[med-svn] [spades] 03/03: use Debian packaged YAML module

[Sascha Steinbiss]

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sascha-guest pushed a commit to branch master
in repository spades.

commit 7ce302488884a6f597a89d2538a67fb40b9fc61f
Author: Sascha Steinbiss <sascha at steinbiss.name>
Date:   Fri Mar 18 14:26:09 2016 +0000

    use Debian packaged YAML module
---
 debian/changelog                                   |  6 ++--
 .../0001_use_debian_packaged_python-yaml.patch     | 38 +++++++++++++++++-----
 2 files changed, 33 insertions(+), 11 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index a54570b..1dee64f 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,10 +1,12 @@
-spades (3.7.1+dfsg-2) unstable; urgency=medium
+spades (3.7.1+dfsg-2) UNRELEASED; urgency=medium
 
   * Use asciidoctor instead of ronn for reproducible man pages
   * enable full hardening
   * add override for pedantic Lintian msg
+  * use correct YAML module
+    Closes: #818584
 
- -- Sascha Steinbiss <sascha at steinbiss.name>  Thu, 17 Mar 2016 23:52:30 +0000
+ -- Sascha Steinbiss <sascha at steinbiss.name>  Fri, 18 Mar 2016 14:25:06 +0000
 
 spades (3.7.1+dfsg-1) unstable; urgency=medium
 
diff --git a/debian/patches/0001_use_debian_packaged_python-yaml.patch b/debian/patches/0001_use_debian_packaged_python-yaml.patch
index 8cba706..252a72f 100644
--- a/debian/patches/0001_use_debian_packaged_python-yaml.patch
+++ b/debian/patches/0001_use_debian_packaged_python-yaml.patch
@@ -35,7 +35,7 @@ Description: We are using Debian packaged python-yaml
  
      data = pyyaml.load(open(filename, 'r'))
      data["dataset"] = cfg.dataset_yaml_filename
-@@ -93,10 +90,13 @@
+@@ -93,10 +90,7 @@
  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)
@@ -43,17 +43,11 @@ Description: We are using Debian packaged python-yaml
 -        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
-+    except:
-+        import yaml as pyyaml
++    import yaml as pyyaml
      dst_configs = os.path.join(cfg.output_dir, "configs")
      if os.path.exists(dst_configs):
          shutil.rmtree(dst_configs)
-@@ -145,4 +145,4 @@
+@@ -145,4 +139,4 @@
      log.info("\n== Dataset description file was created: " + corrected_dataset_yaml_filename + "\n")
  
      if os.path.isdir(cfg.tmp_dir):
@@ -74,3 +68,29 @@ Description: We are using Debian packaged python-yaml
          est_params_data = pyyaml.load(open(est_params_filename, 'r'))
          for reads_library in est_params_data:
              if reads_library['type'] in READS_TYPES_USED_IN_CONSTRUCTION:
+--- a/src/spades_pipeline/corrector_logic.py
++++ b/src/spades_pipeline/corrector_logic.py
+@@ -19,10 +19,7 @@
+ 
+ def prepare_config_corr(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
++    import yaml as pyyaml
+     data = pyyaml.load(open(filename, 'r'))
+     data["dataset"] = cfg.dataset
+     data["output_dir"] = cfg.output_dir
+@@ -39,10 +36,7 @@
+ def run_corrector(configs_dir, execution_home, cfg,
+                 ext_python_modules_home, log, to_correct, result):
+     addsitedir(ext_python_modules_home)
+-    if sys.version.startswith('2.'):
+-        import pyyaml2 as pyyaml
+-    elif sys.version.startswith('3.'):
+-        import pyyaml3 as pyyaml
++    import yaml as pyyaml
+ 
+     dst_configs = os.path.join(cfg.output_dir, "configs")
+     if os.path.exists(dst_configs):

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