initial work for screed release

versioneer install and setup
creation of release procedure notes
creation of known_issues doc

.gitattributes

@@ -0,0 +1 @@
+screed/_version.py export-subst

ChangeLog

@@ -1,3 +1,8 @@
+2014-11-2  Michael Crusoe  <mcrusoe@msu.edu>
+
+    * Doxyfile, .coverage, coverage.xml, diff-cover.html, doc/doxygen/, env/
+    htmlcov/, nosetests.xml, pylint_report.txt, .*.swp: added Doxygen support
+
 2014-10-27  Ben Taylor  <taylo886@msu.edu>
 
 	* benchmarks/fqGen.py, benchmarks/fqToFaConvert.py,
@@ -6,3 +11,7 @@
 	doc/screed.html, doc/screed.txt, screed/conversion.py, screed/fastq.py,
 	screed/tests/test_fastq.py: Changed all uses of "accuracy" to "quality"
 	* screed/tests/test_dna.py: Added basic test coverage for screed/dna.py
+
+2014-5-16  Michael Crusoe  <mcrusoe@msu.edu>
+
+    * screed/openscreed.py: added sniffing of compression types, including zip

MANIFEST.in

@@ -0,0 +1,2 @@
+include versioneer.py
+include screed/_version.py

doc/index.txt

@@ -18,6 +18,7 @@ Contents:
 
    screed
    example
+   releases
 
 Indices and tables
 ==================

doc/known-issues.txt

@@ -0,0 +1,23 @@
+.. vim: set filetype=rst
+============
+Known Issues
+============
+
+This document details the known issues in the current release of screed. All
+issues for screed are tracked at https://github.com/ged-lab/khmer/issues
+
+List of known issues
+====================
+
+Screed currently does not support streaming of any filetypes.
+https://github.com/ged-lab/khmer/issues/654
+https://github.com/ged-lab/khmer/issues/633
+
+Screed has issues with pair checking and Fastq ID stripping
+https://github.com/ged-lab/khmer/issues/23
+https://github.com/ged-lab/khmer/issues/606
+
+Screed is overly tolerant of spaces in fast{q,a} which is against spec.
+https://github.com/ged-lab/khmer/issues/108
+
+

doc/releases.txt

@@ -0,0 +1,24 @@
+=====================
+Release Documentation
+=====================
+
+Notes on this document
+======================
+This is the procedure for cutting a new release of screed. It has been adapted
+from the release documentation for the khmer project, found at
+http://khmer.readthedocs.org/en/v1.1/release.html.
+
+Getting Started
+===============
+
+#. Start with a clean checkout:
+    cd `mktemp -d`
+    git clone git@github.com:ged-lab/screed.git
+    cd screed
+#. Install/update versioneer:
+    pip install versioneer
+    versioneer-installer
+#. Review the git logs since the previous release and that ChangeLog reflects
+the major changes
+#. Review the issue list for any existing bugs that won't be fixed in the
+release and ensure they're documented in ``doc/known-issues.txt``

screed/__init__.py

@@ -31,3 +31,7 @@
 from dna import rc
 
 __version__ = '0.7.1'
+
+from ._version import get_versions
+__version__ = get_versions()['version']
+del get_versions

screed/_version.py

@@ -0,0 +1,183 @@
+
+# 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-0.12 (https://github.com/warner/python-versioneer)
+
+# these strings will be replaced by git during git-archive
+git_refnames = "$Format:%d$"
+git_full = "$Format:%H$"
+
+# these strings are filled in when 'setup.py versioneer' creates _version.py
+tag_prefix = "v"
+parentdir_prefix = "."
+versionfile_source = "screed/_version.py"
+
+import os, sys, re, subprocess, errno
+
+def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False):
+    assert isinstance(commands, list)
+    p = None
+    for c in commands:
+        try:
+            # 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))
+            break
+        except EnvironmentError:
+            e = sys.exc_info()[1]
+            if e.errno == errno.ENOENT:
+                continue
+            if verbose:
+                print("unable to run %s" % args[0])
+                print(e)
+            return None
+    else:
+        if verbose:
+            print("unable to find command, tried %s" % (commands,))
+        return None
+    stdout = p.communicate()[0].strip()
+    if sys.version >= '3':
+        stdout = stdout.decode()
+    if p.returncode != 0:
+        if verbose:
+            print("unable to run %s (error)" % args[0])
+        return None
+    return stdout
+
+
+def versions_from_parentdir(parentdir_prefix, root, verbose=False):
+    # Source tarballs conventionally unpack into a directory that includes
+    # both the project name and a version string.
+    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))
+        return None
+    return {"version": dirname[len(parentdir_prefix):], "full": ""}
+
+def git_get_keywords(versionfile_abs):
+    # 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)
+        f.close()
+    except EnvironmentError:
+        pass
+    return keywords
+
+def git_versions_from_keywords(keywords, tag_prefix, verbose=False):
+    if not keywords:
+        return {} # keyword-finding function failed to find keywords
+    refnames = keywords["refnames"].strip()
+    if refnames.startswith("$Format"):
+        if verbose:
+            print("keywords are unexpanded, not using")
+        return {} # unexpanded, so not in an unpacked 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": keywords["full"].strip() }
+    # no suitable tags, so we use the full revision id
+    if verbose:
+        print("no suitable tags, using full revision id")
+    return { "version": keywords["full"].strip(),
+             "full": keywords["full"].strip() }
+
+
+def git_versions_from_vcs(tag_prefix, root, verbose=False):
+    # this runs 'git' from 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.
+
+    if not os.path.exists(os.path.join(root, ".git")):
+        if verbose:
+            print("no .git in %s" % root)
+        return {}
+
+    GITS = ["git"]
+    if sys.platform == "win32":
+        GITS = ["git.cmd", "git.exe"]
+    stdout = run_command(GITS, ["describe", "--tags", "--dirty", "--always"],
+                         cwd=root)
+    if stdout is None:
+        return {}
+    if not stdout.startswith(tag_prefix):
+        if verbose:
+            print("tag '%s' doesn't start with prefix '%s'" % (stdout, tag_prefix))
+        return {}
+    tag = stdout[len(tag_prefix):]
+    stdout = run_command(GITS, ["rev-parse", "HEAD"], cwd=root)
+    if stdout is None:
+        return {}
+    full = stdout.strip()
+    if tag.endswith("-dirty"):
+        full += "-dirty"
+    return {"version": tag, "full": full}
+
+
+def get_versions(default={"version": "unknown", "full": ""}, verbose=False):
+    # 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.
+
+    keywords = { "refnames": git_refnames, "full": git_full }
+    ver = git_versions_from_keywords(keywords, tag_prefix, verbose)
+    if ver:
+        return ver
+
+    try:
+        root = os.path.abspath(__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 range(len(versionfile_source.split(os.sep))):
+            root = os.path.dirname(root)
+    except NameError:
+        return default
+
+    return (git_versions_from_vcs(tag_prefix, root, verbose)
+            or versions_from_parentdir(parentdir_prefix, root, verbose)
+            or default)

setup.py

@@ -5,8 +5,16 @@
     print '(WARNING: importing distutils, not setuptools!)'
     from distutils.core import setup
 
+import versioneer
+versioneer.VCS = 'git'
+versioneer.versionfile_source = 'screed/_version.py'
+versioneer.versionfile_build = 'screed/_version.py'
+versioneer.tag_prefix = 'v' # i.e. v1.2.0
+versioneer.parentdir_prefix = '.'
+CMDCLASS = versioneer.get_cmdclass()
+
 setup(name='screed',
-      version='0.7.1',
+      version=versioneer.get_version(),
       description='A short read database',
       author='Alex Nolley, C. Titus Brown',
       author_email='ctb@msu.edu',
@@ -16,4 +24,7 @@
       license='BSD',
       test_suite='nose.collector',
       extras_require={'tests': ['nose >= 1.0']},
+      cmdclass=versioneer.get_cmdclass()
       )
+
+