[med-svn] [Git][med-team/spades][master] 3 commits: Specify yaml loader

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / spades


Commits:
2a1a3c6d by Andreas Tille at 2019-11-12T17:57:21Z
Specify yaml loader

- - - - -
54bc9d00 by Andreas Tille at 2019-11-12T18:12:30Z
Hopefully fix

  File "/build/spades-3.13.1/install_spades/../../share/spades/spades_pipeline/spades_logic.
    for src, target in replacements.iteritems():
AttributeError: 'dict' object has no attribute 'iteritems'

- - - - -
9207cab9 by Andreas Tille at 2019-11-12T18:13:25Z
Build-Depends: s/python-all-dev/python3-dev/

- - - - -


5 changed files:

- debian/changelog
- debian/control
- debian/patches/python3.patch
- debian/patches/series
- + debian/patches/yaml_load.patch


Changes:

=====================================
debian/changelog
=====================================
@@ -9,6 +9,7 @@ spades (3.13.1-1) UNRELEASED; urgency=medium
   * Move source package lintian overrides to debian/source.
   * Set upstream metadata fields: Repository.
   * Make sure Python3 interpreter is used in scripts
+  * Specify yaml loader
 
  -- Andreas Tille <tille at debian.org>  Tue, 08 Oct 2019 18:17:07 +0200
 


=====================================
debian/control
=====================================
@@ -9,7 +9,7 @@ Priority: optional
 Build-Depends: debhelper-compat (= 12),
                dh-python,
                cmake,
-               python-all-dev,
+               python3-dev,
                zlib1g-dev,
                libbz2-dev,
                libboost-dev,


=====================================
debian/patches/python3.patch
=====================================
@@ -115,6 +115,24 @@ Description: Make sure Python3 interpreter is used in scripts
  
  ############################################################################
  # Copyright (c) 2015 Saint Petersburg State University
+@@ -214,7 +214,7 @@ def run_iteration(configs_dir, execution
+             lines = []
+             with open(cfg_file) as infile:
+                 for line in infile:
+-                    for src, target in replacements.iteritems():
++                    for src, target in list(replacements.iteritems()):
+                         line = line.replace(src, target)
+                     lines.append(line)
+             with open(cfg_file, 'w') as outfile:
+@@ -275,7 +275,7 @@ def run_scaffold_correction(configs_dir,
+             lines = []
+             with open(cfg_file) as infile:
+                 for line in infile:
+-                    for src, target in replacements.iteritems():
++                    for src, target in list(replacements.iteritems()):
+                         line = line.replace(src, target)
+                     lines.append(line)
+             with open(cfg_file, 'w') as outfile:
 --- a/assembler/src/spades_pipeline/truspades/reference_construction.py
 +++ b/assembler/src/spades_pipeline/truspades/reference_construction.py
 @@ -1,4 +1,4 @@


=====================================
debian/patches/series
=====================================
@@ -19,3 +19,4 @@ fix-bool-cast
 spelling
 gcc7.patch
 python3.patch
+yaml_load.patch


=====================================
debian/patches/yaml_load.patch
=====================================
@@ -0,0 +1,16 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Tue, 12 Nov 2019 17:11:17 +0100
+Description: Specify yaml loader
+ see https://github.com/yaml/pyyaml/wiki/PyYAML-yaml.load(input)-Deprecation
+
+--- a/assembler/spades.py
++++ b/assembler/spades.py
+@@ -107,7 +107,7 @@ def print_used_values(cfg, log):
+                      " or --meta flag if processing metagenomic dataset)")
+ 
+         log.info("  Reads:")
+-        dataset_data = pyyaml.load(open(cfg["dataset"].yaml_filename, 'r'))
++        dataset_data = pyyaml.load(open(cfg["dataset"].yaml_filename, 'r'), Loader=yaml.FullLoader)
+         dataset_data = support.relative2abs_paths(dataset_data, os.path.dirname(cfg["dataset"].yaml_filename))
+         support.pretty_print_reads(dataset_data, log)
+ 



View it on GitLab: https://salsa.debian.org/med-team/spades/compare/533d1e6ed64dde7804e75a149d1eb45661081e2a...9207cab94da2e59b88cc9a282b48efa7b0233e84

-- 
View it on GitLab: https://salsa.debian.org/med-team/spades/compare/533d1e6ed64dde7804e75a149d1eb45661081e2a...9207cab94da2e59b88cc9a282b48efa7b0233e84
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