Polars 1xx#149

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ghuls wants to merge 65 commits intomainfrom

Commits on Jun 10, 2024

Format all python files with "ruff format".
ghuls
committed

Commits on Jun 11, 2024

Cleanup code of get_barcodes_passing_qc_for_sample.
ghuls
committed

Commits on Jul 16, 2024

Reformat TSS profile chained code by adding no opt "clone" calls.
ghuls
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Restrict version numbers for some depencencies.
ghuls
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Expose "engine" option in "pycistopic qc".
ghuls
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Support adding sample ID to cell barcodes when reading fragments or cell barcode files.
ghuls
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Remove unused argument from `get_insert_size_distribution` docstring.
ghuls
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Use greater than or equal for threshold filters in "get_barcodes_passing_qc_for_sample".
ghuls
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Change `pycistopic qc` to `pycistopic qc run`.
ghuls
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Add `pycistopic qc filter` to be able to filter cell barcodes based on QC stats.
ghuls
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Commits on Jul 17, 2024

Commits on Jul 18, 2024

Add "create_fragment_matrix_from_fragments" to create directly a sparse fragment matrix.
ghuls
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Commits on Aug 2, 2024

Add "create_regions_topics_frequency_matrix" function to replace "load_word_topics" in the future.
ghuls
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Commits on Aug 5, 2024

Commits on Aug 22, 2024

Add some basic sanity checking to "convert_binary_matrix_to_mallet_corpus_file".
ghuls
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Commits on Aug 26, 2024

Commits on Aug 27, 2024

Commits on Aug 28, 2024

Commits on Sep 18, 2024

Retrieve also Ensembl gene ID in `get_tss_annotation_from_ensembl`.
ghuls
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Commits on Oct 24, 2024

Commits on Oct 30, 2024

Use`infer_schema=False` instead of `infer_schema_length=0` (polars >= 1.2.0).
ghuls
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Commits on Nov 6, 2024

Commits on Nov 7, 2024

Commits on Nov 8, 2024

Commits on Nov 12, 2024

Commits on Dec 6, 2024

Commits on Dec 10, 2024

Update topic binarization code
SeppeDeWinter
committed

Commits on Dec 13, 2024

Add extra directories to ignore to gitignore.
ghuls
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Commits on Dec 17, 2024

Use "read_fragments_to_pyranges" instead of deprecated "read_fragments_from_file".

SeppeDeWinter
authored and
ghuls
committed
Fix `variables=None` and `color_dictionary=None` cases in "cell_topic_heatmap".

SeppeDeWinter
authored and
ghuls
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Raise error when target is not "cell" or "region" in "find_clusters".

SeppeDeWinter
authored and
ghuls
committed

Commits on Jan 15, 2025

Fix "create_fragment_matrix_from_fragments" in case last (few) region IDs do not overlap with any fragments.
ghuls
committed