Switch to using uv to manage the environment (#67)

Author: tsalo

.github/dependabot.yml

@@ -11,8 +11,9 @@ updates:
     assignees: ["tsalo"]
     schedule:
       interval: "weekly"
-  - package-ecosystem: pip
+  - package-ecosystem: "uv"
     directory: "/"
     labels: ["maintenance", "ignore-for-release"]
+    assignees: ["tsalo"]
     schedule:
       interval: weekly

.gitignore

@@ -115,6 +115,7 @@ venv/
 ENV/
 env.bak/
 venv.bak/
+meda/
 
 # Spyder project settings
 .spyderproject

Makefile

@@ -1,23 +1,41 @@
-.PHONY: help book clean serve sync-docs site-publish
+# Name of the uv-managed project environment directory.
+# `uv` honors UV_PROJECT_ENVIRONMENT to place the venv somewhere other than .venv.
+export UV_PROJECT_ENVIRONMENT := meda
+
+# Reproducible image outputs: matplotlib honors SOURCE_DATE_EPOCH and will stamp
+# PNGs with a fixed timestamp instead of "now", so identical plots produce
+# identical bytes (and identical content-hashed filenames in _images/).
+# 1577836800 == 2020-01-01T00:00:00Z
+export SOURCE_DATE_EPOCH := 1577836800
+
+.PHONY: help check-env book clean serve sync-docs site-publish install runall build site
 
 help:
 	@echo "Please use 'make <target>' where <target> is one of:"
-	@echo "  install     to install the necessary dependencies for jupyter-book to build"
-	@echo "  book        to convert the content/ folder into Jekyll markdown in _build/"
+	@echo "  install     to sync the 'meda' environment from uv.lock"
+	@echo "  check-env   to verify the 'meda' environment matches uv.lock"
+	@echo "  book        to activate 'meda' and build the Jupyter Book into _build/"
 	@echo "  clean       to clean out site build files"
 	@echo "  runall      to run all notebooks in-place, capturing outputs with the notebook"
 	@echo "  serve       to serve the repository locally with Jekyll"
 	@echo "  build       to build the site HTML and store in _site/"
-	@echo "  site 		 to build the site HTML, store in _site/, and serve with Jekyll"
+	@echo "  site        to build the site HTML, store in _site/, and serve with Jekyll"
 	@echo "  sync-docs   to copy _build/html into docs/ for GitHub Pages"
 	@echo "  site-publish to build the book and sync docs/ (book + sync-docs)"
 
 
 install:
-	jupyter-book install ./
+	uv sync --locked
+
+# Verify that the local 'meda' environment is up-to-date with uv.lock.
+# `uv sync --locked --check` exits non-zero if the environment would change.
+check-env:
+	@echo "Checking that '$(UV_PROJECT_ENVIRONMENT)' matches uv.lock..."
+	uv sync --locked --check
 
-book:
-	jupyter-book build ./
+# Activate the 'meda' environment (via `uv run`) and build the book.
+book: check-env
+	uv run --locked jupyter-book build ./
 
 sync-docs:
 	python scripts/sync_docs.py
@@ -33,8 +51,8 @@ clean:
 serve:
 	bundle exec guard
 
-build:
-	jupyter-book build ./ --overwrite
+build: check-env
+	uv run --locked jupyter-book build ./ --overwrite
 
 site: build
 	bundle exec jekyll build

_config.yml

@@ -9,7 +9,7 @@ title                       : "Multi-Echo fMRI Data Analysis"  # The title of th
 author                      : "The tedana community"  # The author of the book
 copyright                   : "2021"  # Copyright year to be placed in the footer
 logo                        : "logo.png"  # A path to the book logo
-exclude_patterns            : ["README.md", "content/*.py", "docs/**", "data/ds*/logs/*.md", "data/ds*/*.md", "content/ds*/logs/*.md", "notebooks/README_notebooks.md", "notebooks/*.ipynb"]
+exclude_patterns            : ["README.md", "content/*.py", "docs/**", "meda/**", ".venv/**", "data/ds*/logs/*.md", "data/ds*/*.md", "content/ds*/logs/*.md", "notebooks/README_notebooks.md", "notebooks/*.ipynb"]
 
 #######################################################################################
 # Execution settings