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Merge pull request #8051 from jmchilton/galaxy_util_libs

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Prepare all packages/ for actual releases.
This commit is contained in:
Martin Cech
2019-06-05 15:29:08 -04:00
committed by GitHub
parent 9c2f142fb8 500a5cc46d
commit 31b7fb0356
37 changed files with 292 additions and 24 deletions
Download Patch File Download Diff File Expand all files Collapse all files
.ci/flake8_blacklist.txt
+4
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@@ -2,6 +2,10 @@
.tox
.venv
.venv3
packages/*/.venv
packages/*/build
packages/*/dist
packages/venv
node_modules
database
doc/build
packages/build_scripts/commit_version.py
+45
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@@ -0,0 +1,45 @@
#!/usr/bin/env python
# Modify version...
import datetime
import os
import re
import subprocess
import sys
DEV_RELEASE = os.environ.get("DEV_RELEASE", None) == "1"
PROJECT_DIRECTORY = os.getcwd()
PROJECT_DIRECTORY_NAME = os.path.basename(os.path.abspath(PROJECT_DIRECTORY))
PROJECT_MODULE_FILENAME = "project_galaxy_%s.py" % PROJECT_DIRECTORY_NAME
PROJECT_NAME = PROJECT_DIRECTORY_NAME.replace("_", "-")
def main(argv):
source_dir = argv[1]
version = argv[2]
mod_path = os.path.join(PROJECT_DIRECTORY, source_dir, PROJECT_MODULE_FILENAME)
if not DEV_RELEASE:
history_path = os.path.join(PROJECT_DIRECTORY, "HISTORY.rst")
history = open(history_path, "r").read()
today = datetime.datetime.today()
today_str = today.strftime('%Y-%m-%d')
history = history.replace(".dev0", " (%s)" % today_str)
open(history_path, "w").write(history)
mod = open(mod_path, "r").read()
mod = re.sub(r"__version__ = '[\d\.]*\.dev0'",
"__version__ = '%s'" % version,
mod)
mod = open(mod_path, "w").write(mod)
tag = "galaxy-%s-%s" % (PROJECT_NAME, version)
shell(["git", "commit", "-m", "Version %s of %s (tag %s)." % (version, PROJECT_NAME, tag),
"HISTORY.rst", mod_path])
shell(["git", "tag", tag])
def shell(cmds, **kwds):
p = subprocess.Popen(cmds, **kwds)
return p.wait()
if __name__ == "__main__":
main(sys.argv)
packages/build_scripts/new_version.py
+70
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@@ -0,0 +1,70 @@
#!/usr/bin/env python
# Modify version...
import os
import re
import subprocess
import sys
from distutils.version import StrictVersion
DEV_RELEASE = os.environ.get("DEV_RELEASE", None) == "1"
PROJECT_DIRECTORY = os.getcwd()
PROJECT_DIRECTORY_NAME = os.path.basename(os.path.abspath(PROJECT_DIRECTORY))
PROJECT_MODULE_FILENAME = "project_galaxy_%s.py" % PROJECT_DIRECTORY_NAME
PROJECT_NAME = PROJECT_DIRECTORY_NAME.replace("_", "-")
def main(argv):
source_dir = argv[1]
version = argv[2]
if not DEV_RELEASE:
old_version = StrictVersion(version)
old_version_tuple = old_version.version
new_version_tuple = list(old_version_tuple)
new_version_tuple[1] = old_version_tuple[1] + 1
new_version_tuple[2] = 0
new_version = ".".join(map(str, new_version_tuple))
new_dev_version = 0
else:
dev_version = re.compile(r'dev([\d]+)').search(version).group(1)
new_dev_version = int(dev_version) + 1
new_version = version.replace("dev%s" % dev_version, "dev%s" % new_dev_version)
history_path = os.path.join(PROJECT_DIRECTORY, "HISTORY.rst")
if not DEV_RELEASE:
history = open(history_path, "r").read()
def extend(from_str, line):
from_str += "\n"
return history.replace(from_str, from_str + line + "\n")
history = extend(".. to_doc", """
---------------------
%s.dev0
---------------------
""" % new_version)
open(history_path, "w").write(history)
mod_path = os.path.join(PROJECT_DIRECTORY, source_dir, PROJECT_MODULE_FILENAME)
mod = open(mod_path, "r").read()
if not DEV_RELEASE:
mod = re.sub(r"__version__ = '[\d\.]+'",
"__version__ = '%s.dev0'" % new_version,
mod, 1)
else:
mod = re.sub("dev%s" % dev_version,
"dev%s" % new_dev_version,
mod, 1)
mod = open(mod_path, "w").write(mod)
shell(["git", "commit", "-m", "Starting work on %s %s" % (PROJECT_NAME, new_version),
"HISTORY.rst", mod_path])
def shell(cmds, **kwds):
p = subprocess.Popen(cmds, **kwds)
return p.wait()
if __name__ == "__main__":
main(sys.argv)
packages/build_scripts/print_version_for_release.py
+27
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@@ -0,0 +1,27 @@
from __future__ import print_function
import ast
import os
import re
import sys
from distutils.version import LooseVersion
DEV_RELEASE = os.environ.get("DEV_RELEASE", None) == "1"
PROJECT_DIRECTORY = os.getcwd()
PROJECT_DIRECTORY_NAME = os.path.basename(os.path.abspath(PROJECT_DIRECTORY))
PROJECT_MODULE_FILENAME = "project_galaxy_%s.py" % PROJECT_DIRECTORY_NAME
source_dir = sys.argv[1]
PROJECT_MODULE_PATH = os.path.join(PROJECT_DIRECTORY, source_dir, PROJECT_MODULE_FILENAME)
_version_re = re.compile(r'__version__\s+=\s+(.*)')
with open(PROJECT_MODULE_PATH, 'rb') as f:
version = str(ast.literal_eval(_version_re.search(
f.read().decode('utf-8')).group(1)))
if not DEV_RELEASE:
# Strip .devN
version_tuple = LooseVersion(version).version[0:3]
print(".".join(map(str, version_tuple)))
else:
print(version)
packages/data/HISTORY.rst
+2 -2
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@@ -6,7 +6,7 @@ History
.. to_doc
---------------------
19.5.0.dev0
19.9.0.dev0
---------------------
* Initial import from dev branch of Galaxy during 19.05 release cycle.
* Initial import from dev branch of Galaxy during 19.09 development cycle.
packages/data/Makefile
Symlink
+1
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@@ -0,0 +1 @@
../package.Makefile
packages/data/dev-requirements.txt
Symlink
+1
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@@ -0,0 +1 @@
../package-dev-requirements.txt
packages/data/galaxy/project_galaxy_data.py
+2 -1
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@@ -1,11 +1,12 @@
# -*- coding: utf-8 -*-
__version__ = '19.5.0.dev0'
__version__ = '19.9.0.dev1'
PROJECT_NAME = "galaxy-data"
PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"
PROJECT_URL = "https://github.com/galaxyproject/galaxy"
PROJECT_AUTHOR = 'Galaxy Project and Community'
PROJECT_DESCRIPTION = 'Galaxy Datatype Framework and Datatypes'
PROJECT_EMAIL = 'jmchilton@gmail.com'
RAW_CONTENT_URL = "https://raw.github.com/%s/%s/master/" % (
PROJECT_USERAME, PROJECT_NAME
packages/data/scripts
Symlink
+1
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@@ -0,0 +1 @@
../build_scripts
packages/data/setup.py
+2 -2
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@@ -26,9 +26,9 @@ with open('%s/project_galaxy_data.py' % SOURCE_DIR, 'rb') as f:
PROJECT_URL = get_var("PROJECT_URL")
PROJECT_AUTHOR = get_var("PROJECT_AUTHOR")
PROJECT_EMAIL = get_var("PROJECT_EMAIL")
PROJECT_DESCRIPTION = get_var("PROJECT_DESCRIPTION")
TEST_DIR = 'tests'
PROJECT_DESCRIPTION = 'Galaxy Datatype Framework and Datatypes'
PACKAGES = [
'galaxy',
'galaxy.datatypes',
@@ -77,6 +77,7 @@ setup(
version=version,
description=PROJECT_DESCRIPTION,
long_description=readme + '\n\n' + history,
long_description_content_type='text/x-rst',
author=PROJECT_AUTHOR,
author_email=PROJECT_EMAIL,
url=PROJECT_URL,
@@ -101,7 +102,6 @@ setup(
'Natural Language :: English',
"Programming Language :: Python :: 2",
'Programming Language :: Python :: 2.7',
'Programming Language :: Python :: 3.4',
'Programming Language :: Python :: 3.5',
'Programming Language :: Python :: 3.6',
'Programming Language :: Python :: 3.7',
packages/job_metrics/HISTORY.rst
+1 -1
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@@ -9,4 +9,4 @@ History
19.9.0.dev0
---------------------
* Initial import from dev branch of Galaxy during 19.09 release cycle.
* Initial import from dev branch of Galaxy during 19.09 development cycle.
packages/job_metrics/Makefile
Symlink
+1
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@@ -0,0 +1 @@
../package.Makefile
packages/job_metrics/dev-requirements.txt
Symlink
+1
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@@ -0,0 +1 @@
../package-dev-requirements.txt
packages/job_metrics/galaxy/project_galaxy_job_metrics.py
+2 -1
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@@ -1,11 +1,12 @@
# -*- coding: utf-8 -*-
__version__ = '19.9.0.dev0'
__version__ = '19.9.0.dev1'
PROJECT_NAME = "galaxy-job-metrics"
PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"
PROJECT_URL = "https://github.com/galaxyproject/galaxy"
PROJECT_AUTHOR = 'Galaxy Project and Community'
PROJECT_DESCRIPTION = 'Galaxy Job Metrics'
PROJECT_EMAIL = 'jmchilton@gmail.com'
RAW_CONTENT_URL = "https://raw.github.com/%s/%s/master/" % (
PROJECT_USERAME, PROJECT_NAME
packages/job_metrics/scripts
Symlink
+1
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@@ -0,0 +1 @@
../build_scripts
packages/job_metrics/setup.py
+3 -3
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@@ -26,13 +26,13 @@ with open('%s/project_galaxy_job_metrics.py' % SOURCE_DIR, 'rb') as f:
PROJECT_URL = get_var("PROJECT_URL")
PROJECT_AUTHOR = get_var("PROJECT_AUTHOR")
PROJECT_EMAIL = get_var("PROJECT_EMAIL")
PROJECT_DESCRIPTION = get_var("PROJECT_DESCRIPTION")
TEST_DIR = 'tests'
PROJECT_DESCRIPTION = 'Galaxy Job Metrics'
PACKAGES = [
'galaxy',
'galaxy.job_metrics',
'galaxy.job_metrics.instrumers',
'galaxy.job_metrics.instrumenters',
'galaxy.job_metrics.collectl',
]
ENTRY_POINTS = '''
@@ -67,6 +67,7 @@ setup(
version=version,
description=PROJECT_DESCRIPTION,
long_description=readme + '\n\n' + history,
long_description_content_type='text/x-rst',
author=PROJECT_AUTHOR,
author_email=PROJECT_EMAIL,
url=PROJECT_URL,
@@ -91,7 +92,6 @@ setup(
'Natural Language :: English',
"Programming Language :: Python :: 2",
'Programming Language :: Python :: 2.7',
'Programming Language :: Python :: 3.4',
'Programming Language :: Python :: 3.5',
'Programming Language :: Python :: 3.6',
'Programming Language :: Python :: 3.7',
packages/objectstore/HISTORY.rst
+2 -2
View File
@@ -6,7 +6,7 @@ History
.. to_doc
---------------------
19.5.0.dev0
19.9.0.dev0
---------------------
* Initial import from dev branch of Galaxy during 19.05 release cycle.
* Initial import from dev branch of Galaxy during 19.09 development cycle.
packages/objectstore/Makefile
Symlink
+1
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@@ -0,0 +1 @@
../package.Makefile
packages/objectstore/dev-requirements.txt
Symlink
+1
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@@ -0,0 +1 @@
../package-dev-requirements.txt
packages/objectstore/galaxy/project_galaxy_objectstore.py
+2 -1
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@@ -1,11 +1,12 @@
# -*- coding: utf-8 -*-
__version__ = '19.5.0.dev0'
__version__ = '19.9.0.dev1'
PROJECT_NAME = "galaxy-objectstore"
PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"
PROJECT_URL = "https://github.com/galaxyproject/galaxy"
PROJECT_AUTHOR = 'Galaxy Project and Community'
PROJECT_DESCRIPTION = 'Galaxy Objectstore Framework and Plugins'
PROJECT_EMAIL = 'jmchilton@gmail.com'
RAW_CONTENT_URL = "https://raw.github.com/%s/%s/master/" % (
PROJECT_USERAME, PROJECT_NAME
packages/objectstore/scripts
Symlink
+1
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@@ -0,0 +1 @@
../build_scripts
packages/objectstore/setup.py
+2 -2
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@@ -26,9 +26,9 @@ with open('%s/project_galaxy_objectstore.py' % SOURCE_DIR, 'rb') as f:
PROJECT_URL = get_var("PROJECT_URL")
PROJECT_AUTHOR = get_var("PROJECT_AUTHOR")
PROJECT_EMAIL = get_var("PROJECT_EMAIL")
PROJECT_DESCRIPTION = get_var("PROJECT_DESCRIPTION")
TEST_DIR = 'tests'
PROJECT_DESCRIPTION = 'Galaxy Datatype Framework and Datatypes'
PACKAGES = [
'galaxy',
'galaxy.objectstore',
@@ -65,6 +65,7 @@ setup(
version=version,
description=PROJECT_DESCRIPTION,
long_description=readme + '\n\n' + history,
long_description_content_type='text/x-rst',
author=PROJECT_AUTHOR,
author_email=PROJECT_EMAIL,
url=PROJECT_URL,
@@ -89,7 +90,6 @@ setup(
'Natural Language :: English',
"Programming Language :: Python :: 2",
'Programming Language :: Python :: 2.7',
'Programming Language :: Python :: 3.4',
'Programming Language :: Python :: 3.5',
'Programming Language :: Python :: 3.6',
'Programming Language :: Python :: 3.7',
packages/package-dev-requirements.txt
+9
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@@ -0,0 +1,9 @@
# For testing
pytest
# For dev
sphinx
# For release
wheel
twine
packages/package.Makefile
+89
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@@ -0,0 +1,89 @@
# Location of virtualenv used for development.
VENV?=.venv
# Open resource on Mac OS X or Linux
OPEN_RESOURCE=bash -c 'open $$0 || xdg-open $$0'
# Source virtualenv to execute command (flake8, sphinx, twine, etc...)
IN_VENV=if [ -f $(VENV)/bin/activate ]; then . $(VENV)/bin/activate; fi;
UPSTREAM?=galaxyproject
SOURCE_DIR?=galaxy
BUILD_SCRIPTS_DIR=scripts
DEV_RELEASE?=0
VERSION?=$(shell DEV_RELEASE=$(DEV_RELEASE) python $(BUILD_SCRIPTS_DIR)/print_version_for_release.py $(SOURCE_DIR) $(DEV_RELEASE))
PROJECT_NAME?="galaxy-$(shell basename $(CURDIR))"
PROJECT_NAME:=$(subst _,-,$(PROJECT_NAME))
TEST_DIR?=test
TESTS?=$(SOURCE_DIR) $(TEST_DIR)
.PHONY: clean-pyc clean-build docs clean
help:
@echo "clean - remove all build, test, coverage and Python artifacts"
@echo "clean-build - remove build artifacts"
@echo "clean-pyc - remove Python file artifacts"
@echo "clean-test - remove test and coverage artifacts"
@echo "setup-venv - setup a development virutalenv in current directory."
@echo "lint-dist - twine check dist results, including validating README content"
@echo "dist - package project for PyPI distribution"
clean: clean-build clean-pyc clean-tests
clean-build:
rm -fr build/
rm -fr dist/
rm -fr galaxy_*.egg-info
clean-pyc:
find . -name '*.pyc' -exec rm -f {} +
find . -name '*.pyo' -exec rm -f {} +
find . -name '*~' -exec rm -f {} +
find . -name '__pycache__' -exec rm -fr {} +
clean-tests:
rm -fr .tox/
setup-venv:
if [ ! -d $(VENV) ]; then virtualenv $(VENV); exit; fi;
$(IN_VENV) pip install -r requirements.txt && pip install -r dev-requirements.txt
test:
$(IN_VENV) pytest $(TESTS)
develop:
python setup.py develop
dist: clean
$(IN_VENV) python setup.py sdist bdist_wheel
ls -l dist
lint-dist: dist
$(IN_VENV) twine check dist/*
_release-test-artifacts:
$(IN_VENV) twine upload -r test dist/*
$(OPEN_RESOURCE) https://testpypi.python.org/pypi/$(PROJECT_NAME)
release-test-artifacts: lint-dist _release-test-artifacts
_release-artifacts:
@while [ -z "$$CONTINUE" ]; do \
read -r -p "Have you executed release-test and reviewed results? [y/N]: " CONTINUE; \
done ; \
[ $$CONTINUE = "y" ] || [ $$CONTINUE = "Y" ] || (echo "Exiting."; exit 1;)
@echo "Releasing"
$(IN_VENV) twine upload dist/*
release-artifacts: release-test-artifacts _release-artifacts
commit-version:
$(IN_VENV) DEV_RELEASE=$(DEV_RELEASE) python $(BUILD_SCRIPTS_DIR)/commit_version.py $(SOURCE_DIR) $(VERSION)
new-version:
$(IN_VENV) DEV_RELEASE=$(DEV_RELEASE) python $(BUILD_SCRIPTS_DIR)/new_version.py $(SOURCE_DIR) $(VERSION)
release-local: commit-version release-artifacts new-version
push-release:
git push $(UPSTREAM) dev
git push upstream $(UPSTREAM)/tags/galaxy-$(PROJECT_NAME)-$(VERSION)
release: release-local push-release
packages/tool_util/HISTORY.rst
+1 -1
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@@ -9,4 +9,4 @@ History
19.9.0.dev0
---------------------
* Initial import from dev branch of Galaxy during 19.09 release cycle.
* Initial import from dev branch of Galaxy during 19.09 development cycle.
packages/tool_util/Makefile
Symlink
+1
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@@ -0,0 +1 @@
../package.Makefile
packages/tool_util/dev-requirements.txt
Symlink
+1
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@@ -0,0 +1 @@
../package-dev-requirements.txt
packages/tool_util/galaxy/project_galaxy_tool_util.py
+2 -1
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@@ -1,11 +1,12 @@
# -*- coding: utf-8 -*-
__version__ = '19.9.0.dev0'
__version__ = '19.9.0.dev1'
PROJECT_NAME = "galaxy-tool-util"
PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"
PROJECT_URL = "https://github.com/galaxyproject/galaxy"
PROJECT_AUTHOR = 'Galaxy Project and Community'
PROJECT_DESCRIPTION = 'Galaxy Tool and Tool Dependency Utilities'
PROJECT_EMAIL = 'jmchilton@gmail.com'
RAW_CONTENT_URL = "https://raw.github.com/%s/%s/master/" % (
PROJECT_USERAME, PROJECT_NAME
packages/tool_util/scripts
Symlink
+1
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@@ -0,0 +1 @@
../build_scripts
packages/tool_util/setup.py
+2 -2
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@@ -26,9 +26,9 @@ with open('%s/project_galaxy_tool_util.py' % SOURCE_DIR, 'rb') as f:
PROJECT_URL = get_var("PROJECT_URL")
PROJECT_AUTHOR = get_var("PROJECT_AUTHOR")
PROJECT_EMAIL = get_var("PROJECT_EMAIL")
PROJECT_DESCRIPTION = get_var("PROJECT_DESCRIPTION")
TEST_DIR = 'tests'
PROJECT_DESCRIPTION = 'Galaxy Tool Utilities'
PACKAGES = [
'galaxy',
'galaxy.tool_util',
@@ -79,6 +79,7 @@ setup(
version=version,
description=PROJECT_DESCRIPTION,
long_description=readme + '\n\n' + history,
long_description_content_type='text/x-rst',
author=PROJECT_AUTHOR,
author_email=PROJECT_EMAIL,
url=PROJECT_URL,
@@ -103,7 +104,6 @@ setup(
'Natural Language :: English',
"Programming Language :: Python :: 2",
'Programming Language :: Python :: 2.7',
'Programming Language :: Python :: 3.4',
'Programming Language :: Python :: 3.5',
'Programming Language :: Python :: 3.6',
'Programming Language :: Python :: 3.7',
packages/util/HISTORY.rst
+2 -2
View File
@@ -6,7 +6,7 @@ History
.. to_doc
---------------------
19.5.0.dev0
19.9.0.dev0
---------------------
* Initial import from dev branch of Galaxy during 19.05 release cycle.
* Initial import from dev branch of Galaxy during 19.09 development cycle.
packages/util/Makefile
Symlink
+1
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@@ -0,0 +1 @@
../package.Makefile
packages/util/dev-requirements.txt
Symlink
+1
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@@ -0,0 +1 @@
../package-dev-requirements.txt
packages/util/galaxy/project_galaxy_util.py
+2 -1
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@@ -1,11 +1,12 @@
# -*- coding: utf-8 -*-
__version__ = '19.5.0.dev0'
__version__ = '19.9.0.dev2'
PROJECT_NAME = "galaxy-util"
PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"
PROJECT_URL = "https://github.com/galaxyproject/galaxy"
PROJECT_AUTHOR = 'Galaxy Project and Community'
PROJECT_DESCRIPTION = 'Galaxy Generic Utilities'
PROJECT_EMAIL = 'jmchilton@gmail.com'
RAW_CONTENT_URL = "https://raw.github.com/%s/%s/master/" % (
PROJECT_USERAME, PROJECT_NAME
packages/util/scripts
Symlink
+1
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@@ -0,0 +1 @@
../build_scripts
packages/util/setup.py
+3 -2
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@@ -26,11 +26,12 @@ with open('%s/project_galaxy_util.py' % SOURCE_DIR, 'rb') as f:
PROJECT_URL = get_var("PROJECT_URL")
PROJECT_AUTHOR = get_var("PROJECT_AUTHOR")
PROJECT_EMAIL = get_var("PROJECT_EMAIL")
PROJECT_DESCRIPTION = get_var("PROJECT_DESCRIPTION")
TEST_DIR = 'tests'
PROJECT_DESCRIPTION = 'Galaxy Datatype Framework and Datatypes'
PACKAGES = [
'galaxy',
'galaxy.exceptions',
'galaxy.util',
'galaxy.util.logging',
'galaxy.util.path',
@@ -69,6 +70,7 @@ setup(
version=version,
description=PROJECT_DESCRIPTION,
long_description=readme + '\n\n' + history,
long_description_content_type='text/x-rst',
author=PROJECT_AUTHOR,
author_email=PROJECT_EMAIL,
url=PROJECT_URL,
@@ -93,7 +95,6 @@ setup(
'Natural Language :: English',
"Programming Language :: Python :: 2",
'Programming Language :: Python :: 2.7',
'Programming Language :: Python :: 3.4',
'Programming Language :: Python :: 3.5',
'Programming Language :: Python :: 3.6',
'Programming Language :: Python :: 3.7',
setup.cfg
+3
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@@ -1,3 +1,6 @@
[wheel]
universal = 1
[flake8]
# These are exceptions allowed by Galaxy style guidelines.
# E128 continuation line under-indented for visual indent