Merge pull request #9 from meyer-lab/UseRye

Remove poetry and move to rye

.github/workflows/build.yml

@@ -8,10 +8,15 @@ jobs:
     runs-on: self-hosted
     steps:
     - uses: actions/checkout@v4
-    - name: Install dependencies
-      run: poetry install
+    - name: Setup rye
+      uses: eifinger/setup-rye@v4
+      with:
+        enable-cache: true
+        version: '0.39.0'
+    - name: Setup environment
+      run: make .venv
     - name: Build figures
-      run: make all
+      run: make all -j 2
     - name: Upload files
       uses: actions/upload-artifact@v4
       with:

makefile

@@ -1,33 +1,26 @@
-SHELL := /bin/bash
+.PHONY: clean test pyright
 
-.PHONY: clean test
-
-flist = $(wildcard pf2rnaseq/figures/figure*.py)
-allOutput = $(patsubst pf2rnaseq/figures/figure%.py, output/figure%.svg, $(flist))
+flist = $(wildcard pf2scrnaseq/figures/figure*.py)
+allOutput = $(patsubst pf2scrnaseq/figures/figure%.py, output/figure%.svg, $(flist))
 
 all: $(allOutput)
 
-output/figure%.svg: pf2rnaseq/figures/figure%.py
+output/figure%.svg: pf2scrnaseq/figures/figure%.py
 	@ mkdir -p ./output
-	poetry run fbuild $*
+	rye run fbuild $*
 
-output/figureCITEseq%.svg: pf2rnaseq/figures/figureCITEseq%.py
-	@ mkdir -p ./output
-	poetry run fbuild CITEseq$*
+test: .venv
+	rye run pytest -s -v -x
+
+.venv:
+	rye sync
 
-test:
-	poetry run pytest -s -x -v
+coverage.xml: .venv
+	rye run pytest --junitxml=junit.xml --cov=pf2scrnaseq --cov-report xml:coverage.xml
 
-coverage.xml:
-	poetry run pytest --cov=pf2rnaseq --cov-report=xml
+pyright: .venv
+	rye run pyright pf2scrnaseq
 
 clean:
 	rm -rf output profile profile.svg
-	rm -rf factor_cache
-
-testprofile:
-	poetry run python3 -m cProfile -o profile -m pytest -s -v -x
-	gprof2dot -f pstats --node-thres=5.0 profile | dot -Tsvg -o profile.svg
-
-mypy:
-	poetry run mypy --install-types --non-interactive --ignore-missing-imports --check-untyped-defs pf2rnaseq
+	rm -rf factor_cache