[med-svn] [Git][med-team/ctdconverter][master] do a final 2to3 conversion, release
Alexandre Detiste (@detiste-guest)
gitlab at salsa.debian.org
Wed Jun 19 10:56:51 BST 2024
Alexandre Detiste pushed to branch master at Debian Med / ctdconverter
Commits:
1e3e897c by Alexandre Detiste at 2024-06-19T11:55:41+02:00
do a final 2to3 conversion, release
- - - - -
5 changed files:
- debian/changelog
- debian/control
- + debian/patches/2to3.patch
- debian/patches/series
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+ctdconverter (2.1-7) unstable; urgency=medium
+
+ * Team upload.
+ * Do a one shot final 2to3 conversion (Closes: #1045042)
+
+ -- Alexandre Detiste <tchet at debian.org> Wed, 19 Jun 2024 11:54:31 +0200
+
ctdconverter (2.1-6) unstable; urgency=medium
* Team upload.
=====================================
debian/control
=====================================
@@ -12,7 +12,6 @@ Build-Depends: debhelper-compat (= 13),
python3-ruamel.yaml,
python3-ctdopts,
help2man,
- 2to3
Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/med-team/ctdconverter
Vcs-Git: https://salsa.debian.org/med-team/ctdconverter.git
=====================================
debian/patches/2to3.patch
=====================================
@@ -0,0 +1,171 @@
+--- a/common/utils.py
++++ b/common/utils.py
+@@ -4,7 +4,7 @@
+ import os
+
+ from lxml import etree
+-from logger import info, error, warning
++from .logger import info, error, warning
+
+ from common.exceptions import ApplicationException
+ from CTDopts.CTDopts import CTDModel, ParameterGroup
+@@ -100,7 +100,7 @@
+ try:
+ info("Loading validation schema from %s" % xsd_location, 0)
+ schema = etree.XMLSchema(etree.parse(xsd_location))
+- except Exception, e:
++ except Exception as e:
+ error("Could not load validation schema %s. Reason: %s" % (xsd_location, str(e)), 0)
+ else:
+ warning("Validation against a schema has not been enabled.", 0)
+@@ -127,7 +127,7 @@
+ try:
+ parser = etree.XMLParser(schema=schema)
+ etree.parse(ctd_file, parser=parser)
+- except etree.XMLSyntaxError, e:
++ except etree.XMLSyntaxError as e:
+ raise ApplicationException("Invalid CTD file %s. Reason: %s" % (ctd_file, str(e)))
+
+
+@@ -195,9 +195,9 @@
+ def extract_tool_help_text(ctd_model):
+ manual = ""
+ doc_url = None
+- if "manual" in ctd_model.opt_attribs.keys():
++ if "manual" in list(ctd_model.opt_attribs.keys()):
+ manual += "%s\n\n" % ctd_model.opt_attribs["manual"]
+- if "docurl" in ctd_model.opt_attribs.keys():
++ if "docurl" in list(ctd_model.opt_attribs.keys()):
+ doc_url = ctd_model.opt_attribs["docurl"]
+
+ help_text = "No help available"
+@@ -258,7 +258,7 @@
+ parameters.append(parameter)
+ else:
+ # append the first-level children of this ParameterGroup
+- pending.extend(parameter.parameters.values())
++ pending.extend(list(parameter.parameters.values()))
+ # returned the reversed list of parameters (as it is now,
+ # we have the last parameter in the CTD as first in the list)
+ return reversed(parameters)
+--- a/convert.py
++++ b/convert.py
+@@ -175,11 +175,11 @@
+ # 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")
+- print("\nUsage: $ {} [TARGET] "
++ print(("\nUsage: $ {} [TARGET] "
+ " [ARGUMENTS]\n\n".format(program_name) +
+ "Where:\n" +
+ " target: one of 'cwl' or 'galaxy'\n\n" +
+- "Run again using the -h/--help option to print more detailed help.\n")
++ "Run again using the -h/--help option to print more detailed help.\n"))
+ return 1
+
+ # TODO: at some point this should look like real software engineering and use a map containing converter instances
+@@ -224,19 +224,19 @@
+ print("Interrupted...")
+ return 0
+
+- except ApplicationException, e:
++ except ApplicationException as e:
+ traceback.print_exc()
+ utils.error("CTDConverter could not complete the requested operation.", 0)
+ utils.error("Reason: " + e.msg, 0)
+ return 1
+
+- except ModelError, e:
++ except ModelError as e:
+ traceback.print_exc()
+ utils.error("There seems to be a problem with one of your input CTDs.", 0)
+ utils.error("Reason: " + e.msg, 0)
+ return 1
+
+- except Exception, e:
++ except Exception as e:
+ traceback.print_exc()
+ utils.error("CTDConverter could not complete the requested operation.", 0)
+ utils.error("Reason: " + e.msg, 0)
+--- a/galaxy/converter.py
++++ b/galaxy/converter.py
+@@ -134,10 +134,10 @@
+ else:
+ logger.info("Macro %s found" % name, 1)
+ macros_to_expand.add(name)
+- except ParseError, e:
++ except ParseError as e:
+ raise ApplicationException("The macros file " + macros_file_name + " could not be parsed. Cause: " +
+ str(e))
+- except IOError, e:
++ except IOError as e:
+ raise ApplicationException("The macros file " + macros_file_name + " could not be opened. Cause: " +
+ str(e))
+
+@@ -281,7 +281,7 @@
+ if galaxy_tool_path is None:
+ galaxy_tool_path = ""
+
+- for category, file_names in categories_to_tools.iteritems():
++ for category, file_names in categories_to_tools.items():
+ section_node = add_child_node(toolbox_node, "section")
+ section_node.attrib["id"] = "section-id-" + "".join(category.split())
+ section_node.attrib["name"] = category
+@@ -322,7 +322,7 @@
+
+
+ def create_description(tool, model):
+- if "description" in model.opt_attribs.keys() and model.opt_attribs["description"] is not None:
++ if "description" in list(model.opt_attribs.keys()) and model.opt_attribs["description"] is not None:
+ description = SubElement(tool,"description")
+ description.text = model.opt_attribs["description"]
+
+@@ -667,7 +667,7 @@
+ def generate_label_and_help(desc):
+ help_text = ""
+ # This tag is found in some descriptions
+- if not isinstance(desc, basestring):
++ if not isinstance(desc, str):
+ desc = str(desc)
+ desc = desc.encode("utf8").replace("#br#", " <br>")
+ # Get rid of dots in the end
+@@ -734,9 +734,9 @@
+
+
+ def get_lowercase_list(some_list):
+- lowercase_list = map(str, some_list)
+- lowercase_list = map(string.lower, lowercase_list)
+- lowercase_list = map(strip, lowercase_list)
++ lowercase_list = list(map(str, some_list))
++ lowercase_list = list(map(string.lower, lowercase_list))
++ lowercase_list = list(map(strip, lowercase_list))
+ return lowercase_list
+
+
+@@ -800,7 +800,7 @@
+ # check if there are formats that have not been registered yet...
+ output = list()
+ for format_name in param.restrictions.formats:
+- if not format_name in supported_file_formats.keys():
++ if not format_name in list(supported_file_formats.keys()):
+ output.append(str(format_name))
+
+ # warn only if there's about to complain
+@@ -833,7 +833,7 @@
+
+ # Get the supported file format for one given format
+ def get_supported_file_type(format_name, supported_file_formats):
+- if format_name in supported_file_formats.keys():
++ if format_name in list(supported_file_formats.keys()):
+ return supported_file_formats.get(format_name, DataType(format_name, format_name)).galaxy_extension
+ else:
+ return None
+@@ -841,7 +841,7 @@
+
+ def get_supported_file_types(formats, supported_file_formats):
+ return set([supported_file_formats.get(format_name, DataType(format_name, format_name)).galaxy_extension
+- for format_name in formats if format_name in supported_file_formats.keys()])
++ for format_name in formats if format_name in list(supported_file_formats.keys())])
+
+
+ def create_change_format_node(parent, data_formats, input_ref):
=====================================
debian/patches/series
=====================================
@@ -3,3 +3,4 @@ upgrade_deprecated_strip
correct_name
py3_compat
python3-syntax.patch
+2to3.patch
=====================================
debian/rules
=====================================
@@ -19,10 +19,6 @@ include /usr/share/dpkg/default.mk
%:
dh $@ --buildsystem=pybuild
-override_dh_auto_build:
- 2to3 --write --nobackups --no-diffs convert.py galaxy/ cwl/ common/
- dh_auto_build
-
debian/CTDConverter.1: debian/rules debian/CTDConverter.help2man
help2man 'python3 convert.py' --include=debian/CTDConverter.help2man \
--no-info --version-string="$(DEB_VERSION_UPSTREAM)" \
View it on GitLab: https://salsa.debian.org/med-team/ctdconverter/-/commit/1e3e897c68078fa2128591afa2e99b60a1f7ecae
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