Merge pull request #42 from AuReMe/m2m_1.5.1

m2m 1.5.1

.github/workflows/pythonpackage.yml

@@ -32,7 +32,7 @@ jobs:
     strategy:
       matrix:
         platform: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: [3.6, 3.7]
+        python-version: [3.7, 3.8]
     runs-on: ${{ matrix.platform }}
 
     steps:

CHANGELOG.md

@@ -1,5 +1,12 @@
 # Changelog
 
+# Metage2Metabo v1.5.1 (2022-09-21)
+
+## Fix
+
+* issue in m2m_analysis where clyngor module uses the clingo module producing [ValueError](https://github.com/Aluriak/PowerGrASP/issues/1).
+* issue in m2m_analysis when incorrect paths for seed and/or target files were given as input. 
+
 # Metage2Metabo v1.5.0 (2021-03-17)
 
 This release focuses on `m2m_analysis` by adding new option, new output files,more documentation and refactoring some functions and output files.

metage2metabo/__init__.py

@@ -14,6 +14,6 @@
 
 from metage2metabo import m2m, m2m_analysis
 
-__version__ = '1.5.0'
+__version__ = '1.5.1'
 """ version of the package
 """ 

metage2metabo/__main_analysis__.py

@@ -237,6 +237,15 @@ def main():
         parser.print_help()
         sys.exit()
 
+    if "seeds" in args and args.seeds is not None:
+        if not utils.is_valid_file(args.seeds):
+            logger.critical('Error: ' + args.seeds + " is not a correct filepath")
+            sys.exit(1)
+    if "targets" in args and args.targets is not None:
+        if not utils.is_valid_file(args.targets):
+            logger.critical('Error: ' + args.targets + " is not a correct filepath")
+            sys.exit(1)
+
     # add logger in file
     formatter = logging.Formatter('%(message)s')
     log_file_path = os.path.join(args.out, f'm2m_analysis_{args.cmd}.log')

metage2metabo/m2m_analysis/graph_compression.py

@@ -26,6 +26,11 @@
 from metage2metabo import utils
 from metage2metabo.m2m_analysis.taxonomy import extract_taxa, get_taxon
 
+# Deactivate clingo module to avoid issue like this one:
+# https://github.com/Aluriak/PowerGrASP/issues/1
+import clyngor
+clyngor.deactivate_clingo_module()
+
 logger = logging.getLogger(__name__)