0.32.0 (#154)

* fix(scrna.SeuratMap2Ref): fix report and add stats to report

* refactor(scrna.Seurat2AnnData): abstract seurat_to_anndata() for reuse

* fix(utils.single_cell.R): fix categorical data when converting seurat to anndata format

* deps: update pipen-runinfo dependency to version 0.8.1

* enh(tcr.TCRClustering): make GIANA compatible with latest BioPython

* feat(scrna): add CellCellCommunication and CellCellCommunicationPlots

* fix(tcr.TCRClstering): fix clusTCR error due to scipy update (v1.14)

* 0.32.0

0.31.7 (#153)

* chore: update pyright configuration to include biopipen/**/*.py

* feat(bam): add BamSubsetByBed process for subsetting bam file by regions in a bed file

* feat(bed): add BedtoolsMakeWindows process for generating windows from a BED file or genome size file

* deps: bump pipen-args to 0.16

* 0.31.7

0.31.6 (#152)

* refactor(regulatory.MotifAffinityTest): optimize code base

* chore(regulatory.MotifAffinityTest): fix arguments when calling ensure_regulator_motifs

* feat(regulatory): add VariantMotifPlot to plot motif and surrounding sequences with mutations

* ci: add verbosal output for tests

* fix(regulatory.motifs-common): handle empty regmotifs argument in ensure_regulator_motifs

* test(regulatory): add motifdb argument to VariantMotifPlot's

* test(regulatory.MotifAffinityTest): add regmotifs argument to VariantMotifPlotAtSNP_WithTFOnly

* test(regulatory): add regmotifs argument to VariantMotifPlotBreakR_WithTFOnly

* feat(vcf): adopt truvari v4+ for related processes

* deps: pin the channels of conda dependencies for tests

* 0.31.6

0.31.5 (#151)

* ci: do not print verbose logs for tests

* feat(protein): add the protein module and Prodigy and ProdigySummary to calculate the binding affinity of a complex structure

* deps: update pipen to version 0.15.3 and xqute to version 0.5.2

* chore(bam.BamMerge): use logger instead of print for logging

* feat(bam): add BamSampling process for sampling a fraction of reads from a bam file

* 0.31.5

* test: exclude ENSG00000230373 from gene name conversion tests as it returns unstable results by mygeneinfo

0.31.4 (#150)

* fix(plot.VennDiagram): update default devpars and fix issues with computed data

* fix(scrna.SeuratMap2Ref): fix identifying the normalization method of reference

* deps: bump pipen-report to 0.20.1 (pipen to 0.15.2)

* 0.31.4

0.31.3 (#149)

* test: fix test not failing when tests failed

* test: fix gene name conversion tests due to external API change

* fix(tcr.CDR3AAPhyschem): fix when chain is not available

* fix(tcr.TCRClustering): fix when chain is not available

* test: fix gene name conversion test due to external API change

* test: fix gene name conversion test due to external API change

* fix(tcr.CDR3AAPhyschem): fix typo in the script

* 0.31.3

0.31.2 (#148)

* fix(tcr.CDR3AAPhyschem): use sequence from TRB chain only

* fix(tcr.TCRClustering): fix for multi-chain TCRs, use TRB only if on_multi is false

* 0.31.2

0.31.1 (#147)

* enh(scrna.SeuratMap2Ref): check if reference has SCTModel if SCTransform'ed (likely prepared by old Seurat)

* 0.31.1

0.31.0 (#146)

* feat(scrna): add ScSimulation process for simulating single-cell data using splatter

* refactor(scrna.CellsDistribution): fix same colors for more than 16 clusters

* BREAKING(scrna.SeuratClusterStats): change envs.stats.frac option to calculate fraction of cells in each group or ident

* feat(scrna.SeuratMap2Ref): run PrepSCTFindMarkers when necessary

* deps: bump pipen to 0.15

* 0.31.0

0.30.0 (#145)

* fix(stats.Mediation): fix when NAs in the data

* BREAKING(scrna): move clustree plots from SeuratClustering/SeuratSubClustering to SeuratClusterStats

* chore(scrna.MetaMarkers): remove `plugin_opts.poplog_max`

* fix(scrna): fix resolution expansion for SeuratClustering and SeuratSubClustering

* chore(tcr.CloneResidency): improve logging when handling subjects

* feat(plot): add Scatter for scatter plots

* tests: use single conda env for tests

* ci: fix CI due to conda env changes

* chore: source the files for Immunarch scripts for better debugging

* tests(scrna.ScFGSEA): fix unavailable urls to GMT files

* docs(web): update docs of `envs.tool` for Download/DownloadList

* chore(scrna.SeuratMap2Ref): optimize memory usage

* feat(web): add GCloudStorageDownloadFile and GCloudStorageDownloadBucket to download files from GCP

* fix(cellranger.CellRangerCount): fix falsy `envs.create_bam` not working for cellranger v7

* feat(scrna.SeuratPreparing): add scDblFinder to detect doublets

* feat(scrna.SeuratMap2Ref): add envs.skip_if_normalized option to skip normalization if query is already normalized using the same method as the reference

* chore(regulatory.MotifAffinityTest): use template filter source_r to source R files

* tests(regulatory.MotifAffinityTest): rename regulation to regulatory

* chore: use template filter source_r to source R files

* fix(stats): handle case when p-value is 0 for MetaPvalue and MetaPvalue1

* feat(scrna.CellTypeAnnotation): allow to merge/not to merge the clusters with the same labels predicted

* fix(scrna): Fix generating PrepSCTFindMarkers  command when no previous commands present

* refactor(scnra.SeuratClustering): refactor the script for better debugging

* refactor(scnra.SeuratPreparing): refactor the script for better debugging

* 0.30.0

* docs: fix CHANGELOG format