2025-12-13T03:59:32,776 Created temporary directory: /tmp/pip-ephem-wheel-cache-zntir_z4 2025-12-13T03:59:32,778 Created temporary directory: /tmp/pip-build-tracker-sj62fjlv 2025-12-13T03:59:32,779 Initialized build tracking at /tmp/pip-build-tracker-sj62fjlv 2025-12-13T03:59:32,779 Created build tracker: /tmp/pip-build-tracker-sj62fjlv 2025-12-13T03:59:32,780 Entered build tracker: /tmp/pip-build-tracker-sj62fjlv 2025-12-13T03:59:32,781 Created temporary directory: /tmp/pip-wheel-gnqde7az 2025-12-13T03:59:32,784 DEPRECATION: --no-binary currently disables reading from the cache of locally built wheels. In the future --no-binary will not influence the wheel cache. pip 23.1 will enforce this behaviour change. A possible replacement is to use the --no-cache-dir option. You can use the flag --use-feature=no-binary-enable-wheel-cache to test the upcoming behaviour. 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https://archive1.piwheels.org/simple/galaxy-tool-util/galaxy_tool_util-19.9.0-py2.py3-none-any.whl#sha256=b9ae70a1744abff6164cab3304cf279e8683944b8cf2d95c26f6df7dfe9eb4c5 (from https://www.piwheels.org/simple/galaxy-tool-util/) 2025-12-13T03:59:33,408 Skipping link: No binaries permitted for galaxy-tool-util: https://archive1.piwheels.org/simple/galaxy-tool-util/galaxy_tool_util-19.9.0.dev5-py2.py3-none-any.whl#sha256=f869574a225f69e7b51f6dba165eec4a58fe6c76d45924aecd9cc44e6513ad77 (from https://www.piwheels.org/simple/galaxy-tool-util/) 2025-12-13T03:59:33,409 Skipping link: No binaries permitted for galaxy-tool-util: https://archive1.piwheels.org/simple/galaxy-tool-util/galaxy_tool_util-19.9.0.dev4-py2.py3-none-any.whl#sha256=f8287860bf6f524db3bd2d9096b97595aecea1a1e321065d5e36d971f5cd7b79 (from https://www.piwheels.org/simple/galaxy-tool-util/) 2025-12-13T03:59:33,410 Skipping link: No binaries permitted for galaxy-tool-util: https://archive1.piwheels.org/simple/galaxy-tool-util/galaxy_tool_util-19.9.0.dev3-py2.py3-none-any.whl#sha256=c11cefb2c969b6e74729ae125693e5bf5401218df9615d22a68b3a5d8ce68122 (from https://www.piwheels.org/simple/galaxy-tool-util/) 2025-12-13T03:59:33,411 Skipping link: No binaries permitted for galaxy-tool-util: https://archive1.piwheels.org/simple/galaxy-tool-util/galaxy_tool_util-19.9.0.dev2-py2.py3-none-any.whl#sha256=62e79b75dc27fa398c1e33a336b253d18de3fc94880fe567b3ee01fd081c6d5c (from https://www.piwheels.org/simple/galaxy-tool-util/) 2025-12-13T03:59:33,412 Skipping link: No binaries permitted for galaxy-tool-util: https://archive1.piwheels.org/simple/galaxy-tool-util/galaxy_tool_util-19.9.0.dev1-py2.py3-none-any.whl#sha256=7ff286949cb2c87a462ef1360b4ff58a3d0fc953dfde646f2b23bc9438d63ada (from https://www.piwheels.org/simple/galaxy-tool-util/) 2025-12-13T03:59:33,412 Skipping link: No binaries permitted for galaxy-tool-util: https://archive1.piwheels.org/simple/galaxy-tool-util/galaxy_tool_util-19.9.0.dev0-py3-none-any.whl#sha256=f3257799e554be8d31f640710ed8672994323cbfda020a3648775c6d156fad4a (from https://www.piwheels.org/simple/galaxy-tool-util/) 2025-12-13T03:59:33,413 Skipping link: not a file: https://www.piwheels.org/simple/galaxy-tool-util/ 2025-12-13T03:59:33,414 Skipping link: not a file: https://pypi.org/simple/galaxy-tool-util/ 2025-12-13T03:59:33,445 Given no hashes to check 1 links for project 'galaxy-tool-util': discarding no candidates 2025-12-13T03:59:33,463 Collecting galaxy-tool-util==25.1.dev0 2025-12-13T03:59:33,465 Created temporary directory: /tmp/pip-unpack-qmo0axky 2025-12-13T03:59:33,601 Downloading galaxy_tool_util-25.1.dev0.tar.gz (469 kB) 2025-12-13T03:59:34,105 Added galaxy-tool-util==25.1.dev0 from https://files.pythonhosted.org/packages/8f/f2/0b92d78f3e61ec3fbe5b8ae071ef3578288e33ee8dfc22894bdec80dcb7a/galaxy_tool_util-25.1.dev0.tar.gz to build tracker '/tmp/pip-build-tracker-sj62fjlv' 2025-12-13T03:59:34,108 Created temporary directory: /tmp/pip-build-env-7i3bxzcx 2025-12-13T03:59:34,112 Installing build dependencies: started 2025-12-13T03:59:34,113 Running command pip subprocess to install build dependencies 2025-12-13T03:59:35,241 Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11) 2025-12-13T03:59:35,882 DEPRECATION: --no-binary currently disables reading from the cache of locally built wheels. In the future --no-binary will not influence the wheel cache. pip 23.1 will enforce this behaviour change. A possible replacement is to use the --no-cache-dir option. You can use the flag --use-feature=no-binary-enable-wheel-cache to test the upcoming behaviour. Discussion can be found at https://github.com/pypa/pip/issues/11453 2025-12-13T03:59:35,906 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-12-13T03:59:37,630 Collecting setuptools 2025-12-13T03:59:37,752 Using cached https://www.piwheels.org/simple/setuptools/setuptools-80.9.0-py3-none-any.whl (1.2 MB) 2025-12-13T03:59:40,652 Installing collected packages: setuptools 2025-12-13T03:59:44,325 Successfully installed setuptools-80.9.0 2025-12-13T03:59:44,591 Installing build dependencies: finished with status 'done' 2025-12-13T03:59:44,598 Getting requirements to build wheel: started 2025-12-13T03:59:44,599 Running command Getting requirements to build wheel 2025-12-13T03:59:45,193 /tmp/pip-build-env-7i3bxzcx/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-12-13T03:59:45,193 !! 2025-12-13T03:59:45,194 ******************************************************************************** 2025-12-13T03:59:45,195 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-12-13T03:59:45,196 License :: OSI Approved :: Academic Free License (AFL) 2025-12-13T03:59:45,197 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-12-13T03:59:45,198 ******************************************************************************** 2025-12-13T03:59:45,199 !! 2025-12-13T03:59:45,200 self._finalize_license_expression() 2025-12-13T03:59:45,261 running egg_info 2025-12-13T03:59:45,268 writing galaxy_tool_util.egg-info/PKG-INFO 2025-12-13T03:59:45,277 writing dependency_links to galaxy_tool_util.egg-info/dependency_links.txt 2025-12-13T03:59:45,280 writing entry points to galaxy_tool_util.egg-info/entry_points.txt 2025-12-13T03:59:45,284 writing requirements to galaxy_tool_util.egg-info/requires.txt 2025-12-13T03:59:45,285 writing top-level names to galaxy_tool_util.egg-info/top_level.txt 2025-12-13T03:59:45,342 reading manifest file 'galaxy_tool_util.egg-info/SOURCES.txt' 2025-12-13T03:59:45,354 reading manifest template 'MANIFEST.in' 2025-12-13T03:59:45,360 adding license file 'LICENSE' 2025-12-13T03:59:45,370 writing manifest file 'galaxy_tool_util.egg-info/SOURCES.txt' 2025-12-13T03:59:45,461 Getting requirements to build wheel: finished with status 'done' 2025-12-13T03:59:45,465 Created temporary directory: /tmp/pip-modern-metadata-hnw2yliv 2025-12-13T03:59:45,467 Preparing metadata (pyproject.toml): started 2025-12-13T03:59:45,469 Running command Preparing metadata (pyproject.toml) 2025-12-13T03:59:46,028 /tmp/pip-build-env-7i3bxzcx/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-12-13T03:59:46,028 !! 2025-12-13T03:59:46,030 ******************************************************************************** 2025-12-13T03:59:46,030 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-12-13T03:59:46,031 License :: OSI Approved :: Academic Free License (AFL) 2025-12-13T03:59:46,032 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-12-13T03:59:46,033 ******************************************************************************** 2025-12-13T03:59:46,034 !! 2025-12-13T03:59:46,034 self._finalize_license_expression() 2025-12-13T03:59:46,055 running dist_info 2025-12-13T03:59:46,067 creating /tmp/pip-modern-metadata-hnw2yliv/galaxy_tool_util.egg-info 2025-12-13T03:59:46,068 writing /tmp/pip-modern-metadata-hnw2yliv/galaxy_tool_util.egg-info/PKG-INFO 2025-12-13T03:59:46,079 writing dependency_links to /tmp/pip-modern-metadata-hnw2yliv/galaxy_tool_util.egg-info/dependency_links.txt 2025-12-13T03:59:46,081 writing entry points to /tmp/pip-modern-metadata-hnw2yliv/galaxy_tool_util.egg-info/entry_points.txt 2025-12-13T03:59:46,084 writing requirements to /tmp/pip-modern-metadata-hnw2yliv/galaxy_tool_util.egg-info/requires.txt 2025-12-13T03:59:46,085 writing top-level names to /tmp/pip-modern-metadata-hnw2yliv/galaxy_tool_util.egg-info/top_level.txt 2025-12-13T03:59:46,087 writing manifest file '/tmp/pip-modern-metadata-hnw2yliv/galaxy_tool_util.egg-info/SOURCES.txt' 2025-12-13T03:59:46,139 reading manifest file '/tmp/pip-modern-metadata-hnw2yliv/galaxy_tool_util.egg-info/SOURCES.txt' 2025-12-13T03:59:46,141 reading manifest template 'MANIFEST.in' 2025-12-13T03:59:46,146 adding license file 'LICENSE' 2025-12-13T03:59:46,154 writing manifest file '/tmp/pip-modern-metadata-hnw2yliv/galaxy_tool_util.egg-info/SOURCES.txt' 2025-12-13T03:59:46,156 creating '/tmp/pip-modern-metadata-hnw2yliv/galaxy_tool_util-25.1.dev0.dist-info' 2025-12-13T03:59:46,304 Preparing metadata (pyproject.toml): finished with status 'done' 2025-12-13T03:59:46,311 Source in /tmp/pip-wheel-gnqde7az/galaxy-tool-util_ca751e6df74744dbb060413aa8406913 has version 25.1.dev0, which satisfies requirement galaxy-tool-util==25.1.dev0 from https://files.pythonhosted.org/packages/8f/f2/0b92d78f3e61ec3fbe5b8ae071ef3578288e33ee8dfc22894bdec80dcb7a/galaxy_tool_util-25.1.dev0.tar.gz 2025-12-13T03:59:46,312 Removed galaxy-tool-util==25.1.dev0 from https://files.pythonhosted.org/packages/8f/f2/0b92d78f3e61ec3fbe5b8ae071ef3578288e33ee8dfc22894bdec80dcb7a/galaxy_tool_util-25.1.dev0.tar.gz from build tracker '/tmp/pip-build-tracker-sj62fjlv' 2025-12-13T03:59:46,321 Created temporary directory: /tmp/pip-unpack-jxn8n704 2025-12-13T03:59:46,322 Building wheels for collected packages: galaxy-tool-util 2025-12-13T03:59:46,327 Created temporary directory: /tmp/pip-wheel-_w_qr8yf 2025-12-13T03:59:46,328 Destination directory: /tmp/pip-wheel-_w_qr8yf 2025-12-13T03:59:46,330 Building wheel for galaxy-tool-util (pyproject.toml): started 2025-12-13T03:59:46,331 Running command Building wheel for galaxy-tool-util (pyproject.toml) 2025-12-13T03:59:46,873 /tmp/pip-build-env-7i3bxzcx/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-12-13T03:59:46,873 !! 2025-12-13T03:59:46,874 ******************************************************************************** 2025-12-13T03:59:46,875 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-12-13T03:59:46,876 License :: OSI Approved :: Academic Free License (AFL) 2025-12-13T03:59:46,877 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-12-13T03:59:46,878 ******************************************************************************** 2025-12-13T03:59:46,879 !! 2025-12-13T03:59:46,880 self._finalize_license_expression() 2025-12-13T03:59:46,903 running bdist_wheel 2025-12-13T03:59:46,933 running build 2025-12-13T03:59:46,934 running build_py 2025-12-13T03:59:46,943 creating build/lib/galaxy 2025-12-13T03:59:46,945 copying galaxy/__init__.py -> build/lib/galaxy 2025-12-13T03:59:46,948 creating build/lib/galaxy/tool_util 2025-12-13T03:59:46,949 copying galaxy/tool_util/lint.py -> build/lib/galaxy/tool_util 2025-12-13T03:59:46,952 copying galaxy/tool_util/loader_directory.py -> build/lib/galaxy/tool_util 2025-12-13T03:59:46,954 copying galaxy/tool_util/model_factory.py -> build/lib/galaxy/tool_util 2025-12-13T03:59:46,956 copying galaxy/tool_util/provided_metadata.py -> build/lib/galaxy/tool_util 2025-12-13T03:59:46,958 copying galaxy/tool_util/__init__.py -> build/lib/galaxy/tool_util 2025-12-13T03:59:46,960 copying galaxy/tool_util/fetcher.py -> build/lib/galaxy/tool_util 2025-12-13T03:59:46,962 copying galaxy/tool_util/output_checker.py -> build/lib/galaxy/tool_util 2025-12-13T03:59:46,964 copying galaxy/tool_util/edam_util.py -> build/lib/galaxy/tool_util 2025-12-13T03:59:46,966 copying galaxy/tool_util/validate_test_format.py -> build/lib/galaxy/tool_util 2025-12-13T03:59:46,968 copying galaxy/tool_util/loader.py -> build/lib/galaxy/tool_util 2025-12-13T03:59:46,970 copying galaxy/tool_util/version.py -> build/lib/galaxy/tool_util 2025-12-13T03:59:46,973 creating build/lib/galaxy/tool_util/verify 2025-12-13T03:59:46,974 copying galaxy/tool_util/verify/test_data.py -> build/lib/galaxy/tool_util/verify 2025-12-13T03:59:46,977 copying galaxy/tool_util/verify/codegen.py -> build/lib/galaxy/tool_util/verify 2025-12-13T03:59:46,980 copying galaxy/tool_util/verify/interactor.py -> build/lib/galaxy/tool_util/verify 2025-12-13T03:59:46,984 copying galaxy/tool_util/verify/script.py -> build/lib/galaxy/tool_util/verify 2025-12-13T03:59:46,987 copying galaxy/tool_util/verify/__init__.py -> build/lib/galaxy/tool_util/verify 2025-12-13T03:59:46,990 copying galaxy/tool_util/verify/_types.py -> build/lib/galaxy/tool_util/verify 2025-12-13T03:59:46,992 copying galaxy/tool_util/verify/parse.py -> build/lib/galaxy/tool_util/verify 2025-12-13T03:59:46,995 copying galaxy/tool_util/verify/wait.py -> build/lib/galaxy/tool_util/verify 2025-12-13T03:59:46,997 creating build/lib/galaxy/tool_util/cwl 2025-12-13T03:59:46,998 copying galaxy/tool_util/cwl/schema.py -> build/lib/galaxy/tool_util/cwl 2025-12-13T03:59:47,001 copying galaxy/tool_util/cwl/util.py -> build/lib/galaxy/tool_util/cwl 2025-12-13T03:59:47,003 copying galaxy/tool_util/cwl/runtime_actions.py -> build/lib/galaxy/tool_util/cwl 2025-12-13T03:59:47,006 copying galaxy/tool_util/cwl/representation.py -> build/lib/galaxy/tool_util/cwl 2025-12-13T03:59:47,009 copying galaxy/tool_util/cwl/parser.py -> build/lib/galaxy/tool_util/cwl 2025-12-13T03:59:47,012 copying galaxy/tool_util/cwl/__init__.py -> build/lib/galaxy/tool_util/cwl 2025-12-13T03:59:47,014 copying galaxy/tool_util/cwl/runnable.py -> build/lib/galaxy/tool_util/cwl 2025-12-13T03:59:47,016 copying galaxy/tool_util/cwl/cwltool_deps.py -> build/lib/galaxy/tool_util/cwl 2025-12-13T03:59:47,019 creating build/lib/galaxy/tool_util/deps 2025-12-13T03:59:47,021 copying galaxy/tool_util/deps/dockerfiles.py -> build/lib/galaxy/tool_util/deps 2025-12-13T03:59:47,023 copying galaxy/tool_util/deps/installable.py -> build/lib/galaxy/tool_util/deps 2025-12-13T03:59:47,025 copying galaxy/tool_util/deps/conda_compat.py -> build/lib/galaxy/tool_util/deps 2025-12-13T03:59:47,027 copying galaxy/tool_util/deps/container_volumes.py -> build/lib/galaxy/tool_util/deps 2025-12-13T03:59:47,029 copying galaxy/tool_util/deps/requirements.py -> build/lib/galaxy/tool_util/deps 2025-12-13T03:59:47,032 copying galaxy/tool_util/deps/conda_util.py -> build/lib/galaxy/tool_util/deps 2025-12-13T03:59:47,035 copying galaxy/tool_util/deps/__init__.py -> build/lib/galaxy/tool_util/deps 2025-12-13T03:59:47,038 copying galaxy/tool_util/deps/docker_util.py -> build/lib/galaxy/tool_util/deps 2025-12-13T03:59:47,041 copying galaxy/tool_util/deps/container_classes.py -> build/lib/galaxy/tool_util/deps 2025-12-13T03:59:47,044 copying galaxy/tool_util/deps/commands.py -> build/lib/galaxy/tool_util/deps 2025-12-13T03:59:47,045 copying galaxy/tool_util/deps/containers.py -> build/lib/galaxy/tool_util/deps 2025-12-13T03:59:47,048 copying galaxy/tool_util/deps/views.py -> build/lib/galaxy/tool_util/deps 2025-12-13T03:59:47,051 copying galaxy/tool_util/deps/singularity_util.py -> build/lib/galaxy/tool_util/deps 2025-12-13T03:59:47,053 copying galaxy/tool_util/deps/dependencies.py -> build/lib/galaxy/tool_util/deps 2025-12-13T03:59:47,056 copying galaxy/tool_util/deps/brew_util.py -> build/lib/galaxy/tool_util/deps 2025-12-13T03:59:47,058 copying galaxy/tool_util/deps/brew_exts.py -> build/lib/galaxy/tool_util/deps 2025-12-13T03:59:47,061 creating build/lib/galaxy/tool_util/ontologies 2025-12-13T03:59:47,062 copying galaxy/tool_util/ontologies/ontology_data.py -> build/lib/galaxy/tool_util/ontologies 2025-12-13T03:59:47,064 copying galaxy/tool_util/ontologies/__init__.py -> build/lib/galaxy/tool_util/ontologies 2025-12-13T03:59:47,066 creating build/lib/galaxy/tool_util/client 2025-12-13T03:59:47,067 copying galaxy/tool_util/client/__init__.py -> build/lib/galaxy/tool_util/client 2025-12-13T03:59:47,068 copying galaxy/tool_util/client/staging.py -> build/lib/galaxy/tool_util/client 2025-12-13T03:59:47,071 copying galaxy/tool_util/client/landing.py -> build/lib/galaxy/tool_util/client 2025-12-13T03:59:47,074 creating build/lib/galaxy/tool_util/parameters 2025-12-13T03:59:47,075 copying galaxy/tool_util/parameters/visitor.py -> build/lib/galaxy/tool_util/parameters 2025-12-13T03:59:47,077 copying galaxy/tool_util/parameters/state.py -> build/lib/galaxy/tool_util/parameters 2025-12-13T03:59:47,080 copying galaxy/tool_util/parameters/__init__.py -> build/lib/galaxy/tool_util/parameters 2025-12-13T03:59:47,082 copying galaxy/tool_util/parameters/json.py -> build/lib/galaxy/tool_util/parameters 2025-12-13T03:59:47,084 copying galaxy/tool_util/parameters/case.py -> build/lib/galaxy/tool_util/parameters 2025-12-13T03:59:47,086 copying galaxy/tool_util/parameters/factory.py -> build/lib/galaxy/tool_util/parameters 2025-12-13T03:59:47,089 copying galaxy/tool_util/parameters/model_validation.py -> build/lib/galaxy/tool_util/parameters 2025-12-13T03:59:47,091 copying galaxy/tool_util/parameters/convert.py -> build/lib/galaxy/tool_util/parameters 2025-12-13T03:59:47,094 creating build/lib/galaxy/tool_util/toolbox 2025-12-13T03:59:47,095 copying galaxy/tool_util/toolbox/integrated_panel.py -> build/lib/galaxy/tool_util/toolbox 2025-12-13T03:59:47,098 copying galaxy/tool_util/toolbox/parser.py -> build/lib/galaxy/tool_util/toolbox 2025-12-13T03:59:47,101 copying galaxy/tool_util/toolbox/base.py -> build/lib/galaxy/tool_util/toolbox 2025-12-13T03:59:47,104 copying galaxy/tool_util/toolbox/panel.py -> build/lib/galaxy/tool_util/toolbox 2025-12-13T03:59:47,107 copying galaxy/tool_util/toolbox/__init__.py -> build/lib/galaxy/tool_util/toolbox 2025-12-13T03:59:47,109 copying galaxy/tool_util/toolbox/watcher.py -> build/lib/galaxy/tool_util/toolbox 2025-12-13T03:59:47,111 creating build/lib/galaxy/tool_util/biotools 2025-12-13T03:59:47,112 copying galaxy/tool_util/biotools/interface.py -> build/lib/galaxy/tool_util/biotools 2025-12-13T03:59:47,115 copying galaxy/tool_util/biotools/__init__.py -> build/lib/galaxy/tool_util/biotools 2025-12-13T03:59:47,116 copying galaxy/tool_util/biotools/source.py -> build/lib/galaxy/tool_util/biotools 2025-12-13T03:59:47,119 creating build/lib/galaxy/tool_util/upgrade 2025-12-13T03:59:47,120 copying galaxy/tool_util/upgrade/script.py -> build/lib/galaxy/tool_util/upgrade 2025-12-13T03:59:47,123 copying galaxy/tool_util/upgrade/__init__.py -> build/lib/galaxy/tool_util/upgrade 2025-12-13T03:59:47,125 creating build/lib/galaxy/tool_util/unittest_utils 2025-12-13T03:59:47,126 copying galaxy/tool_util/unittest_utils/interactor.py -> build/lib/galaxy/tool_util/unittest_utils 2025-12-13T03:59:47,129 copying galaxy/tool_util/unittest_utils/__init__.py -> build/lib/galaxy/tool_util/unittest_utils 2025-12-13T03:59:47,130 copying galaxy/tool_util/unittest_utils/parameters.py -> build/lib/galaxy/tool_util/unittest_utils 2025-12-13T03:59:47,132 copying galaxy/tool_util/unittest_utils/sample_data.py -> build/lib/galaxy/tool_util/unittest_utils 2025-12-13T03:59:47,135 creating build/lib/galaxy/tool_util/locations 2025-12-13T03:59:47,136 copying galaxy/tool_util/locations/http.py -> build/lib/galaxy/tool_util/locations 2025-12-13T03:59:47,137 copying galaxy/tool_util/locations/file.py -> build/lib/galaxy/tool_util/locations 2025-12-13T03:59:47,139 copying galaxy/tool_util/locations/dockstore.py -> build/lib/galaxy/tool_util/locations 2025-12-13T03:59:47,141 copying galaxy/tool_util/locations/__init__.py -> build/lib/galaxy/tool_util/locations 2025-12-13T03:59:47,144 creating build/lib/galaxy/tool_util/linters 2025-12-13T03:59:47,145 copying galaxy/tool_util/linters/inputs.py -> build/lib/galaxy/tool_util/linters 2025-12-13T03:59:47,148 copying galaxy/tool_util/linters/stdio.py -> build/lib/galaxy/tool_util/linters 2025-12-13T03:59:47,150 copying galaxy/tool_util/linters/output.py -> build/lib/galaxy/tool_util/linters 2025-12-13T03:59:47,152 copying galaxy/tool_util/linters/command.py -> build/lib/galaxy/tool_util/linters 2025-12-13T03:59:47,154 copying galaxy/tool_util/linters/citations.py -> build/lib/galaxy/tool_util/linters 2025-12-13T03:59:47,156 copying galaxy/tool_util/linters/__init__.py -> build/lib/galaxy/tool_util/linters 2025-12-13T03:59:47,158 copying galaxy/tool_util/linters/help.py -> build/lib/galaxy/tool_util/linters 2025-12-13T03:59:47,160 copying galaxy/tool_util/linters/xml_order.py -> build/lib/galaxy/tool_util/linters 2025-12-13T03:59:47,162 copying galaxy/tool_util/linters/tests.py -> build/lib/galaxy/tool_util/linters 2025-12-13T03:59:47,165 copying galaxy/tool_util/linters/_util.py -> build/lib/galaxy/tool_util/linters 2025-12-13T03:59:47,167 copying galaxy/tool_util/linters/general.py -> build/lib/galaxy/tool_util/linters 2025-12-13T03:59:47,169 copying galaxy/tool_util/linters/cwl.py -> build/lib/galaxy/tool_util/linters 2025-12-13T03:59:47,171 copying galaxy/tool_util/linters/xsd.py -> build/lib/galaxy/tool_util/linters 2025-12-13T03:59:47,173 copying galaxy/tool_util/linters/datatypes.py -> build/lib/galaxy/tool_util/linters 2025-12-13T03:59:47,176 creating build/lib/galaxy/tool_util/parser 2025-12-13T03:59:47,177 copying galaxy/tool_util/parser/output_objects.py -> build/lib/galaxy/tool_util/parser 2025-12-13T03:59:47,180 copying galaxy/tool_util/parser/stdio.py -> build/lib/galaxy/tool_util/parser 2025-12-13T03:59:47,182 copying galaxy/tool_util/parser/util.py -> build/lib/galaxy/tool_util/parser 2025-12-13T03:59:47,184 copying galaxy/tool_util/parser/yaml.py -> build/lib/galaxy/tool_util/parser 2025-12-13T03:59:47,187 copying galaxy/tool_util/parser/interface.py -> build/lib/galaxy/tool_util/parser 2025-12-13T03:59:47,190 copying galaxy/tool_util/parser/__init__.py -> build/lib/galaxy/tool_util/parser 2025-12-13T03:59:47,192 copying galaxy/tool_util/parser/parameter_validators.py -> build/lib/galaxy/tool_util/parser 2025-12-13T03:59:47,194 copying galaxy/tool_util/parser/factory.py -> build/lib/galaxy/tool_util/parser 2025-12-13T03:59:47,197 copying galaxy/tool_util/parser/output_actions.py -> build/lib/galaxy/tool_util/parser 2025-12-13T03:59:47,200 copying galaxy/tool_util/parser/cwl.py -> build/lib/galaxy/tool_util/parser 2025-12-13T03:59:47,203 copying galaxy/tool_util/parser/output_collection_def.py -> build/lib/galaxy/tool_util/parser 2025-12-13T03:59:47,205 copying galaxy/tool_util/parser/xml.py -> build/lib/galaxy/tool_util/parser 2025-12-13T03:59:47,210 creating build/lib/galaxy/tool_util/data 2025-12-13T03:59:47,211 copying galaxy/tool_util/data/__init__.py -> build/lib/galaxy/tool_util/data 2025-12-13T03:59:47,214 copying galaxy/tool_util/data/_schema.py -> build/lib/galaxy/tool_util/data 2025-12-13T03:59:47,217 creating build/lib/galaxy/tool_util/verify/asserts 2025-12-13T03:59:47,218 copying galaxy/tool_util/verify/asserts/hdf5.py -> build/lib/galaxy/tool_util/verify/asserts 2025-12-13T03:59:47,220 copying galaxy/tool_util/verify/asserts/image.py -> build/lib/galaxy/tool_util/verify/asserts 2025-12-13T03:59:47,223 copying galaxy/tool_util/verify/asserts/archive.py -> build/lib/galaxy/tool_util/verify/asserts 2025-12-13T03:59:47,225 copying galaxy/tool_util/verify/asserts/__init__.py -> build/lib/galaxy/tool_util/verify/asserts 2025-12-13T03:59:47,227 copying galaxy/tool_util/verify/asserts/text.py -> build/lib/galaxy/tool_util/verify/asserts 2025-12-13T03:59:47,229 copying galaxy/tool_util/verify/asserts/json.py -> build/lib/galaxy/tool_util/verify/asserts 2025-12-13T03:59:47,232 copying galaxy/tool_util/verify/asserts/tabular.py -> build/lib/galaxy/tool_util/verify/asserts 2025-12-13T03:59:47,233 copying galaxy/tool_util/verify/asserts/_types.py -> build/lib/galaxy/tool_util/verify/asserts 2025-12-13T03:59:47,235 copying galaxy/tool_util/verify/asserts/_util.py -> build/lib/galaxy/tool_util/verify/asserts 2025-12-13T03:59:47,237 copying galaxy/tool_util/verify/asserts/size.py -> build/lib/galaxy/tool_util/verify/asserts 2025-12-13T03:59:47,239 copying galaxy/tool_util/verify/asserts/xml.py -> build/lib/galaxy/tool_util/verify/asserts 2025-12-13T03:59:47,242 creating build/lib/galaxy/tool_util/deps/mulled 2025-12-13T03:59:47,243 copying galaxy/tool_util/deps/mulled/util.py -> build/lib/galaxy/tool_util/deps/mulled 2025-12-13T03:59:47,246 copying galaxy/tool_util/deps/mulled/mulled_update_singularity_containers.py -> build/lib/galaxy/tool_util/deps/mulled 2025-12-13T03:59:47,249 copying galaxy/tool_util/deps/mulled/mulled_hash.py -> build/lib/galaxy/tool_util/deps/mulled 2025-12-13T03:59:47,251 copying galaxy/tool_util/deps/mulled/_cli.py -> build/lib/galaxy/tool_util/deps/mulled 2025-12-13T03:59:47,252 copying galaxy/tool_util/deps/mulled/mulled_build.py -> build/lib/galaxy/tool_util/deps/mulled 2025-12-13T03:59:47,255 copying galaxy/tool_util/deps/mulled/__init__.py -> build/lib/galaxy/tool_util/deps/mulled 2025-12-13T03:59:47,257 copying galaxy/tool_util/deps/mulled/mulled_build_files.py -> build/lib/galaxy/tool_util/deps/mulled 2025-12-13T03:59:47,259 copying galaxy/tool_util/deps/mulled/get_tests.py -> build/lib/galaxy/tool_util/deps/mulled 2025-12-13T03:59:47,262 copying galaxy/tool_util/deps/mulled/mulled_list.py -> build/lib/galaxy/tool_util/deps/mulled 2025-12-13T03:59:47,264 copying galaxy/tool_util/deps/mulled/mulled_search.py -> build/lib/galaxy/tool_util/deps/mulled 2025-12-13T03:59:47,267 copying galaxy/tool_util/deps/mulled/mulled_build_channel.py -> build/lib/galaxy/tool_util/deps/mulled 2025-12-13T03:59:47,269 copying galaxy/tool_util/deps/mulled/mulled_build_tool.py -> build/lib/galaxy/tool_util/deps/mulled 2025-12-13T03:59:47,272 creating build/lib/galaxy/tool_util/deps/resolvers 2025-12-13T03:59:47,273 copying galaxy/tool_util/deps/resolvers/galaxy_packages.py -> build/lib/galaxy/tool_util/deps/resolvers 2025-12-13T03:59:47,275 copying galaxy/tool_util/deps/resolvers/tool_shed_packages.py -> build/lib/galaxy/tool_util/deps/resolvers 2025-12-13T03:59:47,277 copying galaxy/tool_util/deps/resolvers/resolver_mixins.py -> build/lib/galaxy/tool_util/deps/resolvers 2025-12-13T03:59:47,279 copying galaxy/tool_util/deps/resolvers/unlinked_tool_shed_packages.py -> build/lib/galaxy/tool_util/deps/resolvers 2025-12-13T03:59:47,282 copying galaxy/tool_util/deps/resolvers/__init__.py -> build/lib/galaxy/tool_util/deps/resolvers 2025-12-13T03:59:47,284 copying galaxy/tool_util/deps/resolvers/lmod.py -> build/lib/galaxy/tool_util/deps/resolvers 2025-12-13T03:59:47,287 copying galaxy/tool_util/deps/resolvers/modules.py -> build/lib/galaxy/tool_util/deps/resolvers 2025-12-13T03:59:47,289 copying galaxy/tool_util/deps/resolvers/brewed_tool_shed_packages.py -> build/lib/galaxy/tool_util/deps/resolvers 2025-12-13T03:59:47,291 copying galaxy/tool_util/deps/resolvers/conda.py -> build/lib/galaxy/tool_util/deps/resolvers 2025-12-13T03:59:47,294 copying galaxy/tool_util/deps/resolvers/homebrew.py -> build/lib/galaxy/tool_util/deps/resolvers 2025-12-13T03:59:47,297 creating build/lib/galaxy/tool_util/deps/container_resolvers 2025-12-13T03:59:47,298 copying galaxy/tool_util/deps/container_resolvers/test.py -> build/lib/galaxy/tool_util/deps/container_resolvers 2025-12-13T03:59:47,300 copying galaxy/tool_util/deps/container_resolvers/mulled.py -> build/lib/galaxy/tool_util/deps/container_resolvers 2025-12-13T03:59:47,302 copying galaxy/tool_util/deps/container_resolvers/__init__.py -> build/lib/galaxy/tool_util/deps/container_resolvers 2025-12-13T03:59:47,304 copying galaxy/tool_util/deps/container_resolvers/explicit.py -> build/lib/galaxy/tool_util/deps/container_resolvers 2025-12-13T03:59:47,307 creating build/lib/galaxy/tool_util/parameters/scripts 2025-12-13T03:59:47,308 copying galaxy/tool_util/parameters/scripts/__init__.py -> build/lib/galaxy/tool_util/parameters/scripts 2025-12-13T03:59:47,310 copying galaxy/tool_util/parameters/scripts/validate_test_cases.py -> build/lib/galaxy/tool_util/parameters/scripts 2025-12-13T03:59:47,313 creating build/lib/galaxy/tool_util/toolbox/views 2025-12-13T03:59:47,314 copying galaxy/tool_util/toolbox/views/interface.py -> build/lib/galaxy/tool_util/toolbox/views 2025-12-13T03:59:47,316 copying galaxy/tool_util/toolbox/views/__init__.py -> build/lib/galaxy/tool_util/toolbox/views 2025-12-13T03:59:47,318 copying galaxy/tool_util/toolbox/views/definitions.py -> build/lib/galaxy/tool_util/toolbox/views 2025-12-13T03:59:47,320 copying galaxy/tool_util/toolbox/views/sources.py -> build/lib/galaxy/tool_util/toolbox/views 2025-12-13T03:59:47,322 copying galaxy/tool_util/toolbox/views/static.py -> build/lib/galaxy/tool_util/toolbox/views 2025-12-13T03:59:47,325 copying galaxy/tool_util/toolbox/views/edam.py -> build/lib/galaxy/tool_util/toolbox/views 2025-12-13T03:59:47,327 creating build/lib/galaxy/tool_util/toolbox/lineages 2025-12-13T03:59:47,328 copying galaxy/tool_util/toolbox/lineages/interface.py -> build/lib/galaxy/tool_util/toolbox/lineages 2025-12-13T03:59:47,331 copying galaxy/tool_util/toolbox/lineages/__init__.py -> build/lib/galaxy/tool_util/toolbox/lineages 2025-12-13T03:59:47,333 copying galaxy/tool_util/toolbox/lineages/factory.py -> build/lib/galaxy/tool_util/toolbox/lineages 2025-12-13T03:59:47,335 creating build/lib/galaxy/tool_util/toolbox/filters 2025-12-13T03:59:47,336 copying galaxy/tool_util/toolbox/filters/__init__.py -> build/lib/galaxy/tool_util/toolbox/filters 2025-12-13T03:59:47,339 creating build/lib/galaxy/tool_util/data/bundles 2025-12-13T03:59:47,340 copying galaxy/tool_util/data/bundles/models.py -> build/lib/galaxy/tool_util/data/bundles 2025-12-13T03:59:47,343 copying galaxy/tool_util/data/bundles/__init__.py -> build/lib/galaxy/tool_util/data/bundles 2025-12-13T03:59:47,344 running egg_info 2025-12-13T03:59:47,356 writing galaxy_tool_util.egg-info/PKG-INFO 2025-12-13T03:59:47,363 writing dependency_links to galaxy_tool_util.egg-info/dependency_links.txt 2025-12-13T03:59:47,365 writing entry points to galaxy_tool_util.egg-info/entry_points.txt 2025-12-13T03:59:47,368 writing requirements to galaxy_tool_util.egg-info/requires.txt 2025-12-13T03:59:47,369 writing top-level names to galaxy_tool_util.egg-info/top_level.txt 2025-12-13T03:59:47,405 reading manifest file 'galaxy_tool_util.egg-info/SOURCES.txt' 2025-12-13T03:59:47,415 reading manifest template 'MANIFEST.in' 2025-12-13T03:59:47,421 adding license file 'LICENSE' 2025-12-13T03:59:47,430 writing manifest file 'galaxy_tool_util.egg-info/SOURCES.txt' 2025-12-13T03:59:47,435 /tmp/pip-build-env-7i3bxzcx/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'galaxy.tool_util.xsd' is absent from the `packages` configuration. 2025-12-13T03:59:47,436 !! 2025-12-13T03:59:47,437 ******************************************************************************** 2025-12-13T03:59:47,437 ############################ 2025-12-13T03:59:47,438 # Package would be ignored # 2025-12-13T03:59:47,438 ############################ 2025-12-13T03:59:47,439 Python recognizes 'galaxy.tool_util.xsd' as an importable package[^1], 2025-12-13T03:59:47,439 but it is absent from setuptools' `packages` configuration. 2025-12-13T03:59:47,440 This leads to an ambiguous overall configuration. If you want to distribute this 2025-12-13T03:59:47,441 package, please make sure that 'galaxy.tool_util.xsd' is explicitly added 2025-12-13T03:59:47,441 to the `packages` configuration field. 2025-12-13T03:59:47,442 Alternatively, you can also rely on setuptools' discovery methods 2025-12-13T03:59:47,443 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-12-13T03:59:47,444 instead of `find_packages(...)`/`find:`). 2025-12-13T03:59:47,445 You can read more about "package discovery" on setuptools documentation page: 2025-12-13T03:59:47,446 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-12-13T03:59:47,447 If you don't want 'galaxy.tool_util.xsd' to be distributed and are 2025-12-13T03:59:47,447 already explicitly excluding 'galaxy.tool_util.xsd' via 2025-12-13T03:59:47,448 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-12-13T03:59:47,448 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-12-13T03:59:47,449 combination with a more fine grained `package-data` configuration. 2025-12-13T03:59:47,450 You can read more about "package data files" on setuptools documentation page: 2025-12-13T03:59:47,451 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-12-13T03:59:47,452 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-12-13T03:59:47,453 even if it does not contain any `.py` files. 2025-12-13T03:59:47,453 On the other hand, currently there is no concept of package data 2025-12-13T03:59:47,454 directory, all directories are treated like packages. 2025-12-13T03:59:47,455 ******************************************************************************** 2025-12-13T03:59:47,456 !! 2025-12-13T03:59:47,456 check.warn(importable) 2025-12-13T03:59:47,457 copying galaxy/py.typed -> build/lib/galaxy 2025-12-13T03:59:47,457 creating build/lib/galaxy/tool_util/xsd 2025-12-13T03:59:47,458 copying galaxy/tool_util/xsd/LICENSE -> build/lib/galaxy/tool_util/xsd 2025-12-13T03:59:47,459 copying galaxy/tool_util/xsd/README.md -> build/lib/galaxy/tool_util/xsd 2025-12-13T03:59:47,460 copying galaxy/tool_util/xsd/galaxy.jxb -> build/lib/galaxy/tool_util/xsd 2025-12-13T03:59:47,462 copying galaxy/tool_util/xsd/galaxy.xsd -> build/lib/galaxy/tool_util/xsd 2025-12-13T03:59:47,471 copying galaxy/tool_util/verify/test_config.sample.yml -> build/lib/galaxy/tool_util/verify 2025-12-13T03:59:47,474 copying galaxy/tool_util/ontologies/biotools_mappings.tsv -> build/lib/galaxy/tool_util/ontologies 2025-12-13T03:59:47,478 copying galaxy/tool_util/ontologies/edam_operation_mappings.tsv -> build/lib/galaxy/tool_util/ontologies 2025-12-13T03:59:47,480 copying galaxy/tool_util/ontologies/edam_topic_mappings.tsv -> build/lib/galaxy/tool_util/ontologies 2025-12-13T03:59:47,482 copying galaxy/tool_util/upgrade/upgrade_codes.json -> build/lib/galaxy/tool_util/upgrade 2025-12-13T03:59:47,486 copying galaxy/tool_util/linters/datatypes_conf.xml.sample -> build/lib/galaxy/tool_util/linters 2025-12-13T03:59:47,491 copying galaxy/tool_util/deps/mulled/invfile.lua -> build/lib/galaxy/tool_util/deps/mulled 2025-12-13T03:59:47,494 copying galaxy/tool_util/deps/resolvers/default_conda_mapping.yml -> build/lib/galaxy/tool_util/deps/resolvers 2025-12-13T03:59:47,497 copying galaxy/tool_util/toolbox/filters/examples.py.sample -> build/lib/galaxy/tool_util/toolbox/filters 2025-12-13T03:59:47,526 installing to build/bdist.linux-armv7l/wheel 2025-12-13T03:59:47,527 running install 2025-12-13T03:59:47,550 running install_lib 2025-12-13T03:59:47,560 creating build/bdist.linux-armv7l/wheel 2025-12-13T03:59:47,562 creating build/bdist.linux-armv7l/wheel/galaxy 2025-12-13T03:59:47,564 copying build/lib/galaxy/__init__.py -> build/bdist.linux-armv7l/wheel/./galaxy 2025-12-13T03:59:47,566 copying build/lib/galaxy/py.typed -> build/bdist.linux-armv7l/wheel/./galaxy 2025-12-13T03:59:47,569 creating build/bdist.linux-armv7l/wheel/galaxy/tool_util 2025-12-13T03:59:47,571 creating build/bdist.linux-armv7l/wheel/galaxy/tool_util/verify 2025-12-13T03:59:47,573 copying build/lib/galaxy/tool_util/verify/test_data.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/verify 2025-12-13T03:59:47,576 copying build/lib/galaxy/tool_util/verify/codegen.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/verify 2025-12-13T03:59:47,580 creating build/bdist.linux-armv7l/wheel/galaxy/tool_util/verify/asserts 2025-12-13T03:59:47,582 copying build/lib/galaxy/tool_util/verify/asserts/hdf5.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/verify/asserts 2025-12-13T03:59:47,584 copying build/lib/galaxy/tool_util/verify/asserts/image.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/verify/asserts 2025-12-13T03:59:47,589 copying build/lib/galaxy/tool_util/verify/asserts/archive.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/verify/asserts 2025-12-13T03:59:47,593 copying build/lib/galaxy/tool_util/verify/asserts/__init__.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/verify/asserts 2025-12-13T03:59:47,596 copying build/lib/galaxy/tool_util/verify/asserts/text.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/verify/asserts 2025-12-13T03:59:47,599 copying build/lib/galaxy/tool_util/verify/asserts/json.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/verify/asserts 2025-12-13T03:59:47,603 copying build/lib/galaxy/tool_util/verify/asserts/tabular.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/verify/asserts 2025-12-13T03:59:47,607 copying build/lib/galaxy/tool_util/verify/asserts/_types.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/verify/asserts 2025-12-13T03:59:47,609 copying build/lib/galaxy/tool_util/verify/asserts/_util.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/verify/asserts 2025-12-13T03:59:47,612 copying build/lib/galaxy/tool_util/verify/asserts/size.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/verify/asserts 2025-12-13T03:59:47,614 copying build/lib/galaxy/tool_util/verify/asserts/xml.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/verify/asserts 2025-12-13T03:59:47,617 copying build/lib/galaxy/tool_util/verify/interactor.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/verify 2025-12-13T03:59:47,621 copying build/lib/galaxy/tool_util/verify/script.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/verify 2025-12-13T03:59:47,624 copying build/lib/galaxy/tool_util/verify/__init__.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/verify 2025-12-13T03:59:47,627 copying build/lib/galaxy/tool_util/verify/_types.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/verify 2025-12-13T03:59:47,629 copying build/lib/galaxy/tool_util/verify/parse.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/verify 2025-12-13T03:59:47,633 copying build/lib/galaxy/tool_util/verify/wait.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/verify 2025-12-13T03:59:47,635 copying build/lib/galaxy/tool_util/verify/test_config.sample.yml -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/verify 2025-12-13T03:59:47,637 creating build/bdist.linux-armv7l/wheel/galaxy/tool_util/cwl 2025-12-13T03:59:47,639 copying build/lib/galaxy/tool_util/cwl/schema.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/cwl 2025-12-13T03:59:47,641 copying build/lib/galaxy/tool_util/cwl/util.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/cwl 2025-12-13T03:59:47,644 copying build/lib/galaxy/tool_util/cwl/runtime_actions.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/cwl 2025-12-13T03:59:47,647 copying build/lib/galaxy/tool_util/cwl/representation.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/cwl 2025-12-13T03:59:47,650 copying build/lib/galaxy/tool_util/cwl/parser.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/cwl 2025-12-13T03:59:47,654 copying build/lib/galaxy/tool_util/cwl/__init__.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/cwl 2025-12-13T03:59:47,656 copying build/lib/galaxy/tool_util/cwl/runnable.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/cwl 2025-12-13T03:59:47,658 copying build/lib/galaxy/tool_util/cwl/cwltool_deps.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/cwl 2025-12-13T03:59:47,660 copying build/lib/galaxy/tool_util/lint.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util 2025-12-13T03:59:47,664 creating build/bdist.linux-armv7l/wheel/galaxy/tool_util/deps 2025-12-13T03:59:47,666 creating build/bdist.linux-armv7l/wheel/galaxy/tool_util/deps/mulled 2025-12-13T03:59:47,667 copying build/lib/galaxy/tool_util/deps/mulled/util.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/deps/mulled 2025-12-13T03:59:47,670 copying build/lib/galaxy/tool_util/deps/mulled/mulled_update_singularity_containers.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/deps/mulled 2025-12-13T03:59:47,673 copying build/lib/galaxy/tool_util/deps/mulled/mulled_hash.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/deps/mulled 2025-12-13T03:59:47,675 copying build/lib/galaxy/tool_util/deps/mulled/invfile.lua -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/deps/mulled 2025-12-13T03:59:47,678 copying build/lib/galaxy/tool_util/deps/mulled/_cli.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/deps/mulled 2025-12-13T03:59:47,680 copying build/lib/galaxy/tool_util/deps/mulled/mulled_build.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/deps/mulled 2025-12-13T03:59:47,683 copying build/lib/galaxy/tool_util/deps/mulled/__init__.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/deps/mulled 2025-12-13T03:59:47,684 copying build/lib/galaxy/tool_util/deps/mulled/mulled_build_files.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/deps/mulled 2025-12-13T03:59:47,687 copying build/lib/galaxy/tool_util/deps/mulled/get_tests.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/deps/mulled 2025-12-13T03:59:47,690 copying build/lib/galaxy/tool_util/deps/mulled/mulled_list.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/deps/mulled 2025-12-13T03:59:47,692 copying build/lib/galaxy/tool_util/deps/mulled/mulled_search.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/deps/mulled 2025-12-13T03:59:47,695 copying build/lib/galaxy/tool_util/deps/mulled/mulled_build_channel.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/deps/mulled 2025-12-13T03:59:47,698 copying build/lib/galaxy/tool_util/deps/mulled/mulled_build_tool.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/deps/mulled 2025-12-13T03:59:47,700 copying build/lib/galaxy/tool_util/deps/dockerfiles.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/deps 2025-12-13T03:59:47,703 copying build/lib/galaxy/tool_util/deps/installable.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/deps 2025-12-13T03:59:47,705 copying build/lib/galaxy/tool_util/deps/conda_compat.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/deps 2025-12-13T03:59:47,707 copying build/lib/galaxy/tool_util/deps/container_volumes.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/deps 2025-12-13T03:59:47,709 copying build/lib/galaxy/tool_util/deps/requirements.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/deps 2025-12-13T03:59:47,712 copying build/lib/galaxy/tool_util/deps/conda_util.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/deps 2025-12-13T03:59:47,715 copying build/lib/galaxy/tool_util/deps/__init__.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/deps 2025-12-13T03:59:47,719 copying build/lib/galaxy/tool_util/deps/docker_util.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/deps 2025-12-13T03:59:47,721 copying build/lib/galaxy/tool_util/deps/container_classes.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/deps 2025-12-13T03:59:47,725 creating build/bdist.linux-armv7l/wheel/galaxy/tool_util/deps/resolvers 2025-12-13T03:59:47,726 copying build/lib/galaxy/tool_util/deps/resolvers/galaxy_packages.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/deps/resolvers 2025-12-13T03:59:47,729 copying build/lib/galaxy/tool_util/deps/resolvers/tool_shed_packages.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/deps/resolvers 2025-12-13T03:59:47,731 copying build/lib/galaxy/tool_util/deps/resolvers/default_conda_mapping.yml -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/deps/resolvers 2025-12-13T03:59:47,734 copying build/lib/galaxy/tool_util/deps/resolvers/resolver_mixins.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/deps/resolvers 2025-12-13T03:59:47,736 copying build/lib/galaxy/tool_util/deps/resolvers/unlinked_tool_shed_packages.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/deps/resolvers 2025-12-13T03:59:47,739 copying build/lib/galaxy/tool_util/deps/resolvers/__init__.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/deps/resolvers 2025-12-13T03:59:47,742 copying build/lib/galaxy/tool_util/deps/resolvers/lmod.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/deps/resolvers 2025-12-13T03:59:47,745 copying build/lib/galaxy/tool_util/deps/resolvers/modules.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/deps/resolvers 2025-12-13T03:59:47,748 copying build/lib/galaxy/tool_util/deps/resolvers/brewed_tool_shed_packages.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/deps/resolvers 2025-12-13T03:59:47,750 copying build/lib/galaxy/tool_util/deps/resolvers/conda.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/deps/resolvers 2025-12-13T03:59:47,754 copying build/lib/galaxy/tool_util/deps/resolvers/homebrew.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/deps/resolvers 2025-12-13T03:59:47,758 copying build/lib/galaxy/tool_util/deps/commands.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/deps 2025-12-13T03:59:47,762 copying build/lib/galaxy/tool_util/deps/containers.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/deps 2025-12-13T03:59:47,766 copying build/lib/galaxy/tool_util/deps/views.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/deps 2025-12-13T03:59:47,770 copying build/lib/galaxy/tool_util/deps/singularity_util.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/deps 2025-12-13T03:59:47,773 copying build/lib/galaxy/tool_util/deps/dependencies.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/deps 2025-12-13T03:59:47,775 copying build/lib/galaxy/tool_util/deps/brew_util.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/deps 2025-12-13T03:59:47,779 creating build/bdist.linux-armv7l/wheel/galaxy/tool_util/deps/container_resolvers 2025-12-13T03:59:47,780 copying build/lib/galaxy/tool_util/deps/container_resolvers/test.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/deps/container_resolvers 2025-12-13T03:59:47,782 copying build/lib/galaxy/tool_util/deps/container_resolvers/mulled.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/deps/container_resolvers 2025-12-13T03:59:47,786 copying build/lib/galaxy/tool_util/deps/container_resolvers/__init__.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/deps/container_resolvers 2025-12-13T03:59:47,788 copying build/lib/galaxy/tool_util/deps/container_resolvers/explicit.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/deps/container_resolvers 2025-12-13T03:59:47,791 copying build/lib/galaxy/tool_util/deps/brew_exts.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/deps 2025-12-13T03:59:47,794 copying build/lib/galaxy/tool_util/loader_directory.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util 2025-12-13T03:59:47,796 creating build/bdist.linux-armv7l/wheel/galaxy/tool_util/ontologies 2025-12-13T03:59:47,797 copying build/lib/galaxy/tool_util/ontologies/edam_operation_mappings.tsv -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/ontologies 2025-12-13T03:59:47,799 copying build/lib/galaxy/tool_util/ontologies/ontology_data.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/ontologies 2025-12-13T03:59:47,801 copying build/lib/galaxy/tool_util/ontologies/biotools_mappings.tsv -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/ontologies 2025-12-13T03:59:47,804 copying build/lib/galaxy/tool_util/ontologies/__init__.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/ontologies 2025-12-13T03:59:47,806 copying build/lib/galaxy/tool_util/ontologies/edam_topic_mappings.tsv -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/ontologies 2025-12-13T03:59:47,808 creating build/bdist.linux-armv7l/wheel/galaxy/tool_util/client 2025-12-13T03:59:47,809 copying build/lib/galaxy/tool_util/client/__init__.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/client 2025-12-13T03:59:47,811 copying build/lib/galaxy/tool_util/client/staging.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/client 2025-12-13T03:59:47,813 copying build/lib/galaxy/tool_util/client/landing.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/client 2025-12-13T03:59:47,816 creating build/bdist.linux-armv7l/wheel/galaxy/tool_util/parameters 2025-12-13T03:59:47,817 copying build/lib/galaxy/tool_util/parameters/visitor.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/parameters 2025-12-13T03:59:47,820 creating build/bdist.linux-armv7l/wheel/galaxy/tool_util/parameters/scripts 2025-12-13T03:59:47,821 copying build/lib/galaxy/tool_util/parameters/scripts/__init__.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/parameters/scripts 2025-12-13T03:59:47,822 copying build/lib/galaxy/tool_util/parameters/scripts/validate_test_cases.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/parameters/scripts 2025-12-13T03:59:47,825 copying build/lib/galaxy/tool_util/parameters/state.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/parameters 2025-12-13T03:59:47,827 copying build/lib/galaxy/tool_util/parameters/__init__.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/parameters 2025-12-13T03:59:47,829 copying build/lib/galaxy/tool_util/parameters/json.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/parameters 2025-12-13T03:59:47,831 copying build/lib/galaxy/tool_util/parameters/case.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/parameters 2025-12-13T03:59:47,833 copying build/lib/galaxy/tool_util/parameters/factory.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/parameters 2025-12-13T03:59:47,836 copying build/lib/galaxy/tool_util/parameters/model_validation.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/parameters 2025-12-13T03:59:47,839 copying build/lib/galaxy/tool_util/parameters/convert.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/parameters 2025-12-13T03:59:47,842 copying build/lib/galaxy/tool_util/model_factory.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util 2025-12-13T03:59:47,846 copying build/lib/galaxy/tool_util/provided_metadata.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util 2025-12-13T03:59:47,849 creating build/bdist.linux-armv7l/wheel/galaxy/tool_util/toolbox 2025-12-13T03:59:47,850 copying build/lib/galaxy/tool_util/toolbox/integrated_panel.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/toolbox 2025-12-13T03:59:47,853 creating build/bdist.linux-armv7l/wheel/galaxy/tool_util/toolbox/views 2025-12-13T03:59:47,854 copying build/lib/galaxy/tool_util/toolbox/views/interface.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/toolbox/views 2025-12-13T03:59:47,856 copying build/lib/galaxy/tool_util/toolbox/views/__init__.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/toolbox/views 2025-12-13T03:59:47,857 copying build/lib/galaxy/tool_util/toolbox/views/definitions.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/toolbox/views 2025-12-13T03:59:47,859 copying build/lib/galaxy/tool_util/toolbox/views/sources.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/toolbox/views 2025-12-13T03:59:47,861 copying build/lib/galaxy/tool_util/toolbox/views/static.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/toolbox/views 2025-12-13T03:59:47,863 copying build/lib/galaxy/tool_util/toolbox/views/edam.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/toolbox/views 2025-12-13T03:59:47,865 copying build/lib/galaxy/tool_util/toolbox/parser.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/toolbox 2025-12-13T03:59:47,868 creating build/bdist.linux-armv7l/wheel/galaxy/tool_util/toolbox/lineages 2025-12-13T03:59:47,869 copying build/lib/galaxy/tool_util/toolbox/lineages/interface.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/toolbox/lineages 2025-12-13T03:59:47,871 copying build/lib/galaxy/tool_util/toolbox/lineages/__init__.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/toolbox/lineages 2025-12-13T03:59:47,872 copying build/lib/galaxy/tool_util/toolbox/lineages/factory.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/toolbox/lineages 2025-12-13T03:59:47,874 copying build/lib/galaxy/tool_util/toolbox/base.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/toolbox 2025-12-13T03:59:47,877 copying build/lib/galaxy/tool_util/toolbox/panel.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/toolbox 2025-12-13T03:59:47,880 copying build/lib/galaxy/tool_util/toolbox/__init__.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/toolbox 2025-12-13T03:59:47,881 copying build/lib/galaxy/tool_util/toolbox/watcher.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/toolbox 2025-12-13T03:59:47,885 creating build/bdist.linux-armv7l/wheel/galaxy/tool_util/toolbox/filters 2025-12-13T03:59:47,886 copying build/lib/galaxy/tool_util/toolbox/filters/__init__.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/toolbox/filters 2025-12-13T03:59:47,889 copying build/lib/galaxy/tool_util/toolbox/filters/examples.py.sample -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/toolbox/filters 2025-12-13T03:59:47,892 copying build/lib/galaxy/tool_util/__init__.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util 2025-12-13T03:59:47,894 creating build/bdist.linux-armv7l/wheel/galaxy/tool_util/biotools 2025-12-13T03:59:47,895 copying build/lib/galaxy/tool_util/biotools/interface.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/biotools 2025-12-13T03:59:47,897 copying build/lib/galaxy/tool_util/biotools/__init__.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/biotools 2025-12-13T03:59:47,898 copying build/lib/galaxy/tool_util/biotools/source.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/biotools 2025-12-13T03:59:47,901 creating build/bdist.linux-armv7l/wheel/galaxy/tool_util/upgrade 2025-12-13T03:59:47,902 copying build/lib/galaxy/tool_util/upgrade/script.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/upgrade 2025-12-13T03:59:47,904 copying build/lib/galaxy/tool_util/upgrade/__init__.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/upgrade 2025-12-13T03:59:47,906 copying build/lib/galaxy/tool_util/upgrade/upgrade_codes.json -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/upgrade 2025-12-13T03:59:47,908 copying build/lib/galaxy/tool_util/fetcher.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util 2025-12-13T03:59:47,911 creating build/bdist.linux-armv7l/wheel/galaxy/tool_util/unittest_utils 2025-12-13T03:59:47,912 copying build/lib/galaxy/tool_util/unittest_utils/interactor.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/unittest_utils 2025-12-13T03:59:47,914 copying build/lib/galaxy/tool_util/unittest_utils/__init__.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/unittest_utils 2025-12-13T03:59:47,916 copying build/lib/galaxy/tool_util/unittest_utils/parameters.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/unittest_utils 2025-12-13T03:59:47,917 copying build/lib/galaxy/tool_util/unittest_utils/sample_data.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/unittest_utils 2025-12-13T03:59:47,919 copying build/lib/galaxy/tool_util/output_checker.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util 2025-12-13T03:59:47,922 copying build/lib/galaxy/tool_util/edam_util.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util 2025-12-13T03:59:47,924 creating build/bdist.linux-armv7l/wheel/galaxy/tool_util/locations 2025-12-13T03:59:47,925 copying build/lib/galaxy/tool_util/locations/http.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/locations 2025-12-13T03:59:47,927 copying build/lib/galaxy/tool_util/locations/file.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/locations 2025-12-13T03:59:47,929 copying build/lib/galaxy/tool_util/locations/dockstore.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/locations 2025-12-13T03:59:47,931 copying build/lib/galaxy/tool_util/locations/__init__.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/locations 2025-12-13T03:59:47,933 copying build/lib/galaxy/tool_util/validate_test_format.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util 2025-12-13T03:59:47,935 creating build/bdist.linux-armv7l/wheel/galaxy/tool_util/linters 2025-12-13T03:59:47,936 copying build/lib/galaxy/tool_util/linters/inputs.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/linters 2025-12-13T03:59:47,939 copying build/lib/galaxy/tool_util/linters/stdio.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/linters 2025-12-13T03:59:47,941 copying build/lib/galaxy/tool_util/linters/output.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/linters 2025-12-13T03:59:47,943 copying build/lib/galaxy/tool_util/linters/datatypes_conf.xml.sample -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/linters 2025-12-13T03:59:47,947 copying build/lib/galaxy/tool_util/linters/command.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/linters 2025-12-13T03:59:47,949 copying build/lib/galaxy/tool_util/linters/citations.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/linters 2025-12-13T03:59:47,951 copying build/lib/galaxy/tool_util/linters/__init__.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/linters 2025-12-13T03:59:47,953 copying build/lib/galaxy/tool_util/linters/help.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/linters 2025-12-13T03:59:47,955 copying build/lib/galaxy/tool_util/linters/xml_order.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/linters 2025-12-13T03:59:47,957 copying build/lib/galaxy/tool_util/linters/tests.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/linters 2025-12-13T03:59:47,960 copying build/lib/galaxy/tool_util/linters/_util.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/linters 2025-12-13T03:59:47,962 copying build/lib/galaxy/tool_util/linters/general.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/linters 2025-12-13T03:59:47,964 copying build/lib/galaxy/tool_util/linters/cwl.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/linters 2025-12-13T03:59:47,966 copying build/lib/galaxy/tool_util/linters/xsd.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/linters 2025-12-13T03:59:47,968 copying build/lib/galaxy/tool_util/linters/datatypes.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/linters 2025-12-13T03:59:47,971 creating build/bdist.linux-armv7l/wheel/galaxy/tool_util/parser 2025-12-13T03:59:47,972 copying build/lib/galaxy/tool_util/parser/output_objects.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/parser 2025-12-13T03:59:47,974 copying build/lib/galaxy/tool_util/parser/stdio.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/parser 2025-12-13T03:59:47,977 copying build/lib/galaxy/tool_util/parser/util.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/parser 2025-12-13T03:59:47,979 copying build/lib/galaxy/tool_util/parser/yaml.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/parser 2025-12-13T03:59:47,982 copying build/lib/galaxy/tool_util/parser/interface.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/parser 2025-12-13T03:59:47,984 copying build/lib/galaxy/tool_util/parser/__init__.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/parser 2025-12-13T03:59:47,986 copying build/lib/galaxy/tool_util/parser/parameter_validators.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/parser 2025-12-13T03:59:47,988 copying build/lib/galaxy/tool_util/parser/factory.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/parser 2025-12-13T03:59:47,990 copying build/lib/galaxy/tool_util/parser/output_actions.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/parser 2025-12-13T03:59:47,993 copying build/lib/galaxy/tool_util/parser/cwl.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/parser 2025-12-13T03:59:47,995 copying build/lib/galaxy/tool_util/parser/output_collection_def.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/parser 2025-12-13T03:59:47,997 copying build/lib/galaxy/tool_util/parser/xml.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/parser 2025-12-13T03:59:48,001 copying build/lib/galaxy/tool_util/loader.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util 2025-12-13T03:59:48,003 creating build/bdist.linux-armv7l/wheel/galaxy/tool_util/data 2025-12-13T03:59:48,005 creating build/bdist.linux-armv7l/wheel/galaxy/tool_util/data/bundles 2025-12-13T03:59:48,006 copying build/lib/galaxy/tool_util/data/bundles/models.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/data/bundles 2025-12-13T03:59:48,009 copying build/lib/galaxy/tool_util/data/bundles/__init__.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/data/bundles 2025-12-13T03:59:48,010 copying build/lib/galaxy/tool_util/data/__init__.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/data 2025-12-13T03:59:48,013 copying build/lib/galaxy/tool_util/data/_schema.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/data 2025-12-13T03:59:48,015 copying build/lib/galaxy/tool_util/version.py -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util 2025-12-13T03:59:48,018 creating build/bdist.linux-armv7l/wheel/galaxy/tool_util/xsd 2025-12-13T03:59:48,019 copying build/lib/galaxy/tool_util/xsd/LICENSE -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/xsd 2025-12-13T03:59:48,021 copying build/lib/galaxy/tool_util/xsd/galaxy.xsd -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/xsd 2025-12-13T03:59:48,029 copying build/lib/galaxy/tool_util/xsd/README.md -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/xsd 2025-12-13T03:59:48,031 copying build/lib/galaxy/tool_util/xsd/galaxy.jxb -> build/bdist.linux-armv7l/wheel/./galaxy/tool_util/xsd 2025-12-13T03:59:48,032 running install_egg_info 2025-12-13T03:59:48,046 Copying galaxy_tool_util.egg-info to build/bdist.linux-armv7l/wheel/./galaxy_tool_util-25.1.dev0-py3.11.egg-info 2025-12-13T03:59:48,058 running install_scripts 2025-12-13T03:59:48,070 creating build/bdist.linux-armv7l/wheel/galaxy_tool_util-25.1.dev0.dist-info/WHEEL 2025-12-13T03:59:48,073 creating '/tmp/pip-wheel-_w_qr8yf/.tmp-2cdj5w45/galaxy_tool_util-25.1.dev0-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2025-12-13T03:59:48,076 adding 'galaxy/__init__.py' 2025-12-13T03:59:48,077 adding 'galaxy/py.typed' 2025-12-13T03:59:48,079 adding 'galaxy/tool_util/__init__.py' 2025-12-13T03:59:48,081 adding 'galaxy/tool_util/edam_util.py' 2025-12-13T03:59:48,082 adding 'galaxy/tool_util/fetcher.py' 2025-12-13T03:59:48,085 adding 'galaxy/tool_util/lint.py' 2025-12-13T03:59:48,086 adding 'galaxy/tool_util/loader.py' 2025-12-13T03:59:48,088 adding 'galaxy/tool_util/loader_directory.py' 2025-12-13T03:59:48,089 adding 'galaxy/tool_util/model_factory.py' 2025-12-13T03:59:48,091 adding 'galaxy/tool_util/output_checker.py' 2025-12-13T03:59:48,093 adding 'galaxy/tool_util/provided_metadata.py' 2025-12-13T03:59:48,095 adding 'galaxy/tool_util/validate_test_format.py' 2025-12-13T03:59:48,096 adding 'galaxy/tool_util/version.py' 2025-12-13T03:59:48,098 adding 'galaxy/tool_util/biotools/__init__.py' 2025-12-13T03:59:48,099 adding 'galaxy/tool_util/biotools/interface.py' 2025-12-13T03:59:48,101 adding 'galaxy/tool_util/biotools/source.py' 2025-12-13T03:59:48,102 adding 'galaxy/tool_util/client/__init__.py' 2025-12-13T03:59:48,104 adding 'galaxy/tool_util/client/landing.py' 2025-12-13T03:59:48,106 adding 'galaxy/tool_util/client/staging.py' 2025-12-13T03:59:48,108 adding 'galaxy/tool_util/cwl/__init__.py' 2025-12-13T03:59:48,110 adding 'galaxy/tool_util/cwl/cwltool_deps.py' 2025-12-13T03:59:48,116 adding 'galaxy/tool_util/cwl/parser.py' 2025-12-13T03:59:48,119 adding 'galaxy/tool_util/cwl/representation.py' 2025-12-13T03:59:48,120 adding 'galaxy/tool_util/cwl/runnable.py' 2025-12-13T03:59:48,122 adding 'galaxy/tool_util/cwl/runtime_actions.py' 2025-12-13T03:59:48,123 adding 'galaxy/tool_util/cwl/schema.py' 2025-12-13T03:59:48,127 adding 'galaxy/tool_util/cwl/util.py' 2025-12-13T03:59:48,134 adding 'galaxy/tool_util/data/__init__.py' 2025-12-13T03:59:48,136 adding 'galaxy/tool_util/data/_schema.py' 2025-12-13T03:59:48,138 adding 'galaxy/tool_util/data/bundles/__init__.py' 2025-12-13T03:59:48,139 adding 'galaxy/tool_util/data/bundles/models.py' 2025-12-13T03:59:48,143 adding 'galaxy/tool_util/deps/__init__.py' 2025-12-13T03:59:48,146 adding 'galaxy/tool_util/deps/brew_exts.py' 2025-12-13T03:59:48,147 adding 'galaxy/tool_util/deps/brew_util.py' 2025-12-13T03:59:48,148 adding 'galaxy/tool_util/deps/commands.py' 2025-12-13T03:59:48,149 adding 'galaxy/tool_util/deps/conda_compat.py' 2025-12-13T03:59:48,152 adding 'galaxy/tool_util/deps/conda_util.py' 2025-12-13T03:59:48,155 adding 'galaxy/tool_util/deps/container_classes.py' 2025-12-13T03:59:48,157 adding 'galaxy/tool_util/deps/container_volumes.py' 2025-12-13T03:59:48,159 adding 'galaxy/tool_util/deps/containers.py' 2025-12-13T03:59:48,161 adding 'galaxy/tool_util/deps/dependencies.py' 2025-12-13T03:59:48,162 adding 'galaxy/tool_util/deps/docker_util.py' 2025-12-13T03:59:48,164 adding 'galaxy/tool_util/deps/dockerfiles.py' 2025-12-13T03:59:48,165 adding 'galaxy/tool_util/deps/installable.py' 2025-12-13T03:59:48,167 adding 'galaxy/tool_util/deps/requirements.py' 2025-12-13T03:59:48,169 adding 'galaxy/tool_util/deps/singularity_util.py' 2025-12-13T03:59:48,171 adding 'galaxy/tool_util/deps/views.py' 2025-12-13T03:59:48,173 adding 'galaxy/tool_util/deps/container_resolvers/__init__.py' 2025-12-13T03:59:48,175 adding 'galaxy/tool_util/deps/container_resolvers/explicit.py' 2025-12-13T03:59:48,178 adding 'galaxy/tool_util/deps/container_resolvers/mulled.py' 2025-12-13T03:59:48,179 adding 'galaxy/tool_util/deps/container_resolvers/test.py' 2025-12-13T03:59:48,181 adding 'galaxy/tool_util/deps/mulled/__init__.py' 2025-12-13T03:59:48,182 adding 'galaxy/tool_util/deps/mulled/_cli.py' 2025-12-13T03:59:48,184 adding 'galaxy/tool_util/deps/mulled/get_tests.py' 2025-12-13T03:59:48,186 adding 'galaxy/tool_util/deps/mulled/invfile.lua' 2025-12-13T03:59:48,189 adding 'galaxy/tool_util/deps/mulled/mulled_build.py' 2025-12-13T03:59:48,191 adding 'galaxy/tool_util/deps/mulled/mulled_build_channel.py' 2025-12-13T03:59:48,192 adding 'galaxy/tool_util/deps/mulled/mulled_build_files.py' 2025-12-13T03:59:48,193 adding 'galaxy/tool_util/deps/mulled/mulled_build_tool.py' 2025-12-13T03:59:48,195 adding 'galaxy/tool_util/deps/mulled/mulled_hash.py' 2025-12-13T03:59:48,196 adding 'galaxy/tool_util/deps/mulled/mulled_list.py' 2025-12-13T03:59:48,199 adding 'galaxy/tool_util/deps/mulled/mulled_search.py' 2025-12-13T03:59:48,200 adding 'galaxy/tool_util/deps/mulled/mulled_update_singularity_containers.py' 2025-12-13T03:59:48,203 adding 'galaxy/tool_util/deps/mulled/util.py' 2025-12-13T03:59:48,206 adding 'galaxy/tool_util/deps/resolvers/__init__.py' 2025-12-13T03:59:48,207 adding 'galaxy/tool_util/deps/resolvers/brewed_tool_shed_packages.py' 2025-12-13T03:59:48,210 adding 'galaxy/tool_util/deps/resolvers/conda.py' 2025-12-13T03:59:48,211 adding 'galaxy/tool_util/deps/resolvers/default_conda_mapping.yml' 2025-12-13T03:59:48,213 adding 'galaxy/tool_util/deps/resolvers/galaxy_packages.py' 2025-12-13T03:59:48,214 adding 'galaxy/tool_util/deps/resolvers/homebrew.py' 2025-12-13T03:59:48,215 adding 'galaxy/tool_util/deps/resolvers/lmod.py' 2025-12-13T03:59:48,217 adding 'galaxy/tool_util/deps/resolvers/modules.py' 2025-12-13T03:59:48,219 adding 'galaxy/tool_util/deps/resolvers/resolver_mixins.py' 2025-12-13T03:59:48,220 adding 'galaxy/tool_util/deps/resolvers/tool_shed_packages.py' 2025-12-13T03:59:48,222 adding 'galaxy/tool_util/deps/resolvers/unlinked_tool_shed_packages.py' 2025-12-13T03:59:48,223 adding 'galaxy/tool_util/linters/__init__.py' 2025-12-13T03:59:48,225 adding 'galaxy/tool_util/linters/_util.py' 2025-12-13T03:59:48,226 adding 'galaxy/tool_util/linters/citations.py' 2025-12-13T03:59:48,227 adding 'galaxy/tool_util/linters/command.py' 2025-12-13T03:59:48,229 adding 'galaxy/tool_util/linters/cwl.py' 2025-12-13T03:59:48,230 adding 'galaxy/tool_util/linters/datatypes.py' 2025-12-13T03:59:48,240 adding 'galaxy/tool_util/linters/datatypes_conf.xml.sample' 2025-12-13T03:59:48,243 adding 'galaxy/tool_util/linters/general.py' 2025-12-13T03:59:48,244 adding 'galaxy/tool_util/linters/help.py' 2025-12-13T03:59:48,248 adding 'galaxy/tool_util/linters/inputs.py' 2025-12-13T03:59:48,250 adding 'galaxy/tool_util/linters/output.py' 2025-12-13T03:59:48,252 adding 'galaxy/tool_util/linters/stdio.py' 2025-12-13T03:59:48,254 adding 'galaxy/tool_util/linters/tests.py' 2025-12-13T03:59:48,256 adding 'galaxy/tool_util/linters/xml_order.py' 2025-12-13T03:59:48,257 adding 'galaxy/tool_util/linters/xsd.py' 2025-12-13T03:59:48,259 adding 'galaxy/tool_util/locations/__init__.py' 2025-12-13T03:59:48,260 adding 'galaxy/tool_util/locations/dockstore.py' 2025-12-13T03:59:48,261 adding 'galaxy/tool_util/locations/file.py' 2025-12-13T03:59:48,262 adding 'galaxy/tool_util/locations/http.py' 2025-12-13T03:59:48,264 adding 'galaxy/tool_util/ontologies/__init__.py' 2025-12-13T03:59:48,270 adding 'galaxy/tool_util/ontologies/biotools_mappings.tsv' 2025-12-13T03:59:48,271 adding 'galaxy/tool_util/ontologies/edam_operation_mappings.tsv' 2025-12-13T03:59:48,273 adding 'galaxy/tool_util/ontologies/edam_topic_mappings.tsv' 2025-12-13T03:59:48,274 adding 'galaxy/tool_util/ontologies/ontology_data.py' 2025-12-13T03:59:48,276 adding 'galaxy/tool_util/parameters/__init__.py' 2025-12-13T03:59:48,278 adding 'galaxy/tool_util/parameters/case.py' 2025-12-13T03:59:48,281 adding 'galaxy/tool_util/parameters/convert.py' 2025-12-13T03:59:48,283 adding 'galaxy/tool_util/parameters/factory.py' 2025-12-13T03:59:48,284 adding 'galaxy/tool_util/parameters/json.py' 2025-12-13T03:59:48,286 adding 'galaxy/tool_util/parameters/model_validation.py' 2025-12-13T03:59:48,287 adding 'galaxy/tool_util/parameters/state.py' 2025-12-13T03:59:48,288 adding 'galaxy/tool_util/parameters/visitor.py' 2025-12-13T03:59:48,290 adding 'galaxy/tool_util/parameters/scripts/__init__.py' 2025-12-13T03:59:48,292 adding 'galaxy/tool_util/parameters/scripts/validate_test_cases.py' 2025-12-13T03:59:48,294 adding 'galaxy/tool_util/parser/__init__.py' 2025-12-13T03:59:48,295 adding 'galaxy/tool_util/parser/cwl.py' 2025-12-13T03:59:48,297 adding 'galaxy/tool_util/parser/factory.py' 2025-12-13T03:59:48,301 adding 'galaxy/tool_util/parser/interface.py' 2025-12-13T03:59:48,303 adding 'galaxy/tool_util/parser/output_actions.py' 2025-12-13T03:59:48,305 adding 'galaxy/tool_util/parser/output_collection_def.py' 2025-12-13T03:59:48,308 adding 'galaxy/tool_util/parser/output_objects.py' 2025-12-13T03:59:48,310 adding 'galaxy/tool_util/parser/parameter_validators.py' 2025-12-13T03:59:48,311 adding 'galaxy/tool_util/parser/stdio.py' 2025-12-13T03:59:48,313 adding 'galaxy/tool_util/parser/util.py' 2025-12-13T03:59:48,321 adding 'galaxy/tool_util/parser/xml.py' 2025-12-13T03:59:48,327 adding 'galaxy/tool_util/parser/yaml.py' 2025-12-13T03:59:48,329 adding 'galaxy/tool_util/toolbox/__init__.py' 2025-12-13T03:59:48,337 adding 'galaxy/tool_util/toolbox/base.py' 2025-12-13T03:59:48,339 adding 'galaxy/tool_util/toolbox/integrated_panel.py' 2025-12-13T03:59:48,341 adding 'galaxy/tool_util/toolbox/panel.py' 2025-12-13T03:59:48,342 adding 'galaxy/tool_util/toolbox/parser.py' 2025-12-13T03:59:48,344 adding 'galaxy/tool_util/toolbox/watcher.py' 2025-12-13T03:59:48,346 adding 'galaxy/tool_util/toolbox/filters/__init__.py' 2025-12-13T03:59:48,347 adding 'galaxy/tool_util/toolbox/filters/examples.py.sample' 2025-12-13T03:59:48,349 adding 'galaxy/tool_util/toolbox/lineages/__init__.py' 2025-12-13T03:59:48,350 adding 'galaxy/tool_util/toolbox/lineages/factory.py' 2025-12-13T03:59:48,351 adding 'galaxy/tool_util/toolbox/lineages/interface.py' 2025-12-13T03:59:48,353 adding 'galaxy/tool_util/toolbox/views/__init__.py' 2025-12-13T03:59:48,354 adding 'galaxy/tool_util/toolbox/views/definitions.py' 2025-12-13T03:59:48,356 adding 'galaxy/tool_util/toolbox/views/edam.py' 2025-12-13T03:59:48,357 adding 'galaxy/tool_util/toolbox/views/interface.py' 2025-12-13T03:59:48,358 adding 'galaxy/tool_util/toolbox/views/sources.py' 2025-12-13T03:59:48,360 adding 'galaxy/tool_util/toolbox/views/static.py' 2025-12-13T03:59:48,362 adding 'galaxy/tool_util/unittest_utils/__init__.py' 2025-12-13T03:59:48,363 adding 'galaxy/tool_util/unittest_utils/interactor.py' 2025-12-13T03:59:48,364 adding 'galaxy/tool_util/unittest_utils/parameters.py' 2025-12-13T03:59:48,366 adding 'galaxy/tool_util/unittest_utils/sample_data.py' 2025-12-13T03:59:48,368 adding 'galaxy/tool_util/upgrade/__init__.py' 2025-12-13T03:59:48,369 adding 'galaxy/tool_util/upgrade/script.py' 2025-12-13T03:59:48,371 adding 'galaxy/tool_util/upgrade/upgrade_codes.json' 2025-12-13T03:59:48,375 adding 'galaxy/tool_util/verify/__init__.py' 2025-12-13T03:59:48,377 adding 'galaxy/tool_util/verify/_types.py' 2025-12-13T03:59:48,379 adding 'galaxy/tool_util/verify/codegen.py' 2025-12-13T03:59:48,389 adding 'galaxy/tool_util/verify/interactor.py' 2025-12-13T03:59:48,392 adding 'galaxy/tool_util/verify/parse.py' 2025-12-13T03:59:48,396 adding 'galaxy/tool_util/verify/script.py' 2025-12-13T03:59:48,397 adding 'galaxy/tool_util/verify/test_config.sample.yml' 2025-12-13T03:59:48,398 adding 'galaxy/tool_util/verify/test_data.py' 2025-12-13T03:59:48,400 adding 'galaxy/tool_util/verify/wait.py' 2025-12-13T03:59:48,402 adding 'galaxy/tool_util/verify/asserts/__init__.py' 2025-12-13T03:59:48,403 adding 'galaxy/tool_util/verify/asserts/_types.py' 2025-12-13T03:59:48,404 adding 'galaxy/tool_util/verify/asserts/_util.py' 2025-12-13T03:59:48,406 adding 'galaxy/tool_util/verify/asserts/archive.py' 2025-12-13T03:59:48,407 adding 'galaxy/tool_util/verify/asserts/hdf5.py' 2025-12-13T03:59:48,411 adding 'galaxy/tool_util/verify/asserts/image.py' 2025-12-13T03:59:48,412 adding 'galaxy/tool_util/verify/asserts/json.py' 2025-12-13T03:59:48,413 adding 'galaxy/tool_util/verify/asserts/size.py' 2025-12-13T03:59:48,415 adding 'galaxy/tool_util/verify/asserts/tabular.py' 2025-12-13T03:59:48,416 adding 'galaxy/tool_util/verify/asserts/text.py' 2025-12-13T03:59:48,418 adding 'galaxy/tool_util/verify/asserts/xml.py' 2025-12-13T03:59:48,420 adding 'galaxy/tool_util/xsd/LICENSE' 2025-12-13T03:59:48,421 adding 'galaxy/tool_util/xsd/README.md' 2025-12-13T03:59:48,422 adding 'galaxy/tool_util/xsd/galaxy.jxb' 2025-12-13T03:59:48,462 adding 'galaxy/tool_util/xsd/galaxy.xsd' 2025-12-13T03:59:48,468 adding 'galaxy_tool_util-25.1.dev0.dist-info/licenses/LICENSE' 2025-12-13T03:59:48,473 adding 'galaxy_tool_util-25.1.dev0.dist-info/METADATA' 2025-12-13T03:59:48,474 adding 'galaxy_tool_util-25.1.dev0.dist-info/WHEEL' 2025-12-13T03:59:48,476 adding 'galaxy_tool_util-25.1.dev0.dist-info/entry_points.txt' 2025-12-13T03:59:48,477 adding 'galaxy_tool_util-25.1.dev0.dist-info/top_level.txt' 2025-12-13T03:59:48,479 adding 'galaxy_tool_util-25.1.dev0.dist-info/RECORD' 2025-12-13T03:59:48,488 removing build/bdist.linux-armv7l/wheel 2025-12-13T03:59:48,636 Building wheel for galaxy-tool-util (pyproject.toml): finished with status 'done' 2025-12-13T03:59:48,650 Created wheel for galaxy-tool-util: filename=galaxy_tool_util-25.1.dev0-py3-none-any.whl size=518083 sha256=aec59328149ad7147f16f410f30539ab4537e696bc9cf8b14c749cc0e56a093e 2025-12-13T03:59:48,652 Stored in directory: /tmp/pip-ephem-wheel-cache-pjpwb3t4/wheels/82/8f/ea/c0c58c7354cbb2477e8e63718f2d3de000b1ce581968bea377 2025-12-13T03:59:48,674 Successfully built galaxy-tool-util 2025-12-13T03:59:48,690 Removed build tracker: '/tmp/pip-build-tracker-sj62fjlv'