Merge branch 'main' of https://github.com/jkobject/scDataLoader

jkobject · Nov 19, 2024 · e9f25e2 · e9f25e2
2 parents 052d8f4 + 025074d
commit e9f25e2
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Showing 4 changed files with 4 additions and 5 deletions.
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -37,7 +37,7 @@ jobs:
       - name: Run tests
         run: make test
       - name: "Upload coverage to Codecov"
-        uses: codecov/codecov-action@v4
+        uses: codecov/codecov-action@v5
         with:
           fail_ci_if_error: true
           token: ${{ secrets.CODECOV_TOKEN }}
diff --git a/pyproject.toml b/pyproject.toml
@@ -1,6 +1,6 @@
 [project]
 name = "scdataloader"
-version = "1.6.4"
+version = "1.6.5"
 description = "a dataloader for single cell data in lamindb"
 authors = [
     {name = "jkobject", email = "[email protected]"}

diff --git a/scdataloader/VERSION b/scdataloader/VERSION
@@ -1 +1 @@
-1.6.4
+1.6.5
diff --git a/scdataloader/preprocess.py b/scdataloader/preprocess.py
@@ -96,7 +96,6 @@ def __init__(
         self.filter_gene_by_counts = filter_gene_by_counts
         self.filter_cell_by_counts = filter_cell_by_counts
         self.normalize_sum = normalize_sum
-        self.subset_hvg = subset_hvg
         self.hvg_flavor = hvg_flavor
         self.binning = binning
         self.organisms = organisms
@@ -109,6 +108,7 @@ def __init__(
         self.min_nnz_genes = min_nnz_genes
         self.maxdropamount = maxdropamount
         self.madoutlier = madoutlier
+        self.n_hvg_for_postp = n_hvg_for_postp
         self.pct_mt_outlier = pct_mt_outlier
         self.batch_key = batch_key
         self.length_normalize = length_normalize
@@ -318,7 +318,6 @@ def __call__(self, adata) -> AnnData:
                     flavor=self.hvg_flavor,
                     subset=True,
                     layer="norm",
-
                 )
             sc.pp.log1p(adata, layer="norm")
             sc.pp.pca(