def _install_requirements(plugin_path):
requirement_file = os.path.join(plugin_path, "plugin_requirements.txt")
if os.path.isfile(requirement_file):
LOG.info(
"Installing requirements from: {}".format(requirement_file))
pip_args = ['install', '-r', requirement_file]
pip_main(args=pip_args)
def _preinstall(package_list, options=[]):
""" Pre-install PyPi packages before running cmake.
"""
if not isinstance(package_list, list) or not isinstance(options, list):
raise TypeError('preinstall inputs must be of type list.')
pip_main(['install'] + options + package_list)
def pipinstall(package_list, options=[]):
""" Pip install PyPi packages.
"""
if not isinstance(package_list, list) or not isinstance(options, list):
raise TypeError('preinstall inputs must be of type list.')
pip_main(['install'] + options + package_list)
def marvcli_pip_uninstall(pipargs):
"""Uninstall python package (EE)."""
assert within_pyinstaller_bundle()
siteconf = get_site_config()
sitepackages = make_config(siteconf).marv.sitepackages
load_sitepackages(sitepackages)
ensure_python(siteconf, sitepackages)
from pip._internal.main import main as pip_main # pylint: disable=import-outside-toplevel
sys.argv = [sys.executable, 'uninstall', *pipargs]
sys.exit(pip_main())
def marvcli_pip_install(pipargs):
"""Install python package (EE).
Use -e like with plain pip to install in editable mode.
"""
assert within_pyinstaller_bundle()
siteconf = get_site_config()
config = make_config(siteconf)
sitepackages = config.marv.sitepackages
load_sitepackages(sitepackages)
ensure_python(siteconf, sitepackages)
from pip._internal.main import main as pip_main # pylint: disable=import-outside-toplevel
sys.argv = [
sys.executable, 'install', '--prefix',
str(config.marv.venv), *pipargs
]
sys.exit(pip_main())
def install():
parser = argparse.ArgumentParser(
formatter_class=argparse.RawDescriptionHelpFormatter,
description="""
Install all requirements from specified file with pip. Optionally transform
git+git and git+ssh url to private repo's to use a given Personal Access Token for
github. That way installing them does not depend on a ssh-agent with suitable
keys. Which you don't have when installing requirements in a Docker.
These URLs will also be stripped of the -e flag, so they're installed globally.
Note the -e flag is optional for the git+git//github.com and git+ssh://github.com
urls.
This means that the following URL:
-e [email protected]:MyOrg/my-project.git@my-tag#egg=my_project
would be transformed to:
git+https://<token>:[email protected]/MyOrg/my-project.git@my-tag#egg=my_project
Non-private GitHub URL's (git+https) and non-GitHub URL's are kept as-is, but
are also stripped of the -e flag. If no token is given, private URLs will be
kept, including the -e flag (otherwise they can't be installed at all).
""")
parser.add_argument(
'--token',
'-t',
help='Your Personal Access Token for private GitHub repositories',
default=os.environ.get('GITHUB_TOKEN'))
parser.add_argument('req_file',
help='path to the requirements file to install')
args = parser.parse_args()
# TODO: rewrite to a clear collect and a clear transform phase. Or pass in a transform function
pip_args = ['install'] + collect_requirements(
args.req_file, transform_with_token=args.token)
if pip_main(pip_args) != status_codes.SUCCESS:
raise RuntimeError('Error installing requirements')
def _pip_install_helper(package_names):
for package in package_names:
pip_main(["install", "-q", package])
logger.reset()
# Global parameters
CLASSIFIERS = [
"Development Status :: 1 - Planning", "Environment :: Console",
"Operating System :: OS Independent", "Programming Language :: Python",
"Topic :: Scientific/Engineering"
]
AUTHOR = """
Antoine Grigis <*****@*****.**>
Samuel Farrens <*****@*****.**>
Jean-Luc Starck <*****@*****.**>
Philippe Ciuciu <*****@*****.**>
"""
# Write setup
setup_requires = ["numpy>=1.16.4", "cython>=0.27.3", "pytest-runner"]
pip_main(['install'] + setup_requires)
setup(
name="pysap-mri",
description="Python Sparse data Analysis Package external MRI plugin.",
long_description="Python Sparse data Analysis Package external MRI plugin.",
license="CeCILL-B",
classifiers="CLASSIFIERS",
author=AUTHOR,
author_email="XXX",
version="0.4.0",
url="https://github.com/CEA-COSMIC/pysap-mri",
packages=find_packages(),
setup_requires=setup_requires,
install_requires=[
"scikit-learn>=0.19.1",
def update_plugin(self,
plugin_name,
revision=None,
skip_reqs=False,
hard_reset=False):
"""Updates a Git-based plugin
Pulls changes from the remote, and checkout a specific revision.
(will point to the tip of the branch if revision isn't given)
:param plugin_name: Name of plugin to update.
:param revision: Revision to checkout.
:param skip_reqs: If True, will skip plugin requirements installation.
:param hard_reset: Whether to drop all changes using git hard reset
"""
if plugin_name not in self.PLUGINS_DICT:
raise IRFailedToUpdatePlugin(
"Plugin '{}' isn't installed".format(plugin_name))
plugin = self.get_plugin(plugin_name)
try:
repo = git.Repo(plugin.path, search_parent_directories=True)
except git.InvalidGitRepositoryError:
raise IRFailedToUpdatePlugin(
"Plugin '{}' isn't a Git-based plugin".format(plugin_name))
# microseconds ('%f') required for unit testing
timestamp = \
datetime.datetime.fromtimestamp(
time.time()).strftime('%B-%d-%Y_%H-%M-%S-%f')
update_string = \
'IR_Plugin_update_{plugin_name}_{timestamp}' \
''.format(plugin_name=plugin_name, timestamp=timestamp)
LOG.debug("Checking for changes of tracked files "
"in {}".format(plugin.path))
changed_tracked_files = \
repo.git.status('--porcelain', '--untracked-files=no')
all_changed_files = repo.git.status('--porcelain')
if changed_tracked_files and not hard_reset:
raise IRFailedToUpdatePlugin("Failed to update plugin {}\n"
"Found changes in tracked files, "
"please go to {}, and manually save "
"your changes!".format(
plugin_name, plugin.path))
if hard_reset:
if all_changed_files:
repo.git.stash('save', '-u', update_string)
LOG.warning("All changes have been "
"stashed - '{}'".format(update_string))
repo.git.reset('--hard', 'HEAD')
# checkout revision
self._checkout_git_plugin_revision(repo, revision, update_string)
if not hard_reset:
# pull changes
self._pull_git_plugin_changes(repo)
if repo.git.status('--porcelain', '--untracked-files=no'):
LOG.warning("Changes in tracked files have been found")
if not skip_reqs:
reqs_file = os.path.join(plugin.path, 'requirements.txt')
if os.path.isfile(reqs_file):
pip_main(['install', '-r', reqs_file])
def import_requirements(req_file):
with open(req_file, "r") as requirements:
for req in requirements:
if pip_main(["install", req]) == 1:
raise Exception("Package {} not installed".format(req))
