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BREAKING CHANGE: Complete replacement of cgat-core with Snakemake (#186)
* Fixed bug with keep_aligned. Incorrect parameter specified * Allowed slice_stats to deal with empty df. Typo in remove_non_capture_fragments * Changed parent_read to parent_id for lower memory * Added basic test for slice filters * Added captures property to TiledCSliceFilter * Replaced isna check query with capture_count == 0 * Added ANALYSIS_METHOD placeholder * Added pytest-order * Added tests for all three methods of filtering * Added tests for all three pipeline modes * Fixed bug in cooler storage * Attempting to fix bowtie2 index cache * Engine pyarrow-dataset depreciated now using pyarrow directly * chore: Updated version to 0.2.3 (#165) * chore: pin conda dependency versions to speed up environment solver (#167) * Set minimum python version * Pinned conda dependencies + altered channel order * fix(pipeline): Fixed issues with annotation, filtering, storage and plotting for Tiled-C data (#166) * Bug with bedtools sort. Removing this fixes annotation issue * Increased verbosity of counting. Fixed counting bugs for single viewpoints and merging * Removed un-needed logging * BedIntersection now copes with empty files. Returns invalid intersection. * Updated cooler version * Updated annotation test * Cooler binning step follows wrong task * Missing reporter directory generation for binning * Using pyarrow for collation rather than dask * Pipeline formatting * Binning task not running. Ensured scale_factor exists * Fixed issue with storing as binned cooler * Fixed issue with store binned task. Now will merge with binned version * Removing binned temp file * Fixed issues with CoolerBinner and GenomicBinner * Fixed CCMatrix plotting class and added scaling factor normalisation * Fixed storage bug when creating GenomicBinner * Updated pipeline test to download indicies * Removed un-needed functions * fix(pipeline): Fixed stability issue with generate_bin_conversion_tables task. (#172) * fix(pipeline): Bug fixes for Tiled-C analysis and pipeline dependency updates (#168) * Fixed bug with keep_aligned. Incorrect parameter specified * Allowed slice_stats to deal with empty df. Typo in remove_non_capture_fragments * Changed parent_read to parent_id for lower memory * Added basic test for slice filters * Added captures property to TiledCSliceFilter * Replaced isna check query with capture_count == 0 * Added ANALYSIS_METHOD placeholder * Added pytest-order * Added tests for all three methods of filtering * Added tests for all three pipeline modes * Fixed bug in cooler storage * Attempting to fix bowtie2 index cache * Engine pyarrow-dataset depreciated now using pyarrow directly * chore: Updated version to 0.2.3 (#165) * chore: pin conda dependency versions to speed up environment solver (#167) * Set minimum python version * Pinned conda dependencies + altered channel order * fix(pipeline): Fixed issues with annotation, filtering, storage and plotting for Tiled-C data (#166) * Bug with bedtools sort. Removing this fixes annotation issue * Increased verbosity of counting. Fixed counting bugs for single viewpoints and merging * Removed un-needed logging * BedIntersection now copes with empty files. Returns invalid intersection. * Updated cooler version * Updated annotation test * Cooler binning step follows wrong task * Missing reporter directory generation for binning * Using pyarrow for collation rather than dask * Pipeline formatting * Binning task not running. Ensured scale_factor exists * Fixed issue with storing as binned cooler * Fixed issue with store binned task. Now will merge with binned version * Removing binned temp file * Fixed issues with CoolerBinner and GenomicBinner * Fixed CCMatrix plotting class and added scaling factor normalisation * Fixed storage bug when creating GenomicBinner * Updated pipeline test to download indicies * Removed un-needed functions * chore: prepare for release 0.2.3 (#169) * Fixed bug with keep_aligned. Incorrect parameter specified * Allowed slice_stats to deal with empty df. Typo in remove_non_capture_fragments * Changed parent_read to parent_id for lower memory * Added basic test for slice filters * Added captures property to TiledCSliceFilter * Replaced isna check query with capture_count == 0 * Added ANALYSIS_METHOD placeholder * Added pytest-order * Added tests for all three methods of filtering * Added tests for all three pipeline modes * Fixed bug in cooler storage * Attempting to fix bowtie2 index cache * Engine pyarrow-dataset depreciated now using pyarrow directly * chore: Updated version to 0.2.3 (#165) * chore: pin conda dependency versions to speed up environment solver (#167) * Set minimum python version * Pinned conda dependencies + altered channel order * fix(pipeline): Fixed issues with annotation, filtering, storage and plotting for Tiled-C data (#166) * Bug with bedtools sort. Removing this fixes annotation issue * Increased verbosity of counting. Fixed counting bugs for single viewpoints and merging * Removed un-needed logging * BedIntersection now copes with empty files. Returns invalid intersection. * Updated cooler version * Updated annotation test * Cooler binning step follows wrong task * Missing reporter directory generation for binning * Using pyarrow for collation rather than dask * Pipeline formatting * Binning task not running. Ensured scale_factor exists * Fixed issue with storing as binned cooler * Fixed issue with store binned task. Now will merge with binned version * Removing binned temp file * Fixed issues with CoolerBinner and GenomicBinner * Fixed CCMatrix plotting class and added scaling factor normalisation * Fixed storage bug when creating GenomicBinner * Updated pipeline test to download indicies * Removed un-needed functions * chore: update changelog and readme for release 0.2.3 (#170) * Fixed bug with keep_aligned. Incorrect parameter specified * Allowed slice_stats to deal with empty df. Typo in remove_non_capture_fragments * Changed parent_read to parent_id for lower memory * Added basic test for slice filters * Added captures property to TiledCSliceFilter * Replaced isna check query with capture_count == 0 * Added ANALYSIS_METHOD placeholder * Added pytest-order * Added tests for all three methods of filtering * Added tests for all three pipeline modes * Fixed bug in cooler storage * Attempting to fix bowtie2 index cache * Engine pyarrow-dataset depreciated now using pyarrow directly * chore: Updated version to 0.2.3 (#165) * chore: pin conda dependency versions to speed up environment solver (#167) * Set minimum python version * Pinned conda dependencies + altered channel order * fix(pipeline): Fixed issues with annotation, filtering, storage and plotting for Tiled-C data (#166) * Bug with bedtools sort. Removing this fixes annotation issue * Increased verbosity of counting. Fixed counting bugs for single viewpoints and merging * Removed un-needed logging * BedIntersection now copes with empty files. Returns invalid intersection. * Updated cooler version * Updated annotation test * Cooler binning step follows wrong task * Missing reporter directory generation for binning * Using pyarrow for collation rather than dask * Pipeline formatting * Binning task not running. Ensured scale_factor exists * Fixed issue with storing as binned cooler * Fixed issue with store binned task. Now will merge with binned version * Removing binned temp file * Fixed issues with CoolerBinner and GenomicBinner * Fixed CCMatrix plotting class and added scaling factor normalisation * Fixed storage bug when creating GenomicBinner * Updated pipeline test to download indicies * Removed un-needed functions * Updated changelog and readme * Added checks for bin size * Updated binning set up * Changed bin_size to bin_sizes * Updated tests to ensure cooler files are binned correctly * Removed bad import * Incorrect input files specified for heatmap templates * Making template for each viewpoint and resolution heatmap * Only plotting heatmaps if binning performed * Bumped version to 0.2.4 * Chore add dependabot (#173) * Create dependabot.yml * Moved requirements out of setup.cfg * chore(CI): Updated GitHub actions and dependabot templates * Fixed a bug where the bins of a cooler do not contain a name column * Updated version to 0.2.4a2 * feat(annotation): Improve annotation speed and memory usage by integrating ray+pyranges (#180) * fix(reporters_pileup): Fixes error where cooler bins do not contain the name of the bin (#178) * Fixed bug with keep_aligned. Incorrect parameter specified * Allowed slice_stats to deal with empty df. Typo in remove_non_capture_fragments * Changed parent_read to parent_id for lower memory * Added basic test for slice filters * Added captures property to TiledCSliceFilter * Replaced isna check query with capture_count == 0 * Added ANALYSIS_METHOD placeholder * Added pytest-order * Added tests for all three methods of filtering * Added tests for all three pipeline modes * Fixed bug in cooler storage * Attempting to fix bowtie2 index cache * Engine pyarrow-dataset depreciated now using pyarrow directly * chore: Updated version to 0.2.3 (#165) * chore: pin conda dependency versions to speed up environment solver (#167) * Set minimum python version * Pinned conda dependencies + altered channel order * fix(pipeline): Fixed issues with annotation, filtering, storage and plotting for Tiled-C data (#166) * Bug with bedtools sort. Removing this fixes annotation issue * Increased verbosity of counting. Fixed counting bugs for single viewpoints and merging * Removed un-needed logging * BedIntersection now copes with empty files. Returns invalid intersection. * Updated cooler version * Updated annotation test * Cooler binning step follows wrong task * Missing reporter directory generation for binning * Using pyarrow for collation rather than dask * Pipeline formatting * Binning task not running. Ensured scale_factor exists * Fixed issue with storing as binned cooler * Fixed issue with store binned task. Now will merge with binned version * Removing binned temp file * Fixed issues with CoolerBinner and GenomicBinner * Fixed CCMatrix plotting class and added scaling factor normalisation * Fixed storage bug when creating GenomicBinner * Updated pipeline test to download indicies * Removed un-needed functions * fix(pipeline): Fixed stability issue with generate_bin_conversion_tables task. (#172) * fix(pipeline): Bug fixes for Tiled-C analysis and pipeline dependency updates (#168) * Fixed bug with keep_aligned. Incorrect parameter specified * Allowed slice_stats to deal with empty df. Typo in remove_non_capture_fragments * Changed parent_read to parent_id for lower memory * Added basic test for slice filters * Added captures property to TiledCSliceFilter * Replaced isna check query with capture_count == 0 * Added ANALYSIS_METHOD placeholder * Added pytest-order * Added tests for all three methods of filtering * Added tests for all three pipeline modes * Fixed bug in cooler storage * Attempting to fix bowtie2 index cache * Engine pyarrow-dataset depreciated now using pyarrow directly * chore: Updated version to 0.2.3 (#165) * chore: pin conda dependency versions to speed up environment solver (#167) * Set minimum python version * Pinned conda dependencies + altered channel order * fix(pipeline): Fixed issues with annotation, filtering, storage and plotting for Tiled-C data (#166) * Bug with bedtools sort. Removing this fixes annotation issue * Increased verbosity of counting. Fixed counting bugs for single viewpoints and merging * Removed un-needed logging * BedIntersection now copes with empty files. Returns invalid intersection. * Updated cooler version * Updated annotation test * Cooler binning step follows wrong task * Missing reporter directory generation for binning * Using pyarrow for collation rather than dask * Pipeline formatting * Binning task not running. Ensured scale_factor exists * Fixed issue with storing as binned cooler * Fixed issue with store binned task. Now will merge with binned version * Removing binned temp file * Fixed issues with CoolerBinner and GenomicBinner * Fixed CCMatrix plotting class and added scaling factor normalisation * Fixed storage bug when creating GenomicBinner * Updated pipeline test to download indicies * Removed un-needed functions * chore: prepare for release 0.2.3 (#169) * Fixed bug with keep_aligned. Incorrect parameter specified * Allowed slice_stats to deal with empty df. Typo in remove_non_capture_fragments * Changed parent_read to parent_id for lower memory * Added basic test for slice filters * Added captures property to TiledCSliceFilter * Replaced isna check query with capture_count == 0 * Added ANALYSIS_METHOD placeholder * Added pytest-order * Added tests for all three methods of filtering * Added tests for all three pipeline modes * Fixed bug in cooler storage * Attempting to fix bowtie2 index cache * Engine pyarrow-dataset depreciated now using pyarrow directly * chore: Updated version to 0.2.3 (#165) * chore: pin conda dependency versions to speed up environment solver (#167) * Set minimum python version * Pinned conda dependencies + altered channel order * fix(pipeline): Fixed issues with annotation, filtering, storage and plotting for Tiled-C data (#166) * Bug with bedtools sort. Removing this fixes annotation issue * Increased verbosity of counting. Fixed counting bugs for single viewpoints and merging * Removed un-needed logging * BedIntersection now copes with empty files. Returns invalid intersection. * Updated cooler version * Updated annotation test * Cooler binning step follows wrong task * Missing reporter directory generation for binning * Using pyarrow for collation rather than dask * Pipeline formatting * Binning task not running. Ensured scale_factor exists * Fixed issue with storing as binned cooler * Fixed issue with store binned task. Now will merge with binned version * Removing binned temp file * Fixed issues with CoolerBinner and GenomicBinner * Fixed CCMatrix plotting class and added scaling factor normalisation * Fixed storage bug when creating GenomicBinner * Updated pipeline test to download indicies * Removed un-needed functions * chore: update changelog and readme for release 0.2.3 (#170) * Fixed bug with keep_aligned. Incorrect parameter specified * Allowed slice_stats to deal with empty df. Typo in remove_non_capture_fragments * Changed parent_read to parent_id for lower memory * Added basic test for slice filters * Added captures property to TiledCSliceFilter * Replaced isna check query with capture_count == 0 * Added ANALYSIS_METHOD placeholder * Added pytest-order * Added tests for all three methods of filtering * Added tests for all three pipeline modes * Fixed bug in cooler storage * Attempting to fix bowtie2 index cache * Engine pyarrow-dataset depreciated now using pyarrow directly * chore: Updated version to 0.2.3 (#165) * chore: pin conda dependency versions to speed up environment solver (#167) * Set minimum python version * Pinned conda dependencies + altered channel order * fix(pipeline): Fixed issues with annotation, filtering, storage and plotting for Tiled-C data (#166) * Bug with bedtools sort. Removing this fixes annotation issue * Increased verbosity of counting. Fixed counting bugs for single viewpoints and merging * Removed un-needed logging * BedIntersection now copes with empty files. Returns invalid intersection. * Updated cooler version * Updated annotation test * Cooler binning step follows wrong task * Missing reporter directory generation for binning * Using pyarrow for collation rather than dask * Pipeline formatting * Binning task not running. Ensured scale_factor exists * Fixed issue with storing as binned cooler * Fixed issue with store binned task. Now will merge with binned version * Removing binned temp file * Fixed issues with CoolerBinner and GenomicBinner * Fixed CCMatrix plotting class and added scaling factor normalisation * Fixed storage bug when creating GenomicBinner * Updated pipeline test to download indicies * Removed un-needed functions * Updated changelog and readme * Added checks for bin size * Updated binning set up * Changed bin_size to bin_sizes * Updated tests to ensure cooler files are binned correctly * Removed bad import * Incorrect input files specified for heatmap templates * Making template for each viewpoint and resolution heatmap * Only plotting heatmaps if binning performed * Bumped version to 0.2.4 * Chore add dependabot (#173) * Create dependabot.yml * Moved requirements out of setup.cfg * chore(CI): Updated GitHub actions and dependabot templates * Fixed a bug where the bins of a cooler do not contain a name column * Updated version to 0.2.4a2 * build(deps): Update click requirement from <=8.1.0 to <8.2.0 (#176) Updates the requirements on [click](https://github.com/pallets/click) to permit the latest version. - [Release notes](https://github.com/pallets/click/releases) - [Changelog](https://github.com/pallets/click/blob/main/CHANGES.rst) - [Commits](pallets/click@0.1...8.1.3) --- updated-dependencies: - dependency-name: click dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Alastair Smith <[email protected]> * build(deps): Update pandas requirement from <=1.4.3 to <1.4.5 (#175) Updates the requirements on [pandas](https://github.com/pandas-dev/pandas) to permit the latest version. - [Release notes](https://github.com/pandas-dev/pandas/releases) - [Changelog](https://github.com/pandas-dev/pandas/blob/main/RELEASE.md) - [Commits](pandas-dev/pandas@0.3.0...v1.4.4) --- updated-dependencies: - dependency-name: pandas dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Alastair Smith <[email protected]> * Forcing blacklist to numeric * Forcing numeric blacklist in parent class * Added pyranges conversions to utils * Updated alignments_annotate with ray+pyranges * Added pyranges intersection class * Updated filters to cope with dtype changes * Updated tests * Added ray and pyranges Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * feat(reduce fragment adj memory): Reduces the memory footprint of a restriction fragment adj filtering step (#181) * fix(reporters_pileup): Fixes error where cooler bins do not contain the name of the bin (#178) * Fixed bug with keep_aligned. Incorrect parameter specified * Allowed slice_stats to deal with empty df. Typo in remove_non_capture_fragments * Changed parent_read to parent_id for lower memory * Added basic test for slice filters * Added captures property to TiledCSliceFilter * Replaced isna check query with capture_count == 0 * Added ANALYSIS_METHOD placeholder * Added pytest-order * Added tests for all three methods of filtering * Added tests for all three pipeline modes * Fixed bug in cooler storage * Attempting to fix bowtie2 index cache * Engine pyarrow-dataset depreciated now using pyarrow directly * chore: Updated version to 0.2.3 (#165) * chore: pin conda dependency versions to speed up environment solver (#167) * Set minimum python version * Pinned conda dependencies + altered channel order * fix(pipeline): Fixed issues with annotation, filtering, storage and plotting for Tiled-C data (#166) * Bug with bedtools sort. Removing this fixes annotation issue * Increased verbosity of counting. Fixed counting bugs for single viewpoints and merging * Removed un-needed logging * BedIntersection now copes with empty files. Returns invalid intersection. * Updated cooler version * Updated annotation test * Cooler binning step follows wrong task * Missing reporter directory generation for binning * Using pyarrow for collation rather than dask * Pipeline formatting * Binning task not running. Ensured scale_factor exists * Fixed issue with storing as binned cooler * Fixed issue with store binned task. Now will merge with binned version * Removing binned temp file * Fixed issues with CoolerBinner and GenomicBinner * Fixed CCMatrix plotting class and added scaling factor normalisation * Fixed storage bug when creating GenomicBinner * Updated pipeline test to download indicies * Removed un-needed functions * fix(pipeline): Fixed stability issue with generate_bin_conversion_tables task. (#172) * fix(pipeline): Bug fixes for Tiled-C analysis and pipeline dependency updates (#168) * Fixed bug with keep_aligned. Incorrect parameter specified * Allowed slice_stats to deal with empty df. Typo in remove_non_capture_fragments * Changed parent_read to parent_id for lower memory * Added basic test for slice filters * Added captures property to TiledCSliceFilter * Replaced isna check query with capture_count == 0 * Added ANALYSIS_METHOD placeholder * Added pytest-order * Added tests for all three methods of filtering * Added tests for all three pipeline modes * Fixed bug in cooler storage * Attempting to fix bowtie2 index cache * Engine pyarrow-dataset depreciated now using pyarrow directly * chore: Updated version to 0.2.3 (#165) * chore: pin conda dependency versions to speed up environment solver (#167) * Set minimum python version * Pinned conda dependencies + altered channel order * fix(pipeline): Fixed issues with annotation, filtering, storage and plotting for Tiled-C data (#166) * Bug with bedtools sort. Removing this fixes annotation issue * Increased verbosity of counting. Fixed counting bugs for single viewpoints and merging * Removed un-needed logging * BedIntersection now copes with empty files. Returns invalid intersection. * Updated cooler version * Updated annotation test * Cooler binning step follows wrong task * Missing reporter directory generation for binning * Using pyarrow for collation rather than dask * Pipeline formatting * Binning task not running. Ensured scale_factor exists * Fixed issue with storing as binned cooler * Fixed issue with store binned task. Now will merge with binned version * Removing binned temp file * Fixed issues with CoolerBinner and GenomicBinner * Fixed CCMatrix plotting class and added scaling factor normalisation * Fixed storage bug when creating GenomicBinner * Updated pipeline test to download indicies * Removed un-needed functions * chore: prepare for release 0.2.3 (#169) * Fixed bug with keep_aligned. Incorrect parameter specified * Allowed slice_stats to deal with empty df. Typo in remove_non_capture_fragments * Changed parent_read to parent_id for lower memory * Added basic test for slice filters * Added captures property to TiledCSliceFilter * Replaced isna check query with capture_count == 0 * Added ANALYSIS_METHOD placeholder * Added pytest-order * Added tests for all three methods of filtering * Added tests for all three pipeline modes * Fixed bug in cooler storage * Attempting to fix bowtie2 index cache * Engine pyarrow-dataset depreciated now using pyarrow directly * chore: Updated version to 0.2.3 (#165) * chore: pin conda dependency versions to speed up environment solver (#167) * Set minimum python version * Pinned conda dependencies + altered channel order * fix(pipeline): Fixed issues with annotation, filtering, storage and plotting for Tiled-C data (#166) * Bug with bedtools sort. Removing this fixes annotation issue * Increased verbosity of counting. Fixed counting bugs for single viewpoints and merging * Removed un-needed logging * BedIntersection now copes with empty files. Returns invalid intersection. * Updated cooler version * Updated annotation test * Cooler binning step follows wrong task * Missing reporter directory generation for binning * Using pyarrow for collation rather than dask * Pipeline formatting * Binning task not running. Ensured scale_factor exists * Fixed issue with storing as binned cooler * Fixed issue with store binned task. Now will merge with binned version * Removing binned temp file * Fixed issues with CoolerBinner and GenomicBinner * Fixed CCMatrix plotting class and added scaling factor normalisation * Fixed storage bug when creating GenomicBinner * Updated pipeline test to download indicies * Removed un-needed functions * chore: update changelog and readme for release 0.2.3 (#170) * Fixed bug with keep_aligned. Incorrect parameter specified * Allowed slice_stats to deal with empty df. Typo in remove_non_capture_fragments * Changed parent_read to parent_id for lower memory * Added basic test for slice filters * Added captures property to TiledCSliceFilter * Replaced isna check query with capture_count == 0 * Added ANALYSIS_METHOD placeholder * Added pytest-order * Added tests for all three methods of filtering * Added tests for all three pipeline modes * Fixed bug in cooler storage * Attempting to fix bowtie2 index cache * Engine pyarrow-dataset depreciated now using pyarrow directly * chore: Updated version to 0.2.3 (#165) * chore: pin conda dependency versions to speed up environment solver (#167) * Set minimum python version * Pinned conda dependencies + altered channel order * fix(pipeline): Fixed issues with annotation, filtering, storage and plotting for Tiled-C data (#166) * Bug with bedtools sort. Removing this fixes annotation issue * Increased verbosity of counting. Fixed counting bugs for single viewpoints and merging * Removed un-needed logging * BedIntersection now copes with empty files. Returns invalid intersection. * Updated cooler version * Updated annotation test * Cooler binning step follows wrong task * Missing reporter directory generation for binning * Using pyarrow for collation rather than dask * Pipeline formatting * Binning task not running. Ensured scale_factor exists * Fixed issue with storing as binned cooler * Fixed issue with store binned task. Now will merge with binned version * Removing binned temp file * Fixed issues with CoolerBinner and GenomicBinner * Fixed CCMatrix plotting class and added scaling factor normalisation * Fixed storage bug when creating GenomicBinner * Updated pipeline test to download indicies * Removed un-needed functions * Updated changelog and readme * Added checks for bin size * Updated binning set up * Changed bin_size to bin_sizes * Updated tests to ensure cooler files are binned correctly * Removed bad import * Incorrect input files specified for heatmap templates * Making template for each viewpoint and resolution heatmap * Only plotting heatmaps if binning performed * Bumped version to 0.2.4 * Chore add dependabot (#173) * Create dependabot.yml * Moved requirements out of setup.cfg * chore(CI): Updated GitHub actions and dependabot templates * Fixed a bug where the bins of a cooler do not contain a name column * Updated version to 0.2.4a2 * build(deps): Update click requirement from <=8.1.0 to <8.2.0 (#176) Updates the requirements on [click](https://github.com/pallets/click) to permit the latest version. - [Release notes](https://github.com/pallets/click/releases) - [Changelog](https://github.com/pallets/click/blob/main/CHANGES.rst) - [Commits](pallets/click@0.1...8.1.3) --- updated-dependencies: - dependency-name: click dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Alastair Smith <[email protected]> * build(deps): Update pandas requirement from <=1.4.3 to <1.4.5 (#175) Updates the requirements on [pandas](https://github.com/pandas-dev/pandas) to permit the latest version. - [Release notes](https://github.com/pandas-dev/pandas/releases) - [Changelog](https://github.com/pandas-dev/pandas/blob/main/RELEASE.md) - [Commits](pandas-dev/pandas@0.3.0...v1.4.4) --- updated-dependencies: - dependency-name: pandas dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Alastair Smith <[email protected]> * Reduced memory for remove_viewpoint_adjacent_restriction_fragments Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * fix: turned off ray dashboard * fix: Limited ray version to less than 2.0.1 * Updated environment to downgrade ray * chore: Updated environment.yml * chore: Changed pip section * chore: Updated ray package name * BREAKING_CHANGE: Replace cgatcore with snakemake for pipeline (#182) * Initiated snakemake pipeline * Further progress on snakemake pipeline * Continued with snakemake CC pipeline * Updated snakemake pipeline * Further work on snakemake port * Updated parts of pipeline and cli snakemake * Completed snakemake pipeline up to hub generation * Remomved extra file * Moved tools to API and updated API * Commented old pipeline test * Added pre-commit hooks * Removed linting as this clashes with snakemake * Updated ruff linter defaults * Updated annotation defaults * Updated .gitignore * Ignore 'old' directories * Updated for compliance with linter * Replaced tools module with 'api' * Imported cli in __init__.py * Updated gitignore * Fixed import * Pipeline test now tests all methods * Updated gitignore * Logging displays correctly now * Corrected error with duplicate removal * Updated pyproject.toml * Formatting * Formatting 2 * Ensure fastq files are present for pipeline * Added on error move of log to capcruncher_error.log * Updated pyproject.toml with snakefmt * Updated for snakefmt linting and pre-commit * Added differential interactions cli script * Updated Fastq set-up * Updated test for pipeline * Added snakemake as requirement * Trying to cache bowtie2 indicies better * Updated snakemake in env * Increased pandas version * Added ibis and duckdb. Removed cgat_core * Updated tests for renamed cli * Added MANIFEST.in * Duckdb is python-duckdb * Added annotation_defaults.json to manifest * Fixed numpy version to <=1.23 * Deleted old code and updated cis_and_trans_stats * Formatting * Cleans utils script * Re-write of CoolerBinner class * Attempt to fix deduplicate bugs * Using ray instead of joblib for storing interactions * Updated cli tests * Updates to FastqSamples class * Moved workflow and updated tests * Workflow now in recommended snakemake format * chore: fixed package versioning and logging * feat: added count_identified_viewpoints * Updates to pipeline. Not working yet * pipeline mostly running * feat: using tracknado to make hub * chore: updated threads * fix: fixed data location * feat: using quarto to generate report * fix: fixed output file path for fastqc rule. v1 * Added back duplicated reads * fix: hiding report code * fix: corrected splitting checkpoint * fix: updated tests * feat: increased import ability for api * feat(io): increased bam parsing verbosity * feat(alignments_filter): Better catching of errors * feat(cli_pipeline): added capcruncher pipeline-config * feat(cli_pipeline): added cookiecutter template * feat(pipeline): corrected pipeline errors * feat(pipeline): corrected pipeline test * chore: updated requirements.txt * chore: updated pipeline resources for fastq and qc * feat: added checks for capcruncher-tools * feat: added alternative workflow for capcruncher tools dedup stats * fix: typo in cookiecutter * feat: updated workflow resources with mem_mb * feat: added suffix option to fastq_splitter * feat: added suffix option to fastq_splitter * feat: added re-splitting of partitions to reduce potential issues * fix: better error message on missing fastq * fix: updated Snakefile for tiled-C * feat: temping annotations * feat: reducing counting cores * fix: added check for religation events to tiled-c * fix: increased max slice number for counting * feat: allowed for use of capcruncher-tools for counting interactions * fix: corrects incorrect pixel selection from binned cooler * feat(pipeline): added differential comparisons * chore: updated workflow python version * fix: workflow error with python version * feat: updated plotting api * fix: missing pyranges from env * chore: added bioconda to testing channels * feat: added plotting functionality to the pipeline * feat: placeholder for singularity container * fix: need to not use quotes if variable used * feat: catching errors for plotting in the log * feat: heatmaps are triangular by default * fix: analysis bin_sizes * fix: updated plot command * fix: removed --cov=xml from pytest * fix: removed --cov=xml from pytest * fix: pip installing test components * fix: updated indexes url in test * fix: ignoring ray reinit error * fix: added -el to bash shells * fix(tests): minor edits to initiate testing * fix(plotting): typo * feat(plotting): better logging * feat(plotting): added replicate bigwigs. collection still not possible * chore: bump python version * feat: altered pipeline paths * fix(report): fixed deduplication graph * fix(differential): fix differential interactions script * chore: currently only allowing differential for capture and tri * fix: small fixes and added some minor docs * fix: increased memory requested for count jobs * fix: small fixes for singularity * docs: small fixes for singularity docs * fix: fixed error in bin_sizes * fix: removed old import * feat: reduced storage space required by increasing temp() * fix: updated ibis code to be compatible with v6.0.0 (#183) * fix: replaced by * fix(tests): ensure that all tests pass (#185) * fix: replaced by * fix: replaced by * fix: fixed reporters pilup outfile name * fix: ray: removed logger to stop ray error (serialization) * fix: ray: reupdated deduplicate for new ibis version * fix: fixed logging in annotation worker * updated workflow * fix: corrected many input function errors * fix: git merge related errors corrected * fix: updated cis and trans stats code to ibis v6.0.0 * chore: ibis-framework minimum version set to 6.0.0 * feat: renamed capcruncher success log * chore(pipeline): removed all temp() for bugfixing * fix(pipeline.fastq): temping non- or combined fastq breaks pipeline * fix(pipeline.fastq): temping digestion stats breaks pipeline * chore: added cores argument to tests * chore: temping aligned.smk outputs * chore: temping annotate.smk outputs * chore: temping filter.smk outputs * chore: temping pileup.smk outputs * chore: temping other rules * fix: cores argument in test should be str * fix(test_pipeline): cookiecutter args now strings * fix: updated environment.yml versions * fix: read number is automatically x4 * fix: annotate now increases mem with each retry * fix: removed temp of filtering stats * fix: bigwig location updated * fix: cooler path updated * fix: updated number of expected slices for tiled * fix(pileup): binning never performed * debug: adding log to merge_stats_filtering * fix: added tiled specific cis/trans support * fix: added assay flag to rule * fix: dont remove viewpoint bins from tiled * fix: cis_count changed to count * fix: changed report output path in test * fix: multiple bin sizes added as list to bin_size * fix: updated publish action to latest version * chore: updated github workflow * fix(github-actions): quoted python version * feat: updated CI action * fix: updated codecov action * feat: use pytest-xdist to run tests in parallel * chore: updated gitignore with coverage * chore: cores option added to CI.yml * fix: n reads for rebalance reduced by 4x * fix: removed xdist cores * chore: updated codecov action in CI * chore(test-plotting): added test for plotting * feat: additional type hints added to CCTrack * chore: `type` changed to `file_type` for clarity * fix: ensure file paths are strings * fix: improved track adding capabilities CCFigure * fix: increased plotting window size * fix: corrected plotting test * chore: formatting * fix: updated caching for workflow --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
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