biopipen 0.27.5__py3-none-any.whl → 0.27.6__py3-none-any.whl

biopipen/__init__.py

@@ -1 +1 @@
-__version__ = "0.27.5"
+__version__ = "0.27.6"

biopipen/core/testing.py

@@ -3,7 +3,7 @@ import tempfile
 from functools import wraps
 from pathlib import Path
 
-from pipen import Pipen, plugin
+from pipen import Pipen
 
 TESTING_INDEX_INIT = 1
 TESTING_PARENT_DIR = Path(tempfile.gettempdir())
@@ -40,17 +40,6 @@ def _get_test_dirs(testfile, new):
     return name, workdir, outdir
 
 
-class PipelineSucceeded:
-    """A plugin to check if the pipeline succeeded"""
-
-    name = "succeeded"
-    version = "0.1.0"
-
-    @plugin.impl
-    async def on_complete(pipen, succeeded):
-        pipen._succeeded = succeeded
-
-
 def get_pipeline(testfile, loglevel="debug", enable_report=False, **kwargs):
     """Get a pipeline for a test file"""
     name, workdir, outdir = _get_test_dirs(testfile, False)
@@ -60,7 +49,7 @@ def get_pipeline(testfile, loglevel="debug", enable_report=False, **kwargs):
         "workdir": workdir,
         "outdir": outdir,
         "loglevel": loglevel,
-        "plugins": [PipelineSucceeded, f"{report_plugin_prefix}report"],
+        "plugins": [f"{report_plugin_prefix}report"],
     }
     kws.update(kwargs)
     return Pipen(**kws)

biopipen/scripts/scrna_metabolic_landscape/MetabolicFeatures.R

@@ -52,12 +52,13 @@ do_one_group <- function(obj, features, group, outputdir, h1) {
     if (any(table(classes) < 5)) {
         msg <- paste("Group", group, "has less than 5 cells, or only 5 cells left.")
         log_warn(msg)
-        add_report(
-            list(kind = "error", content = msg),
-            h1 = ifelse(is.null(h1), groupname, h1),
-            h2 = ifelse(is.null(h1), "#", groupname)
+        return(
+            list(
+                list(kind = "error", content = msg),
+                h1 = ifelse(is.null(h1), groupname, h1),
+                h2 = ifelse(is.null(h1), "#", groupname)
+            )
         )
-        return()
     }
 
     exprs = GetAssayData(obj)[features, , drop = FALSE]

biopipen/utils/gsea.R

@@ -172,12 +172,12 @@ runFGSEA = function(
 
     tablefig = file.path(outdir, "gsea_table.png")
     png(tablefig, res=100, width=1000, height=200 + 40 * length(topPathways))
-    print(plotGseaTable(
+    plotGseaTable(
         envs$pathways[topPathways],
         ranks,
         gsea_res,
         gseaParam = if (!is.null(envs$gseaParam)) envs$gseaParam else 1
-    ))
+    )
     dev.off()
 
     for (pathway in topPathways) {

{biopipen-0.27.5.dist-info → biopipen-0.27.6.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: biopipen
-Version: 0.27.5
+Version: 0.27.6
 Summary: Bioinformatics processes/pipelines that can be run from `pipen run`
 License: MIT
 Author: pwwang

{biopipen-0.27.5.dist-info → biopipen-0.27.6.dist-info}/RECORD

@@ -1,11 +1,11 @@
-biopipen/__init__.py,sha256=E1FuUUku2gzKP9EaIByX13BXhDU2SYE99gN_s2YdX7s,23
+biopipen/__init__.py,sha256=BwKhBzWMdVser1JHOUEX0Aa2nBqgua67wsNi17fRle0,23
 biopipen/core/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biopipen/core/config.py,sha256=edK5xnDhM8j27srDzsxubi934NMrglLoKrdcC8qsEPk,1069
 biopipen/core/config.toml,sha256=20RCI30Peee1EQdfb_UbV3Hf74XUPndJnYZlUThytsw,1781
 biopipen/core/defaults.py,sha256=yPeehPLk_OYCf71IgRVCWuQRxLAMixDF81Ium0HtPKI,344
 biopipen/core/filters.py,sha256=HLrjXGsvvjRtTWIAmg_f4IMymWaRD769HlDwsCTh170,12424
 biopipen/core/proc.py,sha256=60lUP3PcUAaKbDETo9N5PEIoeOYrLgcSmuytmrhcx8g,912
-biopipen/core/testing.py,sha256=fZ8lzLwM5AhYapx0LDdYZPumqC0dj7GZpQuabhlqyGI,3665
+biopipen/core/testing.py,sha256=lZ_R5ZbYPO2NPuLHdbzg6HbD_f4j8paVVbyeUqwg6FE,3411
 biopipen/ns/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biopipen/ns/bam.py,sha256=5AsYrB0mtr_mH6mCL6gjJ5rC4NywpjFkpFjUrBGp7Fk,9301
 biopipen/ns/bcftools.py,sha256=puCDfIL-1z6cz2y1Rlz-ESNIr8xJgeIjEQ440qicCvM,3467
@@ -157,7 +157,7 @@ biopipen/scripts/scrna/Subset10X.R,sha256=T2nJBTwOe12AIKC2FZsMSv6xx3s-67CYZokpz5
 biopipen/scripts/scrna/TopExpressingGenes.R,sha256=kXMCYHVytgVgO_Uq66fKKFCFV2PPXE8VREy_0yYPLpU,7475
 biopipen/scripts/scrna/celltypist-wrapper.py,sha256=f5M8f4rU5nC7l17RS0YVmUPpLLz4D6PIcgWtA77UExM,1722
 biopipen/scripts/scrna/sctype.R,sha256=NaUJkABwF5G1UVm1CCtcMbwLSj94Mo24mbYCKFqo1Bw,6524
-biopipen/scripts/scrna_metabolic_landscape/MetabolicFeatures.R,sha256=b77yG5FeRse3bNfFgLIEYGHNZzydAn1OeyyR_n5Ju60,4790
+biopipen/scripts/scrna_metabolic_landscape/MetabolicFeatures.R,sha256=nSBNn1BMwqoApTqmvzLeRhFu2JW_mNhOXICxmBYIP6E,4813
 biopipen/scripts/scrna_metabolic_landscape/MetabolicFeaturesIntraSubset.R,sha256=ic8Fy8QqYDGh_izmvZVJ3KL66podg_CSF5ITL3FZsvo,5196
 biopipen/scripts/scrna_metabolic_landscape/MetabolicPathwayActivity.R,sha256=95DLX1Rz0tobOuDZ8V9YdGgO0KiNthhccoeeOK21tno,16216
 biopipen/scripts/scrna_metabolic_landscape/MetabolicPathwayHeterogeneity.R,sha256=rQ9iwGh9FNRZlJJzM4QItdyXmebfzLAq05ZAjb1kGUw,9831
@@ -230,7 +230,7 @@ biopipen/utils/caching.R,sha256=qANQqH8p-VpvD8V4VSoqSfp0TFr4esujC7x3OFZsJMw,1687
 biopipen/utils/common_docstrs.py,sha256=Ow-g-yS5P7DEO37cP1X-xioRbYWygfQHxIuLIaDdrjs,6288
 biopipen/utils/gene.R,sha256=BzAwlLA8hO12vF-3t6IwEuTEeLa_jBll4zm_5qe3qoE,1243
 biopipen/utils/gene.py,sha256=qE_BqTayrJWxRdniffhcz6OhZcw9GUoOrj2EtFWH9Gw,2246
-biopipen/utils/gsea.R,sha256=UMQOlWGstQTOBScvy1wIzrB7I3CE28Xo2v1sy4lmJ-M,7549
+biopipen/utils/gsea.R,sha256=2sN3AM0XjLWbTv6cB3JHCBWjuhmD4wEjPaaBY7wkhCI,7542
 biopipen/utils/io.R,sha256=jIYdqdn0iRWfQYAZa5CjXi3fikqmYvPPLIXhobRe8sw,537
 biopipen/utils/misc.R,sha256=jXusPDCxSIaYRq_qm4khUsu9nyMhbpBVcj8BVn4j8Ic,10629
 biopipen/utils/misc.py,sha256=KJziAFY4Kl-0ZsO93vteY9gRLZg9BSYig-TDocHY36k,3601
@@ -240,7 +240,7 @@ biopipen/utils/reference.py,sha256=6bPSwQa-GiDfr7xLR9a5T64Ey40y24yn3QfQ5wDFZkU,4
 biopipen/utils/rnaseq.R,sha256=Ro2B2dG-Z2oVaT5tkwp9RHBz4dp_RF-JcizlM5GYXFs,1298
 biopipen/utils/single_cell.R,sha256=pJjYP8bIZpNAtTQ32rOXhZxaM1Y-6D-xUcK3pql9tbk,4316
 biopipen/utils/vcf.py,sha256=ajXs0M_QghEctlvUlSRjWQIABVF02wPdYd-0LP4mIsU,9377
-biopipen-0.27.5.dist-info/METADATA,sha256=V-P-6i9I4Q1OE-KDY39Nkki_Iv_5jpP-65kxeUuCc88,882
-biopipen-0.27.5.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
-biopipen-0.27.5.dist-info/entry_points.txt,sha256=wu70aoBcv1UahVbB_5237MY-9M9_mzqmWjDD-oi3yz0,621
-biopipen-0.27.5.dist-info/RECORD,,
+biopipen-0.27.6.dist-info/METADATA,sha256=t7ROsmFyR6-E4YXGAwiuNxRjZz5IX6_H7mT1rs9OSfE,882
+biopipen-0.27.6.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
+biopipen-0.27.6.dist-info/entry_points.txt,sha256=wu70aoBcv1UahVbB_5237MY-9M9_mzqmWjDD-oi3yz0,621
+biopipen-0.27.6.dist-info/RECORD,,