Set up versioneer

Fixes #47.

.gitattributes

+mhcflurry/_version.py export-subst

MANIFEST.in

+include versioneer.py
+include mhcflurry/_version.py

mhcflurry/__init__.py

@@ -17,7 +17,11 @@ from .class1_affinity_prediction.class1_neural_network import (
 from .class1_affinity_prediction.class1_affinity_predictor import (
     Class1AffinityPredictor)
 
-__version__ = "0.9.2"
+
+from ._version import get_versions
+__version__ = get_versions()['version']
+del get_versions
+
 
 __all__ = [
     "Class1NeuralNetwork",

mhcflurry/_version.py

+
+# This file helps to compute a version number in source trees obtained from
+# git-archive tarball (such as those provided by githubs download-from-tag
+# feature). Distribution tarballs (built by setup.py sdist) and build
+# directories (produced by setup.py build) will contain a much shorter file
+# that just contains the computed version number.
+
+# This file is released into the public domain. Generated by
+# versioneer-0.18 (https://github.com/warner/python-versioneer)
+
+"""Git implementation of _version.py."""
+
+import errno
+import os
+import re
+import subprocess
+import sys
+
+
+def get_keywords():
+    """Get the keywords needed to look up the version information."""
+    # these strings will be replaced by git during git-archive.
+    # setup.py/versioneer.py will grep for the variable names, so they must
+    # each be defined on a line of their own. _version.py will just call
+    # get_keywords().
+    git_refnames = "$Format:%d$"
+    git_full = "$Format:%H$"
+    git_date = "$Format:%ci$"
+    keywords = {"refnames": git_refnames, "full": git_full, "date": git_date}
+    return keywords
+
+
+class VersioneerConfig:
+    """Container for Versioneer configuration parameters."""
+
+
+def get_config():
+    """Create, populate and return the VersioneerConfig() object."""
+    # these strings are filled in when 'setup.py versioneer' creates
+    # _version.py
+    cfg = VersioneerConfig()
+    cfg.VCS = "git"
+    cfg.style = "pep440"
+    cfg.tag_prefix = ""
+    cfg.parentdir_prefix = "mhcflurry-"
+    cfg.versionfile_source = "mhcflurry/_version.py"
+    cfg.verbose = False
+    return cfg
+
+
+class NotThisMethod(Exception):
+    """Exception raised if a method is not valid for the current scenario."""
+
+
+LONG_VERSION_PY = {}
+HANDLERS = {}
+
+
+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
+
+
+def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False,
+                env=None):
+    """Call the given command(s)."""
+    assert isinstance(commands, list)
+    p = None
+    for c in commands:
+        try:
+            dispcmd = str([c] + args)
+            # remember shell=False, so use git.cmd on windows, not just git
+            p = subprocess.Popen([c] + args, cwd=cwd, env=env,
+                                 stdout=subprocess.PIPE,
+                                 stderr=(subprocess.PIPE if hide_stderr
+                                         else None))
+            break
+        except EnvironmentError:
+            e = sys.exc_info()[1]
+            if e.errno == errno.ENOENT:
+                continue
+            if verbose:
+                print("unable to run %s" % dispcmd)
+                print(e)
+            return None, None
+    else:
+        if verbose:
+            print("unable to find command, tried %s" % (commands,))
+        return None, None
+    stdout = p.communicate()[0].strip()
+    if sys.version_info[0] >= 3:
+        stdout = stdout.decode()
+    if p.returncode != 0:
+        if verbose:
+            print("unable to run %s (error)" % dispcmd)
+            print("stdout was %s" % stdout)
+        return None, p.returncode
+    return stdout, p.returncode
+
+
+def versions_from_parentdir(parentdir_prefix, root, verbose):
+    """Try to determine the version from the parent directory name.
+
+    Source tarballs conventionally unpack into a directory that includes both
+    the project name and a version string. We will also support searching up
+    two directory levels for an appropriately named parent directory
+    """
+    rootdirs = []
+
+    for i in range(3):
+        dirname = os.path.basename(root)
+        if dirname.startswith(parentdir_prefix):
+            return {"version": dirname[len(parentdir_prefix):],
+                    "full-revisionid": None,
+                    "dirty": False, "error": None, "date": None}
+        else:
+            rootdirs.append(root)
+            root = os.path.dirname(root)  # up a level
+
+    if verbose:
+        print("Tried directories %s but none started with prefix %s" %
+              (str(rootdirs), parentdir_prefix))
+    raise NotThisMethod("rootdir doesn't start with parentdir_prefix")
+
+
+@register_vcs_handler("git", "get_keywords")
+def git_get_keywords(versionfile_abs):
+    """Extract version information from the given file."""
+    # the code embedded in _version.py can just fetch the value of these
+    # keywords. When used from setup.py, we don't want to import _version.py,
+    # so we do it with a regexp instead. This function is not used from
+    # _version.py.
+    keywords = {}
+    try:
+        f = open(versionfile_abs, "r")
+        for line in f.readlines():
+            if line.strip().startswith("git_refnames ="):
+                mo = re.search(r'=\s*"(.*)"', line)
+                if mo:
+                    keywords["refnames"] = mo.group(1)
+            if line.strip().startswith("git_full ="):
+                mo = re.search(r'=\s*"(.*)"', line)
+                if mo:
+                    keywords["full"] = mo.group(1)
+            if line.strip().startswith("git_date ="):
+                mo = re.search(r'=\s*"(.*)"', line)
+                if mo:
+                    keywords["date"] = mo.group(1)
+        f.close()
+    except EnvironmentError:
+        pass
+    return keywords
+
+
+@register_vcs_handler("git", "keywords")
+def git_versions_from_keywords(keywords, tag_prefix, verbose):
+    """Get version information from git keywords."""
+    if not keywords:
+        raise NotThisMethod("no keywords at all, weird")
+    date = keywords.get("date")
+    if date is not None:
+        # git-2.2.0 added "%cI", which expands to an ISO-8601 -compliant
+        # datestamp. However we prefer "%ci" (which expands to an "ISO-8601
+        # -like" string, which we must then edit to make compliant), because
+        # it's been around since git-1.5.3, and it's too difficult to
+        # discover which version we're using, or to work around using an
+        # older one.
+        date = date.strip().replace(" ", "T", 1).replace(" ", "", 1)
+    refnames = keywords["refnames"].strip()
+    if refnames.startswith("$Format"):
+        if verbose:
+            print("keywords are unexpanded, not using")
+        raise NotThisMethod("unexpanded keywords, not a git-archive tarball")
+    refs = set([r.strip() for r in refnames.strip("()").split(",")])
+    # 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)])
+    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
+        # expansion behaves like git log --decorate=short and strips out the
+        # refs/heads/ and refs/tags/ prefixes that would let us distinguish
+        # 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)])
+        if verbose:
+            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):]
+            if verbose:
+                print("picking %s" % r)
+            return {"version": r,
+                    "full-revisionid": keywords["full"].strip(),
+                    "dirty": False, "error": None,
+                    "date": date}
+    # 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", "date": None}
+
+
+@register_vcs_handler("git", "pieces_from_vcs")
+def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
+    """Get version from 'git describe' in the root of the source tree.
+
+    This only gets called if the git-archive 'subst' keywords were *not*
+    expanded, and _version.py hasn't already been rewritten with a short
+    version string, meaning we're inside a checked out source tree.
+    """
+    GITS = ["git"]
+    if sys.platform == "win32":
+        GITS = ["git.cmd", "git.exe"]
+
+    out, rc = run_command(GITS, ["rev-parse", "--git-dir"], cwd=root,
+                          hide_stderr=True)
+    if rc != 0:
+        if verbose:
+            print("Directory %s not under git control" % root)
+        raise NotThisMethod("'git rev-parse --git-dir' returned error")
+
+    # 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, rc = 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")
+    describe_out = describe_out.strip()
+    full_out, rc = run_command(GITS, ["rev-parse", "HEAD"], cwd=root)
+    if full_out is None:
+        raise NotThisMethod("'git rev-parse' failed")
+    full_out = full_out.strip()
+
+    pieces = {}
+    pieces["long"] = full_out
+    pieces["short"] = full_out[:7]  # maybe improved later
+    pieces["error"] = None
+
+    # parse describe_out. It will be like TAG-NUM-gHEX[-dirty] or HEX[-dirty]
+    # TAG might have hyphens.
+    git_describe = describe_out
+
+    # look for -dirty suffix
+    dirty = git_describe.endswith("-dirty")
+    pieces["dirty"] = dirty
+    if 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)
+        if not mo:
+            # unparseable. Maybe git-describe is misbehaving?
+            pieces["error"] = ("unable to parse git-describe output: '%s'"
+                               % describe_out)
+            return pieces
+
+        # tag
+        full_tag = mo.group(1)
+        if not full_tag.startswith(tag_prefix):
+            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))
+            return pieces
+        pieces["closest-tag"] = full_tag[len(tag_prefix):]
+
+        # distance: number of commits since tag
+        pieces["distance"] = int(mo.group(2))
+
+        # commit: short hex revision ID
+        pieces["short"] = mo.group(3)
+
+    else:
+        # HEX: no tags
+        pieces["closest-tag"] = None
+        count_out, rc = run_command(GITS, ["rev-list", "HEAD", "--count"],
+                                    cwd=root)
+        pieces["distance"] = int(count_out)  # total number of commits
+
+    # commit date: see ISO-8601 comment in git_versions_from_keywords()
+    date = run_command(GITS, ["show", "-s", "--format=%ci", "HEAD"],
+                       cwd=root)[0].strip()
+    pieces["date"] = date.strip().replace(" ", "T", 1).replace(" ", "", 1)
+
+    return pieces
+
+
+def plus_or_dot(pieces):
+    """Return a + if we don't already have one, else return a ."""
+    if "+" in pieces.get("closest-tag", ""):
+        return "."
+    return "+"
+
+
+def render_pep440(pieces):
+    """Build up version string, with post-release "local version identifier".
+
+    Our goal: TAG[+DISTANCE.gHEX[.dirty]] . Note that if you
+    get a tagged build and then dirty it, you'll get TAG+0.gHEX.dirty
+
+    Exceptions:
+    1: no tags. git_describe was just HEX. 0+untagged.DISTANCE.gHEX[.dirty]
+    """
+    if pieces["closest-tag"]:
+        rendered = pieces["closest-tag"]
+        if pieces["distance"] or pieces["dirty"]:
+            rendered += plus_or_dot(pieces)
+            rendered += "%d.g%s" % (pieces["distance"], pieces["short"])
+            if pieces["dirty"]:
+                rendered += ".dirty"
+    else:
+        # exception #1
+        rendered = "0+untagged.%d.g%s" % (pieces["distance"],
+                                          pieces["short"])
+        if pieces["dirty"]:
+            rendered += ".dirty"
+    return rendered
+
+
+def render_pep440_pre(pieces):
+    """TAG[.post.devDISTANCE] -- No -dirty.
+
+    Exceptions:
+    1: no tags. 0.post.devDISTANCE
+    """
+    if pieces["closest-tag"]:
+        rendered = pieces["closest-tag"]
+        if pieces["distance"]:
+            rendered += ".post.dev%d" % pieces["distance"]
+    else:
+        # exception #1
+        rendered = "0.post.dev%d" % pieces["distance"]
+    return rendered
+
+
+def render_pep440_post(pieces):
+    """TAG[.postDISTANCE[.dev0]+gHEX] .
+
+    The ".dev0" means dirty. Note that .dev0 sorts backwards
+    (a dirty tree will appear "older" than the corresponding clean one),
+    but you shouldn't be releasing software with -dirty anyways.
+
+    Exceptions:
+    1: no tags. 0.postDISTANCE[.dev0]
+    """
+    if pieces["closest-tag"]:
+        rendered = pieces["closest-tag"]
+        if pieces["distance"] or pieces["dirty"]:
+            rendered += ".post%d" % pieces["distance"]
+            if pieces["dirty"]:
+                rendered += ".dev0"
+            rendered += plus_or_dot(pieces)
+            rendered += "g%s" % pieces["short"]
+    else:
+        # exception #1
+        rendered = "0.post%d" % pieces["distance"]
+        if pieces["dirty"]:
+            rendered += ".dev0"
+        rendered += "+g%s" % pieces["short"]
+    return rendered
+
+
+def render_pep440_old(pieces):
+    """TAG[.postDISTANCE[.dev0]] .
+
+    The ".dev0" means dirty.
+
+    Eexceptions:
+    1: no tags. 0.postDISTANCE[.dev0]
+    """
+    if pieces["closest-tag"]:
+        rendered = pieces["closest-tag"]
+        if pieces["distance"] or pieces["dirty"]:
+            rendered += ".post%d" % pieces["distance"]
+            if pieces["dirty"]:
+                rendered += ".dev0"
+    else:
+        # exception #1
+        rendered = "0.post%d" % pieces["distance"]
+        if pieces["dirty"]:
+            rendered += ".dev0"
+    return rendered
+
+
+def render_git_describe(pieces):
+    """TAG[-DISTANCE-gHEX][-dirty].
+
+    Like 'git describe --tags --dirty --always'.
+
+    Exceptions:
+    1: no tags. HEX[-dirty]  (note: no 'g' prefix)
+    """
+    if pieces["closest-tag"]:
+        rendered = pieces["closest-tag"]
+        if pieces["distance"]:
+            rendered += "-%d-g%s" % (pieces["distance"], pieces["short"])
+    else:
+        # exception #1
+        rendered = pieces["short"]
+    if pieces["dirty"]:
+        rendered += "-dirty"
+    return rendered
+
+
+def render_git_describe_long(pieces):
+    """TAG-DISTANCE-gHEX[-dirty].
+
+    Like 'git describe --tags --dirty --always -long'.
+    The distance/hash is unconditional.
+
+    Exceptions:
+    1: no tags. HEX[-dirty]  (note: no 'g' prefix)
+    """
+    if pieces["closest-tag"]:
+        rendered = pieces["closest-tag"]
+        rendered += "-%d-g%s" % (pieces["distance"], pieces["short"])
+    else:
+        # exception #1
+        rendered = pieces["short"]
+    if pieces["dirty"]:
+        rendered += "-dirty"
+    return rendered
+
+
+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"],
+                "date": None}
+
+    if not style or style == "default":
+        style = "pep440"  # the default
+
+    if style == "pep440":
+        rendered = render_pep440(pieces)
+    elif style == "pep440-pre":
+        rendered = render_pep440_pre(pieces)
+    elif style == "pep440-post":
+        rendered = render_pep440_post(pieces)
+    elif style == "pep440-old":
+        rendered = render_pep440_old(pieces)
+    elif style == "git-describe":
+        rendered = render_git_describe(pieces)
+    elif style == "git-describe-long":
+        rendered = render_git_describe_long(pieces)
+    else:
+        raise ValueError("unknown style '%s'" % style)
+
+    return {"version": rendered, "full-revisionid": pieces["long"],
+            "dirty": pieces["dirty"], "error": None,
+            "date": pieces.get("date")}
+
+
+def get_versions():
+    """Get version information or return default if unable to do so."""
+    # I am in _version.py, which lives at ROOT/VERSIONFILE_SOURCE. If we have
+    # __file__, we can work backwards from there to the root. Some
+    # py2exe/bbfreeze/non-CPython implementations don't do __file__, in which
+    # case we can only use expanded keywords.
+
+    cfg = get_config()
+    verbose = cfg.verbose
+
+    try:
+        return git_versions_from_keywords(get_keywords(), cfg.tag_prefix,
+                                          verbose)
+    except NotThisMethod:
+        pass
+
+    try:
+        root = os.path.realpath(__file__)
+        # 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('/'):
+            root = os.path.dirname(root)
+    except NameError:
+        return {"version": "0+unknown", "full-revisionid": None,
+                "dirty": None,
+                "error": "unable to find root of source tree",
+                "date": None}
+
+    try:
+        pieces = git_pieces_from_vcs(cfg.tag_prefix, root, verbose)
+        return render(pieces, cfg.style)
+    except NotThisMethod:
+        pass
+
+    try:
+        if cfg.parentdir_prefix:
+            return versions_from_parentdir(cfg.parentdir_prefix, root, verbose)
+    except NotThisMethod:
+        pass
+
+    return {"version": "0+unknown", "full-revisionid": None,
+            "dirty": None,
+            "error": "unable to compute version", "date": None}

setup.cfg

+[versioneer]
+VCS = git
+style = pep440
+versionfile_source = mhcflurry/_version.py
+versionfile_build = mhcflurry/_version.py
+tag_prefix =
+parentdir_prefix = mhcflurry-

setup.py

@@ -18,6 +18,7 @@ import re
 import sys
 
 from setuptools import setup
+import versioneer
 
 # normally we would import six.PY2 but can't yet assume that six
 # is installed here
@@ -40,13 +41,6 @@ except:
     logging.warn("Conversion of long_description from MD to RST failed")
     pass
 
-
-with open('mhcflurry/__init__.py', 'r') as f:
-    version = re.search(
-        r'^__version__\s*=\s*[\'"]([^\'"]*)[\'"]',
-        f.read(),
-        re.MULTILINE).group(1)
-
 if __name__ == '__main__':
     required_packages = [
         'six',
@@ -66,7 +60,8 @@ if __name__ == '__main__':
 
     setup(
         name='mhcflurry',
-        version=version,
+        version=versioneer.get_version(),
+        cmdclass=versioneer.get_cmdclass(),
         description="MHC Binding Predictor",
         author="Alex Rubinsteyn <alex@hammerlab.org>, Tim O'Donnell <tim@hammerlab.org>",
         author_email="tim@hammerlab.org",