biopipen 0.32.0__tar.gz → 0.32.1__tar.gz

{biopipen-0.32.0 → biopipen-0.32.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: biopipen
-Version: 0.32.0
+Version: 0.32.1
 Summary: Bioinformatics processes/pipelines that can be run from `pipen run`
 License: MIT
 Author: pwwang
@@ -12,6 +12,7 @@ Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
 Provides-Extra: runinfo
 Requires-Dist: datar[pandas] (>=0.15.6,<0.16.0)
 Requires-Dist: pipen-board[report] (>=0.16,<0.17)

biopipen-0.32.1/biopipen/__init__.py

@@ -0,0 +1 @@
+__version__ = "0.32.1"

{biopipen-0.32.0 → biopipen-0.32.1}/biopipen/reports/scrna/TopExpressingGenes.svelte

@@ -2,7 +2,7 @@
 {% from "utils/gsea.liq" import enrichr_report -%}
 <script>
     import { Image, DataTable, Descr } from "$libs";
-    import { Accordion, AccordionItem, Tabs, Tab, TabContent } from "$ccs";
+    import { Accordion, AccordionItem, Tabs, Tab, TabContent, InlineNotification } from "$ccs";
 </script>
 
 

{biopipen-0.32.0 → biopipen-0.32.1}/biopipen/scripts/scrna/ScFGSEA.R

@@ -180,7 +180,7 @@ do_case <- function(name, case) {
     case$rest$maxSize <- case$maxsize
     case$rest$eps <- case$eps
     case$rest$nproc <- case$ncores
-    runFGSEA(ranks, gmtfile, case$top, info$casedir, case$rest)
+    runFGSEA(ranks, case$gmtfile, case$top, info$casedir, case$rest)
 
     add_report(
         list(kind = "fgsea", dir = info$casedir),

{biopipen-0.32.0 → biopipen-0.32.1}/biopipen/scripts/scrna/SeuratClusterStats-features.R

@@ -414,7 +414,7 @@ do_one_features = function(name) {
             p = p + eval(parse(text = pls))
         }
     }
-    figfile = file.path(odir, paste0(slugify(name), ".", slugify(case$kind), ".png"))
+    figfile = file.path(odir, paste0(slugify(name), ".", slugify(kind), ".png"))
     png(figfile, width=devpars$width, height=devpars$height, res=devpars$res)
     tryCatch({
         print(p)

{biopipen-0.32.0 → biopipen-0.32.1}/biopipen/scripts/scrna/SeuratPreparing-common.R

@@ -35,10 +35,10 @@ rename_files = function(e, sample, path) {
 perform_cell_qc <- function(sobj, per_sample = FALSE) {
     log_prefix <- ifelse(per_sample, "  ", "- ")
     log_info("{log_prefix}Adding metadata for QC ...")
-    sobj$percent.mt <- PercentageFeatureSet(sobj, pattern = "^MT-")
-    sobj$percent.ribo <- PercentageFeatureSet(sobj, pattern = "^RP[SL]")
-    sobj$percent.hb <- PercentageFeatureSet(sobj, pattern = "^HB[^(P)]")
-    sobj$percent.plat <- PercentageFeatureSet(sobj, pattern = "PECAM1|PF4")
+    sobj$percent.mt <- PercentageFeatureSet(sobj, pattern = "^MT-|^Mt-|^mt-")
+    sobj$percent.ribo <- PercentageFeatureSet(sobj, pattern = "^RP[SL]|^Rp[sl]")
+    sobj$percent.hb <- PercentageFeatureSet(sobj, pattern = "^HB[^P]|^Hb[^p]")
+    sobj$percent.plat <- PercentageFeatureSet(sobj, pattern = "PECAM1|PF4|Pecam1|Pf4")
 
     if (is.null(envs$cell_qc) || length(envs$cell_qc) == 0) {
         log_warn("{log_prefix}No cell QC criteria is provided. All cells will be kept.")
@@ -210,7 +210,7 @@ load_sample = function(sample) {
 
     if (isTRUE(envs$cell_qc_per_sample)) {
         log_info("- Perform cell QC for sample: {sample} ...")
-        obj = perform_cell_qc(obj, TRUE)
+        obj = perform_cell_qc(obj, per_sample = TRUE)
     }
 
     if (isTRUE(envs$use_sct)) {
@@ -287,7 +287,7 @@ run_cell_qc <- function(sobj) {
 
         if (!envs$cell_qc_per_sample) {
             log_info("Performing cell QC ...")
-            sobj = perform_cell_qc(sobj)
+            sobj = perform_cell_qc(sobj, per_sample = FALSE)
         }
 
         cached$data <- list(sobj = sobj, cell_qc_df = cell_qc_df)

{biopipen-0.32.0 → biopipen-0.32.1}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "biopipen"
-version = "0.32.0"
+version = "0.32.1"
 description = "Bioinformatics processes/pipelines that can be run from `pipen run`"
 authors = ["pwwang <pwwang@pwwang.com>"]
 license = "MIT"

{biopipen-0.32.0 → biopipen-0.32.1}/setup.py

@@ -85,7 +85,7 @@ entry_points = \
 
 setup_kwargs = {
     'name': 'biopipen',
-    'version': '0.32.0',
+    'version': '0.32.1',
     'description': 'Bioinformatics processes/pipelines that can be run from `pipen run`',
     'long_description': 'None',
     'author': 'pwwang',

biopipen-0.32.0/biopipen/__init__.py

@@ -1 +0,0 @@
-__version__ = "0.32.0"