Merge branch 'main' of https://github.com/cantinilab/scPRINT

.gitignore

@@ -178,3 +178,8 @@ data/main/bias_sparse.npz
 *.gv
 data/log/
 file.txt
+*.dataset
+*.arrow
+tests/data/step_0__predict_part_0_0.h5ad
+data/human_dcm_hcm_nf/
+data/geneformertest.csv

.gitmodules

@@ -1,3 +1,18 @@
 [submodule "RNABERT"]
 path = scprint/tokenizers/RNABERT
 url = https://github.com/jkobject/RNABERT
+[submodule "tools/DeepSEM"]
+path = tools/DeepSEM
+url = https://github.com/jkobject/DeepSEM
+[submodule "tools/SERGIO"]
+path = tools/SERGIO
+url = https://github.com/jkobject/SERGIO
+[submodule "tools/scFoundation"]
+	path = tools/scFoundation
+	url = https://github.com/biomap-research/scFoundation
+[submodule "tools/scGPT"]
+	path = tools/scGPT
+	url = https://github.com/jkobject/scGPT
+[submodule "tools/Geneformer"]
+	path = tools/Geneformer
+	url = https://huggingface.co/ctheodoris/Geneformer/

Makefile

@@ -76,7 +76,7 @@ release:          ## Create a new tag for release.
 	@git commit -m "release: version $${TAG} 🚀"
 	@echo "creating git tag : $${TAG}"
 	@git tag $${TAG}
-	@git push -u origin HEAD --tags
+	@git push -u cantini HEAD --tags
 	@echo "Github Actions will detect the new tag and release the new version."
 	@mkdocs gh-deploy
 	@echo "Documentation deployed to https://jkobject.github.io/scPRINT/"