Immunopipe

- ci/test: add tests in CI and deploy output in a different branch
- ci: re-arrange workflows
- deps: bump biopipen to 0.27.4
- choir(delim.SampleInfo): add alpha to the colors of the plots using biopipen color pallete
- docs(tcr/scrna/scrna_metabolic_landscape): update links of images in docs

What's Changed
* 1.3.5-pre1 by pwwang in https://github.com/pwwang/immunopipe/pull/55
* 1.3.5 by pwwang in https://github.com/pwwang/immunopipe/pull/58


**Full Changelog**: https://github.com/pwwang/immunopipe/compare/1.3.4-post4...1.3.5

- deps: bump biopipen to 0.27.3
- deps: bump pipen-poplog to 0.1.2 (quick fix for populating logs when job fails)
- deps: temporary fix copier breaks with pyyaml-include v2 (copier-org/copier1568)
- choir(scrna.ScFGSEA): Skip cases when no cells found (50)
- choir(scrna.MarkersFinder): Skip cases when no cells found (50)
- choir(scrna.MetaMarkers): Skip cases when no cells found (50)
- feat(scrna.SeuratPreparing): support `DoubletFinder` (52)

What's Changed
* 1.3.4 by pwwang in https://github.com/pwwang/immunopipe/pull/53


**Full Changelog**: https://github.com/pwwang/immunopipe/compare/1.3.3...1.3.4

- deps: temporary fix copier breaks with pyyaml-include v2 (copier-org/copier1568)
- docs: update FAQ.md with instructions for running pipeline on a cluster
- deps: bump biopipen to 0.27.2
- fix(scrna.RadarPlots): fix mutaters not working
- feat(tcr.CloneResidency): support `envs.upset_ymax` to set the max value of y axis in upset bar plot.

What's Changed
* 1.3.3 by pwwang in https://github.com/pwwang/immunopipe/pull/51


**Full Changelog**: https://github.com/pwwang/immunopipe/compare/1.3.2...1.3.3

- deps: bump pipen to 0.14.5
- deps: add r-complexupset package to environment.yml and environment_full.yml for CloneResidency
- deps: pin tensorflow to 2.15 for TESSA
- deps: bump biopipen to 0.27.1
- depr(scrna.MarkersFinder): remove `envs.use_presto` as it's used by Seurat v5 by default
- enh(tcr.CloneResidency): support log scale for y axis of upset bar plots
- enh(scrna.SeuratClusterStats): allow to rotate labels in circos plot (pwwang/immunopipe48) li.yingmayo.edu
- enh(scrna.SeuratClusterStats): use `pal_biopipen` for ident colors in circos plot
- fix(scrna.CellsDistribution): fix the row order of the heatmaps
- fix(scrna.SeuratClusterStats): fix when `envs.split-by` is specified
- feat(scrna.CellsDistribution): support `envs.prefix_each`
- feat(scrna.MarkersFinder): allow to set max number of genes to plot in dotplots
- feat(scrna.MarkersFinder): support setting detailed arguments for overlapping plots
- feat(scrna.MarkersFinder): support `envs.prefix_group`
- feat(scrna.ScFGSEA): support `envs.prefix_each`
- feat(scrna.RadarPlots): support `envs.prefix_each` and `envs.subset`
- choir(scrna.SeuratClusterStats): use logger instead of print for log messages
- choir(tcr.TCRClustering): print session info for `clustcr` script
- choir(scrna.MarkersFinder): flatten toc when no `section` and no `ident-1` specified
- docs: add more detailed docs for `envs.section` for multiple processes
- BREAKING(scrna.SeuratMap2Ref): rename envs.name to envs.ident so envs.MapQuery.refdata is not required anymore. It will be inferred from envs.ident and envs.use. li.yingmayo.edu

What's Changed
* 1.3.2 by pwwang in https://github.com/pwwang/immunopipe/pull/49


**Full Changelog**: https://github.com/pwwang/immunopipe/compare/1.3.1...1.3.2

- deps: bump pipen to 0.14.3
- deps: pin ggplot2 to 3.4 for docker due to breaking changes of 3.5
- deps: bump biopipen to 0.26.2
- deps: bump datar-pandas to 0.5.5 to dismiss deprecated warnings
- fix(utils.misc.R): replace latin and greek characters with closest ascii chars for slugify()
- feat(scrna.TopExpressingGenes): support `subset`
- fix(scrna.CellsDistribution): fix the row order of the heatmaps.
- enh(tcr.CloneResidency): add legend for multiplets in upset plots.
- feat(scrna.SeuratClusterStats): add circos plot for cell composition stats (46).

What's Changed
* 1.3.1 by pwwang in https://github.com/pwwang/immunopipe/pull/47


**Full Changelog**: https://github.com/pwwang/immunopipe/compare/1.3.0...1.3.1

- deps: bump pipen to 0.14.1
- deps: bump pipen-report to 0.18.2
- deps: bump biopipen to 0.26.0
- fix(scrna.CellTypeAnnotation): keep factor meta data when input and output are RDS for celltypist
- deps: bump datar to 0.15.4 (support pandas 2.2)
- fix(utils.single_cell.R): fix `immdata_from_expanded` missing other data columns
- fix(tcr.Immunarch): fix `mutaters` not working when no subset is set
- fix(scrna.CellsDistribution): fix `hm_devpars` not working
- fix(scrna.CellsDistribution): fix multiple `cells_by` columns and speed up plotting
- choir(tcr.CloneResidency): mark singletons in Venn diagrams more clear
- fix(scrna.RadarPlots): fix the order of groups on radar plots
- choir(scrna.RadarPlots): transpose the count/percentage table to save to files
- fix(scrna.MarkersFinder): fix generating report json file when no significant genes found
- choir(scrna.MarkersFinder): Plot maximum 20 genes in dotplots
- choir(scrna.MarkersFinder): Do not convert dashes in case names to dots
- see more at <https://github.com/pwwang/biopipen/releases/tag/0.26.0>

What's Changed
* 0.13.0 by pwwang in https://github.com/pwwang/immunopipe/pull/45


**Full Changelog**: https://github.com/pwwang/immunopipe/compare/1.2.0...1.3.0