cpg-utils 5.8.0__tar.gz → 5.8.2__tar.gz

{cpg_utils-5.8.0 → cpg_utils-5.8.2}/PKG-INFO

@@ -1,13 +1,12 @@
 Metadata-Version: 2.4
 Name: cpg-utils
-Version: 5.8.0
+Version: 5.8.2
 Summary: Library of convenience functions specific to the CPG
-Home-page: https://github.com/populationgenomics/cpg-utils
-License: MIT
+License-Expression: MIT
+Project-URL: Homepage, https://github.com/populationgenomics/cpg-utils
 Keywords: bioinformatics
 Classifier: Environment :: Console
 Classifier: Intended Audience :: Science/Research
-Classifier: License :: OSI Approved :: MIT License
 Classifier: Natural Language :: English
 Classifier: Operating System :: MacOS :: MacOS X
 Classifier: Operating System :: POSIX
@@ -15,6 +14,7 @@ Classifier: Operating System :: Unix
 Classifier: Programming Language :: Python
 Classifier: Topic :: Scientific/Engineering
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.11
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: boto3>=1.28.56
@@ -33,26 +33,12 @@ Requires-Dist: requests
 Requires-Dist: tabulate
 Requires-Dist: toml
 Requires-Dist: deprecated
-Dynamic: classifier
-Dynamic: description
-Dynamic: description-content-type
-Dynamic: home-page
-Dynamic: keywords
-Dynamic: license
 Dynamic: license-file
-Dynamic: requires-dist
-Dynamic: summary
 
 # cpg-utils
 
 This is a Python library containing convenience functions that are specific to the CPG.
 
-In order to install the library in a conda environment, run:
-
-```bash
-conda install -c cpg cpg-utils
-```
-
 To use the library, import functions like this:
 
 ```python
@@ -61,7 +47,7 @@ from cpg_utils.cloud import email_from_id_token
 _email_string = email_from_id_token(id_token_jwt='TOKEN_STRING')
 ```
 
-We use `bumpversion` for incrementing the library's semantic version. A new conda package gets published automatically in the `cpg` conda channel whenever a version bump commit is merged with the `main` branch.
+We use `bump-my-version` for incrementing the library's semantic version. A new PyPi package gets published whenever a version bump commit is merged with the `main` branch.
 
 
 ## Contents

{cpg_utils-5.8.0 → cpg_utils-5.8.2}/README.md

@@ -2,12 +2,6 @@
 
 This is a Python library containing convenience functions that are specific to the CPG.
 
-In order to install the library in a conda environment, run:
-
-```bash
-conda install -c cpg cpg-utils
-```
-
 To use the library, import functions like this:
 
 ```python
@@ -16,7 +10,7 @@ from cpg_utils.cloud import email_from_id_token
 _email_string = email_from_id_token(id_token_jwt='TOKEN_STRING')
 ```
 
-We use `bumpversion` for incrementing the library's semantic version. A new conda package gets published automatically in the `cpg` conda channel whenever a version bump commit is merged with the `main` branch.
+We use `bump-my-version` for incrementing the library's semantic version. A new PyPi package gets published whenever a version bump commit is merged with the `main` branch.
 
 
 ## Contents

{cpg_utils-5.8.0 → cpg_utils-5.8.2}/cpg_utils/cromwell.py

@@ -792,6 +792,7 @@ def _copy_resource_group_into_batch(
         jq_els,
         error_descriptions,
         rg.keys(),
+        strict=True,
     ):
         j.command(
             f"""

{cpg_utils-5.8.0 → cpg_utils-5.8.2}/cpg_utils/dataproc.py

@@ -3,8 +3,9 @@
 import os
 import re
 import uuid
+from collections.abc import Collection
 from shlex import quote
-from typing import Any, Collection
+from typing import Any
 
 import hailtop.batch as hb
 

{cpg_utils-5.8.0 → cpg_utils-5.8.2}/cpg_utils/dataproc_runner.py

@@ -341,6 +341,7 @@ class HailDataprocCluster:
         job_client: dataproc_v1.JobControllerClient | None = None,
         storage_client: storage.Client | None = None,
         preemptible_workers: bool = True,
+        internal_ip_only: bool = True,
     ) -> None:
         self._project = project
         self._region = region
@@ -391,6 +392,7 @@ class HailDataprocCluster:
         self._cluster: dataproc_v1.Cluster | None = None
         self._job_ids: list[str] = []
         self._preemptible_workers = preemptible_workers
+        self._internal_ip_only = internal_ip_only
 
     @property
     def name(self) -> str:
@@ -490,6 +492,7 @@ class HailDataprocCluster:
             'config': {
                 'gce_cluster_config': {
                     'zone_uri': '',  # Let Dataproc auto-zone within region.
+                    'internal_ip_only': self._internal_ip_only,
                     'metadata': {
                         'WHEEL': self.wheel,
                     },

{cpg_utils-5.8.0 → cpg_utils-5.8.2}/cpg_utils.egg-info/PKG-INFO

@@ -1,13 +1,12 @@
 Metadata-Version: 2.4
 Name: cpg-utils
-Version: 5.8.0
+Version: 5.8.2
 Summary: Library of convenience functions specific to the CPG
-Home-page: https://github.com/populationgenomics/cpg-utils
-License: MIT
+License-Expression: MIT
+Project-URL: Homepage, https://github.com/populationgenomics/cpg-utils
 Keywords: bioinformatics
 Classifier: Environment :: Console
 Classifier: Intended Audience :: Science/Research
-Classifier: License :: OSI Approved :: MIT License
 Classifier: Natural Language :: English
 Classifier: Operating System :: MacOS :: MacOS X
 Classifier: Operating System :: POSIX
@@ -15,6 +14,7 @@ Classifier: Operating System :: Unix
 Classifier: Programming Language :: Python
 Classifier: Topic :: Scientific/Engineering
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.11
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: boto3>=1.28.56
@@ -33,26 +33,12 @@ Requires-Dist: requests
 Requires-Dist: tabulate
 Requires-Dist: toml
 Requires-Dist: deprecated
-Dynamic: classifier
-Dynamic: description
-Dynamic: description-content-type
-Dynamic: home-page
-Dynamic: keywords
-Dynamic: license
 Dynamic: license-file
-Dynamic: requires-dist
-Dynamic: summary
 
 # cpg-utils
 
 This is a Python library containing convenience functions that are specific to the CPG.
 
-In order to install the library in a conda environment, run:
-
-```bash
-conda install -c cpg cpg-utils
-```
-
 To use the library, import functions like this:
 
 ```python
@@ -61,7 +47,7 @@ from cpg_utils.cloud import email_from_id_token
 _email_string = email_from_id_token(id_token_jwt='TOKEN_STRING')
 ```
 
-We use `bumpversion` for incrementing the library's semantic version. A new conda package gets published automatically in the `cpg` conda channel whenever a version bump commit is merged with the `main` branch.
+We use `bump-my-version` for incrementing the library's semantic version. A new PyPi package gets published whenever a version bump commit is merged with the `main` branch.
 
 
 ## Contents

{cpg_utils-5.8.0 → cpg_utils-5.8.2}/cpg_utils.egg-info/SOURCES.txt

@@ -1,7 +1,6 @@
 LICENSE
 README.md
 pyproject.toml
-setup.py
 cpg_utils/__init__.py
 cpg_utils/cloud.py
 cpg_utils/cloudpath_hail_az.py
@@ -23,7 +22,6 @@ cpg_utils.egg-info/SOURCES.txt
 cpg_utils.egg-info/dependency_links.txt
 cpg_utils.egg-info/requires.txt
 cpg_utils.egg-info/top_level.txt
-test/__init__.py
 test/test_config.py
 test/test_cromwell.py
 test/test_dataproc_runner.py

{cpg_utils-5.8.0 → cpg_utils-5.8.2}/cpg_utils.egg-info/top_level.txt

@@ -1,2 +1 @@
 cpg_utils
-test

{cpg_utils-5.8.0 → cpg_utils-5.8.2}/pyproject.toml

@@ -1,3 +1,67 @@
+[project]
+name = "cpg-utils"
+# This tag is automatically updated by bumpversion
+version = "5.8.2"
+requires-python = '>=3.11'
+description = "Library of convenience functions specific to the CPG"
+readme = "README.md"
+license = "MIT"
+license-files = ["LICENSE"]
+keywords = ["bioinformatics"]
+classifiers = [
+    "Environment :: Console",
+    "Intended Audience :: Science/Research",
+    "Natural Language :: English",
+    "Operating System :: MacOS :: MacOS X",
+    "Operating System :: POSIX",
+    "Operating System :: Unix",
+    "Programming Language :: Python",
+    "Topic :: Scientific/Engineering",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+]
+dependencies = [
+    "boto3>=1.28.56",
+    "botocore>=1.31.56",
+    "cloudpathlib[all]",
+    "frozendict",
+    "google-auth>=1.27.0",
+    "google-auth-oauthlib",
+    "google-cloud-artifact-registry",
+    "google-cloud-dataproc",
+    "google-cloud-secret-manager",
+    "google-cloud-storage",
+    "metamist",
+    "python-slugify",
+    "requests",
+    "tabulate",
+    "toml",
+    "deprecated",
+]
+
+[dependency-groups]
+dev = [
+    "bump-my-version",
+    "coverage",
+    "hail",
+    "pip-audit>=2.7.3",
+    "pre-commit",
+    "pytest",
+    "setuptools>=77",
+]
+
+[project.urls]
+Homepage = "https://github.com/populationgenomics/cpg-utils"
+
+[build-system]
+requires = ["setuptools>=77"]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools.packages.find]
+include = ["cpg_utils*"]
+
+[tool.setuptools.package-data]
+cpg_utils = ["py.typed"]
+
 [tool.black]
 line-length = 88
 skip-string-normalization = true
@@ -33,7 +97,6 @@ ignore = [
 ]
 
 [tool.ruff.lint.isort]
-
 section-order = ["future", "standard-library", "third-party", "hail", "cpg", "first-party", "local-folder"]
 
 [tool.ruff.lint.isort.sections]
@@ -56,3 +119,21 @@ cpg = [
 [tool.pytest.ini_options]
 addopts = "--doctest-modules"
 testpaths = ["test", "cpg_utils"]
+
+[tool.bumpversion]
+current_version = "5.8.2"
+parse = "(?P<major>\\d+)\\.(?P<minor>\\d+)\\.(?P<patch>\\d+)"
+serialize = ["{major}.{minor}.{patch}"]
+commit = true
+message = "Bump version: {current_version} → {new_version}"
+commit_args = ""
+
+[[tool.bumpversion.files]]
+filename = "pyproject.toml"
+search = 'version = "{current_version}"'
+replace = 'version = "{new_version}"'
+
+[[tool.bumpversion.files]]
+filename = ".github/workflows/docker.yaml"
+search = 'VERSION: {current_version}'
+replace = 'VERSION: {new_version}'

cpg_utils-5.8.0/setup.py

@@ -1,52 +0,0 @@
-#!/usr/bin/env python
-
-from setuptools import find_packages, setup
-
-with open('README.md') as f:
-    long_description = f.read()
-
-setup(
-    name='cpg-utils',
-    # This tag is automatically updated by bumpversion
-    version='5.8.0',
-    description='Library of convenience functions specific to the CPG',
-    long_description=long_description,
-    long_description_content_type='text/markdown',
-    url='https://github.com/populationgenomics/cpg-utils',
-    license='MIT',
-    packages=find_packages(),
-    package_data={
-        'cpg_utils': ['py.typed'],
-    },
-    install_requires=[
-        'boto3>=1.28.56',
-        'botocore>=1.31.56',
-        'cloudpathlib[all]',
-        'frozendict',
-        'google-auth>=1.27.0',
-        'google-auth-oauthlib',
-        'google-cloud-artifact-registry',
-        'google-cloud-dataproc',
-        'google-cloud-secret-manager',
-        'google-cloud-storage',
-        'metamist',
-        'python-slugify',
-        'requests',
-        'tabulate',
-        'toml',
-        'deprecated',
-    ],
-    keywords='bioinformatics',
-    classifiers=[
-        'Environment :: Console',
-        'Intended Audience :: Science/Research',
-        'License :: OSI Approved :: MIT License',
-        'Natural Language :: English',
-        'Operating System :: MacOS :: MacOS X',
-        'Operating System :: POSIX',
-        'Operating System :: Unix',
-        'Programming Language :: Python',
-        'Topic :: Scientific/Engineering',
-        'Topic :: Scientific/Engineering :: Bio-Informatics',
-    ],
-)