'refs/heads/main' && github.repository == 'cytomining/pycytominer'
+        if: github.event_name == 'push' && github.ref == 'refs/heads/main' && github.repository == 'cytomining/pycytominer'
         uses: peter-evans/dockerhub-description@v3
         with:
           username: ${{ secrets.DOCKER_USER }}
           password: ${{ secrets.DOCKER_TOKEN }}
           repository: cytomining/pycytominer
+          readme-filepath: "${{ env.sdist_extracted_name }}/README.md"

Makefile

@@ -1,25 +1,44 @@
-# Minimal makefile for Sphinx documentation
-#
+install: .devcontainer/postCreateCommand.sh ## Install the poetry environment and install the pre-commit hooks
+	@echo "🛠️ Creating virtual environment using poetry and installing pre-commit hooks"
+	@bash .devcontainer/postCreateCommand.sh
+	@echo "🐢 Launching poetry shell"
+	@poetry shell
 
-# You can set these variables from the command line, and also
-# from the environment for the first two.
-SPHINXOPTS    ?=
-SPHINXBUILD   ?= sphinx-build
-SOURCEDIR     = docs
-BUILDDIR      = build
+.PHONY: check
+check: ## Run code quality tools.
+	@echo "🔒 Checking Poetry lock file consistency with 'pyproject.toml': Running poetry lock --check"
+	@poetry check --lock
+	@echo "🔎 Linting code: Running pre-commit"
+	@poetry run pre-commit run -a
 
-# Put it first so that "make" without argument is like "make help".
-help:
-	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+.PHONY: test
+test: ## Test the code with pytest
+	@echo "🧪 Testing code: Running pytest"
+	@poetry run pytest --cov --cov-config=pyproject.toml --cov-report=xml
+
+.PHONY: docs
+docs: ## Build the documentation
+	@echo "📚 Building documentation"
+	@poetry run sphinx-build docs build
+
+.PHONY: build
+build: clean-build ## Build wheel file using poetry
+	@echo "🛞 Creating wheel and sdist files"
+	@poetry build
 
-.PHONY: help Makefile
+.PHONY: clean-build
+clean-build: ## clean build artifacts
+	@echo "🧹 Cleaning build artifacts"
+	@rm -rf dist
 
-# Catch-all target: route all unknown targets to Sphinx using the new
-# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
-%: Makefile
-	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+.PHONY: docker-build
+test_docker_build: ## Build the docker image and run the tests
+	@echo "🐳 Building docker image and running tests"
+	@docker build -f build/docker/Dockerfile -t pycytominer:latest .
+	@docker run pycytominer:latest poetry run pytest
+
+.PHONY: help
+help:
+	@grep -E '^[a-zA-Z_-]+:.*?## .*$$' "$(MAKEFILE_LIST)" | awk 'BEGIN {FS = ":.*?## "}; {printf "\033[36m%-20s\033[0m %s\n", $$1, $$2}'
 
-# note: presumes the existence of docker daemon to receive docker commands
-test_docker_build:
-	docker build -f build/docker/Dockerfile -t pycytominer:latest . && \
-	docker run pycytominer:latest poetry run pytest
+.DEFAULT_GOAL := help

build/docker/Dockerfile

@@ -25,13 +25,17 @@ RUN pip install --no-cache-dir poetry
 FROM base as production
 
 # copy the pycytominer source into image
-COPY . .
+COPY README.md pyproject.toml poetry.lock ./
+COPY pycytominer ./pycytominer
 
 # install pycytominer using poetry root dependencies and all extras
 RUN poetry install --all-extras -v --no-interaction
 
 # create stage for production build (no dev or non-essential deps)
 FROM production as testing
 
+# copy the tests dir for testing purposes
+COPY tests ./tests
+
 # install pycytominer from poetry with group deps and all extras for testing
 RUN poetry install --with dev --all-extras -v --no-interaction