From 6bc732af5543ee685634b80533ba2ccfdfd77d63 Mon Sep 17 00:00:00 2001 From: jkobject Date: Wed, 13 Nov 2024 12:07:53 +0100 Subject: [PATCH] debug --- pyproject.toml | 13 +- scprint/tasks/grn.py | 4 +- scprint/utils/utils.py | 1 - uv.lock | 427 ++++++++++++++++++++++++++++++++++++++++- 4 files changed, 434 insertions(+), 11 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 8ce767c..869e6ee 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -84,6 +84,9 @@ flash = [ [project.urls] repository = "https://github.com/jkobject/scPRINT" +[project.scripts] +scprint = "scprint.__main__:main" + [tool.ruff] line-length = 88 @@ -91,9 +94,15 @@ line-length = 88 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" + diff --git a/scprint/tasks/grn.py b/scprint/tasks/grn.py index 0680efb..c6a904f 100644 --- a/scprint/tasks/grn.py +++ b/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 ) diff --git a/scprint/utils/utils.py b/scprint/utils/utils.py index 7433ee7..3ed368b 100644 --- a/scprint/utils/utils.py +++ b/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( [ diff 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