8000 Polars 1xx by ghuls · Pull Request #149 · aertslab/pycisTopic · GitHub

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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

Add longer explanation for tss "--no-cache" option.
ghuls
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Catch likely BioMart request caching problems and give "--no-cache" hint.

committed

Commits on Dec 6, 2024

Commits on Dec 10, 2024

Update topic binarization code
SeppeDeWinter
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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
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Fix `variables=None` and `color_dictionary=None` cases in "cell_topic_heatmap".

SeppeDeWinter
authored and
ghuls
committed
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

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