Run of fresh-snapshots for ctdconverter

Try this locally (using silver-platter):

debian-svp new-upstream --snapshot ctdconverter 

Merge these changes:

git pull https://janitor.debian.net/git/ctdconverter fresh-snapshots/main

Summary

Merged new upstream version: 2.0+git20180606.d7ac29e (was: 2.0).

Diff

diff --git a/README.md b/README.md
index 0c62d18..f6c671b 100644
--- a/README.md
+++ b/README.md
@@ -9,9 +9,11 @@ Given one or more CTD files, `CTD2Converter` generates the needed wrappers to in
 - `ruamel.yaml`
 
 ### Installing Dependencies
-We recommend the use of `conda` to manage all dependencies. If you're not sure what `conda` is, make sure to read the [using-conda](conda documentation).
+We recommend the use of `conda` to manage all dependencies. If you're not sure what `conda` is, make sure to read about the [conda project](https://conda.io/docs/index.html).
 
-The easiest way to get you started with CTD conversion is to create a `conda` environment on which you'll install all dependencies. Using environments in `conda` allows you to have parallel, independent python environments, thus avoiding conflicts between libraries. If you haven't installed `conda`, check [conda-install](conda's installation guide).
+The easiest way to get you started with CTD conversion is to create a `conda` environment on which you'll install all dependencies.  Using environments in `conda` allows you to have parallel, independent python environments, thus avoiding conflicts between libraries. 
+
+If you haven't installed `conda`, check [conda-install](conda's installation guide). See [this guide](https://conda.io/docs/user-guide/tasks/manage-environments.html) if you need help creating a `conda` environment.
 
 Once you've installed `conda`, create an environment named `ctd-converter`, like so:
 
@@ -181,4 +183,4 @@ The following invocation of the converter will use `/opt/suite/bin` as a prefix
 [CTDopts]: https://github.com/genericworkflownodes/CTDopts
 [CTDSchema]: https://github.com/WorkflowConversion/CTDSchema
 [conda-install]: https://conda.io/docs/install/quick.html
-[using-conda]: https://conda.io/docs/using/envs.html
\ No newline at end of file
+[using-conda]: https://conda.io/docs/using/envs.html
diff --git a/debian/changelog b/debian/changelog
index f528181..ba3829e 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,8 +1,12 @@
-ctdconverter (2.0-5) UNRELEASED; urgency=medium
+ctdconverter (2.0+git20180606.d7ac29e-1) UNRELEASED; urgency=medium
 
+  [ Jelmer Vernooij ]
   * Remove unnecessary X-Python{,3}-Version field in debian/control.
 
- -- Jelmer Vernooij <jelmer@debian.org>  Sat, 20 Oct 2018 14:03:06 +0000
+  [ Debian Janitor ]
+  * New upstream snapshot.
+
+ -- Debian Janitor <janitor@jelmer.uk>  Wed, 08 May 2019 22:09:30 +0000
 
 ctdconverter (2.0-4) unstable; urgency=medium
 
diff --git a/debian/patches/add_setup.py.patch b/debian/patches/add_setup.py.patch
index 8e84a52..994123f 100644
--- a/debian/patches/add_setup.py.patch
+++ b/debian/patches/add_setup.py.patch
@@ -1,9 +1,11 @@
 From: Michael R. Crusoe <michael.crusoe@gmail.com>
 Subject: Add setup.py
 Forwarded: https://github.com/WorkflowConversion/CTDConverter/pull/40
+Index: ctdconverter/convert.py
+===================================================================
 --- ctdconverter.orig/convert.py
 +++ ctdconverter/convert.py
-@@ -8,7 +8,7 @@
+@@ -8,7 +8,7 @@ from argparse import RawDescriptionHelpF
  from common.exceptions import ApplicationException, ModelError
  
  __all__ = []
@@ -12,13 +14,15 @@ Forwarded: https://github.com/WorkflowConversion/CTDConverter/pull/40
  __date__ = '2014-09-17'
  __updated__ = '2017-08-09'
  
-@@ -269,4 +269,4 @@
+@@ -269,4 +269,4 @@ def validate_and_prepare_common_argument
  
  
  if __name__ == "__main__":
 -    sys.exit(main())
 \ No newline at end of file
 +    sys.exit(main())
+Index: ctdconverter/setup.py
+===================================================================
 --- /dev/null
 +++ ctdconverter/setup.py
 @@ -0,0 +1,170 @@
diff --git a/debian/patches/correct_name b/debian/patches/correct_name
index a517c09..e92b980 100644
--- a/debian/patches/correct_name
+++ b/debian/patches/correct_name
@@ -1,8 +1,10 @@
 From: Michael R. Crusoe <michael.crusoe@gmail.com>
 Subject: unify script name reporting
+Index: ctdconverter/convert.py
+===================================================================
 --- ctdconverter.orig/convert.py
 +++ ctdconverter/convert.py
-@@ -17,10 +17,11 @@
+@@ -17,10 +17,11 @@ program_build_date = str(__updated__)
  program_version_message = '%%(prog)s %s (%s)' % (program_version, program_build_date)
  program_short_description = "CTDConverter - A project from the WorkflowConversion family " \
                                  "(https://github.com/WorkflowConversion/CTDConverter)"
@@ -15,7 +17,7 @@ Subject: unify script name reporting
  
  FORMAT can be either one of the supported output formats: cwl, galaxy.
  
-@@ -30,12 +31,12 @@
+@@ -30,12 +31,12 @@ documentation for each of the converters
  
  I - Parsing a single CTD file and convert it:
  
@@ -30,7 +32,7 @@ Subject: unify script name reporting
  
  
  III - Hardcoding parameters
-@@ -141,7 +142,7 @@
+@@ -141,7 +142,7 @@ III - Hardcoding parameters
  
        There are, for now, no CWL-specific parameters or options.
  
@@ -39,7 +41,7 @@ Subject: unify script name reporting
  
  program_license = '''%(short_description)s
  
-@@ -174,7 +175,8 @@
+@@ -174,7 +175,8 @@ def main(argv=None):
      # converter will register its own parameters after we've registered the basic ones... we have to do it old school
      if len(argv) < 2:
          utils.error("Not enough arguments provided")
diff --git a/debian/patches/py3_compat b/debian/patches/py3_compat
index 65ba38a..92473eb 100644
--- a/debian/patches/py3_compat
+++ b/debian/patches/py3_compat
@@ -1,8 +1,10 @@
 From: Michael R. Crusoe <michael.crusoe@gmail.com>
 Subject: use `open` instead of `file`
+Index: ctdconverter/cwl/converter.py
+===================================================================
 --- ctdconverter.orig/cwl/converter.py
 +++ ctdconverter/cwl/converter.py
-@@ -72,7 +72,7 @@
+@@ -72,7 +72,7 @@ def convert_models(args, parsed_ctds):
  
          logger.info("Writing to %s" % utils.get_filename(output_file), 1)
  
@@ -11,7 +13,7 @@ Subject: use `open` instead of `file`
          stream.write(CWL_SHEBANG + '\n\n')
          stream.write("# This CWL file was automatically generated using CTDConverter.\n")
          stream.write("# Visit https://github.com/WorkflowConversion/CTDConverter for more information.\n\n")
-@@ -103,6 +103,8 @@
+@@ -103,6 +103,8 @@ def convert_to_cwl(ctd_model, args):
          param_name = utils.extract_param_name(param)
          cwl_fixed_param_name = fix_param_name(param_name)
          hardcoded_value = args.parameter_hardcoder.get_hardcoded_value(param_name, ctd_model.name)
diff --git a/debian/patches/upgrade_deprecated_strip b/debian/patches/upgrade_deprecated_strip
index d39b370..89a0727 100644
--- a/debian/patches/upgrade_deprecated_strip
+++ b/debian/patches/upgrade_deprecated_strip
@@ -1,18 +1,18 @@
 From: Michael R. Crusoe <michael.crusoe@gmail.com>
 Subject: Upgrade deprecated using of string.strip()
+Index: ctdconverter/common/utils.py
+===================================================================
 --- ctdconverter.orig/common/utils.py
 +++ ctdconverter/common/utils.py
-@@ -4,8 +4,7 @@
+@@ -4,7 +4,6 @@ import ntpath
  import os
  
  from lxml import etree
 -from string import strip
--from logger import info, error, warning
-+from logger import info, error, warning
+ from logger import info, error, warning
  
  from common.exceptions import ApplicationException
- from CTDopts.CTDopts import CTDModel, ParameterGroup
-@@ -73,9 +72,9 @@
+@@ -73,9 +72,9 @@ def validate_argument_is_valid_path(args
      if member_value is not None:
          if isinstance(member_value, list):
              for file_name in member_value:
@@ -24,4 +24,3 @@ Subject: Upgrade deprecated using of string.strip()
  
          for path_to_check in paths_to_check:
              validate_path_exists(path_to_check)
-
diff --git a/galaxy/converter.py b/galaxy/converter.py
index 7f3e542..7dfd1cb 100755
--- a/galaxy/converter.py
+++ b/galaxy/converter.py
@@ -510,7 +510,7 @@ def create_repeat_attribute_list(rep_node, param):
         rep_node.attrib["min"] = "0"
     # for the ITEMLISTs which have LISTITEM children we only
     # need one parameter as it is given as a string
-    if param.default is not None: 
+    if param.default is not None and param.default is not _Null:  
         rep_node.attrib["max"] = "1"
     rep_node.attrib["title"] = get_galaxy_parameter_name(param)
 

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