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Packages: finish migration from `setup.cfg to pyproject.toml`

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Also:
- Drop now unnecessary ``packages/sync_pyprojects.py`` script.
This commit is contained in:
Nicola Soranzo
2026-06-08 02:34:36 +01:00
parent 788ba05979
commit c329529e51
55 changed files with 1046 additions and 1378 deletions
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packages/app/pyproject.toml
+89 -11
View File
@@ -1,19 +1,71 @@
[build-system]
build-backend = "setuptools.build_meta"
requires = ["setuptools", "setuptools-scm>=8"]
requires = ["setuptools>=77.0.0", "setuptools-scm>=8"]
[project]
dynamic = [
"authors",
"dependencies",
"description",
"license",
"optional-dependencies",
"readme",
"requires-python",
"version",
]
dynamic = ["readme"]
name = "galaxy-app"
version = "26.1.dev0"
description = "Galaxy application (backend)"
requires-python = ">=3.10"
license = "MIT"
license-files = [
"LICENSE",
]
authors = [
{name = "Galaxy Project and Community", email = "galaxy-committers@lists.galaxyproject.org"},
]
dependencies = [
"galaxy-auth",
"galaxy-config",
"galaxy-data",
"galaxy-files",
"galaxy-job-execution",
"galaxy-job-metrics",
"galaxy-objectstore",
"galaxy-tool-util[cwl,edam]",
"galaxy-tool-shed-schema",
"galaxy-tours",
"galaxy-util[image-util,jstree]",
"galaxy-web-framework",
"galaxy-web-stack",
"Beaker",
"boltons",
"bx-python",
"celery",
"cloudauthz==0.6.0",
"cwl-utils",
"dparse",
"gxformat2>=0.27.0",
"kombu>=5.3",
"lagom",
"lxml!=4.2.2",
"Mako",
"Markdown",
"MarkupSafe",
"mercurial>=7.2",
"more-itertools",
"nodejs-wheel>=22,<23",
"packaging",
"paramiko!=2.9.0,!=2.9.1",
"pebble",
"pulsar-galaxy-lib>=0.15.0.dev0",
"pydantic>=2.7.4",
"pydantic-ai>=0.1.16",
"pysam>=0.21",
"python-slugify",
"PyJWT",
"PyYAML",
"refgenconf>=0.13.0",
"regex",
"requests",
"SQLAlchemy>=2.0.37,<2.1,!=2.0.41",
"starlette",
"svgwrite",
"typing-extensions",
"WebOb>=1.8.9",
"Whoosh",
]
classifiers = [
"Development Status :: 5 - Production/Stable",
"Environment :: Console",
@@ -32,7 +84,33 @@ classifiers = [
]
keywords = ["Galaxy"]
[project.optional-dependencies]
test = [
"galaxy-test-base",
"mock-ssh-server",
"pkce",
"pykwalify",
"pytest",
"pytest-asyncio",
"pytest-mock",
"responses",
"testfixtures",
]
[project.scripts]
galaxy-main = "galaxy.main:main"
galaxy-dependencies = "galaxy.dependencies.script:main"
galaxy-sse-monitor = "galaxy.sse_monitor.__main__:main"
[project.urls]
Homepage = "https://github.com/galaxyproject/galaxy"
[tool.setuptools.dynamic]
readme = {content-type = "text/x-rst", file = ["README.rst", "HISTORY.rst"]}
[tool.setuptools.packages.find]
where = ["src"]
exclude = [
"galaxy.tools.bundled*",
"galaxy.tools.parameters.test*",
]
packages/app/setup.cfg
-87
View File
@@ -1,87 +0,0 @@
[metadata]
author = Galaxy Project and Community
author_email = galaxy-committers@lists.galaxyproject.org
description = Galaxy application (backend)
license = MIT
license_files =
LICENSE
long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-app
url = https://github.com/galaxyproject/galaxy
version = 26.1.dev0
[options]
include_package_data = True
install_requires =
galaxy-auth
galaxy-config
galaxy-data
galaxy-files
galaxy-job-execution
galaxy-job-metrics
galaxy-objectstore
galaxy-tool-util[cwl,edam]
galaxy-tool-shed-schema
galaxy-tours
galaxy-util[image-util,jstree]
galaxy-web-framework
galaxy-web-stack
Beaker
boltons
bx-python
celery
cloudauthz==0.6.0
cwl-utils
dparse
gxformat2>=0.27.0
kombu>=5.3
lagom
lxml!=4.2.2
Mako
Markdown
MarkupSafe
mercurial>=7.2
more-itertools
nodejs-wheel>=22,<23
packaging
paramiko!=2.9.0,!=2.9.1
pebble
pulsar-galaxy-lib>=0.15.0.dev0
pydantic>=2.7.4
pydantic-ai>=0.1.16
pysam>=0.21
python-slugify
PyJWT
PyYAML
refgenconf>=0.13.0
regex
requests
SQLAlchemy>=2.0.37,<2.1,!=2.0.41
starlette
svgwrite
typing-extensions
WebOb>=1.8.9
Whoosh
package_dir =
=src
packages = find_namespace:
python_requires = >=3.10
[options.extras_require]
test =
galaxy-test-base
mock-ssh-server
pkce
pykwalify
pytest
pytest-asyncio
pytest-mock
responses
testfixtures
[options.packages.find]
where = src
exclude =
galaxy.tools.bundled*
galaxy.tools.parameters.test*
packages/auth/pyproject.toml
+30 -11
View File
@@ -1,19 +1,24 @@
[build-system]
build-backend = "setuptools.build_meta"
requires = ["setuptools", "setuptools-scm>=8"]
requires = ["setuptools>=77.0.0", "setuptools-scm>=8"]
[project]
dynamic = [
"authors",
"dependencies",
"description",
"license",
"optional-dependencies",
"readme",
"requires-python",
"version",
]
dynamic = ["readme"]
name = "galaxy-auth"
version = "26.1.dev0"
description = "Galaxy auth framework and implementations"
requires-python = ">=3.10"
license = "MIT"
license-files = [
"LICENSE",
]
authors = [
{name = "Galaxy Project and Community", email = "galaxy-committers@lists.galaxyproject.org"},
]
dependencies = [
"galaxy-data",
"galaxy-util",
]
classifiers = [
"Development Status :: 5 - Production/Stable",
"Environment :: Console",
@@ -31,3 +36,17 @@ classifiers = [
"Topic :: Software Development :: Testing",
]
keywords = ["Galaxy"]
[project.optional-dependencies]
test = [
"pytest",
]
[project.urls]
Homepage = "https://github.com/galaxyproject/galaxy"
[tool.setuptools.dynamic]
readme = {content-type = "text/x-rst", file = ["README.rst", "HISTORY.rst"]}
[tool.setuptools.packages.find]
where = ["src"]
packages/auth/setup.cfg
-30
View File
@@ -1,30 +0,0 @@
[metadata]
author = Galaxy Project and Community
author_email = galaxy-committers@lists.galaxyproject.org
description = Galaxy auth framework and implementations
license = MIT
license_files =
LICENSE
long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-auth
url = https://github.com/galaxyproject/galaxy
version = 26.1.dev0
[options]
include_package_data = True
install_requires =
galaxy-data
galaxy-util
package_dir =
=src
packages = find_namespace:
python_requires = >=3.10
[options.extras_require]
test =
pytest
[options.packages.find]
where = src
packages/config/pyproject.toml
+34 -11
View File
@@ -1,19 +1,27 @@
[build-system]
build-backend = "setuptools.build_meta"
requires = ["setuptools", "setuptools-scm>=8"]
requires = ["setuptools>=77.0.0", "setuptools-scm>=8"]
[project]
dynamic = [
"authors",
"dependencies",
"description",
"license",
"optional-dependencies",
"readme",
"requires-python",
"version",
]
dynamic = ["readme"]
name = "galaxy-config"
version = "26.1.dev0"
description = "Galaxy configuration"
requires-python = ">=3.10"
license = "MIT"
license-files = [
"LICENSE",
]
authors = [
{name = "Galaxy Project and Community", email = "galaxy-committers@lists.galaxyproject.org"},
]
dependencies = [
"galaxy-util",
"boltons",
"jinja2",
"pykwalify",
"PyYAML",
]
classifiers = [
"Development Status :: 5 - Production/Stable",
"Environment :: Console",
@@ -32,5 +40,20 @@ classifiers = [
]
keywords = ["Galaxy"]
[project.optional-dependencies]
test = [
"pytest",
"gravity>=1.2.0",
]
[project.scripts]
galaxy-config = "galaxy.config.script:main"
[project.urls]
Homepage = "https://github.com/galaxyproject/galaxy"
[tool.setuptools.dynamic]
readme = {content-type = "text/x-rst", file = ["README.rst", "HISTORY.rst"]}
[tool.setuptools.packages.find]
where = ["src"]
packages/config/setup.cfg
-33
View File
@@ -1,33 +0,0 @@
[metadata]
author = Galaxy Project and Community
author_email = galaxy-committers@lists.galaxyproject.org
description = Galaxy configuration
license = MIT
license_files =
LICENSE
long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-config
url = https://github.com/galaxyproject/galaxy
version = 26.1.dev0
[options]
include_package_data = True
install_requires =
galaxy-util
boltons
jinja2
pykwalify
PyYAML
package_dir =
=src
packages = find_namespace:
python_requires = >=3.10
[options.extras_require]
test =
pytest
gravity>=1.2.0
[options.packages.find]
where = src
packages/data/pyproject.toml
+67 -11
View File
@@ -1,19 +1,55 @@
[build-system]
build-backend = "setuptools.build_meta"
requires = ["setuptools", "setuptools-scm>=8"]
requires = ["setuptools>=77.0.0", "setuptools-scm>=8"]
[project]
dynamic = [
"authors",
"dependencies",
"description",
"license",
"optional-dependencies",
"readme",
"requires-python",
"version",
]
dynamic = ["readme"]
name = "galaxy-data"
version = "26.1.dev0"
description = "Galaxy datatype framework and datatypes"
requires-python = ">=3.10"
license = "MIT"
license-files = [
"LICENSE",
]
authors = [
{name = "Galaxy Project and Community", email = "galaxy-committers@lists.galaxyproject.org"},
]
dependencies = [
"galaxy-files",
"galaxy-objectstore",
"galaxy-schema",
"galaxy-tool-util",
"galaxy-util[image-util,template]",
"alembic",
"bdbag>=1.6.3",
"bx-python",
"dnspython",
"galaxy-sequence-utils",
"h5grove>=1.2.1",
"h5py",
"ijson",
"isa-rwval>=0.10.11",
"isal>=1.7.0",
"MarkupSafe",
"msal",
"mrcfile",
"numpy",
"openpyxl>=3.1.5",
"parsley",
"pycryptodome",
"pydantic[email]>=2.7.4",
"pydicom",
"pylibmagic",
"pypng",
"python-magic",
"pysam>=0.21",
"rocrate<0.15.0",
"social-auth-core>=4.5.0",
"SQLAlchemy>=2.0.37,<2.1,!=2.0.41",
"tifffile",
"typing-extensions",
]
classifiers = [
"Development Status :: 5 - Production/Stable",
"Environment :: Console",
@@ -32,6 +68,14 @@ classifiers = [
]
keywords = ["Galaxy"]
[project.optional-dependencies]
test = [
"galaxy-config",
"hvac",
"pytest",
"roc-validator",
]
[project.scripts]
galaxy-build-objects = "galaxy.model.store.build_objects:main"
galaxy-load-objects = "galaxy.model.store.load_objects:main"
@@ -39,3 +83,15 @@ galaxy-manage-db = "galaxy.model.orm.scripts:manage_db"
galaxy-prune-histories = "galaxy.model.scripts:prune_history_table"
galaxy-delete-sessions = "galaxy.model.scripts:delete_galaxy_sessions"
galaxy-delete-job-metrics = "galaxy.model.scripts:delete_job_metrics"
[project.urls]
Homepage = "https://github.com/galaxyproject/galaxy"
[tool.setuptools.dynamic]
readme = {content-type = "text/x-rst", file = ["README.rst", "HISTORY.rst"]}
[tool.setuptools.packages.find]
where = ["src"]
exclude = [
"galaxy.datatypes.test",
]
packages/data/setup.cfg
-65
View File
@@ -1,65 +0,0 @@
[metadata]
author = Galaxy Project and Community
author_email = galaxy-committers@lists.galaxyproject.org
description = Galaxy datatype framework and datatypes
license = MIT
license_files =
LICENSE
long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-data
url = https://github.com/galaxyproject/galaxy
version = 26.1.dev0
[options]
include_package_data = True
install_requires =
galaxy-files
galaxy-objectstore
galaxy-schema
galaxy-tool-util
galaxy-util[image-util,template]
alembic
bdbag>=1.6.3
bx-python
dnspython
galaxy-sequence-utils
h5grove>=1.2.1
h5py
ijson
isa-rwval>=0.10.11
isal>=1.7.0
MarkupSafe
msal
mrcfile
numpy
openpyxl>=3.1.5
parsley
pycryptodome
pydantic[email]>=2.7.4
pydicom
pylibmagic
pypng
python-magic
pysam>=0.21
rocrate<0.15.0
social-auth-core>=4.5.0
SQLAlchemy>=2.0.37,<2.1,!=2.0.41
tifffile
typing-extensions
package_dir =
=src
packages = find_namespace:
python_requires = >=3.10
[options.extras_require]
test =
galaxy-config
hvac
pytest
roc-validator
[options.packages.find]
where = src
exclude =
galaxy.datatypes.test
packages/files/LICENSE.txt → packages/files/LICENSE
View File
packages/files/pyproject.toml
+38 -11
View File
@@ -1,19 +1,28 @@
[build-system]
build-backend = "setuptools.build_meta"
requires = ["setuptools", "setuptools-scm>=8"]
requires = ["setuptools>=77.0.0", "setuptools-scm>=8"]
[project]
dynamic = [
"authors",
"dependencies",
"description",
"license",
"optional-dependencies",
"readme",
"requires-python",
"version",
]
dynamic = ["readme"]
name = "galaxy-files"
version = "26.1.dev0"
description = "Galaxy file source framework and default plugins"
requires-python = ">=3.10"
license = "MIT"
license-files = [
"LICENSE",
]
authors = [
{name = "Galaxy Project and Community", email = "galaxy-committers@lists.galaxyproject.org"},
]
dependencies = [
"galaxy-util[config-template,template]",
"fs",
"setuptools<82", # TODO: remove once pyfilesystem2 drops pkg_resources (https://github.com/PyFilesystem/pyfilesystem2/issues/597)
"pydantic>=2.7.4",
"typing-extensions",
"fsspec",
]
classifiers = [
"Development Status :: 5 - Production/Stable",
"Environment :: Console",
@@ -32,5 +41,23 @@ classifiers = [
]
keywords = ["Galaxy"]
[project.optional-dependencies]
test = [
"galaxy-test-base",
"pytest",
"gcsfs",
"responses",
"s3fs>=2023.1.0",
]
[project.scripts]
galaxy-file-sources-conf-validation = "galaxy.files.validate.script:main"
[project.urls]
Homepage = "https://github.com/galaxyproject/galaxy"
[tool.setuptools.dynamic]
readme = {content-type = "text/x-rst", file = ["README.rst", "HISTORY.rst"]}
[tool.setuptools.packages.find]
where = ["src"]
packages/files/setup.cfg
-37
View File
@@ -1,37 +0,0 @@
[metadata]
author = Galaxy Project and Community
author_email = galaxy-committers@lists.galaxyproject.org
description = Galaxy file source framework and default plugins
license = MIT
license_files =
LICENSE
long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-files
url = https://github.com/galaxyproject/galaxy
version = 26.1.dev0
[options]
include_package_data = True
install_requires =
galaxy-util[config-template,template]
fs
setuptools<82 # TODO: remove once pyfilesystem2 drops pkg_resources (https://github.com/PyFilesystem/pyfilesystem2/issues/597)
pydantic>=2.7.4
typing-extensions
fsspec
package_dir =
=src
packages = find_namespace:
python_requires = >=3.10
[options.extras_require]
test =
galaxy-test-base
pytest
gcsfs
responses
s3fs>=2023.1.0
[options.packages.find]
where = src
packages/job_execution/pyproject.toml
+35 -11
View File
@@ -1,19 +1,29 @@
[build-system]
build-backend = "setuptools.build_meta"
requires = ["setuptools", "setuptools-scm>=8"]
requires = ["setuptools>=77.0.0", "setuptools-scm>=8"]
[project]
dynamic = [
"authors",
"dependencies",
"description",
"license",
"optional-dependencies",
"readme",
"requires-python",
"version",
]
dynamic = ["readme"]
name = "galaxy-job-execution"
version = "26.1.dev0"
description = "Galaxy job execution runtime utilities"
requires-python = ">=3.10"
license = "MIT"
license-files = [
"LICENSE",
]
authors = [
{name = "Galaxy Project and Community", email = "galaxy-committers@lists.galaxyproject.org"},
]
dependencies = [
"galaxy-data",
"galaxy-files",
"galaxy-objectstore",
"galaxy-tool-util",
"galaxy-util",
"MarkupSafe",
"SQLAlchemy>=2.0.37,<2.1,!=2.0.41",
]
classifiers = [
"Development Status :: 5 - Production/Stable",
"Environment :: Console",
@@ -32,6 +42,20 @@ classifiers = [
]
keywords = ["Galaxy"]
[project.optional-dependencies]
test = [
"pytest",
]
[project.scripts]
galaxy-set-metadata = "galaxy.metadata.set_metadata:set_metadata"
galaxy-container-monitor = "galaxy.job_execution.container_monitor:main"
[project.urls]
Homepage = "https://github.com/galaxyproject/galaxy"
[tool.setuptools.dynamic]
readme = {content-type = "text/x-rst", file = ["README.rst", "HISTORY.rst"]}
[tool.setuptools.packages.find]
where = ["src"]
packages/job_execution/setup.cfg
-34
View File
@@ -1,34 +0,0 @@
[metadata]
author = Galaxy Project and Community
author_email = galaxy-committers@lists.galaxyproject.org
description = Galaxy job execution runtime utilities
license = MIT
license_files =
LICENSE
long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-job-execution
url = https://github.com/galaxyproject/galaxy
version = 26.1.dev0
[options]
include_package_data = True
install_requires =
galaxy-data
galaxy-files
galaxy-objectstore
galaxy-tool-util
galaxy-util
MarkupSafe
SQLAlchemy>=2.0.37,<2.1,!=2.0.41
package_dir =
=src
packages = find_namespace:
python_requires = >=3.10
[options.extras_require]
test =
pytest
[options.packages.find]
where = src
packages/job_metrics/pyproject.toml
+26 -10
View File
@@ -3,17 +3,19 @@ build-backend = "setuptools.build_meta"
requires = ["setuptools", "setuptools-scm>=8"]
[project]
dynamic = [
"authors",
"dependencies",
"description",
"license",
"optional-dependencies",
"readme",
"requires-python",
"version",
]
dynamic = ["readme"]
name = "galaxy-job-metrics"
version = "26.1.dev0"
description = "Galaxy job metrics"
requires-python = ">=3.8"
license = {"text" = "MIT"}
authors = [
{name = "Galaxy Project and Community", email = "galaxy-committers@lists.galaxyproject.org"},
]
dependencies = [
"galaxy-util",
"backports.zoneinfo;python_version<'3.9'",
]
classifiers = [
"Development Status :: 5 - Production/Stable",
"Environment :: Console",
@@ -33,3 +35,17 @@ classifiers = [
"Topic :: Software Development :: Testing",
]
keywords = ["Galaxy"]
[project.optional-dependencies]
test = [
"pytest",
]
[project.urls]
Homepage = "https://github.com/galaxyproject/galaxy"
[tool.setuptools.dynamic]
readme = {content-type = "text/x-rst", file = ["README.rst", "HISTORY.rst"]}
[tool.setuptools.packages.find]
where = ["src"]
packages/job_metrics/setup.cfg
-29
View File
@@ -1,29 +0,0 @@
[metadata]
author = Galaxy Project and Community
author_email = galaxy-committers@lists.galaxyproject.org
description = Galaxy job metrics
license = MIT
license_files =
LICENSE
long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-job-metrics
url = https://github.com/galaxyproject/galaxy
version = 26.1.dev0
[options]
include_package_data = True
install_requires =
galaxy-util
backports.zoneinfo;python_version<'3.9'
package_dir =
=src
packages = find_namespace:
python_requires = >=3.8
[options.extras_require]
test =
pytest
[options.packages.find]
where = src
packages/meta/pyproject.toml
+31 -11
View File
@@ -1,19 +1,22 @@
[build-system]
build-backend = "setuptools.build_meta"
requires = ["setuptools", "setuptools-scm>=8"]
requires = ["setuptools>=77.0.0", "setuptools-scm>=8"]
[project]
dynamic = [
"authors",
"dependencies",
"description",
"license",
"optional-dependencies",
"readme",
"requires-python",
"version",
]
dynamic = ["readme"]
name = "galaxy"
version = "26.1.dev0"
description = "Galaxy server metapackage"
requires-python = ">=3.10"
license = "MIT"
license-files = [
"LICENSE",
]
authors = [
{name = "Galaxy Project and Community", email = "galaxy-committers@lists.galaxyproject.org"},
]
dependencies = [
]
classifiers = [
"Development Status :: 5 - Production/Stable",
"Environment :: Console",
@@ -33,3 +36,20 @@ classifiers = [
"Topic :: Software Development :: Testing",
]
keywords = ["Galaxy"]
[project.optional-dependencies]
postgresql = [
"psycopg[binary]",
]
[project.urls]
Homepage = "https://github.com/galaxyproject/galaxy"
[tool.setuptools.dynamic]
readme = {content-type = "text/x-rst", file = ["README.rst", "HISTORY.rst"]}
[tool.setuptools.packages.find]
where = ["src"]
exclude = [
"tests*",
]
packages/meta/setup.cfg
-25
View File
@@ -1,25 +0,0 @@
[metadata]
author = Galaxy Project and Community
author_email = galaxy-committers@lists.galaxyproject.org
description = Galaxy server metapackage
license = MIT
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 = 26.1.dev0
[options]
include_package_data = True
packages = find:
python_requires = >=3.10
[options.extras_require]
postgresql =
psycopg[binary]
[options.packages.find]
exclude =
tests*
packages/navigation/pyproject.toml
+31 -11
View File
@@ -1,19 +1,25 @@
[build-system]
build-backend = "setuptools.build_meta"
requires = ["setuptools", "setuptools-scm>=8"]
requires = ["setuptools>=77.0.0", "setuptools-scm>=8"]
[project]
dynamic = [
"authors",
"dependencies",
"description",
"license",
"optional-dependencies",
"readme",
"requires-python",
"version",
]
dynamic = ["readme"]
name = "galaxy-navigation"
version = "26.1.dev0"
description = "Galaxy client DOM navigation framework"
requires-python = ">=3.10"
license = "MIT"
license-files = [
"LICENSE",
]
authors = [
{name = "Galaxy Project and Community", email = "galaxy-committers@lists.galaxyproject.org"},
]
dependencies = [
"galaxy-util",
"PyYAML",
"seletools",
]
classifiers = [
"Development Status :: 5 - Production/Stable",
"Environment :: Console",
@@ -31,3 +37,17 @@ classifiers = [
"Topic :: Software Development :: Testing",
]
keywords = ["Galaxy"]
[project.optional-dependencies]
test = [
"pytest",
]
[project.urls]
Homepage = "https://github.com/galaxyproject/galaxy"
[tool.setuptools.dynamic]
readme = {content-type = "text/x-rst", file = ["README.rst", "HISTORY.rst"]}
[tool.setuptools.packages.find]
where = ["src"]
packages/navigation/setup.cfg
-30
View File
@@ -1,30 +0,0 @@
[metadata]
author = Galaxy Project and Community
author_email = galaxy-committers@lists.galaxyproject.org
description = Galaxy client DOM navigation framework
license = MIT
license_files =
LICENSE
long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-navigation
url = https://github.com/galaxyproject/galaxy
version = 26.1.dev0
[options.extras_require]
test =
pytest
[options]
include_package_data = True
install_requires =
galaxy-util
PyYAML
seletools
package_dir =
=src
packages = find_namespace:
python_requires = >=3.10
[options.packages.find]
where = src
packages/objectstore/pyproject.toml
+32 -10
View File
@@ -3,17 +3,20 @@ build-backend = "setuptools.build_meta"
requires = ["setuptools", "setuptools-scm>=8"]
[project]
dynamic = [
"authors",
"dependencies",
"description",
"license",
"optional-dependencies",
"readme",
"requires-python",
"version",
]
dynamic = ["readme"]
name = "galaxy-objectstore"
version = "26.1.dev0"
description = "Galaxy objectstore framework and plugins"
requires-python = ">=3.8"
license = {"text" = "MIT"}
authors = [
{name = "Galaxy Project and Community", email = "galaxy-committers@lists.galaxyproject.org"},
]
dependencies = [
"galaxy-util[config-template]",
"pydantic>=2.7.4",
"PyYAML",
]
classifiers = [
"Development Status :: 5 - Production/Stable",
"Environment :: Console",
@@ -33,3 +36,22 @@ classifiers = [
"Topic :: Software Development :: Testing",
]
keywords = ["Galaxy"]
[project.optional-dependencies]
test = [
"pytest",
"boto3",
"azure-storage-blob",
]
[project.urls]
Homepage = "https://github.com/galaxyproject/galaxy"
[tool.setuptools.dynamic]
readme = {content-type = "text/x-rst", file = ["README.rst", "HISTORY.rst"]}
[tool.setuptools.packages.find]
where = ["src"]
exclude = [
"galaxy.objectstore.examples*",
]
packages/objectstore/setup.cfg
-34
View File
@@ -1,34 +0,0 @@
[metadata]
author = Galaxy Project and Community
author_email = galaxy-committers@lists.galaxyproject.org
description = Galaxy objectstore framework and plugins
license = MIT
license_files =
LICENSE
long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-objectstore
url = https://github.com/galaxyproject/galaxy
version = 26.1.dev0
[options]
include_package_data = True
install_requires =
galaxy-util[config-template]
pydantic>=2.7.4
PyYAML
package_dir =
=src
packages = find_namespace:
python_requires = >=3.8
[options.extras_require]
test =
pytest
boto3
azure-storage-blob
[options.packages.find]
where = src
exclude =
galaxy.objectstore.examples*
packages/schema/pyproject.toml
+31 -11
View File
@@ -1,19 +1,25 @@
[build-system]
build-backend = "setuptools.build_meta"
requires = ["setuptools", "setuptools-scm>=8"]
requires = ["setuptools>=77.0.0", "setuptools-scm>=8"]
[project]
dynamic = [
"authors",
"dependencies",
"description",
"license",
"optional-dependencies",
"readme",
"requires-python",
"version",
]
dynamic = ["readme"]
name = "galaxy-schema"
version = "26.1.dev0"
description = "Pydantic models for Galaxy"
requires-python = ">=3.10"
license = "MIT"
license-files = [
"LICENSE",
]
authors = [
{name = "Galaxy Project and Community", email = "galaxy-committers@lists.galaxyproject.org"},
]
dependencies = [
"galaxy-tool-util-models",
"galaxy-util",
"pydantic[email]>=2.7.4",
]
classifiers = [
"Development Status :: 5 - Production/Stable",
"Environment :: Console",
@@ -31,3 +37,17 @@ classifiers = [
"Topic :: Software Development :: Testing",
]
keywords = ["Galaxy"]
[project.optional-dependencies]
test = [
"pytest",
]
[project.urls]
Homepage = "https://github.com/galaxyproject/galaxy"
[tool.setuptools.dynamic]
readme = {content-type = "text/x-rst", file = ["README.rst", "HISTORY.rst"]}
[tool.setuptools.packages.find]
where = ["src"]
packages/schema/setup.cfg
-30
View File
@@ -1,30 +0,0 @@
[metadata]
author = Galaxy Project and Community
author_email = galaxy-committers@lists.galaxyproject.org
description = Pydantic models for Galaxy
license = MIT
license_files =
LICENSE
long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-schema
url = https://github.com/galaxyproject/galaxy
version = 26.1.dev0
[options]
include_package_data = True
install_requires =
galaxy-tool-util-models
galaxy-util
pydantic[email]>=2.7.4
package_dir =
=src
packages = find_namespace:
python_requires = >=3.10
[options.extras_require]
test =
pytest
[options.packages.find]
where = src
packages/selenium/pyproject.toml
+35 -11
View File
@@ -1,19 +1,29 @@
[build-system]
build-backend = "setuptools.build_meta"
requires = ["setuptools", "setuptools-scm>=8"]
requires = ["setuptools>=77.0.0", "setuptools-scm>=8"]
[project]
dynamic = [
"authors",
"dependencies",
"description",
"license",
"optional-dependencies",
"readme",
"requires-python",
"version",
]
dynamic = ["readme"]
name = "galaxy-selenium"
version = "26.1.dev0"
description = "Galaxy Selenium interaction framework"
requires-python = ">=3.10"
license = "MIT"
license-files = [
"LICENSE",
]
authors = [
{name = "Galaxy Project and Community", email = "galaxy-committers@lists.galaxyproject.org"},
]
dependencies = [
"galaxy-navigation",
"galaxy-util",
"axe-selenium-python",
"PyYAML",
"requests",
"selenium!=4.11.0,!=4.11.1,!=4.11.2",
"playwright",
]
classifiers = [
"Development Status :: 5 - Production/Stable",
"Environment :: Console",
@@ -32,5 +42,19 @@ classifiers = [
]
keywords = ["Galaxy"]
[project.optional-dependencies]
test = [
"pytest",
]
[project.scripts]
gx-dump-tour = "galaxy.selenium.scripts.dump_tour:main"
[project.urls]
Homepage = "https://github.com/galaxyproject/galaxy"
[tool.setuptools.dynamic]
readme = {content-type = "text/x-rst", file = ["README.rst", "HISTORY.rst"]}
[tool.setuptools.packages.find]
where = ["src"]
packages/selenium/setup.cfg
-34
View File
@@ -1,34 +0,0 @@
[metadata]
author = Galaxy Project and Community
author_email = galaxy-committers@lists.galaxyproject.org
description = Galaxy Selenium interaction framework
license = MIT
license_files =
LICENSE
long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-selenium
url = https://github.com/galaxyproject/galaxy
version = 26.1.dev0
[options]
include_package_data = True
install_requires =
galaxy-navigation
galaxy-util
axe-selenium-python
PyYAML
requests
selenium!=4.11.0,!=4.11.1,!=4.11.2
playwright
package_dir =
=src
packages = find_namespace:
python_requires = >=3.10
[options.extras_require]
test =
pytest
[options.packages.find]
where = src
packages/sync_pyprojects.py
-76
View File
@@ -1,76 +0,0 @@
import configparser
import tomllib
from pathlib import Path
from string import Template
PACKAGES_DIR = Path(__file__).parent
WORKSPACE_ROOT_PYPROJECT = PACKAGES_DIR / "pyproject.toml"
PYPROJECT_TOML = Template(
"""[build-system]
build-backend = "setuptools.build_meta"
requires = ["setuptools"]
[project]
dynamic = [
"authors",
"dependencies",
"description",
"license",
"optional-dependencies",
"readme",
"requires-python",
"version",
]
name = "${project_name}"
"""
)
def get_workspace_members(pyproject_path: Path):
pyproject_file = Path(pyproject_path)
if not pyproject_file.exists():
raise FileNotFoundError(f"{pyproject_path} not found.")
data = tomllib.load(pyproject_file.open("rb"))
try:
members = data["tool"]["uv"]["workspace"]["members"]
if not isinstance(members, list):
raise ValueError("Expected 'members' to be a list.")
return members
except KeyError:
raise KeyError("Could not find [tool.uv.workspace] members in pyproject.toml.")
def update_project(project_directory: Path):
if not project_directory.exists():
raise Exception(f"Skipping {project_directory}, not found.")
setup_cfg = project_directory / "setup.cfg"
if not setup_cfg.exists():
raise Exception(f"No setup.cfg found in {project_directory}")
config = configparser.ConfigParser()
config.read(setup_cfg)
try:
project_name = config["metadata"]["name"]
print(f"Project name in {setup_cfg}: {project_name}")
except KeyError:
print(f"No [metadata] section or 'name' field in {setup_cfg}")
pyproject_path = project_directory / "pyproject.toml"
with pyproject_path.open("w") as f:
f.write(PYPROJECT_TOML.substitute(project_name=project_name))
if "options.extras_require" in config:
extra_requires = config["options.extras_require"]
if "test" in extra_requires:
print("'" + extra_requires["test"] + "'")
def main():
members = get_workspace_members(WORKSPACE_ROOT_PYPROJECT)
for member in members:
update_project(PACKAGES_DIR / Path(member))
if __name__ == "__main__":
main()
packages/test.sh
+1 -1
View File
@@ -84,7 +84,7 @@ while read -r package_dir || [ -n "$package_dir" ]; do # https://stackoverflow.
${PIP_CMD} install ${PIP_EXTRA_ARGS} '.[image-util,template,jstree,config-template,test]'
elif [ "$package_dir" = "tool_util" ]; then
${PIP_CMD} install ${PIP_EXTRA_ARGS} '.[cwl,mulled,edam,extended-assertions,test]'
elif grep -q 'test =' setup.cfg 2>/dev/null; then
elif grep -q '^test = \[' pyproject.toml 2>/dev/null; then
${PIP_CMD} install ${PIP_EXTRA_ARGS} '.[test]'
else
${PIP_CMD} install ${PIP_EXTRA_ARGS} .
packages/test_api/pyproject.toml
+36 -11
View File
@@ -1,19 +1,27 @@
[build-system]
build-backend = "setuptools.build_meta"
requires = ["setuptools", "setuptools-scm>=8"]
requires = ["setuptools>=77.0.0", "setuptools-scm>=8"]
[project]
dynamic = [
"authors",
"dependencies",
"description",
"license",
"optional-dependencies",
"readme",
"requires-python",
"version",
]
dynamic = ["readme"]
name = "galaxy-test-api"
version = "26.1.dev0"
description = "Galaxy API tests"
requires-python = ">=3.10"
license = "MIT"
license-files = [
"LICENSE",
]
authors = [
{name = "Galaxy Project and Community", email = "galaxy-committers@lists.galaxyproject.org"},
]
dependencies = [
"galaxy-test-base",
"pytest",
"python-dateutil",
"requests",
"tuspy",
]
classifiers = [
"Development Status :: 5 - Production/Stable",
"Environment :: Console",
@@ -31,3 +39,20 @@ classifiers = [
"Topic :: Software Development :: Testing",
]
keywords = ["Galaxy"]
[project.optional-dependencies]
driver = [
"galaxy-test-driver",
]
test = [
"pytest",
]
[project.urls]
Homepage = "https://github.com/galaxyproject/galaxy"
[tool.setuptools.dynamic]
readme = {content-type = "text/x-rst", file = ["README.rst", "HISTORY.rst"]}
[tool.setuptools.packages.find]
where = ["src"]
packages/test_api/setup.cfg
-34
View File
@@ -1,34 +0,0 @@
[metadata]
author = Galaxy Project and Community
author_email = galaxy-committers@lists.galaxyproject.org
description = Galaxy API tests
license = MIT
license_files =
LICENSE
long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-test-api
url = https://github.com/galaxyproject/galaxy
version = 26.1.dev0
[options]
include_package_data = True
install_requires =
galaxy-test-base
pytest
python-dateutil
requests
tuspy
package_dir =
=src
packages = find_namespace:
python_requires = >=3.10
[options.extras_require]
driver =
galaxy-test-driver
test =
pytest
[options.packages.find]
where = src
packages/test_base/pyproject.toml
+38 -11
View File
@@ -1,19 +1,32 @@
[build-system]
build-backend = "setuptools.build_meta"
requires = ["setuptools", "setuptools-scm>=8"]
requires = ["setuptools>=77.0.0", "setuptools-scm>=8"]
[project]
dynamic = [
"authors",
"dependencies",
"description",
"license",
"optional-dependencies",
"readme",
"requires-python",
"version",
]
dynamic = ["readme"]
name = "galaxy-test-base"
version = "26.1.dev0"
description = "Galaxy testing utilities"
requires-python = ">=3.10"
license = "MIT"
license-files = [
"LICENSE",
]
authors = [
{name = "Galaxy Project and Community", email = "galaxy-committers@lists.galaxyproject.org"},
]
dependencies = [
"galaxy-tool-util",
"galaxy-util",
"bioblend",
"cwltest>=2.5.20240906231108",
"gxformat2>=0.27.0",
"pytest",
"pytest-celery",
"PyYAML",
"requests",
"jsonschema",
]
classifiers = [
"Development Status :: 5 - Production/Stable",
"Environment :: Console",
@@ -31,3 +44,17 @@ classifiers = [
"Topic :: Software Development :: Testing",
]
keywords = ["Galaxy"]
[project.optional-dependencies]
test = [
"pytest",
]
[project.urls]
Homepage = "https://github.com/galaxyproject/galaxy"
[tool.setuptools.dynamic]
readme = {content-type = "text/x-rst", file = ["README.rst", "HISTORY.rst"]}
[tool.setuptools.packages.find]
where = ["src"]
packages/test_base/setup.cfg
-37
View File
@@ -1,37 +0,0 @@
[metadata]
author = Galaxy Project and Community
author_email = galaxy-committers@lists.galaxyproject.org
description = Galaxy testing utilities
license = MIT
license_files =
LICENSE
long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-test-base
url = https://github.com/galaxyproject/galaxy
version = 26.1.dev0
[options]
include_package_data = True
install_requires =
galaxy-tool-util
galaxy-util
bioblend
cwltest>=2.5.20240906231108
gxformat2>=0.27.0
pytest
pytest-celery
PyYAML
requests
jsonschema
package_dir =
=src
packages = find_namespace:
python_requires = >=3.10
[options.extras_require]
test =
pytest
[options.packages.find]
where = src
packages/test_driver/pyproject.toml
+36 -11
View File
@@ -1,19 +1,30 @@
[build-system]
build-backend = "setuptools.build_meta"
requires = ["setuptools", "setuptools-scm>=8"]
requires = ["setuptools>=77.0.0", "setuptools-scm>=8"]
[project]
dynamic = [
"authors",
"dependencies",
"description",
"license",
"optional-dependencies",
"readme",
"requires-python",
"version",
]
dynamic = ["readme"]
name = "galaxy-test-driver"
version = "26.1.dev0"
description = "Galaxy test driver"
requires-python = ">=3.10"
license = "MIT"
license-files = [
"LICENSE",
]
authors = [
{name = "Galaxy Project and Community", email = "galaxy-committers@lists.galaxyproject.org"},
]
dependencies = [
"galaxy-app",
"galaxy-config",
"galaxy-data",
"galaxy-test-base",
"galaxy-tool-util",
"galaxy-util",
"galaxy-web-apps",
"pytest",
]
classifiers = [
"Development Status :: 5 - Production/Stable",
"Environment :: Console",
@@ -31,3 +42,17 @@ classifiers = [
"Topic :: Software Development :: Testing",
]
keywords = ["Galaxy"]
[project.optional-dependencies]
test = [
"pytest",
]
[project.urls]
Homepage = "https://github.com/galaxyproject/galaxy"
[tool.setuptools.dynamic]
readme = {content-type = "text/x-rst", file = ["README.rst", "HISTORY.rst"]}
[tool.setuptools.packages.find]
where = ["src"]
packages/test_driver/setup.cfg
-35
View File
@@ -1,35 +0,0 @@
[metadata]
author = Galaxy Project and Community
author_email = galaxy-committers@lists.galaxyproject.org
description = Galaxy test driver
license = MIT
license_files =
LICENSE
long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-test-driver
url = https://github.com/galaxyproject/galaxy
version = 26.1.dev0
[options]
include_package_data = True
install_requires =
galaxy-app
galaxy-config
galaxy-data
galaxy-test-base
galaxy-tool-util
galaxy-util
galaxy-web-apps
pytest
package_dir =
=src
packages = find_namespace:
python_requires = >=3.10
[options.extras_require]
test =
pytest
[options.packages.find]
where = src
packages/test_selenium/pyproject.toml
+41 -11
View File
@@ -1,19 +1,32 @@
[build-system]
build-backend = "setuptools.build_meta"
requires = ["setuptools", "setuptools-scm>=8"]
requires = ["setuptools>=77.0.0", "setuptools-scm>=8"]
[project]
dynamic = [
"authors",
"dependencies",
"description",
"license",
"optional-dependencies",
"readme",
"requires-python",
"version",
]
dynamic = ["readme"]
name = "galaxy-test-selenium"
version = "26.1.dev0"
description = "Galaxy Selenium tests"
requires-python = ">=3.10"
license = "MIT"
license-files = [
"LICENSE",
]
authors = [
{name = "Galaxy Project and Community", email = "galaxy-committers@lists.galaxyproject.org"},
]
dependencies = [
"galaxy-data",
"galaxy-tool-util",
"galaxy-selenium",
"galaxy-test-base",
"galaxy-util",
"gxformat2>=0.27.0",
"pytest",
"PyYAML",
"requests",
"selenium!=4.11.0,!=4.11.1,!=4.11.2",
]
classifiers = [
"Development Status :: 5 - Production/Stable",
"Environment :: Console",
@@ -31,3 +44,20 @@ classifiers = [
"Topic :: Software Development :: Testing",
]
keywords = ["Galaxy"]
[project.optional-dependencies]
driver = [
"galaxy-test-driver",
]
test = [
"pytest",
]
[project.urls]
Homepage = "https://github.com/galaxyproject/galaxy"
[tool.setuptools.dynamic]
readme = {content-type = "text/x-rst", file = ["README.rst", "HISTORY.rst"]}
[tool.setuptools.packages.find]
where = ["src"]
packages/test_selenium/setup.cfg
-39
View File
@@ -1,39 +0,0 @@
[metadata]
author = Galaxy Project and Community
author_email = galaxy-committers@lists.galaxyproject.org
description = Galaxy Selenium tests
license = MIT
license_files =
LICENSE
long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-test-selenium
url = https://github.com/galaxyproject/galaxy
version = 26.1.dev0
[options]
include_package_data = True
install_requires =
galaxy-data
galaxy-tool-util
galaxy-selenium
galaxy-test-base
galaxy-util
gxformat2>=0.27.0
pytest
PyYAML
requests
selenium!=4.11.0,!=4.11.1,!=4.11.2
package_dir =
=src
packages = find:
python_requires = >=3.10
[options.extras_require]
driver =
galaxy-test-driver
test =
pytest
[options.packages.find]
where = src
packages/tool_shed/pyproject.toml
+59 -11
View File
@@ -1,19 +1,46 @@
[build-system]
build-backend = "setuptools.build_meta"
requires = ["setuptools", "setuptools-scm>=8"]
requires = ["setuptools>=77.0.0", "setuptools-scm>=8"]
[project]
dynamic = [
"authors",
"dependencies",
"description",
"license",
"optional-dependencies",
"readme",
"requires-python",
"version",
]
dynamic = ["readme"]
name = "galaxy-tool-shed"
version = "26.1.dev0"
description = "Galaxy Tool Shed"
requires-python = ">=3.10"
license = "MIT"
license-files = [
"LICENSE",
]
authors = [
{name = "Galaxy Project and Community", email = "galaxy-committers@lists.galaxyproject.org"},
]
dependencies = [
"galaxy-app",
"galaxy-auth",
"galaxy-config",
"galaxy-data",
"galaxy-util[image-util]",
"galaxy-web-framework",
"galaxy-web-stack",
"galaxy-web-apps",
"a2wsgi",
"alembic",
"fastapi>=0.133.0",
"Mako",
"MarkupSafe",
"mercurial>=7.2",
"Paste",
"pydantic>=2.7.4",
"Routes",
"SQLAlchemy>=2.0.37,<2.1,!=2.0.41",
"slowapi",
"starlette>=1.0.1",
"starlette-context",
"typing-extensions",
"WebOb",
"Whoosh",
]
classifiers = [
"Development Status :: 5 - Production/Stable",
"Environment :: Console",
@@ -31,3 +58,24 @@ classifiers = [
"Topic :: Software Development :: Testing",
]
keywords = ["Galaxy"]
[project.optional-dependencies]
test = [
"galaxy-test-base",
"galaxy-test-driver",
"playwright",
"pytest",
"pytest-playwright",
]
[project.urls]
Homepage = "https://github.com/galaxyproject/galaxy"
[tool.setuptools.dynamic]
readme = {content-type = "text/x-rst", file = ["README.rst", "HISTORY.rst"]}
[tool.setuptools.packages.find]
where = ["src"]
exclude = [
"tool_shed.test*",
]
packages/tool_shed/setup.cfg
-57
View File
@@ -1,57 +0,0 @@
[metadata]
author = Galaxy Project and Community
author_email = galaxy-committers@lists.galaxyproject.org
description = Galaxy Tool Shed
license = MIT
license_files =
LICENSE
long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-tool-shed
url = https://github.com/galaxyproject/galaxy
version = 26.1.dev0
[options]
include_package_data = True
install_requires =
galaxy-app
galaxy-auth
galaxy-config
galaxy-data
galaxy-util[image-util]
galaxy-web-framework
galaxy-web-stack
galaxy-web-apps
a2wsgi
alembic
fastapi>=0.133.0
Mako
MarkupSafe
mercurial>=7.2
Paste
pydantic>=2.7.4
Routes
SQLAlchemy>=2.0.37,<2.1,!=2.0.41
slowapi
starlette>=1.0.1
starlette-context
typing-extensions
WebOb
Whoosh
package_dir =
=src
packages = find:
python_requires = >=3.10
[options.extras_require]
test =
galaxy-test-base
galaxy-test-driver
playwright
pytest
pytest-playwright
[options.packages.find]
where = src
exclude =
tool_shed.test*
packages/tool_shed_schema/pyproject.toml
+31 -11
View File
@@ -1,19 +1,25 @@
[build-system]
build-backend = "setuptools.build_meta"
requires = ["setuptools", "setuptools-scm>=8"]
requires = ["setuptools>=77.0.0", "setuptools-scm>=8"]
[project]
dynamic = [
"authors",
"dependencies",
"description",
"license",
"optional-dependencies",
"readme",
"requires-python",
"version",
]
dynamic = ["readme"]
name = "galaxy-tool-shed-schema"
version = "26.1.dev0"
description = "Pydantic models for the Galaxy Tool Shed"
requires-python = ">=3.10"
license = "MIT"
license-files = [
"LICENSE",
]
authors = [
{name = "Galaxy Project and Community", email = "galaxy-committers@lists.galaxyproject.org"},
]
dependencies = [
"galaxy-tool-util-models",
"pydantic>=2.7.4",
"typing-extensions",
]
classifiers = [
"Development Status :: 5 - Production/Stable",
"Environment :: Console",
@@ -31,3 +37,17 @@ classifiers = [
"Topic :: Software Development :: Testing",
]
keywords = ["Galaxy"]
[project.optional-dependencies]
test = [
"pytest",
]
[project.urls]
Homepage = "https://github.com/galaxyproject/galaxy"
[tool.setuptools.dynamic]
readme = {content-type = "text/x-rst", file = ["README.rst", "HISTORY.rst"]}
[tool.setuptools.packages.find]
where = ["src"]
packages/tool_shed_schema/setup.cfg
-30
View File
@@ -1,30 +0,0 @@
[metadata]
author = Galaxy Project and Community
author_email = galaxy-committers@lists.galaxyproject.org
description = Pydantic models for the Galaxy Tool Shed
license = MIT
license_files =
LICENSE
long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-tool-shed-schema
url = https://github.com/galaxyproject/galaxy
version = 26.1.dev0
[options]
include_package_data = True
install_requires =
galaxy-tool-util-models
pydantic>=2.7.4
typing-extensions
package_dir =
=src
packages = find:
python_requires = >=3.10
[options.extras_require]
test =
pytest
[options.packages.find]
where = src
packages/tool_util/pyproject.toml
+55 -10
View File
@@ -3,17 +3,29 @@ build-backend = "setuptools.build_meta"
requires = ["setuptools", "setuptools-scm>=8"]
[project]
dynamic = [
"authors",
"dependencies",
"description",
"license",
"optional-dependencies",
"readme",
"requires-python",
"version",
]
dynamic = ["readme"]
name = "galaxy-tool-util"
version = "26.1.dev0"
description = "Galaxy tool and tool dependency utilities"
requires-python = ">=3.8"
license = {"text" = "MIT"}
authors = [
{name = "Galaxy Project and Community", email = "galaxy-committers@lists.galaxyproject.org"},
]
dependencies = [
"galaxy-tool-util-models",
"galaxy-util[template,image-util]>=22.1",
"conda-package-streaming",
"jsonschema",
"lxml!=4.2.2",
"MarkupSafe",
"packaging",
"pydantic>=2.7.4",
"PyYAML",
"requests",
"sortedcontainers",
"typing-extensions",
]
classifiers = [
"Development Status :: 5 - Production/Stable",
"Environment :: Console",
@@ -34,6 +46,30 @@ classifiers = [
]
keywords = ["Galaxy"]
[project.optional-dependencies]
cwl = [
"cwl-utils",
"cwltool>=3.1.20230624081518",
]
mulled = [
"jinja2",
"Whoosh",
]
edam = [
"edam-ontology",
]
extended-assertions = [
"numpy",
"pysam",
"pillow",
"tifffile",
]
test = [
"Beaker",
"pytest",
"pytest-mock",
]
[project.scripts]
galaxy-tool-format = "galaxy.tool_util.format:main"
galaxy-tool-test = "galaxy.tool_util.verify.script:main"
@@ -48,3 +84,12 @@ mulled-hash = "galaxy.tool_util.deps.mulled.mulled_hash:main"
mulled-list = "galaxy.tool_util.deps.mulled.mulled_list:main"
mulled-search = "galaxy.tool_util.deps.mulled.mulled_search:main"
mulled-update-singularity-containers = "galaxy.tool_util.deps.mulled.mulled_update_singularity_containers:main"
[project.urls]
Homepage = "https://github.com/galaxyproject/galaxy"
[tool.setuptools.dynamic]
readme = {content-type = "text/x-rst", file = ["README.rst", "HISTORY.rst"]}
[tool.setuptools.packages.find]
where = ["src"]
packages/tool_util/setup.cfg
-53
View File
@@ -1,53 +0,0 @@
[metadata]
author = Galaxy Project and Community
author_email = galaxy-committers@lists.galaxyproject.org
description = Galaxy tool and tool dependency utilities
license = MIT
license_files =
LICENSE
long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-tool-util
url = https://github.com/galaxyproject/galaxy
version = 26.1.dev0
[options]
include_package_data = True
install_requires =
galaxy-tool-util-models
galaxy-util[template,image-util]>=22.1
conda-package-streaming
jsonschema
lxml!=4.2.2
MarkupSafe
packaging
pydantic>=2.7.4
PyYAML
requests
sortedcontainers
typing-extensions
package_dir =
=src
packages = find_namespace:
python_requires = >=3.8
[options.extras_require]
cwl =
cwl-utils
cwltool>=3.1.20230624081518
mulled =
jinja2
Whoosh
edam =
edam-ontology
extended-assertions =
numpy
pysam
pillow
tifffile
test =
Beaker
pytest
pytest-mock
[options.packages.find]
where = src
packages/tool_util_models/pyproject.toml
+26 -10
View File
@@ -3,17 +3,19 @@ build-backend = "setuptools.build_meta"
requires = ["setuptools", "setuptools-scm>=8"]
[project]
dynamic = [
"authors",
"dependencies",
"description",
"license",
"optional-dependencies",
"readme",
"requires-python",
"version",
]
dynamic = ["readme"]
name = "galaxy-tool-util-models"
version = "26.1.dev0"
description = "Pydantic models for Galaxy tools"
requires-python = ">=3.8"
license = {"text" = "MIT"}
authors = [
{name = "Galaxy Project and Community", email = "galaxy-committers@lists.galaxyproject.org"},
]
dependencies = [
"pydantic>=2.7.4",
"typing-extensions",
]
classifiers = [
"Development Status :: 5 - Production/Stable",
"Environment :: Console",
@@ -33,3 +35,17 @@ classifiers = [
"Topic :: Software Development :: Testing",
]
keywords = ["Galaxy"]
[project.optional-dependencies]
test = [
"pytest",
]
[project.urls]
Homepage = "https://github.com/galaxyproject/galaxy"
[tool.setuptools.dynamic]
readme = {content-type = "text/x-rst", file = ["README.rst", "HISTORY.rst"]}
[tool.setuptools.packages.find]
where = ["src"]
packages/tool_util_models/setup.cfg
-29
View File
@@ -1,29 +0,0 @@
[metadata]
author = Galaxy Project and Community
author_email = galaxy-committers@lists.galaxyproject.org
description = Pydantic models for Galaxy tools
license = MIT
license_files =
LICENSE
long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-tool-util-models
url = https://github.com/galaxyproject/galaxy
version = 26.1.dev0
[options]
include_package_data = True
install_requires =
pydantic>=2.7.4
typing-extensions
package_dir =
=src
packages = find_namespace:
python_requires = >=3.8
[options.extras_require]
test =
pytest
[options.packages.find]
where = src
packages/tours/pyproject.toml
+33 -11
View File
@@ -1,19 +1,27 @@
[build-system]
build-backend = "setuptools.build_meta"
requires = ["setuptools", "setuptools-scm>=8"]
requires = ["setuptools>=77.0.0", "setuptools-scm>=8"]
[project]
dynamic = [
"authors",
"dependencies",
"description",
"license",
"optional-dependencies",
"readme",
"requires-python",
"version",
]
dynamic = ["readme"]
name = "galaxy-tours"
version = "26.1.dev0"
description = "Galaxy tours backend framework"
requires-python = ">=3.10"
license = "MIT"
license-files = [
"LICENSE",
]
authors = [
{name = "Galaxy Project and Community", email = "galaxy-committers@lists.galaxyproject.org"},
]
dependencies = [
"galaxy-navigation",
"galaxy-schema",
"galaxy-util",
"pydantic>=2.7.4",
"PyYAML",
]
classifiers = [
"Development Status :: 5 - Production/Stable",
"Environment :: Console",
@@ -32,5 +40,19 @@ classifiers = [
]
keywords = ["Galaxy"]
[project.optional-dependencies]
test = [
"pytest",
]
[project.scripts]
gx-validate-tours = "galaxy.tours.validate:main"
[project.urls]
Homepage = "https://github.com/galaxyproject/galaxy"
[tool.setuptools.dynamic]
readme = {content-type = "text/x-rst", file = ["README.rst", "HISTORY.rst"]}
[tool.setuptools.packages.find]
where = ["src"]
packages/tours/setup.cfg
-32
View File
@@ -1,32 +0,0 @@
[metadata]
author = Galaxy Project and Community
author_email = galaxy-committers@lists.galaxyproject.org
description = Galaxy tours backend framework
license = MIT
license_files =
LICENSE
long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-tours
url = https://github.com/galaxyproject/galaxy
version = 26.1.dev0
[options]
include_package_data = True
install_requires =
galaxy-navigation
galaxy-schema
galaxy-util
pydantic>=2.7.4
PyYAML
package_dir =
=src
packages = find_namespace:
python_requires = >=3.10
[options.extras_require]
test =
pytest
[options.packages.find]
where = src
packages/util/pyproject.toml
+53 -10
View File
@@ -3,17 +3,27 @@ build-backend = "setuptools.build_meta"
requires = ["setuptools", "setuptools-scm>=8"]
[project]
dynamic = [
"authors",
"dependencies",
"description",
"license",
"optional-dependencies",
"readme",
"requires-python",
"version",
]
dynamic = ["readme"]
name = "galaxy-util"
version = "26.1.dev0"
description = "Galaxy generic utilities"
requires-python = ">=3.8"
license = {"text" = "MIT"}
authors = [
{name = "Galaxy Project and Community", email = "galaxy-committers@lists.galaxyproject.org"},
]
dependencies = [
"bleach",
"boltons",
"docutils!=0.17,!=0.17.1",
"importlib-resources>=5.10.0; python_version<'3.12'",
"packaging",
"pyparsing>=3.0.0",
"PyYAML",
"requests",
"typing-extensions",
"zipstream-new",
]
classifiers = [
"Development Status :: 5 - Production/Stable",
"Environment :: Console",
@@ -33,3 +43,36 @@ classifiers = [
"Topic :: Software Development :: Testing",
]
keywords = ["Galaxy"]
[project.optional-dependencies]
image-util = [
"pillow",
]
jstree = [
"dictobj",
]
template = [
"CT3>=3.3.3",
"fissix; python_version>='3.13'",
"future>=1.0.0",
]
config-template = [
"galaxy-tool-util-models",
"Jinja2",
"pydantic>=2.7.4",
]
test = [
"pytest",
"pytest-httpserver",
"responses",
"Werkzeug",
]
[project.urls]
Homepage = "https://github.com/galaxyproject/galaxy"
[tool.setuptools.dynamic]
readme = {content-type = "text/x-rst", file = ["README.rst", "HISTORY.rst"]}
[tool.setuptools.packages.find]
where = ["src"]
packages/util/setup.cfg
-52
View File
@@ -1,52 +0,0 @@
[metadata]
author = Galaxy Project and Community
author_email = galaxy-committers@lists.galaxyproject.org
description = Galaxy generic utilities
license = MIT
license_files =
LICENSE
long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-util
url = https://github.com/galaxyproject/galaxy
version = 26.1.dev0
[options]
include_package_data = True
install_requires =
bleach
boltons
docutils!=0.17,!=0.17.1
importlib-resources>=5.10.0;python_version<'3.12'
packaging
pyparsing>=3.0.0
PyYAML
requests
typing-extensions
zipstream-new
package_dir =
=src
packages = find_namespace:
python_requires = >=3.8
[options.extras_require]
image-util =
pillow
jstree =
dictobj
template =
CT3>=3.3.3
fissix;python_version>='3.13'
future>=1.0.0
config-template =
galaxy-tool-util-models
Jinja2
pydantic>=2.7.4
test =
pytest
pytest-httpserver
responses
Werkzeug
[options.packages.find]
where = src
packages/web_apps/pyproject.toml
+64 -11
View File
@@ -1,19 +1,56 @@
[build-system]
build-backend = "setuptools.build_meta"
requires = ["setuptools", "setuptools-scm>=8"]
requires = ["setuptools>=77.0.0", "setuptools-scm>=8"]
[project]
dynamic = [
"authors",
"dependencies",
"description",
"license",
"optional-dependencies",
"readme",
"requires-python",
"version",
]
dynamic = ["readme"]
name = "galaxy-web-apps"
version = "26.1.dev0"
description = "Galaxy web apps"
requires-python = ">=3.10"
license = "MIT"
license-files = [
"LICENSE",
]
authors = [
{name = "Galaxy Project and Community", email = "galaxy-committers@lists.galaxyproject.org"},
]
dependencies = [
"galaxy-app",
"galaxy-data",
"galaxy-job-execution",
"galaxy-tool-util",
"galaxy-util[jstree,template]",
"galaxy-web-framework",
"galaxy-web-stack",
"a2wsgi",
"apispec",
"Babel",
"CT3>=3.3.3",
"fastapi>=0.133.0",
"gunicorn!=25.1.0",
"httpx",
"gxformat2>=0.27.0",
"Mako",
"MarkupSafe",
"Paste",
"pydantic>=2.7.4",
"PyJWT",
"python-dateutil",
"python-multipart", # required to support form parsing in FastAPI/Starlette
"PyYAML",
"requests",
"Routes",
"slowapi",
"SQLAlchemy>=2.0.37,<2.1,!=2.0.41",
"starlette>=1.0.1",
"starlette-context",
"tuspyserver",
"typing-extensions",
"uvicorn",
"uvloop>=0.21.0",
"WebOb>=1.8.9",
]
classifiers = [
"Development Status :: 5 - Production/Stable",
"Environment :: Console",
@@ -32,5 +69,21 @@ classifiers = [
]
keywords = ["Galaxy"]
[project.optional-dependencies]
test = [
"httpx",
"pytest",
"pytest-asyncio",
]
[project.scripts]
galaxy-web = "galaxy.webapps.galaxy.script:main"
[project.urls]
Homepage = "https://github.com/galaxyproject/galaxy"
[tool.setuptools.dynamic]
readme = {content-type = "text/x-rst", file = ["README.rst", "HISTORY.rst"]}
[tool.setuptools.packages.find]
where = ["src"]
packages/web_apps/setup.cfg
-63
View File
@@ -1,63 +0,0 @@
[metadata]
author = Galaxy Project and Community
author_email = galaxy-committers@lists.galaxyproject.org
description = Galaxy web apps
license = MIT
license_files =
LICENSE
long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-web-apps
url = https://github.com/galaxyproject/galaxy
version = 26.1.dev0
[options]
include_package_data = True
install_requires =
galaxy-app
galaxy-data
galaxy-job-execution
galaxy-tool-util
galaxy-util[jstree,template]
galaxy-web-framework
galaxy-web-stack
a2wsgi
apispec
Babel
CT3>=3.3.3
fastapi>=0.133.0
gunicorn!=25.1.0
httpx
gxformat2>=0.27.0
Mako
MarkupSafe
Paste
pydantic>=2.7.4
PyJWT
python-dateutil
python-multipart # required to support form parsing in FastAPI/Starlette
PyYAML
requests
Routes
slowapi
SQLAlchemy>=2.0.37,<2.1,!=2.0.41
starlette>=1.0.1
starlette-context
tuspyserver
typing-extensions
uvicorn
uvloop>=0.21.0
WebOb>=1.8.9
package_dir =
=src
packages = find_namespace:
python_requires = >=3.10
[options.extras_require]
test =
httpx
pytest
pytest-asyncio
[options.packages.find]
where = src
packages/web_client/pyproject.toml
+23 -11
View File
@@ -1,19 +1,22 @@
[build-system]
build-backend = "setuptools.build_meta"
requires = ["setuptools", "setuptools-scm>=8"]
requires = ["setuptools>=77.0.0", "setuptools-scm>=8"]
[project]
dynamic = [
"authors",
"dependencies",
"description",
"license",
"optional-dependencies",
"readme",
"requires-python",
"version",
]
dynamic = ["readme"]
name = "galaxy-web-client"
version = "26.1.dev0"
description = "Galaxy web client (frontend)"
requires-python = ">=3.10"
license = "MIT"
license-files = [
"LICENSE",
]
authors = [
{name = "Galaxy Project and Community", email = "galaxy-committers@lists.galaxyproject.org"},
]
dependencies = [
]
classifiers = [
"Development Status :: 5 - Production/Stable",
"Environment :: Console",
@@ -34,3 +37,12 @@ keywords = ["Galaxy"]
[project.scripts]
galaxy-web-client-install = "galaxy.web_client.install:main"
[project.urls]
Homepage = "https://github.com/galaxyproject/galaxy"
[tool.setuptools.dynamic]
readme = {content-type = "text/x-rst", file = ["README.rst", "HISTORY.rst"]}
[tool.setuptools.packages.find]
where = ["src"]
packages/web_client/setup.cfg
-22
View File
@@ -1,22 +0,0 @@
[metadata]
author = Galaxy Project and Community
author_email = galaxy-committers@lists.galaxyproject.org
description = Galaxy web client (frontend)
license = MIT
license_files =
LICENSE
long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-web-client
url = https://github.com/galaxyproject/galaxy
version = 26.1.dev0
[options]
include_package_data = True
package_dir =
=src
packages = find_namespace:
python_requires = >=3.10
[options.packages.find]
where = src
packages/web_framework/pyproject.toml
+39 -11
View File
@@ -1,19 +1,33 @@
[build-system]
build-backend = "setuptools.build_meta"
requires = ["setuptools", "setuptools-scm>=8"]
requires = ["setuptools>=77.0.0", "setuptools-scm>=8"]
[project]
dynamic = [
"authors",
"dependencies",
"description",
"license",
"optional-dependencies",
"readme",
"requires-python",
"version",
]
dynamic = ["readme"]
name = "galaxy-web-framework"
version = "26.1.dev0"
description = "Galaxy web framework"
requires-python = ">=3.10"
license = "MIT"
license-files = [
"LICENSE",
]
authors = [
{name = "Galaxy Project and Community", email = "galaxy-committers@lists.galaxyproject.org"},
]
dependencies = [
"galaxy-data",
"galaxy-util",
"babel",
"MarkupSafe",
"paste",
"pydantic>=2.7.4",
"requests",
"Routes",
"SQLAlchemy>=2.0.37,<2.1,!=2.0.41",
"starlette",
"WebOb",
]
classifiers = [
"Development Status :: 5 - Production/Stable",
"Environment :: Console",
@@ -31,3 +45,17 @@ classifiers = [
"Topic :: Software Development :: Testing",
]
keywords = ["Galaxy"]
[project.optional-dependencies]
test = [
"pytest",
]
[project.urls]
Homepage = "https://github.com/galaxyproject/galaxy"
[tool.setuptools.dynamic]
readme = {content-type = "text/x-rst", file = ["README.rst", "HISTORY.rst"]}
[tool.setuptools.packages.find]
where = ["src"]
packages/web_framework/setup.cfg
-38
View File
@@ -1,38 +0,0 @@
[metadata]
author = Galaxy Project and Community
author_email = galaxy-committers@lists.galaxyproject.org
description = Galaxy web framework
license = MIT
license_files =
LICENSE
long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-web-framework
url = https://github.com/galaxyproject/galaxy
version = 26.1.dev0
[options]
include_package_data = True
install_requires =
galaxy-data
galaxy-util
babel
MarkupSafe
paste
pydantic>=2.7.4
requests
Routes
SQLAlchemy>=2.0.37,<2.1,!=2.0.41
starlette
WebOb
package_dir =
=src
packages = find_namespace:
python_requires = >=3.10
[options.extras_require]
test =
pytest
[options.packages.find]
where = src
packages/web_stack/pyproject.toml
+32 -11
View File
@@ -1,19 +1,25 @@
[build-system]
build-backend = "setuptools.build_meta"
requires = ["setuptools", "setuptools-scm>=8"]
requires = ["setuptools>=77.0.0", "setuptools-scm>=8"]
[project]
dynamic = [
"authors",
"dependencies",
"description",
"license",
"optional-dependencies",
"readme",
"requires-python",
"version",
]
dynamic = ["readme"]
name = "galaxy-web-stack"
version = "26.1.dev0"
description = "Galaxy web stack abstraction"
requires-python = ">=3.10"
license = "MIT"
license-files = [
"LICENSE",
]
authors = [
{name = "Galaxy Project and Community", email = "galaxy-committers@lists.galaxyproject.org"},
]
dependencies = [
"galaxy-data",
"galaxy-util",
"SQLAlchemy>=2.0.37,<2.1,!=2.0.41",
]
classifiers = [
"Development Status :: 5 - Production/Stable",
"Environment :: Console",
@@ -31,3 +37,18 @@ classifiers = [
"Topic :: Software Development :: Testing",
]
keywords = ["Galaxy"]
[project.optional-dependencies]
test = [
"pytest",
"gunicorn!=25.1.0",
]
[project.urls]
Homepage = "https://github.com/galaxyproject/galaxy"
[tool.setuptools.dynamic]
readme = {content-type = "text/x-rst", file = ["README.rst", "HISTORY.rst"]}
[tool.setuptools.packages.find]
where = ["src"]
packages/web_stack/setup.cfg
-31
View File
@@ -1,31 +0,0 @@
[metadata]
author = Galaxy Project and Community
author_email = galaxy-committers@lists.galaxyproject.org
description = Galaxy web stack abstraction
license = MIT
license_files =
LICENSE
long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-web-stack
url = https://github.com/galaxyproject/galaxy
version = 26.1.dev0
[options]
include_package_data = True
install_requires =
galaxy-data
galaxy-util
SQLAlchemy>=2.0.37,<2.1,!=2.0.41
package_dir =
=src
packages = find_namespace:
python_requires = >=3.10
[options.extras_require]
test =
pytest
gunicorn!=25.1.0
[options.packages.find]
where = src