Package: spades / 3.13.1+dfsg-2

0002_use_debian_packaged_python-joblib.patch Patch series | download
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Author: Andreas Tille <tille@debian.org>
Last-Changed: Tue, 03 Mar 2015 20:55:53 +0100
Description: We are using Debian packaged python-joblib
 Debian has its own way to distinguish Python versions and there is no point
 in doing this inside the code.
 .
 The patch is non-intrusive since it conserves the original code and uses
 Debian pyyaml only if the original method fails.

--- a/assembler/src/spades_pipeline/hammer_logic.py
+++ b/assembler/src/spades_pipeline/hammer_logic.py
@@ -46,10 +46,13 @@ def compress_dataset_files(dataset_data,
                 support.sys_call([pigz_path, '-f', '-7', '-p', str(max_threads), reads_file], log)
         else:
             addsitedir(ext_python_modules_home)
-            if sys.version.startswith('2.'):
-                from joblib2 import Parallel, delayed
-            elif sys.version.startswith('3.'):
-                from joblib3 import Parallel, delayed
+            try:
+                if sys.version.startswith('2.'):
+                    from joblib2 import Parallel, delayed
+                elif sys.version.startswith('3.'):
+                    from joblib3 import Parallel, delayed
+            except:
+                from joblib import Parallel, delayed
             n_jobs = min(len(to_compress), max_threads)
             outputs = Parallel(n_jobs=n_jobs)(delayed(support.sys_call)(['gzip', '-f', '-7', reads_file]) for reads_file in to_compress)
             for output in outputs:
--- a/assembler/src/spades_pipeline/lucigen_nxmate.py
+++ b/assembler/src/spades_pipeline/lucigen_nxmate.py
@@ -43,12 +43,14 @@ except ImportError:
     support.error("Can't process Lucigen NxMate reads! Python module regex is not installed!")
 
 addsitedir(spades_init.ext_python_modules_home)
-if sys.version.startswith('2.'):
-    from joblib2 import Parallel, delayed
-elif sys.version.startswith('3.'):
-    from joblib3 import Parallel, delayed
+try:
+    if sys.version.startswith('2.'):
+        from joblib2 import Parallel, delayed
+    elif sys.version.startswith('3.'):
+        from joblib3 import Parallel, delayed
+except:
+    from joblib import Parallel, delayed
 
-    
 # CONSTANTS
 READS_PER_THREAD = 25000
 READS_PER_BATCH = READS_PER_THREAD * options_storage.threads  # e.g. 100000 for 4 threads