Bump to v0.1.14

Author: Lucas Camillo

.gitignore

@@ -6,7 +6,6 @@ clocks/weights/
 *.pt
 *.json
 pyaging_data/
-example_data/
 testing.ipynb
 .ipynb_checkpoints/
 *.pyc

Makefile

@@ -0,0 +1,87 @@
+.PHONY: lint format update build install update-clocks-notebooks update-all-clocks process-tutorials test test-tutorials docs version commit tag release
+
+VERSION ?= v0.1.14
+COMMIT_MSG ?= "Bump to $(VERSION)"
+RELEASE_MSG ?= "Release $(VERSION)"
+
+lint:
+	@echo "Running ruff for linting..."
+	ruff check pyaging --fix
+
+format:
+	@echo "Running ruff for code formatting..."
+	ruff format pyaging
+
+update:
+	@echo "Running poetry update..."
+	poetry update
+
+build: lint format
+	@echo "Building the package..."
+	poetry build
+
+install: build
+	@echo "Installing the package..."
+	poetry install
+
+update-clocks-notebooks:
+	@echo "Updating clocks and notebooks..."
+	@cd clocks/notebooks && \
+	total=$$(ls *.ipynb | wc -l) && \
+	counter=1 && \
+	for notebook in *.ipynb; do \
+		if [ "$$notebook" = "template.ipynb" ]; then \
+			echo "Skipping template.ipynb"; \
+			continue; \
+		fi; \
+		echo "Processing clock notebook ($$counter/$$total): $$notebook"; \
+		jupyter nbconvert --execute --inplace "$$notebook" || { echo "Error processing $$notebook"; exit 1; }; \
+		counter=$$((counter+1)); \
+	done && cd ../..
+
+update-all-clocks:
+	@echo "Running script to update all clocks..."
+	@cd clocks && python3 update_all_clocks.py $(VERSION) || { echo "Updating clocks failed"; exit 1; } && cd ..
+	@echo "Reminder: Upload all clocks and metadata to S3!"
+
+process-tutorials:
+	@echo "Processing tutorials..."
+	@cd tutorials && \
+	for notebook in *.ipynb; do \
+		echo "Processing tutorial notebook: $$notebook"; \
+		jupyter nbconvert --ExecutePreprocessor.timeout=600 --to notebook --execute --inplace "$$notebook" || { echo "Error processing $$notebook"; exit 1; }; \
+	done && cd ..
+
+test:
+	@echo "Running gold standard tests..."
+	poetry run pytest || { echo "Gold standard tests failed"; exit 1; }
+
+test-tutorials:
+	@echo "Running tutorial tests..."
+	poetry run pytest --nbmake tutorials/ || { echo "Tutorial tests failed"; exit 1; }
+
+docs:
+	@echo "Building documentation..."
+	cp tutorials/*.ipynb docs/source/tutorials
+	cp clocks/notebooks/*.ipynb docs/source/clock_notebooks
+	@cd docs && make html || { echo "Documentation build failed"; exit 1; }
+
+version:
+	@echo "Updating version in pyproject.toml to $(VERSION)..."
+	sed -i '' "s/^version = \".*\"/version = \"$(patsubst v%,%,$(VERSION))\"/" pyproject.toml || { echo "Error updating version in pyproject.toml"; exit 1; }
+	@echo "Updating version in pyaging/__init__.py to $(VERSION)..."
+	sed -i '' "s/^__version__ = \".*\"/__version__ = \"$(patsubst v%,%,$(VERSION))\"/" pyaging/__init__.py || { echo "Error updating version in pyaging/__init__.py"; exit 1; }
+
+commit:
+	@echo "Committing and pushing changes..."
+	git add .
+	git commit -m $(COMMIT_MSG) || { echo "Git commit failed"; exit 1; }
+	git push || { echo "Git push failed"; exit 1; }
+
+tag:
+	@echo "Creating and pushing tag $(VERSION)..."
+	git tag -a "$(VERSION)" -m $(RELEASE_MSG)
+	git push origin "$(VERSION)" || { echo "Git tag creation or push failed"; exit 1; }
+
+release: version lint format update build install update-clocks-notebooks update-all-clocks process-tutorials test test-tutorials docs commit tag
+	@echo "Release $(VERSION) completed successfully"

README.md

@@ -46,9 +46,4 @@ To cite `pyaging`, please use the following:
     url = {https://doi.org/10.1093/bioinformatics/btae200},
     eprint = {https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae200/57218155/btae200.pdf},
 }
-```
-
-## 📝 To-Do List
-
-- [ ] Add SymphonyAge
-
+```