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Don't complain when writing a bgzip file and the extension is gz
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@jdidion
jdidion committed Apr 6, 2019
1 parent f99b743 commit 0580a35
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Showing 8 changed files with 1,376 additions and 964 deletions.
447 changes: 270 additions & 177 deletions xphyle/__init__.py
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132 changes: 83 additions & 49 deletions xphyle/_version.py
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Original file line number Diff line number Diff line change
Expand Up @@ -57,12 +57,14 @@ class NotThisMethod(Exception):

def register_vcs_handler(vcs, method): # decorator
"""Decorator to mark a method as the handler for a particular VCS."""

def decorate(f):
"""Store f in HANDLERS[vcs][method]."""
if vcs not in HANDLERS:
HANDLERS[vcs] = {}
HANDLERS[vcs][method] = f
return f

return decorate


Expand All @@ -74,9 +76,12 @@ def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False):
try:
dispcmd = str([c] + args)
# remember shell=False, so use git.cmd on windows, not just git
p = subprocess.Popen([c] + args, cwd=cwd, stdout=subprocess.PIPE,
stderr=(subprocess.PIPE if hide_stderr
else None))
p = subprocess.Popen(
[c] + args,
cwd=cwd,
stdout=subprocess.PIPE,
stderr=(subprocess.PIPE if hide_stderr else None),
)
break
except EnvironmentError:
e = sys.exc_info()[1]
Expand Down Expand Up @@ -109,12 +114,17 @@ def versions_from_parentdir(parentdir_prefix, root, verbose):
dirname = os.path.basename(root)
if not dirname.startswith(parentdir_prefix):
if verbose:
print("guessing rootdir is '%s', but '%s' doesn't start with "
"prefix '%s'" % (root, dirname, parentdir_prefix))
print(
"guessing rootdir is '%s', but '%s' doesn't start with "
"prefix '%s'" % (root, dirname, parentdir_prefix)
)
raise NotThisMethod("rootdir doesn't start with parentdir_prefix")
return {"version": dirname[len(parentdir_prefix):],
"full-revisionid": None,
"dirty": False, "error": None}
return {
"version": dirname[len(parentdir_prefix) :],
"full-revisionid": None,
"dirty": False,
"error": None,
}


@register_vcs_handler("git", "get_keywords")
Expand Down Expand Up @@ -156,7 +166,7 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose):
# starting in git-1.8.3, tags are listed as "tag: foo-1.0" instead of
# just "foo-1.0". If we see a "tag: " prefix, prefer those.
TAG = "tag: "
tags = set([r[len(TAG):] for r in refs if r.startswith(TAG)])
tags = set([r[len(TAG) :] for r in refs if r.startswith(TAG)])
if not tags:
# Either we're using git < 1.8.3, or there really are no tags. We use
# a heuristic: assume all version tags have a digit. The old git %d
Expand All @@ -165,27 +175,32 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose):
# between branches and tags. By ignoring refnames without digits, we
# filter out many common branch names like "release" and
# "stabilization", as well as "HEAD" and "master".
tags = set([r for r in refs if re.search(r'\d', r)])
tags = set([r for r in refs if re.search(r"\d", r)])
if verbose:
print("discarding '%s', no digits" % ",".join(refs-tags))
print("discarding '%s', no digits" % ",".join(refs - tags))
if verbose:
print("likely tags: %s" % ",".join(sorted(tags)))
for ref in sorted(tags):
# sorting will prefer e.g. "2.0" over "2.0rc1"
if ref.startswith(tag_prefix):
r = ref[len(tag_prefix):]
r = ref[len(tag_prefix) :]
if verbose:
print("picking %s" % r)
return {"version": r,
"full-revisionid": keywords["full"].strip(),
"dirty": False, "error": None
}
return {
"version": r,
"full-revisionid": keywords["full"].strip(),
"dirty": False,
"error": None,
}
# no suitable tags, so version is "0+unknown", but full hex is still there
if verbose:
print("no suitable tags, using unknown + full revision id")
return {"version": "0+unknown",
"full-revisionid": keywords["full"].strip(),
"dirty": False, "error": "no suitable tags"}
return {
"version": "0+unknown",
"full-revisionid": keywords["full"].strip(),
"dirty": False,
"error": "no suitable tags",
}


@register_vcs_handler("git", "pieces_from_vcs")
Expand All @@ -206,10 +221,19 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
GITS = ["git.cmd", "git.exe"]
# if there is a tag matching tag_prefix, this yields TAG-NUM-gHEX[-dirty]
# if there isn't one, this yields HEX[-dirty] (no NUM)
describe_out = run_command(GITS, ["describe", "--tags", "--dirty",
"--always", "--long",
"--match", "%s*" % tag_prefix],
cwd=root)
describe_out = run_command(
GITS,
[
"describe",
"--tags",
"--dirty",
"--always",
"--long",
"--match",
"%s*" % tag_prefix,
],
cwd=root,
)
# --long was added in git-1.5.5
if describe_out is None:
raise NotThisMethod("'git describe' failed")
Expand All @@ -229,17 +253,16 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
dirty = git_describe.endswith("-dirty")
pieces["dirty"] = dirty
if dirty:
git_describe = git_describe[:git_describe.rindex("-dirty")]
git_describe = git_describe[: git_describe.rindex("-dirty")]

# now we have TAG-NUM-gHEX or HEX

if "-" in git_describe:
# TAG-NUM-gHEX
mo = re.search(r'^(.+)-(\d+)-g([0-9a-f]+)$', git_describe)
mo = re.search(r"^(.+)-(\d+)-g([0-9a-f]+)$", git_describe)
if not mo:
# unparseable. Maybe git-describe is misbehaving?
pieces["error"] = ("unable to parse git-describe output: '%s'"
% describe_out)
pieces["error"] = "unable to parse git-describe output: '%s'" % describe_out
return pieces

# tag
Expand All @@ -248,10 +271,12 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
if verbose:
fmt = "tag '%s' doesn't start with prefix '%s'"
print(fmt % (full_tag, tag_prefix))
pieces["error"] = ("tag '%s' doesn't start with prefix '%s'"
% (full_tag, tag_prefix))
pieces["error"] = "tag '%s' doesn't start with prefix '%s'" % (
full_tag,
tag_prefix,
)
return pieces
pieces["closest-tag"] = full_tag[len(tag_prefix):]
pieces["closest-tag"] = full_tag[len(tag_prefix) :]

# distance: number of commits since tag
pieces["distance"] = int(mo.group(2))
Expand All @@ -262,8 +287,7 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
else:
# HEX: no tags
pieces["closest-tag"] = None
count_out = run_command(GITS, ["rev-list", "HEAD", "--count"],
cwd=root)
count_out = run_command(GITS, ["rev-list", "HEAD", "--count"], cwd=root)
pieces["distance"] = int(count_out) # total number of commits

return pieces
Expand Down Expand Up @@ -294,8 +318,7 @@ def render_pep440(pieces):
rendered += ".dirty"
else:
# exception #1
rendered = "0+untagged.%d.g%s" % (pieces["distance"],
pieces["short"])
rendered = "0+untagged.%d.g%s" % (pieces["distance"], pieces["short"])
if pieces["dirty"]:
rendered += ".dirty"
return rendered
Expand Down Expand Up @@ -409,10 +432,12 @@ def render_git_describe_long(pieces):
def render(pieces, style):
"""Render the given version pieces into the requested style."""
if pieces["error"]:
return {"version": "unknown",
"full-revisionid": pieces.get("long"),
"dirty": None,
"error": pieces["error"]}
return {
"version": "unknown",
"full-revisionid": pieces.get("long"),
"dirty": None,
"error": pieces["error"],
}

if not style or style == "default":
style = "pep440" # the default
Expand All @@ -432,8 +457,12 @@ def render(pieces, style):
else:
raise ValueError("unknown style '%s'" % style)

return {"version": rendered, "full-revisionid": pieces["long"],
"dirty": pieces["dirty"], "error": None}
return {
"version": rendered,
"full-revisionid": pieces["long"],
"dirty": pieces["dirty"],
"error": None,
}


def get_versions():
Expand All @@ -447,8 +476,7 @@ def get_versions():
verbose = cfg.verbose

try:
return git_versions_from_keywords(get_keywords(), cfg.tag_prefix,
verbose)
return git_versions_from_keywords(get_keywords(), cfg.tag_prefix, verbose)
except NotThisMethod:
pass

Expand All @@ -457,12 +485,15 @@ def get_versions():
# versionfile_source is the relative path from the top of the source
# tree (where the .git directory might live) to this file. Invert
# this to find the root from __file__.
for i in cfg.versionfile_source.split('/'):
for i in cfg.versionfile_source.split("/"):
root = os.path.dirname(root)
except NameError:
return {"version": "0+unknown", "full-revisionid": None,
"dirty": None,
"error": "unable to find root of source tree"}
return {
"version": "0+unknown",
"full-revisionid": None,
"dirty": None,
"error": "unable to find root of source tree",
}

try:
pieces = git_pieces_from_vcs(cfg.tag_prefix, root, verbose)
Expand All @@ -476,6 +507,9 @@ def get_versions():
except NotThisMethod:
pass

return {"version": "0+unknown", "full-revisionid": None,
"dirty": None,
"error": "unable to compute version"}
return {
"version": "0+unknown",
"full-revisionid": None,
"dirty": None,
"error": "unable to compute version",
}

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