Refactor to make genomicsdb_query and genomicsdb_cache console scripts

.github/scripts/setup_azurite.sh

@@ -60,7 +60,7 @@ tar xzvf $GITHUB_WORKSPACE/test/inputs/sanity.test.tgz -C oldstyle_dir
 az storage blob upload-batch -d test/oldstyle-dir -s oldstyle_dir --connection-string $AZURE_CONNECTION_STRING
 export  OLDSTYLE_DIR=az://test/oldstyle-dir
 
-cd $GITHUB_WORKSPACE/examples
+cd $GITHUB_WORKSPACE/test/scripts
 tar xzvf examples_ws.tgz
 az storage blob upload-batch -d test/ws -s ws --connection-string $AZURE_CONNECTION_STRING
 export WORKSPACE=az://test/ws

.github/workflows/basic.yml

@@ -96,14 +96,14 @@ jobs:
       run: |
         PYTHONPATH=. pytest
         PYTHONPATH=. python test/test.py
-        PYTHONPATH=. examples/test.sh
+        PYTHONPATH=. test/scripts/test.sh
 
     - name: Cloud Test - Azurite
       run: |
         source .github/scripts/setup_azurite.sh
         echo "Testing on Azurite..."
         echo "WORKSPACE=$WORKSPACE OLDSTYLE_DIR=$OLDSTYLE_DIR"
-        PYTHONPATH=. ./examples/test.sh
+        PYTHONPATH=. test/scripts/test.sh
         ls -l /tmp/tiledb_bookkeeping
         echo "Testing on Azurite DONE"
 

Makefile

@@ -55,14 +55,14 @@ clean-test: ## remove test and coverage artifacts
 	rm -fr .pytest_cache
 
 format: ## format files with black and isort
-	black --line-length 120 setup.py src test examples/genomicsdb_*
-	isort --profile black --line-length 120 setup.py src test examples/genomicsdb_*
+	black --line-length 120 setup.py src test genomicsdb/scripts
+	isort --profile black --line-length 120 setup.py src test genomicsdb/scripts
 
 lint: ## check style with flake8 and vulnerabilities with bandit
 	bandit -r setup.py src
-	flake8 --extend-ignore='E203, N803, N806, E402' --max-line-length=120 setup.py src test examples/genomicsdb_*
-	black --check --line-length 120 setup.py src test examples/genomicsdb_*
-	isort --profile black --line-length 120 -c setup.py src test examples/genomicsdb_*
+	flake8 --extend-ignore='E203, N803, N806, E402' --max-line-length=120 setup.py src test genomicsdb/scripts
+	black --check --line-length 120 setup.py src test genomicsdb/scripts
+	isort --profile black --line-length 120 -c setup.py src test genomicsdb/scripts
 	cython-lint --max-line-length 120 src/*.pyx
 
 test: FORCE ## run tests quickly with the default Python

README.md

@@ -2,7 +2,7 @@
 [![pypi](https://img.shields.io/pypi/v/genomicsdb.svg)](https://pypi.org/project/genomicsdb/) 
 
 # GenomicsDB-Python
-Experimental Python 3 Bindings to the native [GenomicsDB](https://github.com/GenomicsDB/GenomicsDB) library. Only queries are supported for now. For importing vcf files into GenomicsDB, use the command line tools - `vcf2genomicsdb` or `gatk GenomicsDBImport`.
+Python 3 Bindings to the native [GenomicsDB](https://github.com/GenomicsDB/GenomicsDB) library. Only queries are supported for now. For importing vcf files into GenomicsDB, use the command line tools - `vcf2genomicsdb` or `gatk GenomicsDBImport`.
 
 ## Installation : Only Linux and MacOS are currently supported
 Install `genomicsdb` binary wheels from PyPi with pip:
@@ -19,5 +19,8 @@ cd genomicsdb-<version>
 python setup.py install
 ```
 
+## GenomicsDB console scripts
+See [GenomicsDB query tool](https://github.com/GenomicsDB/GenomicsDB-Python/blob/master/genomicsdb/scripts/README.md). The available scripts are `genomicsdb_query` and `genomicsdb_cache` with the supported output options being csv, json and parquet files.
+
 ## Development
 See [instructions](https://github.com/GenomicsDB/GenomicsDB-Python/blob/master/INSTALL.md) for local builds and running tests.

examples/genomicsdb_cache → genomicsdb/scripts/genomicsdb_cache.py

@@ -5,7 +5,7 @@
 #
 # The MIT License
 #
-# Copyright (c) 2024 dātma, inc™
+# Copyright (c) 2024-2025 dātma, inc™
 #
 # Permission is hereby granted, free of charge, to any person obtaining a copy
 # of this software and associated documentation files (the "Software"), to deal
@@ -29,9 +29,8 @@
 import argparse
 import json
 
-import genomicsdb_common
-
 import genomicsdb
+from genomicsdb.scripts import genomicsdb_common
 
 
 def is_cloud_path(path):

examples/genomicsdb_query → genomicsdb/scripts/genomicsdb_query.py

@@ -5,7 +5,7 @@
 #
 # The MIT License
 #
-# Copyright (c) 2024 dātma, inc™
+# Copyright (c) 2024-2025 dātma, inc™
 #
 # Permission is hereby granted, free of charge, to any person obtaining a copy
 # of this software and associated documentation files (the "Software"), to deal
@@ -35,14 +35,14 @@
 import sys
 from typing import List, NamedTuple
 
-import genomicsdb_common
 import pyarrow as pa
 import pyarrow.parquet as pq
 
 import genomicsdb
 from genomicsdb import json_output_mode
 from genomicsdb.protobuf import genomicsdb_coordinates_pb2 as query_coords
 from genomicsdb.protobuf import genomicsdb_export_config_pb2 as query_pb
+from genomicsdb.scripts import genomicsdb_common
 
 logging.basicConfig(
     format="%(asctime)s.%(msecs)03d %(levelname)-5s GenomicsDB Python - pid=%(process)d tid=%(thread)d %(message)s",

setup.py

@@ -3,7 +3,7 @@
 #
 # The MIT License (MIT)
 #
-# Copyright (c) 2023 dātma, inc™
+# Copyright (c) 2023-2025 dātma, inc™
 #
 # Permission is hereby granted, free of charge, to any person obtaining a copy of
 # this software and associated documentation files (the "Software"), to deal in
@@ -146,7 +146,7 @@ def run_cythonize(src):
 
 setup(
     name="genomicsdb",
-    description="Experimental Python Bindings for querying GenomicsDB",
+    description="Python Bindings for querying GenomicsDB",
     long_description=long_description,
     long_description_content_type="text/markdown",
     author="GenomicsDB.org",
@@ -159,12 +159,18 @@ def run_cythonize(src):
     setup_requires=["cython>=0.27"],
     install_requires=install_requirements,
     python_requires=">=3.9",
-    packages=find_packages(exclude=["package", "test"]),
+    packages=find_packages(include=["genomicsdb", "genomicsdb.*"], exclude=["package", "test"]),
     keywords=["genomics", "genomicsdb", "variant", "vcf", "variant calls"],
     include_package_data=True,
     version=with_version,
+    entry_points={
+        "console_scripts": [
+            "genomicsdb_query=genomicsdb.scripts.genomicsdb_query:main",
+            "genomicsdb_cache=genomicsdb.scripts.genomicsdb_cache:main",
+        ],
+    },
     classifiers=[
-        "Development Status :: 3 - Alpha",
+        "Development Status :: 5 - Production/Stable",
         "Intended Audience :: Developers",
         "Intended Audience :: Information Technology",
         "Intended Audience :: Science/Research",

test/scripts/genomicsdb_cache

@@ -0,0 +1,34 @@
+#!/usr/bin/env python
+
+#
+# genomicsdb_cache wrappper
+#
+# The MIT License
+#
+# Copyright (c) 2025 dātma, inc™
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+
+import sys
+
+from genomicsdb.scripts.genomicsdb_cache import main
+
+if __name__ == '__main__':
+    sys.exit(main())

test/scripts/genomicsdb_query

@@ -0,0 +1,34 @@
+#!/usr/bin/env python
+
+#
+# genomicsdb_query wrapper
+#
+# The MIT License
+#
+# Copyright (c) 2025 dātma, inc™
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+
+import sys
+
+from genomicsdb.scripts.genomicsdb_query import main
+
+if __name__ == '__main__':
+    sys.exit(main())

examples/test.sh → test/scripts/test.sh

@@ -205,7 +205,7 @@ rm -f loader.json callset.json vidmap.json
 if [[ -z $OLDSTYLE_DIR ]]; then
   OLDSTYLE_DIR=$TEMP_DIR/old_style
   mkdir -p $OLDSTYLE_DIR
-  tar xzf $(dirname $0)/../test/inputs/sanity.test.tgz -C $OLDSTYLE_DIR
+  tar xzf $(dirname $0)/../inputs/sanity.test.tgz -C $OLDSTYLE_DIR
 fi
 WORKSPACE=$OLDSTYLE_DIR/ws