From 79660bb58d13df709a211eb45830bb5cc13d16ff Mon Sep 17 00:00:00 2001 From: Sergey Golitsynskiy Date: Sat, 6 Jul 2019 11:44:03 +0200 Subject: [PATCH] Move linters from tools into tool_util Also, update setup.py for tool_util package. Ref: https://github.com/galaxyproject/galaxy/issues/8240 Note: `make updaterst` has not been run; waiting on https://github.com/galaxyproject/galaxy/pull/8270 --- lib/galaxy/{tools => tool_util}/lint.py | 4 ++-- lib/galaxy/{tools => tool_util}/linters/__init__.py | 0 lib/galaxy/{tools/lint_util.py => tool_util/linters/_util.py} | 0 lib/galaxy/{tools => tool_util}/linters/citations.py | 0 lib/galaxy/{tools => tool_util}/linters/command.py | 0 lib/galaxy/{tools => tool_util}/linters/cwl.py | 0 lib/galaxy/{tools => tool_util}/linters/general.py | 0 lib/galaxy/{tools => tool_util}/linters/help.py | 0 lib/galaxy/{tools => tool_util}/linters/inputs.py | 2 +- lib/galaxy/{tools => tool_util}/linters/outputs.py | 0 lib/galaxy/{tools => tool_util}/linters/stdio.py | 0 lib/galaxy/{tools => tool_util}/linters/tests.py | 2 +- lib/galaxy/{tools => tool_util}/linters/xml_order.py | 0 packages/tool_util/setup.py | 1 + 14 files changed, 5 insertions(+), 4 deletions(-) rename lib/galaxy/{tools => tool_util}/lint.py (97%) rename lib/galaxy/{tools => tool_util}/linters/__init__.py (100%) rename lib/galaxy/{tools/lint_util.py => tool_util/linters/_util.py} (100%) rename lib/galaxy/{tools => tool_util}/linters/citations.py (100%) rename lib/galaxy/{tools => tool_util}/linters/command.py (100%) rename lib/galaxy/{tools => tool_util}/linters/cwl.py (100%) rename lib/galaxy/{tools => tool_util}/linters/general.py (100%) rename lib/galaxy/{tools => tool_util}/linters/help.py (100%) rename lib/galaxy/{tools => tool_util}/linters/inputs.py (99%) rename lib/galaxy/{tools => tool_util}/linters/outputs.py (100%) rename lib/galaxy/{tools => tool_util}/linters/stdio.py (100%) rename lib/galaxy/{tools => tool_util}/linters/tests.py (98%) rename lib/galaxy/{tools => tool_util}/linters/xml_order.py (100%) diff --git a/lib/galaxy/tools/lint.py b/lib/galaxy/tool_util/lint.py similarity index 97% rename from lib/galaxy/tools/lint.py rename to lib/galaxy/tool_util/lint.py index 7a808dad744..fee04c77ea0 100644 --- a/lib/galaxy/tools/lint.py +++ b/lib/galaxy/tool_util/lint.py @@ -28,9 +28,9 @@ def lint_xml(tool_xml, level=LEVEL_ALL, fail_level=LEVEL_WARN, extra_modules=[], def lint_tool_source_with(lint_context, tool_source, extra_modules=[]): - import galaxy.tools.linters + import galaxy.tool_util.linters tool_xml = getattr(tool_source, "xml_tree", None) - linter_modules = submodules.import_submodules(galaxy.tools.linters, ordered=True) + linter_modules = submodules.import_submodules(galaxy.tool_util.linters, ordered=True) linter_modules.extend(extra_modules) for module in linter_modules: tool_type = tool_source.parse_tool_type() or "default" diff --git a/lib/galaxy/tools/linters/__init__.py b/lib/galaxy/tool_util/linters/__init__.py similarity index 100% rename from lib/galaxy/tools/linters/__init__.py rename to lib/galaxy/tool_util/linters/__init__.py diff --git a/lib/galaxy/tools/lint_util.py b/lib/galaxy/tool_util/linters/_util.py similarity index 100% rename from lib/galaxy/tools/lint_util.py rename to lib/galaxy/tool_util/linters/_util.py diff --git a/lib/galaxy/tools/linters/citations.py b/lib/galaxy/tool_util/linters/citations.py similarity index 100% rename from lib/galaxy/tools/linters/citations.py rename to lib/galaxy/tool_util/linters/citations.py diff --git a/lib/galaxy/tools/linters/command.py b/lib/galaxy/tool_util/linters/command.py similarity index 100% rename from lib/galaxy/tools/linters/command.py rename to lib/galaxy/tool_util/linters/command.py diff --git a/lib/galaxy/tools/linters/cwl.py b/lib/galaxy/tool_util/linters/cwl.py similarity index 100% rename from lib/galaxy/tools/linters/cwl.py rename to lib/galaxy/tool_util/linters/cwl.py diff --git a/lib/galaxy/tools/linters/general.py b/lib/galaxy/tool_util/linters/general.py similarity index 100% rename from lib/galaxy/tools/linters/general.py rename to lib/galaxy/tool_util/linters/general.py diff --git a/lib/galaxy/tools/linters/help.py b/lib/galaxy/tool_util/linters/help.py similarity index 100% rename from lib/galaxy/tools/linters/help.py rename to lib/galaxy/tool_util/linters/help.py diff --git a/lib/galaxy/tools/linters/inputs.py b/lib/galaxy/tool_util/linters/inputs.py similarity index 99% rename from lib/galaxy/tools/linters/inputs.py rename to lib/galaxy/tool_util/linters/inputs.py index ffcc5c974d5..542320ef9b1 100644 --- a/lib/galaxy/tools/linters/inputs.py +++ b/lib/galaxy/tool_util/linters/inputs.py @@ -1,6 +1,6 @@ """This module contains a linting functions for tool inputs.""" from galaxy.util import string_as_bool -from ..lint_util import is_datasource +from ._util import is_datasource def lint_inputs(tool_xml, lint_ctx): diff --git a/lib/galaxy/tools/linters/outputs.py b/lib/galaxy/tool_util/linters/outputs.py similarity index 100% rename from lib/galaxy/tools/linters/outputs.py rename to lib/galaxy/tool_util/linters/outputs.py diff --git a/lib/galaxy/tools/linters/stdio.py b/lib/galaxy/tool_util/linters/stdio.py similarity index 100% rename from lib/galaxy/tools/linters/stdio.py rename to lib/galaxy/tool_util/linters/stdio.py diff --git a/lib/galaxy/tools/linters/tests.py b/lib/galaxy/tool_util/linters/tests.py similarity index 98% rename from lib/galaxy/tools/linters/tests.py rename to lib/galaxy/tool_util/linters/tests.py index aca2351e7a8..8fc60317419 100644 --- a/lib/galaxy/tools/linters/tests.py +++ b/lib/galaxy/tool_util/linters/tests.py @@ -1,5 +1,5 @@ """This module contains a linting functions for tool tests.""" -from ..lint_util import is_datasource +from ._util import is_datasource # Misspelled so as not be picked up by nosetests. diff --git a/lib/galaxy/tools/linters/xml_order.py b/lib/galaxy/tool_util/linters/xml_order.py similarity index 100% rename from lib/galaxy/tools/linters/xml_order.py rename to lib/galaxy/tool_util/linters/xml_order.py diff --git a/packages/tool_util/setup.py b/packages/tool_util/setup.py index 33bf10b7794..3a07bdc2b5c 100644 --- a/packages/tool_util/setup.py +++ b/packages/tool_util/setup.py @@ -37,6 +37,7 @@ PACKAGES = [ 'galaxy.tool_util.deps.container_resolvers', 'galaxy.tool_util.deps.mulled', 'galaxy.tool_util.deps.resolvers', + 'galaxy.tool_util.linters', 'galaxy.tool_util.locations', 'galaxy.tool_util.parser', ]