├── .all-contributorsrc ├── .github ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── FUNDING.yml ├── ISSUE_TEMPLATE │ ├── bug_report.md │ ├── documentation-or-tutorial-request.md │ ├── feature_request.md │ └── question.md ├── dev-requirements.txt ├── old-workflows │ └── update.yaml ├── stale.yml ├── test-centos.yml ├── update-multiple-pr.yml └── workflows │ ├── alert-action-updates.yaml │ ├── docs.yml │ ├── main.yml │ ├── release.yaml │ ├── test-container.yml │ ├── test-core.yml │ ├── test.yml │ └── update-contributors.yaml ├── .gitignore ├── .pre-commit-config.yaml ├── CHANGELOG.md ├── CITATION.cff ├── Dockerfile ├── Dockerfile.tcl ├── LICENSE ├── MANIFEST.in ├── README.md ├── actions └── cache-update │ ├── action.yaml │ └── scripts │ ├── helpers.py │ ├── update-from-cache.py │ └── update-from-listing.py ├── docs ├── Makefile ├── _static │ ├── sphinx-argparse.css │ └── theme.css ├── api_reference │ ├── internal │ │ ├── modules.rst │ │ └── shpc.rst │ └── shpc.rst ├── assets │ └── img │ │ ├── shpc.png │ │ ├── shpc.svg │ │ └── shpc.xcf ├── conf.py ├── getting_started │ ├── developer-guide.rst │ ├── index.rst │ ├── installation.rst │ ├── use-cases.rst │ └── user-guide.rst ├── index.rst └── requirements.txt ├── entrypoint.sh ├── example ├── README.md ├── biocontainer-match.py └── google-cloud-storage │ ├── README.md │ ├── google-cloud-storage.py │ └── img │ └── storage.png ├── paper ├── paper.bib └── paper.md ├── pyproject.toml ├── setup.cfg ├── setup.py └── shpc ├── __init__.py ├── client ├── __init__.py ├── add.py ├── check.py ├── config.py ├── docgen.py ├── get.py ├── help.py ├── inspect.py ├── install.py ├── listing.py ├── namespace.py ├── pull.py ├── remove.py ├── shell.py ├── show.py ├── sync.py ├── test.py ├── uninstall.py ├── update.py └── view.py ├── defaults.py ├── logger.py ├── main ├── __init__.py ├── client.py ├── container │ ├── __init__.py │ ├── base.py │ ├── config.py │ ├── docker.py │ ├── podman.py │ ├── singularity.py │ ├── templates │ │ ├── __init__.py │ │ └── container.yaml │ └── update │ │ ├── __init__.py │ │ ├── diff.py │ │ ├── docker.py │ │ └── versions.py ├── modules │ ├── __init__.py │ ├── base.py │ ├── lmod.py │ ├── module.py │ ├── tcl.py │ ├── template.py │ ├── templates │ │ ├── __init__.py │ │ ├── default_version │ │ ├── docker.lua │ │ ├── docker.tcl │ │ ├── docs.md │ │ ├── includes │ │ │ ├── default_version.lua │ │ │ ├── load_view.lua │ │ │ └── load_view.tcl │ │ ├── singularity.lua │ │ ├── singularity.tcl │ │ ├── test.sh │ │ ├── view_module.lua │ │ └── view_module.tcl │ ├── versions.py │ └── views.py ├── registry │ ├── __init__.py │ ├── filesystem.py │ ├── provider.py │ └── remote.py ├── schemas.py ├── settings.py ├── templates.py └── wrappers │ ├── __init__.py │ ├── base.py │ ├── generators.py │ └── templates │ ├── __init__.py │ ├── bases │ ├── __init__.py │ └── shell-script-base.sh │ ├── docker.sh │ ├── docker │ ├── container.sh │ ├── exec.sh │ ├── inspect.sh │ ├── run.sh │ └── shell.sh │ ├── singularity.sh │ ├── singularity │ ├── container.sh │ ├── exec.sh │ ├── inspect-deffile.sh │ ├── inspect-runscript.sh │ ├── run.sh │ └── shell.sh │ └── snippets │ └── __init__.py ├── settings.yml ├── tests ├── __init__.py ├── helpers.py ├── helpers.sh ├── test-registry-module.sh ├── test_client.py ├── test_client.sh ├── test_config.py ├── test_container.py ├── test_container_config.py ├── test_settings.py ├── test_sync.py ├── test_utils.py ├── test_views.py ├── test_wrappers.py └── testdata │ ├── alias-container.yaml │ ├── empty_singularity.sh │ ├── hashtest.txt │ ├── overrides-invalid.yaml │ ├── overrides.yaml │ ├── python-container.yaml │ ├── quay-container.yaml │ ├── registry │ └── dinosaur │ │ └── salad │ │ └── container.yaml │ ├── salad_latest.sif │ ├── samtools │ ├── 1.14--hb421002_0.yaml │ ├── 1.15--h3843a85_0.yaml │ └── container.yaml │ └── view.yaml ├── utils ├── __init__.py ├── fileio.py └── terminal.py └── version.py /.all-contributorsrc: 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