biopipen 0.27.5__tar.gz → 0.27.6__tar.gz

{biopipen-0.27.5 → biopipen-0.27.6}/PKG-INFO

@@ -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-0.27.6/biopipen/__init__.py

@@ -0,0 +1 @@
+__version__ = "0.27.6"

{biopipen-0.27.5 → biopipen-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-0.27.5 → biopipen-0.27.6}/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-0.27.5 → biopipen-0.27.6}/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 → biopipen-0.27.6}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "biopipen"
-version = "0.27.5"
+version = "0.27.6"
 description = "Bioinformatics processes/pipelines that can be run from `pipen run`"
 authors = ["pwwang <pwwang@pwwang.com>"]
 license = "MIT"

{biopipen-0.27.5 → biopipen-0.27.6}/setup.py

@@ -81,7 +81,7 @@ entry_points = \
 
 setup_kwargs = {
     'name': 'biopipen',
-    'version': '0.27.5',
+    'version': '0.27.6',
     'description': 'Bioinformatics processes/pipelines that can be run from `pipen run`',
     'long_description': 'None',
     'author': 'pwwang',

biopipen-0.27.5/biopipen/__init__.py

@@ -1 +0,0 @@
-__version__ = "0.27.5"