From 2070fec1d50bda186582d44e386757bfae71efbe Mon Sep 17 00:00:00 2001
From: Josh Loecker <joshloecker@icloud.com>
Date: Thu, 2 Oct 2025 10:38:38 -0500
Subject: [PATCH 1/2] chore: update lock file

Signed-off-by: Josh Loecker <joshloecker@icloud.com>
---
 uv.lock | 1411 ++++++++++++++++++++++++++++---------------------------
 1 file changed, 731 insertions(+), 680 deletions(-)

diff --git a/uv.lock b/uv.lock
index 8d226ed8..1d7b10e3 100644
--- a/uv.lock
+++ b/uv.lock
@@ -1,5 +1,5 @@
 version = 1
-revision = 2
+revision = 3
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From 2e8357ba74c834b9c6eaf5d1a5f31f7c97e955b1 Mon Sep 17 00:00:00 2001
From: Josh Loecker <joshloecker@icloud.com>
Date: Thu, 2 Oct 2025 10:43:35 -0500
Subject: [PATCH 2/2] chore: fix ruff check errors

Signed-off-by: Josh Loecker <joshloecker@icloud.com>
---
 main/como/combine_distributions.py |  2 +-
 main/como/merge_xomics.py          | 50 +++++++++++++-----------------
 main/como/rnaseq_gen.py            |  3 ++
 main/como/rnaseq_preprocess.py     |  2 +-
 4 files changed, 26 insertions(+), 31 deletions(-)

diff --git a/main/como/combine_distributions.py b/main/como/combine_distributions.py
index c747e071..cfdebe22 100644
--- a/main/como/combine_distributions.py
+++ b/main/como/combine_distributions.py
@@ -203,7 +203,7 @@ def _combine_z_distribution_for_context(
     return combined_z_matrix_df
 
 
-async def _begin_combining_distributions(
+def _begin_combining_distributions(
     context_name: str,
     input_matrices: InputMatrices,
     batch_names: BatchNames,
diff --git a/main/como/merge_xomics.py b/main/como/merge_xomics.py
index 0188504f..71ddd776 100644
--- a/main/como/merge_xomics.py
+++ b/main/como/merge_xomics.py
@@ -432,7 +432,7 @@ async def _process(
 
     if merge_zfpkm_distribution:
         logger.trace("Merging Z-Scores")
-        await _begin_combining_distributions(
+        _begin_combining_distributions(
             context_name=context_name,
             input_matrices=input_matrices,
             batch_names=batch_names,
@@ -650,50 +650,42 @@ async def merge_xomics(  # noqa: C901
     trna_matrix: pd.DataFrame | None
     trna_boolean_matrix: pd.DataFrame | None
     trna_metadata: pd.DataFrame | None
-    trna_matrix, trna_boolean_matrix, trna_metadata = await asyncio.gather(
-        *[
-            read_file(trna_matrix_or_filepath),
-            read_file(trna_boolean_matrix_or_filepath),
-            read_file(trna_metadata_filepath_or_df),
-        ]
-    )
+    trna_matrix, trna_boolean_matrix, trna_metadata = await asyncio.gather(*[
+        read_file(trna_matrix_or_filepath),
+        read_file(trna_boolean_matrix_or_filepath),
+        read_file(trna_metadata_filepath_or_df),
+    ])
 
     # Build mrna items
     mrna_matrix: pd.DataFrame | None
     mrna_boolean_matrix: pd.DataFrame | None
     mrna_metadata: pd.DataFrame | None
-    mrna_matrix, mrna_boolean_matrix, mrna_metadata = await asyncio.gather(
-        *[
-            read_file(mrna_matrix_or_filepath),
-            read_file(mrna_boolean_matrix_or_filepath),
-            read_file(mrna_metadata_filepath_or_df),
-        ]
-    )
+    mrna_matrix, mrna_boolean_matrix, mrna_metadata = await asyncio.gather(*[
+        read_file(mrna_matrix_or_filepath),
+        read_file(mrna_boolean_matrix_or_filepath),
+        read_file(mrna_metadata_filepath_or_df),
+    ])
 
     # build scrna items
 
     scrna_matrix: pd.DataFrame | None
     scrna_boolean_matrix: pd.DataFrame | None
     scrna_metadata: pd.DataFrame | None
-    scrna_matrix, scrna_boolean_matrix, scrna_metadata = await asyncio.gather(
-        *[
-            read_file(scrna_matrix_or_filepath),
-            read_file(scrna_boolean_matrix_or_filepath),
-            read_file(scrna_metadata_filepath_or_df),
-        ]
-    )
+    scrna_matrix, scrna_boolean_matrix, scrna_metadata = await asyncio.gather(*[
+        read_file(scrna_matrix_or_filepath),
+        read_file(scrna_boolean_matrix_or_filepath),
+        read_file(scrna_metadata_filepath_or_df),
+    ])
 
     # build proteomic items
     proteomic_matrix: pd.DataFrame | None
     proteomic_boolean_matrix: pd.DataFrame | None
     proteomic_metadata: pd.DataFrame | None
-    proteomic_matrix, proteomic_boolean_matrix, proteomic_metadata = await asyncio.gather(
-        *[
-            read_file(proteomic_matrix_or_filepath),
-            read_file(proteomic_boolean_matrix_or_filepath),
-            read_file(proteomic_metadata_filepath_or_df),
-        ]
-    )
+    proteomic_matrix, proteomic_boolean_matrix, proteomic_metadata = await asyncio.gather(*[
+        read_file(proteomic_matrix_or_filepath),
+        read_file(proteomic_boolean_matrix_or_filepath),
+        read_file(proteomic_metadata_filepath_or_df),
+    ])
 
     source_weights = SourceWeights(trna=trna_weight, mrna=mrna_weight, scrna=scrna_weight, proteomics=proteomic_weight)
     input_matrices = InputMatrices(trna=trna_matrix, mrna=mrna_matrix, scrna=scrna_matrix, proteomics=proteomic_matrix)
diff --git a/main/como/rnaseq_gen.py b/main/como/rnaseq_gen.py
index 2ea307b4..957f7e8c 100644
--- a/main/como/rnaseq_gen.py
+++ b/main/como/rnaseq_gen.py
@@ -145,6 +145,9 @@ async def _build_count_metrics(
 
     Returns:
         A dataclass `ReadMatrixResults`
+
+    Raises:
+        ValueError: If no columns to merge on are found, or if no sample columns are found after merging with gene information.
     """
     matrix.dropna(subset="ensembl_gene_id", inplace=True)
     conversion = await ensembl_to_gene_id_and_symbol(ids=matrix["ensembl_gene_id"].tolist(), taxon=taxon)
diff --git a/main/como/rnaseq_preprocess.py b/main/como/rnaseq_preprocess.py
index a04f0df3..b58a8a6d 100644
--- a/main/como/rnaseq_preprocess.py
+++ b/main/como/rnaseq_preprocess.py
@@ -65,7 +65,7 @@ async def build_from_tab(cls, filepath: Path) -> _STARinformation:
             num_ambiguous = [int(i) for i in ambiguous.removesuffix("\n").split("\t")[1:]]
 
         df: pd.DataFrame = await read_file(
-            fiepath,
+            filepath,
             h5ad_as_df=True,
             sep="\t",
             header=None,