[med-svn] r18900 - trunk/packages/spades/trunk/debian/patches

[Andreas Tille]

Author: tille
Date: 2015-03-03 21:36:23 +0000 (Tue, 03 Mar 2015)
New Revision: 18900

Modified:
   trunk/packages/spades/trunk/debian/patches/0001_use_debian_packaged_python-yaml.patch
   trunk/packages/spades/trunk/debian/patches/0002_use_debian_packaged_python-joblib.patch
Log:
Fix spacing in patches


Modified: trunk/packages/spades/trunk/debian/patches/0001_use_debian_packaged_python-yaml.patch
===================================================================
--- trunk/packages/spades/trunk/debian/patches/0001_use_debian_packaged_python-yaml.patch	2015-03-03 20:03:50 UTC (rev 18899)
+++ trunk/packages/spades/trunk/debian/patches/0001_use_debian_packaged_python-yaml.patch	2015-03-03 21:36:23 UTC (rev 18900)
@@ -25,12 +25,14 @@
  import options_storage
  addsitedir(ext_python_modules_home)
 -if sys.version.startswith('2.'):
+-    import pyyaml2 as pyyaml
+-elif sys.version.startswith('3.'):
+-    import pyyaml3 as pyyaml
 +try:
 +    if sys.version.startswith('2.'):
-     import pyyaml2 as pyyaml
--elif sys.version.startswith('3.'):
++        import pyyaml2 as pyyaml
 +    elif sys.version.startswith('3.'):
-     import pyyaml3 as pyyaml
++        import pyyaml3 as pyyaml
 +except:
 +    import yaml as pyyaml
  
@@ -42,11 +44,15 @@
  
  def prepare_config_ih(filename, cfg, ext_python_modules_home):
      addsitedir(ext_python_modules_home)
+-    if sys.version.startswith('2.'):
+-        import pyyaml2 as pyyaml
+-    elif sys.version.startswith('3.'):
+-        import pyyaml3 as pyyaml
 +    try:
-     if sys.version.startswith('2.'):
-         import pyyaml2 as pyyaml
-     elif sys.version.startswith('3.'):
-         import pyyaml3 as pyyaml
++        if sys.version.startswith('2.'):
++            import pyyaml2 as pyyaml
++        elif sys.version.startswith('3.'):
++            import pyyaml3 as pyyaml
 +    except:
 +        import yaml as pyyaml
  
@@ -56,27 +62,42 @@
  def run_hammer(corrected_dataset_yaml_filename, configs_dir, execution_home, cfg,
                 not_used_dataset_data, ext_python_modules_home, log):
      addsitedir(ext_python_modules_home)
+-    if sys.version.startswith('2.'):
+-        import pyyaml2 as pyyaml
+-    elif sys.version.startswith('3.'):
+-        import pyyaml3 as pyyaml
 +    try:
-     if sys.version.startswith('2.'):
-         import pyyaml2 as pyyaml
-     elif sys.version.startswith('3.'):
-         import pyyaml3 as pyyaml
++        if sys.version.startswith('2.'):
++            import pyyaml2 as pyyaml
++        elif sys.version.startswith('3.'):
++            import pyyaml3 as pyyaml
 +    except:
 +        import yaml as pyyaml
      dst_configs = os.path.join(cfg.output_dir, "configs")
      if os.path.exists(dst_configs):
          shutil.rmtree(dst_configs)
+@@ -142,4 +148,4 @@ def run_hammer(corrected_dataset_yaml_fi
+     log.info("\n== Dataset description file was created: " + corrected_dataset_yaml_filename + "\n")
+ 
+     if os.path.isdir(cfg.tmp_dir):
+-        shutil.rmtree(cfg.tmp_dir)
+\ No newline at end of file
++        shutil.rmtree(cfg.tmp_dir)
 --- a/src/spades_pipeline/spades_logic.py
 +++ b/src/spades_pipeline/spades_logic.py
 @@ -68,10 +68,13 @@ def get_read_length(output_dir, K, ext_p
      max_read_length = 0
      if os.path.isfile(est_params_filename):
          addsitedir(ext_python_modules_home)
+-        if sys.version.startswith('2.'):
+-            import pyyaml2 as pyyaml
+-        elif sys.version.startswith('3.'):
+-            import pyyaml3 as pyyaml
 +        try:
-         if sys.version.startswith('2.'):
-             import pyyaml2 as pyyaml
-         elif sys.version.startswith('3.'):
-             import pyyaml3 as pyyaml
++            if sys.version.startswith('2.'):
++                import pyyaml2 as pyyaml
++            elif sys.version.startswith('3.'):
++                import pyyaml3 as pyyaml
 +        except:
 +            import yaml as pyyaml
          est_params_data = pyyaml.load(open(est_params_filename, 'r'))

Modified: trunk/packages/spades/trunk/debian/patches/0002_use_debian_packaged_python-joblib.patch
===================================================================
--- trunk/packages/spades/trunk/debian/patches/0002_use_debian_packaged_python-joblib.patch	2015-03-03 20:03:50 UTC (rev 18899)
+++ trunk/packages/spades/trunk/debian/patches/0002_use_debian_packaged_python-joblib.patch	2015-03-03 21:36:23 UTC (rev 18900)
@@ -27,13 +27,6 @@
              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:
-@@ -148,4 +151,4 @@ def run_hammer(corrected_dataset_yaml_fi
-     log.info("\n== Dataset description file was created: " + corrected_dataset_yaml_filename + "\n")
- 
-     if os.path.isdir(cfg.tmp_dir):
--        shutil.rmtree(cfg.tmp_dir)
-\ No newline at end of file
-+        shutil.rmtree(cfg.tmp_dir)
 --- a/src/spades_pipeline/lucigen_nxmate.py
 +++ b/src/spades_pipeline/lucigen_nxmate.py
 @@ -36,12 +36,14 @@ except ImportError: