Old engine for Continuous Time Bayesian Networks. Superseded by reCTBN. 🐍
https://github.com/madlabunimib/PyCTBN
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434 lines
15 KiB
434 lines
15 KiB
# The following comment should be removed at some point in the future.
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# mypy: disallow-untyped-defs=False
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from __future__ import absolute_import
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import logging
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import os.path
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import re
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from pip._vendor.packaging.version import parse as parse_version
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from pip._vendor.six.moves.urllib import parse as urllib_parse
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from pip._vendor.six.moves.urllib import request as urllib_request
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from pip._internal.exceptions import BadCommand, SubProcessError
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from pip._internal.utils.misc import display_path, hide_url
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from pip._internal.utils.subprocess import make_command
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from pip._internal.utils.temp_dir import TempDirectory
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from pip._internal.utils.typing import MYPY_CHECK_RUNNING
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from pip._internal.vcs.versioncontrol import (
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RemoteNotFoundError,
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VersionControl,
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find_path_to_setup_from_repo_root,
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vcs,
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)
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if MYPY_CHECK_RUNNING:
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from typing import Optional, Tuple
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from pip._internal.utils.misc import HiddenText
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from pip._internal.vcs.versioncontrol import AuthInfo, RevOptions
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urlsplit = urllib_parse.urlsplit
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urlunsplit = urllib_parse.urlunsplit
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logger = logging.getLogger(__name__)
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HASH_REGEX = re.compile('^[a-fA-F0-9]{40}$')
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def looks_like_hash(sha):
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return bool(HASH_REGEX.match(sha))
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class Git(VersionControl):
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name = 'git'
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dirname = '.git'
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repo_name = 'clone'
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schemes = (
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'git', 'git+http', 'git+https', 'git+ssh', 'git+git', 'git+file',
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)
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# Prevent the user's environment variables from interfering with pip:
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# https://github.com/pypa/pip/issues/1130
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unset_environ = ('GIT_DIR', 'GIT_WORK_TREE')
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default_arg_rev = 'HEAD'
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@staticmethod
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def get_base_rev_args(rev):
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return [rev]
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def is_immutable_rev_checkout(self, url, dest):
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# type: (str, str) -> bool
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_, rev_options = self.get_url_rev_options(hide_url(url))
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if not rev_options.rev:
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return False
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if not self.is_commit_id_equal(dest, rev_options.rev):
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# the current commit is different from rev,
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# which means rev was something else than a commit hash
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return False
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# return False in the rare case rev is both a commit hash
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# and a tag or a branch; we don't want to cache in that case
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# because that branch/tag could point to something else in the future
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is_tag_or_branch = bool(
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self.get_revision_sha(dest, rev_options.rev)[0]
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)
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return not is_tag_or_branch
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def get_git_version(self):
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VERSION_PFX = 'git version '
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version = self.run_command(['version'])
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if version.startswith(VERSION_PFX):
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version = version[len(VERSION_PFX):].split()[0]
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else:
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version = ''
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# get first 3 positions of the git version because
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# on windows it is x.y.z.windows.t, and this parses as
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# LegacyVersion which always smaller than a Version.
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version = '.'.join(version.split('.')[:3])
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return parse_version(version)
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@classmethod
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def get_current_branch(cls, location):
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"""
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Return the current branch, or None if HEAD isn't at a branch
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(e.g. detached HEAD).
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"""
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# git-symbolic-ref exits with empty stdout if "HEAD" is a detached
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# HEAD rather than a symbolic ref. In addition, the -q causes the
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# command to exit with status code 1 instead of 128 in this case
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# and to suppress the message to stderr.
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args = ['symbolic-ref', '-q', 'HEAD']
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output = cls.run_command(
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args, extra_ok_returncodes=(1, ), cwd=location,
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)
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ref = output.strip()
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if ref.startswith('refs/heads/'):
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return ref[len('refs/heads/'):]
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return None
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def export(self, location, url):
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# type: (str, HiddenText) -> None
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"""Export the Git repository at the url to the destination location"""
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if not location.endswith('/'):
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location = location + '/'
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with TempDirectory(kind="export") as temp_dir:
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self.unpack(temp_dir.path, url=url)
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self.run_command(
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['checkout-index', '-a', '-f', '--prefix', location],
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cwd=temp_dir.path
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)
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@classmethod
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def get_revision_sha(cls, dest, rev):
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"""
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Return (sha_or_none, is_branch), where sha_or_none is a commit hash
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if the revision names a remote branch or tag, otherwise None.
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Args:
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dest: the repository directory.
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rev: the revision name.
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"""
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# Pass rev to pre-filter the list.
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output = ''
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try:
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output = cls.run_command(['show-ref', rev], cwd=dest)
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except SubProcessError:
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pass
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refs = {}
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for line in output.strip().splitlines():
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try:
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sha, ref = line.split()
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except ValueError:
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# Include the offending line to simplify troubleshooting if
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# this error ever occurs.
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raise ValueError('unexpected show-ref line: {!r}'.format(line))
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refs[ref] = sha
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branch_ref = 'refs/remotes/origin/{}'.format(rev)
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tag_ref = 'refs/tags/{}'.format(rev)
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sha = refs.get(branch_ref)
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if sha is not None:
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return (sha, True)
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sha = refs.get(tag_ref)
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return (sha, False)
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@classmethod
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def _should_fetch(cls, dest, rev):
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"""
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Return true if rev is a ref or is a commit that we don't have locally.
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Branches and tags are not considered in this method because they are
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assumed to be always available locally (which is a normal outcome of
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``git clone`` and ``git fetch --tags``).
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"""
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if rev.startswith("refs/"):
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# Always fetch remote refs.
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return True
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if not looks_like_hash(rev):
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# Git fetch would fail with abbreviated commits.
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return False
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if cls.has_commit(dest, rev):
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# Don't fetch if we have the commit locally.
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return False
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return True
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@classmethod
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def resolve_revision(cls, dest, url, rev_options):
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# type: (str, HiddenText, RevOptions) -> RevOptions
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"""
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Resolve a revision to a new RevOptions object with the SHA1 of the
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branch, tag, or ref if found.
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Args:
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rev_options: a RevOptions object.
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"""
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rev = rev_options.arg_rev
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# The arg_rev property's implementation for Git ensures that the
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# rev return value is always non-None.
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assert rev is not None
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sha, is_branch = cls.get_revision_sha(dest, rev)
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if sha is not None:
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rev_options = rev_options.make_new(sha)
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rev_options.branch_name = rev if is_branch else None
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return rev_options
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# Do not show a warning for the common case of something that has
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# the form of a Git commit hash.
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if not looks_like_hash(rev):
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logger.warning(
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"Did not find branch or tag '%s', assuming revision or ref.",
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rev,
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)
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if not cls._should_fetch(dest, rev):
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return rev_options
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# fetch the requested revision
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cls.run_command(
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make_command('fetch', '-q', url, rev_options.to_args()),
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cwd=dest,
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)
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# Change the revision to the SHA of the ref we fetched
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sha = cls.get_revision(dest, rev='FETCH_HEAD')
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rev_options = rev_options.make_new(sha)
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return rev_options
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@classmethod
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def is_commit_id_equal(cls, dest, name):
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"""
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Return whether the current commit hash equals the given name.
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Args:
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dest: the repository directory.
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name: a string name.
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"""
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if not name:
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# Then avoid an unnecessary subprocess call.
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return False
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return cls.get_revision(dest) == name
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def fetch_new(self, dest, url, rev_options):
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# type: (str, HiddenText, RevOptions) -> None
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rev_display = rev_options.to_display()
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logger.info('Cloning %s%s to %s', url, rev_display, display_path(dest))
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self.run_command(make_command('clone', '-q', url, dest))
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if rev_options.rev:
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# Then a specific revision was requested.
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rev_options = self.resolve_revision(dest, url, rev_options)
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branch_name = getattr(rev_options, 'branch_name', None)
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if branch_name is None:
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# Only do a checkout if the current commit id doesn't match
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# the requested revision.
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if not self.is_commit_id_equal(dest, rev_options.rev):
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cmd_args = make_command(
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'checkout', '-q', rev_options.to_args(),
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)
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self.run_command(cmd_args, cwd=dest)
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elif self.get_current_branch(dest) != branch_name:
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# Then a specific branch was requested, and that branch
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# is not yet checked out.
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track_branch = 'origin/{}'.format(branch_name)
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cmd_args = [
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'checkout', '-b', branch_name, '--track', track_branch,
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]
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self.run_command(cmd_args, cwd=dest)
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#: repo may contain submodules
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self.update_submodules(dest)
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def switch(self, dest, url, rev_options):
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# type: (str, HiddenText, RevOptions) -> None
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self.run_command(
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make_command('config', 'remote.origin.url', url),
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cwd=dest,
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)
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cmd_args = make_command('checkout', '-q', rev_options.to_args())
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self.run_command(cmd_args, cwd=dest)
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self.update_submodules(dest)
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def update(self, dest, url, rev_options):
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# type: (str, HiddenText, RevOptions) -> None
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# First fetch changes from the default remote
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if self.get_git_version() >= parse_version('1.9.0'):
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# fetch tags in addition to everything else
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self.run_command(['fetch', '-q', '--tags'], cwd=dest)
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else:
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self.run_command(['fetch', '-q'], cwd=dest)
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# Then reset to wanted revision (maybe even origin/master)
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rev_options = self.resolve_revision(dest, url, rev_options)
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cmd_args = make_command('reset', '--hard', '-q', rev_options.to_args())
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self.run_command(cmd_args, cwd=dest)
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#: update submodules
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self.update_submodules(dest)
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@classmethod
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def get_remote_url(cls, location):
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"""
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Return URL of the first remote encountered.
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Raises RemoteNotFoundError if the repository does not have a remote
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url configured.
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"""
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# We need to pass 1 for extra_ok_returncodes since the command
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# exits with return code 1 if there are no matching lines.
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stdout = cls.run_command(
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['config', '--get-regexp', r'remote\..*\.url'],
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extra_ok_returncodes=(1, ), cwd=location,
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)
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remotes = stdout.splitlines()
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try:
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found_remote = remotes[0]
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except IndexError:
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raise RemoteNotFoundError
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for remote in remotes:
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if remote.startswith('remote.origin.url '):
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found_remote = remote
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break
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url = found_remote.split(' ')[1]
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return url.strip()
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@classmethod
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def has_commit(cls, location, rev):
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"""
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Check if rev is a commit that is available in the local repository.
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"""
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try:
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cls.run_command(
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['rev-parse', '-q', '--verify', "sha^" + rev], cwd=location
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)
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except SubProcessError:
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return False
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else:
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return True
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@classmethod
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def get_revision(cls, location, rev=None):
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if rev is None:
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rev = 'HEAD'
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current_rev = cls.run_command(
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['rev-parse', rev], cwd=location,
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)
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return current_rev.strip()
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@classmethod
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def get_subdirectory(cls, location):
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"""
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Return the path to setup.py, relative to the repo root.
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Return None if setup.py is in the repo root.
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"""
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# find the repo root
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git_dir = cls.run_command(
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['rev-parse', '--git-dir'],
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cwd=location).strip()
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if not os.path.isabs(git_dir):
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git_dir = os.path.join(location, git_dir)
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repo_root = os.path.abspath(os.path.join(git_dir, '..'))
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return find_path_to_setup_from_repo_root(location, repo_root)
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@classmethod
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def get_url_rev_and_auth(cls, url):
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# type: (str) -> Tuple[str, Optional[str], AuthInfo]
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"""
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Prefixes stub URLs like 'user@hostname:user/repo.git' with 'ssh://'.
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That's required because although they use SSH they sometimes don't
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work with a ssh:// scheme (e.g. GitHub). But we need a scheme for
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parsing. Hence we remove it again afterwards and return it as a stub.
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"""
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# Works around an apparent Git bug
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# (see https://article.gmane.org/gmane.comp.version-control.git/146500)
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scheme, netloc, path, query, fragment = urlsplit(url)
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if scheme.endswith('file'):
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initial_slashes = path[:-len(path.lstrip('/'))]
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newpath = (
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initial_slashes +
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urllib_request.url2pathname(path)
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.replace('\\', '/').lstrip('/')
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)
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after_plus = scheme.find('+') + 1
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url = scheme[:after_plus] + urlunsplit(
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(scheme[after_plus:], netloc, newpath, query, fragment),
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)
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if '://' not in url:
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assert 'file:' not in url
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url = url.replace('git+', 'git+ssh://')
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url, rev, user_pass = super(Git, cls).get_url_rev_and_auth(url)
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url = url.replace('ssh://', '')
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else:
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url, rev, user_pass = super(Git, cls).get_url_rev_and_auth(url)
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return url, rev, user_pass
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@classmethod
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def update_submodules(cls, location):
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if not os.path.exists(os.path.join(location, '.gitmodules')):
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return
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cls.run_command(
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['submodule', 'update', '--init', '--recursive', '-q'],
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cwd=location,
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)
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@classmethod
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def get_repository_root(cls, location):
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loc = super(Git, cls).get_repository_root(location)
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if loc:
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return loc
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try:
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r = cls.run_command(
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['rev-parse', '--show-toplevel'],
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cwd=location,
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log_failed_cmd=False,
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)
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except BadCommand:
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logger.debug("could not determine if %s is under git control "
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"because git is not available", location)
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return None
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except SubProcessError:
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return None
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return os.path.normpath(r.rstrip('\r\n'))
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vcs.register(Git)
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