debug

pyproject.toml

@@ -84,16 +84,25 @@ flash = [
 [project.urls]
 repository = "https://github.com/jkobject/scPRINT"
 
+[project.scripts]
+scprint = "scprint.__main__:main"
+
 [tool.ruff]
 line-length = 88
 
 [tool.ruff.lint]
 select = ["E", "F", "I"]
 ignore = ["E501", "E203", "E266", "E265", "F401", "F403", "E722", "E741", "E731", "E721"]
 
+[tool.hatch.build.targets.wheel]
+only-include = [
+    "/scprint",
+    "/slurm",
+    "/config",
+]
+
 [build-system]
 requires = ["hatchling"]
 build-backend = "hatchling.build"
 
-[project.scripts]
-scprint = "scprint.__main__:main"
+

scprint/tasks/grn.py

@@ -275,6 +275,7 @@ def aggregate(self, attn, genes):
             return attn.detach().cpu().numpy()
         badloc = torch.isnan(attn.sum((0, 2, 3, 4)))
         attn = attn[:, ~badloc, :, :, :]
+        badloc = badloc.detach().cpu().numpy()
         self.curr_genes = (
             np.array(self.curr_genes)[~badloc[self.add_emb_in_model :]]
             if self.how == "random expr"
@@ -399,9 +400,6 @@ def filter(self, adj, gt=None):
         return adj
 
     def save(self, grn, subadata, loc=""):
-        import pdb
-
-        pdb.set_trace()
         grn = GRNAnnData(
             subadata[:, subadata.var.index.isin(self.curr_genes)].copy(), grn=grn
         )

scprint/utils/utils.py

@@ -133,7 +133,6 @@ def get_free_gpu():
     import sys
     from io import StringIO
 
-    import pandas as pd
 
     gpu_stats = subprocess.check_output(
         [