Merge pull request #1491 from jdavcs/galaxy_24.2

Bump requirements for galaxy packages to 24.2

planemo/linters/doi.py

@@ -1,5 +1,4 @@
-""" Tool linting module that lints Galaxy tools for their DOIs (if a DOI type citation is present)
-"""
+"""Tool linting module that lints Galaxy tools for their DOIs (if a DOI type citation is present)"""
 
 import planemo.lint
 

planemo/linters/urls.py

@@ -1,5 +1,4 @@
-""" Tool linting module that lints Galaxy tools for their URLs
-"""
+"""Tool linting module that lints Galaxy tools for their URLs"""
 
 import planemo.lint
 

planemo/shed2tap/__init__.py

@@ -1,2 +1 @@
-"""
-"""
+""" """

planemo/virtualenv.py

@@ -1,5 +1,4 @@
-""" Utilities for using virtualenv as library and planemo command.
-"""
+"""Utilities for using virtualenv as library and planemo command."""
 
 import os
 import sys

requirements.txt

@@ -3,8 +3,8 @@ bioblend>=1.0.0
 click!=8.0.2
 cwltool>=1.0.20191225192155
 ephemeris>=0.10.3
-galaxy-tool-util[edam,extended-assertions]>=24.1,<24.2
-galaxy-util[template]>=24.1,<24.2
+galaxy-tool-util[edam,extended-assertions]>=24.1,<25.0
+galaxy-util[template]>=24.1,<25.0
 glob2
 gxformat2>=0.14.0
 h5py

tests/data/lint_skip_list.txt

@@ -1,4 +1,4 @@
 # check that comments work
-xml_order
+XMLOrder
 # check the white spaces are ignored
- citations 
+ CitationsMissing 

tests/data/tools/empty_cdata.xml

@@ -16,10 +16,10 @@
     </outputs>
     <tests>
         <test>
-            <param name="select_opt" value="Hello World!" />
+            <param name="select_opt" value="moo" />
             <output name="output">
                 <assert_contents>
-                    <has_line line="Hello World!" />
+                    <has_line line="moo" />
                 </assert_contents>
             </output>
         </test>

tests/data/tools/ok_conditional.xml

@@ -17,10 +17,10 @@
     </outputs>
     <tests>
         <test>
-            <param name="select_opt" value="Hello World!" />
+            <param name="conditional|select_opt" value="moo" />
             <output name="output">
                 <assert_contents>
-                    <has_line line="Hello World!" />
+                    <has_line line="moo" />
                 </assert_contents>
             </output>
         </test>

tests/data/tools/ok_param_argument.xml

@@ -13,6 +13,7 @@
     <tests>
         <test expect_failure="true" expect_exit_code="1">
             <param name="input1" value="1.bed"/>
+            <param name="r" value="1.bed"/>
             <assert_stdout>
                 <has_line line="Indexed 0 sequences" />
             </assert_stdout>

tests/data/tools/ok_select_param.xml

@@ -13,10 +13,10 @@
     </outputs>
     <tests>
         <test>
-            <param name="select_opt" value="Hello World!" />
+            <param name="select_opt" value="moo" />
             <output name="output">
                 <assert_contents>
-                    <has_line line="Hello World!" />
+                    <has_line line="moo" />
                 </assert_contents>
             </output>
         </test>

tests/data/tools/url.xml

@@ -13,10 +13,10 @@
     </outputs>
     <tests>
         <test>
-            <param name="select_opt" value="Hello World!" />
+            <param name="select_opt" value="moo" />
             <output name="output">
                 <assert_contents>
-                    <has_line line="Hello World!" />
+                    <has_line line="moo" />
                 </assert_contents>
             </output>
         </test>

tests/shed_app.py

@@ -1,6 +1,4 @@
-""" Test app to emulate planemo-relevant portions of the
-the ToolShed API... for now :).
-"""
+"""Test app to emulate planemo-relevant portions of the ToolShedAPI... for now :)."""
 
 import json
 import os

tests/test_external_galaxy_commands.py

@@ -1,5 +1,4 @@
-"""Tests for planemo commands relating to external Galaxy instances
-"""
+"""Tests for planemo commands relating to external Galaxy instances"""
 
 import os
 

tests/test_lint.py

@@ -48,18 +48,18 @@ def test_lint_multiple(self):
         names = ["fail_citation.xml", "fail_order.xml"]
         paths = list(map(lambda p: os.path.join(TEST_TOOLS_DIR, p), names))
         self._check_exit_code(["lint"] + paths, exit_code=1)
-        self._check_exit_code(["lint", "--skip", "citations,xml_order"] + paths, exit_code=0)
+        self._check_exit_code(["lint", "--skip", "CitationsMissing,XMLOrder"] + paths, exit_code=0)
 
     def test_skips(self):
         fail_citation = os.path.join(TEST_TOOLS_DIR, "fail_citation.xml")
         lint_cmd = ["lint", fail_citation]
         self._check_exit_code(lint_cmd, exit_code=1)
 
-        lint_cmd = ["lint", "--skip", "citations", fail_citation]
+        lint_cmd = ["lint", "--skip", "CitationsMissing", fail_citation]
         self._check_exit_code(lint_cmd, exit_code=0)
 
         # Check string splitting and stuff.
-        lint_cmd = ["lint", "--skip", "xml_order, citations", fail_citation]
+        lint_cmd = ["lint", "--skip", "XMLOrder, CitationsMissing", fail_citation]
         self._check_exit_code(lint_cmd, exit_code=0)
 
         # Check skip_file (containing the same skips)
@@ -71,16 +71,16 @@ def test_recursive(self):
         nested_dir = os.path.join(TEST_REPOS_DIR, "multi_repos_nested")
 
         # Fails to find any tools without -r.
-        lint_cmd = ["lint", "--skip", "citations", nested_dir]
+        lint_cmd = ["lint", "--skip", "CitationsMissing", nested_dir]
         self._check_exit_code(lint_cmd, exit_code=2)
 
         # Works with -r.
-        lint_cmd = ["lint", "--skip", "citations", "-r", nested_dir]
+        lint_cmd = ["lint", "--skip", "CitationsMissing", "-r", nested_dir]
         self._check_exit_code(lint_cmd, exit_code=0)
 
     def test_empty_cdata(self):
         empty_cdata = os.path.join(TEST_TOOLS_DIR, "empty_cdata.xml")
-        lint_cmd = ["lint", "--skip", "citations,help", empty_cdata]
+        lint_cmd = ["lint", "--skip", "HelpEmpty", empty_cdata]
         self._check_exit_code(lint_cmd, exit_code=0)
 
     def test_lint_doi(self):

tests/test_normalize.py

@@ -1,5 +1,4 @@
-""" Integration tests for normalize command.
-"""
+"""Integration tests for normalize command."""
 
 import os
 

tests/test_shed.py

@@ -1,5 +1,4 @@
-"""
-"""
+""" """
 
 import os
 import random

tests/test_shed_diff.py

@@ -1,5 +1,4 @@
-""" Integration tests for shed_diff command.
-"""
+"""Integration tests for shed_diff command."""
 
 import os
 import sys