Move CLI from scripts to entrypoints

This make these easier to test and also means we are using a non-deprecated pyproject.toml configuration for them.
wtsi-npg · Nov 20, 2023 · b89641c · b89641c
1 parent bb8aa7d
commit b89641c
Show file tree

Hide file tree

Showing 17 changed files with 34 additions and 90 deletions.
diff --git a/pyproject.toml b/pyproject.toml
@@ -34,14 +34,29 @@ test = [
 homepage = "https://github.com/wtsi-npg/npg-irods-python"
 repository = "https://github.com/wtsi-npg/npg-irods-python.git"
 
+[project.scripts]
+"apply-ont-metadata" = "npg_irods.cli.apply_ont_metadata:main"
+"check-checksums" = "npg_irods.cli.check_checksums:main"
+"check-common-metadata" = "npg_irods.cli.check_common_metadata:main"
+"check-consent-withdrawn" = "npg_irods.cli.check_consent_withdrawn:main"
+"check-replicas" = "npg_irods.cli.check_replicas:main"
+"copy-confirm" = "npg_irods.cli.copy_confirm:main"
+"locate-data-objects" = "npg_irods.cli.locate_data_objects:main"
+"repair-common-metadata" = "npg_irods.cli.repair_common_metadata:main"
+"repair-checksums" = "npg_irods.cli.repair_checksums:main"
+"repair-replicas" = "npg_irods.cli.repair_replicas:main"
+"safe-remove-script" = "npg_irods.cli.safe_remove_script:main"
+"update-secondary-metadata" = "npg_irods.cli.update_secondary_metadata:main"
+"withdraw-consent" = "npg_irods.cli.withdraw_consent:main"
+
 [build-system]
 requires = ["setuptools>=41", "wheel", "setuptools-git-versioning<2"]
 build-backend = "setuptools.build_meta"
 
 [tool.setuptools]
 # Note: we are relying on setuptools' automatic package discovery, so no further
-# configuration is required. This is possible because partisan uses a standard src
-# layout. See the following for more information:
+# configuration is required. This is possible because npg-irods-python uses a standard
+# src layout. See the following for more information:
 #
 # https://setuptools.pypa.io/en/latest/userguide/package_discovery.html#src-layout
 
@@ -50,21 +65,8 @@ build-backend = "setuptools.build_meta"
 # "project.scripts", but that only supports automatcially generating wrapper scripts
 # for entry points, not installing existing scripts.
 script-files = [
-    "scripts/apply-ont-metadata",
     "scripts/backfill_illumina_locations.py",
     "scripts/backfill_pacbio_ids",
-    "scripts/check-checksums",
-    "scripts/check-common-metadata",
-    "scripts/check-consent-withdrawn",
-    "scripts/check-replicas",
-    "scripts/copy-confirm",
-    "scripts/locate-data-objects",
-    "scripts/repair-checksums",
-    "scripts/repair-common-metadata",
-    "scripts/repair-replicas",
-    "scripts/safe-remove-script",
-    "scripts/update-secondary-metadata",
-    "scripts/withdraw-consent",
 ]
 
 [tool.setuptools-git-versioning]

diff --git a/scripts/backfill_pacbio_ids b/scripts/backfill_pacbio_ids
@@ -22,7 +22,7 @@ import argparse
 import logging
 import structlog
 
-from npg_irods.cli import configure_logging, add_logging_arguments
+from npg_irods.cli.util import configure_logging, add_logging_arguments
 from npg_irods.metadata.pacbio import backfill_id_products
 from npg_irods.version import version
 

diff --git a/src/npg_irods/cli/__init__.py b/src/npg_irods/cli/__init__.py
@@ -0,0 +1 @@
+"""Command line interface for npg-irods-python."""
diff --git a/scripts/apply-ont-metadata → src/npg_irods/cli/apply_ont_metadata.py b/scripts/apply-ont-metadata → src/npg_irods/cli/apply_ont_metadata.py
@@ -1,4 +1,3 @@
-#!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
 # Copyright © 2023 Genome Research Ltd. All rights reserved.
@@ -25,7 +24,7 @@
 import structlog
 from sqlalchemy.orm import Session
 
-from npg_irods.cli import add_logging_arguments, configure_logging, parse_iso_date
+from npg_irods.cli.util import add_logging_arguments, configure_logging, parse_iso_date
 from npg_irods.db import DBConfig
 from npg_irods.ont import apply_metadata
 from npg_irods.version import version
@@ -130,7 +129,3 @@ def main():
             num_updated=num_updated,
             num_errors=num_errors,
         )
-
-
-if __name__ == "__main__":
-    main()
diff --git a/scripts/check-checksums → src/npg_irods/cli/check_checksums.py b/scripts/check-checksums → src/npg_irods/cli/check_checksums.py
@@ -1,4 +1,3 @@
-#!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
 # Copyright © 2022, 2023 Genome Research Ltd. All rights reserved.
@@ -24,7 +23,7 @@
 import structlog
 
 from npg_irods.utilities import check_checksums
-from npg_irods.cli import add_logging_arguments, configure_logging
+from npg_irods.cli.util import add_logging_arguments, configure_logging
 from npg_irods.version import version
 
 description = """
@@ -132,7 +131,3 @@ def main():
         num_passed=num_passed,
         num_errors=num_errors,
     )
-
-
-if __name__ == "__main__":
-    main()
diff --git a/scripts/check-common-metadata → src/npg_irods/cli/check_common_metadata.py b/scripts/check-common-metadata → src/npg_irods/cli/check_common_metadata.py
@@ -1,4 +1,3 @@
-#!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
 # Copyright © 2022, 2023 Genome Research Ltd. All rights reserved.
@@ -24,7 +23,7 @@
 import structlog
 
 from npg_irods.utilities import check_common_metadata
-from npg_irods.cli import add_logging_arguments, configure_logging
+from npg_irods.cli.util import add_logging_arguments, configure_logging
 from npg_irods.version import version
 
 description = """
@@ -130,7 +129,3 @@ def main():
         num_passed=num_passed,
         num_errors=num_errors,
     )
-
-
-if __name__ == "__main__":
-    main()
diff --git a/scripts/check-consent-withdrawn → src/npg_irods/cli/check_consent_withdrawn.py b/scripts/check-consent-withdrawn → src/npg_irods/cli/check_consent_withdrawn.py
@@ -1,4 +1,3 @@
-#!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
 # Copyright © 2023 Genome Research Ltd. All rights reserved.
@@ -26,7 +25,7 @@
 from npg_irods.utilities import (
     check_consent_withdrawn,
 )
-from npg_irods.cli import add_logging_arguments, configure_logging
+from npg_irods.cli.util import add_logging_arguments, configure_logging
 from npg_irods.version import version
 
 description = """
@@ -124,7 +123,3 @@ def main():
         num_passed=num_passed,
         num_errors=num_errors,
     )
-
-
-if __name__ == "__main__":
-    main()
diff --git a/scripts/check-replicas → src/npg_irods/cli/check_replicas.py b/scripts/check-replicas → src/npg_irods/cli/check_replicas.py
@@ -1,4 +1,3 @@
-#!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
 # Copyright © 2023 Genome Research Ltd. All rights reserved.
@@ -24,7 +23,7 @@
 import structlog
 
 from npg_irods.utilities import check_replicas
-from npg_irods.cli import add_logging_arguments, configure_logging
+from npg_irods.cli.util import add_logging_arguments, configure_logging
 from npg_irods.version import version
 
 description = """
@@ -140,7 +139,3 @@ def main():
         num_passed=num_passed,
         num_errors=num_errors,
     )
-
-
-if __name__ == "__main__":
-    main()
diff --git a/scripts/copy-confirm → src/npg_irods/cli/copy_confirm.py b/scripts/copy-confirm → src/npg_irods/cli/copy_confirm.py
@@ -1,4 +1,3 @@
-#!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
 # Copyright © 2022, 2023 Genome Research Ltd. All rights reserved.
@@ -25,7 +24,7 @@
 
 from npg_irods.exception import ChecksumError
 from npg_irods.utilities import copy
-from npg_irods.cli import add_logging_arguments, configure_logging, rods_path
+from npg_irods.cli.util import add_logging_arguments, configure_logging, rods_path
 from npg_irods.version import version
 
 description = """
@@ -126,7 +125,3 @@ def main():
     except Exception as e:
         log.error(e)
         exit(1)
-
-
-if __name__ == "__main__":
-    main()
diff --git a/scripts/locate-data-objects → src/npg_irods/cli/locate_data_objects.py b/scripts/locate-data-objects → src/npg_irods/cli/locate_data_objects.py
@@ -1,4 +1,3 @@
-#!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
 # Copyright © 2023 Genome Research Ltd. All rights reserved.
@@ -18,6 +17,7 @@
 #
 # @author Keith James <[email protected]>
 
+
 import argparse
 from collections import defaultdict
 from datetime import datetime, timedelta, timezone
@@ -28,7 +28,7 @@
 from sqlalchemy.orm import Session
 
 from npg_irods import illumina, ont
-from npg_irods.cli import (
+from npg_irods.cli.util import (
     add_logging_arguments,
     configure_logging,
     integer_in_range,
@@ -42,6 +42,7 @@
 from npg_irods.ont import barcode_collections
 from npg_irods.version import version
 
+
 description = """
 A utility for locating sets of data objects in iRODS.
 
@@ -359,7 +360,3 @@ def main():
         print(version())
         exit(0)
     args.func(args)
-
-
-if __name__ == "__main__":
-    main()
diff --git a/scripts/repair-common-metadata → src/npg_irods/cli/repair-common-metadata.py b/scripts/repair-common-metadata → src/npg_irods/cli/repair-common-metadata.py
@@ -1,4 +1,3 @@
-#!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
 # Copyright © 2022, 2023 Genome Research Ltd. All rights reserved.
@@ -24,7 +23,7 @@
 import structlog
 
 from npg_irods.utilities import repair_common_metadata
-from npg_irods.cli import add_logging_arguments, configure_logging
+from npg_irods.cli.util import add_logging_arguments, configure_logging
 from npg_irods.version import version
 
 description = """

diff --git a/scripts/repair-checksums → src/npg_irods/cli/repair_checksums.py b/scripts/repair-checksums → src/npg_irods/cli/repair_checksums.py
@@ -1,4 +1,3 @@
-#!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
 # Copyright © 2022, 2023 Genome Research Ltd. All rights reserved.
@@ -24,7 +23,7 @@
 import structlog
 
 from npg_irods.utilities import repair_checksums
-from npg_irods.cli import add_logging_arguments, configure_logging
+from npg_irods.cli.util import add_logging_arguments, configure_logging
 from npg_irods.version import version
 
 description = """
@@ -140,7 +139,3 @@ def main():
         num_repaired=num_repaired,
         num_errors=num_errors,
     )
-
-
-if __name__ == "__main__":
-    main()
diff --git a/scripts/repair-replicas → src/npg_irods/cli/repair_replicas.py b/scripts/repair-replicas → src/npg_irods/cli/repair_replicas.py
@@ -1,4 +1,3 @@
-#!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
 # Copyright © 2023 Genome Research Ltd. All rights reserved.
@@ -24,7 +23,7 @@
 import structlog
 
 from npg_irods.utilities import repair_replicas
-from npg_irods.cli import add_logging_arguments, configure_logging
+from npg_irods.cli.util import add_logging_arguments, configure_logging
 from npg_irods.version import version
 
 description = """
@@ -140,7 +139,3 @@ def main():
         num_repaired=num_repaired,
         num_errors=num_errors,
     )
-
-
-if __name__ == "__main__":
-    main()
diff --git a/scripts/safe-remove-script → src/npg_irods/cli/safe_remove_script.py b/scripts/safe-remove-script → src/npg_irods/cli/safe_remove_script.py
@@ -1,4 +1,3 @@
-#!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
 # Copyright © 2022, 2023 Genome Research Ltd. All rights reserved.
@@ -23,7 +22,7 @@
 import structlog
 
 from npg_irods.utilities import write_safe_remove_script
-from npg_irods.cli import add_logging_arguments, configure_logging
+from npg_irods.cli.util import add_logging_arguments, configure_logging
 from npg_irods.version import version
 
 description = """
@@ -100,7 +99,3 @@ def main():
     except Exception as e:
         log.error(e)
         exit(1)
-
-
-if __name__ == "__main__":
-    main()
diff --git a/scripts/update-secondary-metadata → ...pg_irods/cli/update_secondary_metadata.py b/scripts/update-secondary-metadata → ...pg_irods/cli/update_secondary_metadata.py
@@ -1,4 +1,3 @@
-#!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
 # Copyright © 2023 Genome Research Ltd. All rights reserved.
@@ -25,7 +24,7 @@
 import structlog
 from sqlalchemy.orm import Session
 
-from npg_irods.cli import add_logging_arguments, configure_logging
+from npg_irods.cli.util import add_logging_arguments, configure_logging
 from npg_irods.db import DBConfig
 from npg_irods.utilities import update_secondary_metadata
 from npg_irods.version import version
@@ -158,7 +157,3 @@ def main():
             num_updated=num_updated,
             num_errors=num_errors,
         )
-
-
-if __name__ == "__main__":
-    main()
diff --git a/src/npg_irods/cli.py → src/npg_irods/cli/util.py b/src/npg_irods/cli.py → src/npg_irods/cli/util.py
diff --git a/scripts/withdraw-consent → src/npg_irods/cli/withdraw_consent.py b/scripts/withdraw-consent → src/npg_irods/cli/withdraw_consent.py
@@ -1,4 +1,3 @@
-#!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
 # Copyright © 2023 Genome Research Ltd. All rights reserved.
@@ -26,7 +25,7 @@
 from npg_irods.utilities import (
     withdraw_consent,
 )
-from npg_irods.cli import add_logging_arguments, configure_logging
+from npg_irods.cli.util import add_logging_arguments, configure_logging
 from npg_irods.version import version
 
 description = """
@@ -118,7 +117,3 @@ def main():
         num_withdrawn=num_withdrawn,
         num_errors=num_errors,
     )
-
-
-if __name__ == "__main__":
-    main()
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		"""Command line interface for npg-irods-python."""