diff --git a/packages/galaxy/HISTORY.rst b/packages/galaxy/HISTORY.rst new file mode 100644 index 000000000000..4b79bb9627f0 --- /dev/null +++ b/packages/galaxy/HISTORY.rst @@ -0,0 +1,8 @@ +History +------- + +.. to_doc + +--------- +24.2.dev0 +--------- diff --git a/packages/galaxy/LICENSE.txt b/packages/galaxy/LICENSE.txt new file mode 120000 index 000000000000..1ef648f64b34 --- /dev/null +++ b/packages/galaxy/LICENSE.txt @@ -0,0 +1 @@ +../../LICENSE.txt \ No newline at end of file diff --git a/packages/galaxy/MANIFEST.in b/packages/galaxy/MANIFEST.in new file mode 100644 index 000000000000..12302eb8dff0 --- /dev/null +++ b/packages/galaxy/MANIFEST.in @@ -0,0 +1 @@ +include *.rst *.txt LICENSE */py.typed diff --git a/packages/galaxy/Makefile b/packages/galaxy/Makefile new file mode 120000 index 000000000000..37af8bae5baa --- /dev/null +++ b/packages/galaxy/Makefile @@ -0,0 +1 @@ +../package.Makefile \ No newline at end of file diff --git a/packages/galaxy/README.rst b/packages/galaxy/README.rst new file mode 100644 index 000000000000..4464de118ce6 --- /dev/null +++ b/packages/galaxy/README.rst @@ -0,0 +1,13 @@ + +.. image:: https://badge.fury.io/py/galaxy.svg + :target: https://pypi.python.org/pypi/galaxy/ + + +Overview +-------- + +The Galaxy_ Web Server. + +* Code: https://github.com/galaxyproject/galaxy + +.. _Galaxy: http://galaxyproject.org/ diff --git a/packages/galaxy/mypy.ini b/packages/galaxy/mypy.ini new file mode 120000 index 000000000000..141a30f41afc --- /dev/null +++ b/packages/galaxy/mypy.ini @@ -0,0 +1 @@ +../../mypy.ini \ No newline at end of file diff --git a/packages/galaxy/package-dev-requirements.txt b/packages/galaxy/package-dev-requirements.txt new file mode 120000 index 000000000000..467b90d7a232 --- /dev/null +++ b/packages/galaxy/package-dev-requirements.txt @@ -0,0 +1 @@ +../package-dev-requirements.txt \ No newline at end of file diff --git a/packages/galaxy/pyproject.toml b/packages/galaxy/pyproject.toml new file mode 120000 index 000000000000..01a3b08b8872 --- /dev/null +++ b/packages/galaxy/pyproject.toml @@ -0,0 +1 @@ +../package-pyproject.toml \ No newline at end of file diff --git a/packages/galaxy/scripts b/packages/galaxy/scripts new file mode 120000 index 000000000000..9aec9dc5a067 --- /dev/null +++ b/packages/galaxy/scripts @@ -0,0 +1 @@ +../build_scripts \ No newline at end of file diff --git a/packages/galaxy/setup.cfg b/packages/galaxy/setup.cfg new file mode 100644 index 000000000000..4e5e895e47b8 --- /dev/null +++ b/packages/galaxy/setup.cfg @@ -0,0 +1,261 @@ +[metadata] +author = Galaxy Project and Community +author_email = galaxy-committers@lists.galaxyproject.org +classifiers = + Development Status :: 5 - Production/Stable + Environment :: Console + Intended Audience :: Developers + License :: OSI Approved :: Academic Free License (AFL) + Natural Language :: English + Operating System :: POSIX + Programming Language :: Python :: 3 + Programming Language :: Python :: 3.8 + Programming Language :: Python :: 3.9 + Programming Language :: Python :: 3.10 + Programming Language :: Python :: 3.11 + Programming Language :: Python :: 3.12 + Topic :: Software Development + Topic :: Software Development :: Code Generators + Topic :: Software Development :: Testing +description = Galaxy +keywords = + Galaxy +license = AFL +license_files = + LICENSE +long_description = file: README.rst, HISTORY.rst +long_description_content_type = text/x-rst +name = galaxy +url = https://github.com/galaxyproject/galaxy +version = 24.1.2 + +[options] +include_package_data = True +install_requires = + galaxy-web-apps==24.1.2 + galaxy-app==24.1.2 + galaxy-data==24.1.2 + galaxy-job-execution==24.1.2 + galaxy-tool-util==24.1.2 + galaxy-util[jstree,template]==24.1.2 + galaxy-web-framework==24.1.2 + a2wsgi==1.10.4 ; python_version >= "3.8" and python_version < "3.13" + adal==1.2.7 ; python_version >= "3.8" and python_version < "3.13" + aiobotocore==2.13.0 ; python_version >= "3.8" and python_version < "3.13" + aiodataloader==0.4.0 ; python_version >= "3.8" and python_version < "3.13" + aiofiles==23.2.1 ; python_version >= "3.8" and python_version < "3.13" + aiohttp==3.9.5 ; python_version >= "3.8" and python_version < "3.13" + aioitertools==0.11.0 ; python_version >= "3.8" and python_version < "3.13" + aiosignal==1.3.1 ; python_version >= "3.8" and python_version < "3.13" + alembic==1.13.1 ; python_version >= "3.8" and python_version < "3.13" + amqp==5.2.0 ; python_version >= "3.8" and python_version < "3.13" + aniso8601==9.0.1 ; python_version >= "3.8" and python_version < "3.13" + annotated-types==0.6.0 ; python_version >= "3.8" and python_version < "3.13" + anyio==4.3.0 ; python_version >= "3.8" and python_version < "3.13" + apispec==6.6.1 ; python_version >= "3.8" and python_version < "3.13" + appdirs==1.4.4 ; python_version >= "3.8" and python_version < "3.13" + arcp==0.2.1 ; python_version >= "3.8" and python_version < "3.13" + argcomplete==3.3.0 ; python_version >= "3.8" and python_version < "3.13" + async-timeout==4.0.3 ; python_version >= "3.8" and python_version < "3.11" + attmap==0.13.2 ; python_version >= "3.8" and python_version < "3.13" + attrs==23.2.0 ; python_version >= "3.8" and python_version < "3.13" + babel==2.15.0 ; python_version >= "3.8" and python_version < "3.13" + backports-zoneinfo==0.2.1 ; python_version >= "3.8" and python_version < "3.9" + backports-zoneinfo[tzdata]==0.2.1 ; python_version >= "3.8" and python_version < "3.9" + bagit-profile==1.3.1 ; python_version >= "3.8" and python_version < "3.13" + bagit==1.8.1 ; python_version >= "3.8" and python_version < "3.13" + bcrypt==4.1.3 ; python_version >= "3.8" and python_version < "3.13" + bdbag==1.7.3 ; python_version >= "3.8" and python_version < "3.13" + beaker==1.13.0 ; python_version >= "3.8" and python_version < "3.13" + billiard==4.2.0 ; python_version >= "3.8" and python_version < "3.13" + bioblend==1.3.0 ; python_version >= "3.8" and python_version < "3.13" + bleach==6.1.0 ; python_version >= "3.8" and python_version < "3.13" + boltons==24.0.0 ; python_version >= "3.8" and python_version < "3.13" + boto==2.49.0 ; python_version >= "3.8" and python_version < "3.13" + botocore==1.34.106 ; python_version >= "3.8" and python_version < "3.13" + bx-python==0.11.0 ; python_version >= "3.8" and python_version < "3.13" + cachecontrol[filecache]==0.14.0 ; python_version >= "3.8" and python_version < "3.13" + celery==5.4.0 ; python_version >= "3.8" and python_version < "3.13" + certifi==2024.2.2 ; python_version >= "3.8" and python_version < "3.13" + cffi==1.16.0 ; python_version >= "3.8" and python_version < "3.13" + charset-normalizer==3.3.2 ; python_version >= "3.8" and python_version < "3.13" + cheetah3==3.2.6.post1 ; python_version >= "3.8" and python_version < "3.13" + circus==0.18.0 ; python_version >= "3.8" and python_version < "3.13" + click-didyoumean==0.3.1 ; python_version >= "3.8" and python_version < "3.13" + click-plugins==1.1.1 ; python_version >= "3.8" and python_version < "3.13" + click-repl==0.3.0 ; python_version >= "3.8" and python_version < "3.13" + click==8.1.7 ; python_version >= "3.8" and python_version < "3.13" + cloudauthz==0.6.0 ; python_version >= "3.8" and python_version < "3.13" + cloudbridge==3.2.0 ; python_version >= "3.8" and python_version < "3.13" + colorama==0.4.6 ; python_version >= "3.8" and python_version < "3.13" and platform_system == "Windows" + coloredlogs==15.0.1 ; python_version >= "3.8" and python_version < "3.13" + conda-package-streaming==0.9.0 ; python_version >= "3.8" and python_version < "3.13" + cryptography==42.0.7 ; python_version >= "3.8" and python_version < "3.13" + cwl-upgrader==1.2.11 ; python_version >= "3.8" and python_version < "3.13" + cwl-utils==0.33 ; python_version >= "3.8" and python_version < "3.13" + cwltool==3.1.20240508115724 ; python_version >= "3.8" and python_version < "3.13" + decorator==5.1.1 ; python_version >= "3.8" and python_version < "3.13" + defusedxml==0.7.1 ; python_version >= "3.8" and python_version < "3.13" + deprecation==2.1.0 ; python_version >= "3.8" and python_version < "3.13" + dictobj==0.4 ; python_version >= "3.8" and python_version < "3.13" + dnspython==2.6.1 ; python_version >= "3.8" and python_version < "3.13" + docopt==0.6.2 ; python_version >= "3.8" and python_version < "3.13" + docutils==0.20.1 ; python_version >= "3.8" and python_version < "3.13" + dparse==0.6.3 ; python_version >= "3.8" and python_version < "3.13" + edam-ontology==1.25.2 ; python_version >= "3.8" and python_version < "3.13" + email-validator==2.1.1 ; python_version >= "3.8" and python_version < "3.13" + exceptiongroup==1.2.1 ; python_version >= "3.8" and python_version < "3.11" + fastapi-slim==0.111.0 ; python_version >= "3.8" and python_version < "3.13" + filelock==3.14.0 ; python_version >= "3.8" and python_version < "3.13" + frozenlist==1.4.1 ; python_version >= "3.8" and python_version < "3.13" + fs==2.4.16 ; python_version >= "3.8" and python_version < "3.13" + fsspec==2024.5.0 ; python_version >= "3.8" and python_version < "3.13" + future==1.0.0 ; python_version >= "3.8" and python_version < "3.13" + galaxy-sequence-utils==1.1.5 ; python_version >= "3.8" and python_version < "3.13" + galaxy2cwl==0.1.4 ; python_version >= "3.8" and python_version < "3.13" + graphene-sqlalchemy==3.0.0rc1 ; python_version >= "3.8" and python_version < "3.13" + graphene==3.3 ; python_version >= "3.8" and python_version < "3.13" + graphql-core==3.2.3 ; python_version >= "3.8" and python_version < "3.13" + graphql-relay==3.2.0 ; python_version >= "3.8" and python_version < "3.13" + gravity==1.0.6 ; python_version >= "3.8" and python_version < "3.13" + greenlet==3.0.3 ; python_version >= "3.8" and python_version < "3.13" and (platform_machine == "aarch64" or platform_machine == "ppc64le" or platform_machine == "x86_64" or platform_machine == "amd64" or platform_machine == "AMD64" or platform_machine == "win32" or platform_machine == "WIN32") + gunicorn==22.0.0 ; python_version >= "3.8" and python_version < "3.13" + gxformat2==0.18.0 ; python_version >= "3.8" and python_version < "3.13" + h11==0.14.0 ; python_version >= "3.8" and python_version < "3.13" + h5grove==2.2.0 ; python_version >= "3.8" and python_version < "3.13" + h5py==3.11.0 ; python_version >= "3.8" and python_version < "3.13" + humanfriendly==10.0 ; python_version >= "3.8" and python_version < "3.13" + idna==3.7 ; python_version >= "3.8" and python_version < "3.13" + importlib-metadata==7.1.0 ; python_version >= "3.8" and python_version < "3.13" + importlib-resources==6.4.0 ; python_version >= "3.8" and python_version < "3.9" + isa-rwval==0.10.10 ; python_version >= "3.8" and python_version < "3.13" + isal==1.6.1 ; python_version >= "3.8" and python_version < "3.13" + isodate==0.6.1 ; python_version >= "3.8" and python_version < "3.13" + jinja2==3.1.4 ; python_version >= "3.8" and python_version < "3.13" + jmespath==1.0.1 ; python_version >= "3.8" and python_version < "3.13" + jsonref==1.1.0 ; python_version >= "3.8" and python_version < "3.13" + jsonschema-specifications==2023.12.1 ; python_version >= "3.8" and python_version < "3.13" + jsonschema==4.20.0 ; python_version >= "3.8" and python_version < "3.13" + kombu==5.3.7 ; python_version >= "3.8" and python_version < "3.13" + lagom==2.6.0 ; python_version >= "3.8" and python_version < "3.13" + lxml==4.9.4 ; python_version >= "3.8" and python_version < "3.13" + mako==1.3.5 ; python_version >= "3.8" and python_version < "3.13" + markdown-it-py==3.0.0 ; python_version >= "3.8" and python_version < "3.13" + markdown==3.6 ; python_version >= "3.8" and python_version < "3.13" + markupsafe==2.1.5 ; python_version >= "3.8" and python_version < "3.13" + mdurl==0.1.2 ; python_version >= "3.8" and python_version < "3.13" + mercurial==6.7.4 ; python_version >= "3.8" and python_version < "3.13" + mistune==3.0.2 ; python_version >= "3.8" and python_version < "3.13" + mrcfile==1.5.0 ; python_version >= "3.8" and python_version < "3.13" + msal==1.28.0 ; python_version >= "3.8" and python_version < "3.13" + msgpack==1.0.8 ; python_version >= "3.8" and python_version < "3.13" + multidict==6.0.5 ; python_version >= "3.8" and python_version < "3.13" + mypy-extensions==1.0.0 ; python_version >= "3.8" and python_version < "3.13" + networkx==2.5 ; python_version >= "3.8" and python_version < "3.13" + nodeenv==1.8.0 ; python_version >= "3.8" and python_version < "3.13" + numpy==1.24.4 ; python_version >= "3.8" and python_version < "3.9" + numpy==1.26.4 ; python_version >= "3.9" and python_version < "3.13" + oauthlib==3.2.2 ; python_version >= "3.8" and python_version < "3.13" + orjson==3.10.3 ; python_version >= "3.8" and python_version < "3.13" + oyaml==1.0 ; python_version >= "3.8" and python_version < "3.13" + packaging==24.0 ; python_version >= "3.8" and python_version < "3.13" + paramiko==3.4.0 ; python_version >= "3.8" and python_version < "3.13" + parsley==1.3 ; python_version >= "3.8" and python_version < "3.13" + paste==3.10.1 ; python_version >= "3.8" and python_version < "3.13" + pastedeploy==3.1.0 ; python_version >= "3.8" and python_version < "3.13" + pebble==5.0.7 ; python_version >= "3.8" and python_version < "3.13" + pillow==10.3.0 ; python_version >= "3.8" and python_version < "3.13" + promise==2.3 ; python_version >= "3.8" and python_version < "3.13" + prompt-toolkit==3.0.43 ; python_version >= "3.8" and python_version < "3.13" + prov==1.5.1 ; python_version >= "3.8" and python_version < "3.13" + psutil==5.9.8 ; python_version >= "3.8" and python_version < "3.13" + pulsar-galaxy-lib==0.15.6 ; python_version >= "3.8" and python_version < "3.13" + pycparser==2.22 ; python_version >= "3.8" and python_version < "3.13" + pycryptodome==3.20.0 ; python_version >= "3.8" and python_version < "3.13" + pydantic-core==2.18.4 ; python_version >= "3.8" and python_version < "3.13" + pydantic-tes==0.1.5 ; python_version >= "3.8" and python_version < "3.13" + pydantic==2.7.4 ; python_version >= "3.8" and python_version < "3.13" + pydantic[email]==2.7.4 ; python_version >= "3.8" and python_version < "3.13" + pydot==2.0.0 ; python_version >= "3.8" and python_version < "3.13" + pyeventsystem==0.1.0 ; python_version >= "3.8" and python_version < "3.13" + pyfaidx==0.8.1.1 ; python_version >= "3.8" and python_version < "3.13" + pygments==2.18.0 ; python_version >= "3.8" and python_version < "3.13" + pyjwt==2.8.0 ; python_version >= "3.8" and python_version < "3.13" + pyjwt[crypto]==2.8.0 ; python_version >= "3.8" and python_version < "3.13" + pykwalify==1.8.0 ; python_version >= "3.8" and python_version < "3.13" + pylibmagic==0.5.0 ; python_version >= "3.8" and python_version < "3.13" + pynacl==1.5.0 ; python_version >= "3.8" and python_version < "3.13" + pyparsing==3.1.2 ; python_version >= "3.8" and python_version < "3.13" + pyreadline3==3.4.1 ; sys_platform == "win32" and python_version >= "3.8" and python_version < "3.13" + pysam==0.22.1 ; python_version >= "3.8" and python_version < "3.13" + python-dateutil==2.9.0.post0 ; python_version >= "3.8" and python_version < "3.13" + python-magic==0.4.27 ; python_version >= "3.8" and python_version < "3.13" + python-multipart==0.0.9 ; python_version >= "3.8" and python_version < "3.13" + python3-openid==3.2.0 ; python_version >= "3.8" and python_version < "3.13" + pytz==2024.1 ; python_version >= "3.8" and python_version < "3.13" + pyyaml==6.0.1 ; python_version >= "3.8" and python_version < "3.13" + pyzmq==26.0.3 ; python_version >= "3.8" and python_version < "3.13" + rdflib==6.3.2 ; python_version >= "3.8" and python_version < "3.13" + referencing==0.35.1 ; python_version >= "3.8" and python_version < "3.13" + refgenconf==0.12.2 ; python_version >= "3.8" and python_version < "3.13" + regex==2024.5.15 ; python_version >= "3.8" and python_version < "3.13" + repoze-lru==0.7 ; python_version >= "3.8" and python_version < "3.13" + requests-oauthlib==2.0.0 ; python_version >= "3.8" and python_version < "3.13" + requests-toolbelt==1.0.0 ; python_version >= "3.8" and python_version < "3.13" + requests-unixsocket==0.3.0 ; python_version >= "3.8" and python_version < "3.13" + requests==2.31.0 ; python_version >= "3.8" and python_version < "3.13" + rich==13.7.1 ; python_version >= "3.8" and python_version < "3.13" + rocrate==0.10.0 ; python_version >= "3.8" and python_version < "3.13" + routes==2.5.1 ; python_version >= "3.8" and python_version < "3.13" + rpds-py==0.18.1 ; python_version >= "3.8" and python_version < "3.13" + ruamel-yaml-clib==0.2.8 ; platform_python_implementation == "CPython" and python_version < "3.13" and python_version >= "3.8" + ruamel-yaml==0.18.6 ; python_version >= "3.8" and python_version < "3.13" + s3fs==2024.5.0 ; python_version >= "3.8" and python_version < "3.13" + schema-salad==8.5.20240503091721 ; python_version >= "3.8" and python_version < "3.13" + setuptools-scm==5.0.2 ; python_version >= "3.8" and python_version < "3.13" + setuptools==69.5.1 ; python_version >= "3.8" and python_version < "3.13" + shellescape==3.8.1 ; python_version >= "3.8" and python_version < "3.13" + six==1.16.0 ; python_version >= "3.8" and python_version < "3.13" + sniffio==1.3.1 ; python_version >= "3.8" and python_version < "3.13" + social-auth-core==4.5.4 ; python_version >= "3.8" and python_version < "3.13" + sortedcontainers==2.4.0 ; python_version >= "3.8" and python_version < "3.13" + spython==0.3.13 ; python_version >= "3.8" and python_version < "3.13" + sqlalchemy==2.0.30 ; python_version >= "3.8" and python_version < "3.13" + sqlitedict==2.1.0 ; python_version >= "3.8" and python_version < "3.13" + sqlparse==0.5.0 ; python_version >= "3.8" and python_version < "3.13" + starlette-context==0.3.6 ; python_version >= "3.8" and python_version < "3.13" + starlette-graphene3==0.6.0 ; python_version >= "3.8" and python_version < "3.13" + starlette==0.37.2 ; python_version >= "3.8" and python_version < "3.13" + supervisor==4.2.5 ; python_version >= "3.8" and python_version < "3.13" + svgwrite==1.4.3 ; python_version >= "3.8" and python_version < "3.13" + tenacity==8.3.0 ; python_version >= "3.8" and python_version < "3.13" + tifffile==2023.7.10 ; python_version >= "3.8" and python_version < "3.13" + tinydb==4.8.0 ; python_version >= "3.8" and python_version < "3.13" + tomli==2.0.1 ; python_version >= "3.8" and python_version < "3.11" + tornado==6.4 ; python_version >= "3.8" and python_version < "3.13" + tqdm==4.66.4 ; python_version >= "3.8" and python_version < "3.13" + tuspy==1.0.3 ; python_version >= "3.8" and python_version < "3.13" + tuswsgi==0.5.5 ; python_version >= "3.8" and python_version < "3.13" + typing-extensions==4.11.0 ; python_version >= "3.8" and python_version < "3.13" + tzdata==2024.1 ; python_version >= "3.8" and python_version < "3.13" + tzlocal==5.2 ; python_version >= "3.8" and python_version < "3.13" + ubiquerg==0.8.0 ; python_version >= "3.8" and python_version < "3.13" + urllib3==1.26.18 ; python_version >= "3.8" and python_version < "3.13" + uvicorn==0.29.0 ; python_version >= "3.8" and python_version < "3.13" + uvloop==0.19.0 ; python_version >= "3.8" and python_version < "3.13" + vine==5.1.0 ; python_version >= "3.8" and python_version < "3.13" + wcwidth==0.2.13 ; python_version >= "3.8" and python_version < "3.13" + webencodings==0.5.1 ; python_version >= "3.8" and python_version < "3.13" + webob==1.8.7 ; python_version >= "3.8" and python_version < "3.13" + whoosh==2.7.4 ; python_version >= "3.8" and python_version < "3.13" + wrapt==1.16.0 ; python_version >= "3.8" and python_version < "3.13" + yacman==0.9.3 ; python_version >= "3.8" and python_version < "3.13" + yarl==1.9.4 ; python_version >= "3.8" and python_version < "3.13" + zipp==3.18.2 ; python_version >= "3.8" and python_version < "3.13" + zipstream-new==1.1.8 ; python_version >= "3.8" and python_version < "3.13" + zstandard==0.22.0 ; python_version >= "3.8" and python_version < "3.13" +python_requires = >=3.8 + +[options.packages.find] +exclude = + tests*