diff --git a/docs/source/conf.py b/docs/source/conf.py index 7d24502..9e099d9 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -79,6 +79,7 @@ "use_repository_button": True, } + # app setup hook def setup(app): app.add_config_value( diff --git a/muon/_atac/plot.py b/muon/_atac/plot.py index 29d1e20..4de1350 100644 --- a/muon/_atac/plot.py +++ b/muon/_atac/plot.py @@ -257,7 +257,6 @@ def tss_enrichment( title: str = "TSS Enrichment", ax: Optional[Axes] = None, ): - """ Plot relative enrichment scores around a TSS. diff --git a/muon/_atac/tools.py b/muon/_atac/tools.py index 225281b..a941512 100644 --- a/muon/_atac/tools.py +++ b/muon/_atac/tools.py @@ -520,7 +520,6 @@ def scan_sequences( def get_sequences(data: Union[AnnData, MuData], bed: str, fasta_file: str, bed_file: str = None): - try: import pybedtools except ImportError: @@ -999,7 +998,6 @@ def _tss_pileup( for i in tqdm( range(features.shape[0]), desc="Fetching Regions..." ): # iterate over features (e.g. genes) - f = features.iloc[i] tss_start = f.Start - extend_upstream # First position of the TSS region for fr in fragments.fetch( diff --git a/muon/_core/io.py b/muon/_core/io.py index 127d289..321c0ac 100644 --- a/muon/_core/io.py +++ b/muon/_core/io.py @@ -47,7 +47,6 @@ def read_10x_h5(filename: PathLike, extended: bool = True, *args, **kwargs) -> M # - attempt to locate fragments file if extended: - # 1) Read interval field from the HDF5 file h5file = h5py.File(filename, "r") diff --git a/tests/test_key_parsing.py b/tests/test_key_parsing.py index abd90ac..23dcc9e 100644 --- a/tests/test_key_parsing.py +++ b/tests/test_key_parsing.py @@ -63,7 +63,6 @@ def mdata(request): class TestTraitParsing: - # Observations def test_global_obs(self, mdata): diff --git a/tests/test_muon_preproc.py b/tests/test_muon_preproc.py index be5b2eb..5640384 100644 --- a/tests/test_muon_preproc.py +++ b/tests/test_muon_preproc.py @@ -22,7 +22,6 @@ def mdata(): @pytest.mark.usefixtures("filepath_h5mu") class TestInPlaceFiltering: - # Observations def test_filter_obs_adata(self, mdata, filepath_h5mu):