Immunopipe

- docs: remove -w option for apptainer/singularity as no writing is necessary since pipen-board 0.15.1
- deps: update biopipen to version 0.27.8
- fix(scrna.SeuratClusterStats): fix selected columns not unique for stats
- feat(scrna.SeuratMap2Ref): allow non-SCTransform'ed reference
- feat(scrna.SeuratMap2Ref): allow splitting query object for mapping (pwwang/immunopipe61)
- deps: update pipen-board to version 0.15.1 (allow configuration file path in the URL box on Web UI)

**Full Changelog**: https://github.com/pwwang/immunopipe/compare/1.3.7...1.3.8

- ci: fix docker images building when no essential changes made

**Full Changelog**: https://github.com/pwwang/immunopipe/compare/1.3.6...1.3.7

- ci: fix deploy workflow (59)
- ci: add README.md to tests-output branch
- ci: fix test/test workflow
- tests: add `make test`
- tests: init test data preparation
- tests: add test for ImmunarchLoading
- tests: add tests for SeuratPreparing
- tests: Update configs for SeuratPreparing test to subset cells so tests can run on CI
- tests: update SeuratPreparing test to disable export
- tests: add tests for SeuratClusteringOfAllCells/SeuratClustering
- docs: update installation instructions (stein.mariammayo.edu)
- deps: bump biopipen to version 0.27.7 (0.27.5-0.27.7)
- fix(scrna.SeuratClusterStats): fix color palette for ridge plots (stein.mariammayo.edu)
- feat(scrna.SeuratPreparing): add envs.cell_qc_per_sample to filter cells before merging instead after
- fix(scrna_metabolic_landscape.MetabolicFeatures): fix return value of groups with less than 5 cells in `do_one_group`
- fix(scrna_metabolic_landscape): fix mutaters not working.
- fix(scrna_metabolic_landscape.MetabolicFeatures/MetabolicFeaturesIntraSubset): skip groups with less than 5 cells in `do_one_group` and save a warning file under the case
- chore: fix typo in class name `ExprImpution` to `ExprImputation`

What's Changed
* 1.3.6 by pwwang in https://github.com/pwwang/immunopipe/pull/60


**Full Changelog**: https://github.com/pwwang/immunopipe/compare/1.3.5...1.3.6

- 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