From 1cfe3037e342af42eaa216e23a810d77ebafaf4a Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Wed, 3 Apr 2024 12:17:07 +0200 Subject: [PATCH 1/5] bump galaxy packages to allow for 24.0 --- requirements.txt | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/requirements.txt b/requirements.txt index c6887d07b..ea8e2c974 100644 --- a/requirements.txt +++ b/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>=23.1,<24.0 -galaxy-util[template]>=23.1,<24.0 +galaxy-tool-util>=23.1,<24.1 +galaxy-util[template]>=23.1,<24.1 glob2 gxformat2>=0.14.0 h5py From 011f332b85cf9059e7438e0ddeb2dd4c438c3c4b Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Thu, 2 May 2024 16:35:25 +0200 Subject: [PATCH 2/5] adapt linter names in tests --- tests/test_lint.py | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/tests/test_lint.py b/tests/test_lint.py index dc8ec9aff..2d5e52ccc 100644 --- a/tests/test_lint.py +++ b/tests/test_lint.py @@ -39,7 +39,7 @@ def test_fail_tools(self): def test_lint_default(self): with self._isolate_repo("single_tool"): - self._check_exit_code(["lint", "--skip", "citations"]) + self._check_exit_code(["lint", "--skip", "CitationsMissing"]) with self._isolate_repo("single_tool"): self._check_exit_code(["lint"], exit_code=1) @@ -47,34 +47,34 @@ 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) 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", "CitationsMissing,HelpEmpty", empty_cdata] self._check_exit_code(lint_cmd, exit_code=0) def test_lint_doi(self): From 6113107f999b53629f703b12c51f01fb714ea844 Mon Sep 17 00:00:00 2001 From: M Bernt Date: Fri, 3 May 2024 16:43:15 +0200 Subject: [PATCH 3/5] Test skip-name-restore branch Co-authored-by: Marius van den Beek --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index ea8e2c974..350b3a081 100644 --- a/requirements.txt +++ b/requirements.txt @@ -3,7 +3,7 @@ bioblend>=1.0.0 click!=8.0.2 cwltool>=1.0.20191225192155 ephemeris>=0.10.3 -galaxy-tool-util>=23.1,<24.1 +galaxy-tool-util @ git+https://github.com/bernt-matthias/galaxy.git@skip-name-restore#egg=galaxy-tool-util&subdirectory=packages/tool_util galaxy-util[template]>=23.1,<24.1 glob2 gxformat2>=0.14.0 From 0b7522baf4f43d969cf7c69f4ec90d864449b134 Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Fri, 3 May 2024 17:11:02 +0200 Subject: [PATCH 4/5] Revert "adapt linter names in tests" This reverts commit d323516c44af586e88824f07530b3e09c97a0f9b. --- tests/test_lint.py | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/tests/test_lint.py b/tests/test_lint.py index 2d5e52ccc..dc8ec9aff 100644 --- a/tests/test_lint.py +++ b/tests/test_lint.py @@ -39,7 +39,7 @@ def test_fail_tools(self): def test_lint_default(self): with self._isolate_repo("single_tool"): - self._check_exit_code(["lint", "--skip", "CitationsMissing"]) + self._check_exit_code(["lint", "--skip", "citations"]) with self._isolate_repo("single_tool"): self._check_exit_code(["lint"], exit_code=1) @@ -47,34 +47,34 @@ 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", "CitationsMissing,XMLOrder"] + paths, exit_code=0) + self._check_exit_code(["lint", "--skip", "citations,xml_order"] + 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", "CitationsMissing", fail_citation] + lint_cmd = ["lint", "--skip", "citations", fail_citation] self._check_exit_code(lint_cmd, exit_code=0) # Check string splitting and stuff. - lint_cmd = ["lint", "--skip", "XMLOrder, CitationsMissing", fail_citation] + lint_cmd = ["lint", "--skip", "xml_order, citations", fail_citation] self._check_exit_code(lint_cmd, exit_code=0) 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", "CitationsMissing", nested_dir] + lint_cmd = ["lint", "--skip", "citations", nested_dir] self._check_exit_code(lint_cmd, exit_code=2) # Works with -r. - lint_cmd = ["lint", "--skip", "CitationsMissing", "-r", nested_dir] + lint_cmd = ["lint", "--skip", "citations", "-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", "CitationsMissing,HelpEmpty", empty_cdata] + lint_cmd = ["lint", "--skip", "citations,help", empty_cdata] self._check_exit_code(lint_cmd, exit_code=0) def test_lint_doi(self): From a429767521b6998dba539211ec13812564b86ae1 Mon Sep 17 00:00:00 2001 From: Marius van den Beek Date: Tue, 7 May 2024 16:53:50 +0200 Subject: [PATCH 5/5] Exclude 24.0.0 and 24.0.1 Since they each had linting issues --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 350b3a081..e10afa480 100644 --- a/requirements.txt +++ b/requirements.txt @@ -3,7 +3,7 @@ bioblend>=1.0.0 click!=8.0.2 cwltool>=1.0.20191225192155 ephemeris>=0.10.3 -galaxy-tool-util @ git+https://github.com/bernt-matthias/galaxy.git@skip-name-restore#egg=galaxy-tool-util&subdirectory=packages/tool_util +galaxy-tool-util>=23.1,!=24.0.0,!=24.0.1,<24.1 galaxy-util[template]>=23.1,<24.1 glob2 gxformat2>=0.14.0