Merge pull request #34 from microbial-pangenomes-lab/fork

Avoid troubles with python 3.14+

Author: mgalardini

panfeed/__main__.py

@@ -7,6 +7,7 @@
 import logging.handlers
 from functools import partial
 import itertools
+import multiprocessing
 from multiprocessing import Process, Queue
 
 from .__init__ import __version__
@@ -296,13 +297,15 @@ def main():
                      compress=args.compress)
 
     if args.cores > 2:
+        ctx = multiprocessing.get_context('fork')
+
         # thanks to @SamStudio8 for the inspiration
         read_q = Queue(maxsize = qlimit * args.cores)
         write_q = Queue(maxsize = qlimit)
 
         processes = []
 
-        reader_process = Process(
+        reader_process = ctx.Process(
             target=reader,
             args=(
                 iter_i,
@@ -312,7 +315,7 @@ def main():
         )
         processes.append(reader_process)
 
-        writer_process = Process(
+        writer_process = ctx.Process(
             target=writer,
             args=(
                 func_w,
@@ -323,7 +326,7 @@ def main():
         processes.append(writer_process)
 
         for i in range(args.cores - 2):
-            p = Process(
+            p = ctx.Process(
                 target=worker,
                 args=(
                     iter_o,

tests/test_files.tar.gz

@@ -1,38 +1,53 @@
 #!/bin/bash
 argumentarray=()
+
+green="\033[1;32m"
+red="\033[1;31m"
+reset="\033[0m"
+
+die () {
+        echo -e $red"############"$reset
+	echo -e $red$1$reset
+	echo -e $red"Test failed!"$reset
+	echo -e $red"############"$reset
+	exit 1
+}
 ##############single argument changes
 #basic
-python ../panfeed-runner.py --gff test_files/gffs/ --presence-absence test_files/gene_presence_absence.csv --targets test_files/stroi.txt --output test_files/comp_data/panfeed_out/basic &> test_files/comp_data/logs/basic.log
+python ../panfeed-runner.py --gff test_files/gffs/ --presence-absence test_files/gene_presence_absence.csv --targets test_files/stroi.txt --output test_files/comp_data/panfeed_out/basic &> test_files/comp_data/logs/basic.log || die "Basic run failed"
 argumentarray+=("basic")
+#cores
+python ../panfeed-runner.py --gff test_files/gffs/ --presence-absence test_files/gene_presence_absence.csv --targets test_files/stroi.txt --cores 4 --output test_files/comp_data/panfeed_out/cores &> test_files/comp_data/logs/cores.log || die "Multiple cores run failed"
+argumentarray+=("cores")
 #no k-mers logged
-python ../panfeed-runner.py --gff test_files/gffs/ --presence-absence test_files/gene_presence_absence.csv --output test_files/comp_data/panfeed_out/nolog &> test_files/comp_data/logs/nolog.log
+python ../panfeed-runner.py --gff test_files/gffs/ --presence-absence test_files/gene_presence_absence.csv --output test_files/comp_data/panfeed_out/nolog &> test_files/comp_data/logs/nolog.log || die "No k-mers logged run failed"
 argumentarray+=("nolog")
 #upstream
-python ../panfeed-runner.py --gff test_files/gffs/ --presence-absence test_files/gene_presence_absence.csv --targets test_files/stroi.txt --upstream 100 --downstream 0 --output test_files/comp_data/panfeed_out/upstream &> test_files/comp_data/logs/upstream.log
+python ../panfeed-runner.py --gff test_files/gffs/ --presence-absence test_files/gene_presence_absence.csv --targets test_files/stroi.txt --upstream 100 --downstream 0 --output test_files/comp_data/panfeed_out/upstream &> test_files/comp_data/logs/upstream.log || die "Upstream run failed"
 argumentarray+=("upstream")
 #downstream
-python ../panfeed-runner.py --gff test_files/gffs/ --presence-absence test_files/gene_presence_absence.csv --targets test_files/stroi.txt --upstream 0 --downstream 100 --output test_files/comp_data/panfeed_out/downstream &> test_files/comp_data/logs/downstream.log
+python ../panfeed-runner.py --gff test_files/gffs/ --presence-absence test_files/gene_presence_absence.csv --targets test_files/stroi.txt --upstream 0 --downstream 100 --output test_files/comp_data/panfeed_out/downstream &> test_files/comp_data/logs/downstream.log || die "Downstream run failed"
 argumentarray+=("downstream")
 #up-/downstream
-python ../panfeed-runner.py --gff test_files/gffs/ --presence-absence test_files/gene_presence_absence.csv --targets test_files/stroi.txt --upstream 100 --downstream 100 --output test_files/comp_data/panfeed_out/updownstream &> test_files/comp_data/logs/updownstream.log
+python ../panfeed-runner.py --gff test_files/gffs/ --presence-absence test_files/gene_presence_absence.csv --targets test_files/stroi.txt --upstream 100 --downstream 100 --output test_files/comp_data/panfeed_out/updownstream &> test_files/comp_data/logs/updownstream.log || die "Up-/downstream run failed"
 argumentarray+=("updownstream")
 #up-/downstream
-python ../panfeed-runner.py --gff test_files/gffs/ --presence-absence test_files/gene_presence_absence.csv --targets test_files/stroi.txt --upstream 100 --downstream 100 --downstream-start-codon --output test_files/comp_data/panfeed_out/downstart &> test_files/comp_data/logs/downstart.log
+python ../panfeed-runner.py --gff test_files/gffs/ --presence-absence test_files/gene_presence_absence.csv --targets test_files/stroi.txt --upstream 100 --downstream 100 --downstream-start-codon --output test_files/comp_data/panfeed_out/downstart &> test_files/comp_data/logs/downstart.log || die "Downstream start codon run failed"
 argumentarray+=("downstart")
 #non-canonical
-python ../panfeed-runner.py --gff test_files/gffs/ --presence-absence test_files/gene_presence_absence.csv --targets test_files/stroi.txt --non-canonical --output test_files/comp_data/panfeed_out/noncanonical &> test_files/comp_data/logs/noncanonical.log
-argumentarray+=("noncanonical")
+python ../panfeed-runner.py --gff test_files/gffs/ --presence-absence test_files/gene_presence_absence.csv --targets test_files/stroi.txt --non-canonical --output test_files/comp_data/panfeed_out/noncanonical &> test_files/comp_data/logs/noncanonical.log || die "Non-canonical run failed"
+argumentarray+=("noncanonical") 
 #no filter
-python ../panfeed-runner.py --gff test_files/gffs/ --presence-absence test_files/gene_presence_absence.csv --targets test_files/stroi.txt --no-filter --output test_files/comp_data/panfeed_out/nofilter &> test_files/comp_data/logs/nofilter.log
+python ../panfeed-runner.py --gff test_files/gffs/ --presence-absence test_files/gene_presence_absence.csv --targets test_files/stroi.txt --no-filter --output test_files/comp_data/panfeed_out/nofilter &> test_files/comp_data/logs/nofilter.log || die "No filter run failed"
 argumentarray+=("nofilter")
 #high maf
-python ../panfeed-runner.py --gff test_files/gffs/ --presence-absence test_files/gene_presence_absence.csv --targets test_files/stroi.txt --maf 0.1 --output test_files/comp_data/panfeed_out/highmaf &> test_files/comp_data/logs/highmaf.log
+python ../panfeed-runner.py --gff test_files/gffs/ --presence-absence test_files/gene_presence_absence.csv --targets test_files/stroi.txt --maf 0.1 --output test_files/comp_data/panfeed_out/highmaf &> test_files/comp_data/logs/highmaf.log || die "High MAF run failed"
 argumentarray+=("highmaf")
 #consider missing
-python ../panfeed-runner.py --gff test_files/gffs/ --presence-absence test_files/gene_presence_absence.csv --targets test_files/stroi.txt --consider-missing --output test_files/comp_data/panfeed_out/considermissing &> test_files/comp_data/logs/considermissing.log
+python ../panfeed-runner.py --gff test_files/gffs/ --presence-absence test_files/gene_presence_absence.csv --targets test_files/stroi.txt --consider-missing --output test_files/comp_data/panfeed_out/considermissing &> test_files/comp_data/logs/considermissing.log || die "Consider missing run failed"
 argumentarray+=("considermissing")
 #fileoffiles
-python ../panfeed-runner.py --gff test_files/input_gffs.txt --fasta test_files/input_fastas.txt --presence-absence test_files/gene_presence_absence.csv --targets test_files/stroi.txt --output test_files/comp_data/panfeed_out/fileoffiles &> test_files/comp_data/logs/fileoffiles.log
+python ../panfeed-runner.py --gff test_files/input_gffs.txt --fasta test_files/input_fastas.txt --presence-absence test_files/gene_presence_absence.csv --targets test_files/stroi.txt --output test_files/comp_data/panfeed_out/fileoffiles &> test_files/comp_data/logs/fileoffiles.log || die "File of files run failed"
 argumentarray+=("fileoffiles")
 ##############multiple argument changes
 ##############compare output files