From 8181bb53e9c558db3c76a30031eefea6de0f4d5c Mon Sep 17 00:00:00 2001 From: Andrea Rizzi Date: Wed, 29 May 2019 10:38:40 +0200 Subject: [PATCH 1/9] Update setup.py to use cookiecutter and versioneer --- setup.py | 199 +++++++++++++++---------------------------------------- 1 file changed, 52 insertions(+), 147 deletions(-) diff --git a/setup.py b/setup.py index aa6d60ef2..f5648c8f7 100644 --- a/setup.py +++ b/setup.py @@ -1,22 +1,32 @@ """ Various Python tools for OpenMM. """ -from __future__ import print_function -import sys import distutils.extension -from setuptools import setup -import os -from os.path import relpath, join -import subprocess from Cython.Build import cythonize -DOCLINES = __doc__.split("\n") +import sys +from setuptools import setup, find_packages +import versioneer + +short_description = __doc__.split("\n") + +# from https://github.com/pytest-dev/pytest-runner#conditional-requirement +needs_pytest = {'pytest', 'test', 'ptr'}.intersection(sys.argv) +pytest_runner = ['pytest-runner'] if needs_pytest else [] + +try: + with open("README.md", "r") as handle: + long_description = handle.read() +except: + long_description = "\n".join(short_description[2:]), + +################################################################################ +# SETUP +################################################################################ + +extensions = distutils.extension.Extension("openmmtools.multistate.mixing._mix_replicas", + ['./openmmtools/multistate/mixing/_mix_replicas.pyx']) -######################## -VERSION = "0.19.0" -ISRELEASED = False -__version__ = VERSION -######################## CLASSIFIERS = """\ Development Status :: 3 - Alpha Intended Audience :: Science/Research @@ -32,151 +42,46 @@ Operating System :: MacOS """ -################################################################################ -# Writing version control information to the module -################################################################################ - -def git_version(): - # Return the git revision as a string - # copied from numpy setup.py - def _minimal_ext_cmd(cmd): - # construct minimal environment - env = {} - for k in ['SYSTEMROOT', 'PATH']: - v = os.environ.get(k) - if v is not None: - env[k] = v - # LANGUAGE is used on win32 - env['LANGUAGE'] = 'C' - env['LANG'] = 'C' - env['LC_ALL'] = 'C' - out = subprocess.Popen( - cmd, stdout=subprocess.PIPE, env=env).communicate()[0] - return out - - try: - out = _minimal_ext_cmd(['git', 'rev-parse', 'HEAD']) - GIT_REVISION = out.strip().decode('ascii') - except OSError: - GIT_REVISION = 'Unknown' - - return GIT_REVISION - - -def write_version_py(filename): - cnt = """ -# This file is automatically generated by setup.py -short_version = '%(version)s' -version = '%(version)s' -full_version = '%(full_version)s' -git_revision = '%(git_revision)s' -release = %(isrelease)s - -if not release: - version = full_version -""" - # Adding the git rev number needs to be done inside write_version_py(), - # otherwise the import of numpy.version messes up the build under Python 3. - FULLVERSION = VERSION - if os.path.exists('.git'): - GIT_REVISION = git_version() - else: - GIT_REVISION = 'Unknown' - - if not ISRELEASED: - FULLVERSION += '.dev-' + GIT_REVISION[:7] - - a = open(filename, 'w') - try: - contents = cnt % {'version': VERSION, - 'full_version': FULLVERSION, - 'git_revision': GIT_REVISION, - 'isrelease': str(ISRELEASED)} - a.write(contents) - print("Writing version.py to %s :" % os.path.abspath(filename)) - print('------------version.py-----------------') - print(contents) - print('---------------------------------------') - finally: - a.close() - -################################################################################ -# USEFUL SUBROUTINES -################################################################################ - -def find_package_data(data_root, package_root): - files = [] - for root, dirnames, filenames in os.walk(data_root): - for fn in filenames: - files.append(relpath(join(root, fn), package_root)) - return files - - -def check_dependencies(): - from distutils.version import StrictVersion - found_openmm = True - found_openmm_61_or_later = True - found_numpy = True - - try: - from simtk import openmm - openmm_version = StrictVersion(openmm.Platform.getOpenMMVersion()) - if openmm_version < StrictVersion('6.1.0'): - found_openmm_61_or_later = False - except ImportError as err: - found_openmm = False - - try: - import numpy - except: - found_numpy = False - - msg = None - bar = ('-' * 70) + "\n" + ('-' * 70) - if found_openmm: - if not found_openmm_61_or_later: - msg = [bar, '[Unmet Dependency] openmmtools requires OpenMM version 6.1 or later. You have version %s.' % openmm_version, bar] - else: - msg = [bar, '[Unmet Dependency] openmmtools requires the OpenMM python package. Refer to for details and installation instructions.', bar] - - if not found_numpy: - msg = [bar, '[Unmet Dependency] openmmtools requires the numpy python package. Refer to for numpy installation instructions.', bar] - - if msg is not None: - import textwrap - print() - print(os.linesep.join([line for e in msg for line in textwrap.wrap(e)]), file=sys.stderr) - #print('\n'.join(list(textwrap.wrap(e) for e in msg))) - -################################################################################ -# SETUP -################################################################################ - -extensions = distutils.extension.Extension("openmmtools.multistate.mixing._mix_replicas", - ['./openmmtools/multistate/mixing/_mix_replicas.pyx']) - -write_version_py('openmmtools/version.py') - setup( name='openmmtools', author='John Chodera', author_email='john.chodera@choderalab.org', - description=DOCLINES[0], - long_description="\n".join(DOCLINES[2:]), - version=__version__, + description=short_description, + long_description=long_description, + long_description_content_type="text/markdown", + version=versioneer.get_version(), + cmdclass=versioneer.get_cmdclass(), license='MIT', - url='https://github.com/choderalab/openmmtools', - platforms=['Linux', 'Mac OS-X', 'Unix', 'Windows'], + + # Which Python importable modules should be included when your package is installed + # Handled automatically by setuptools. Use 'exclude' to prevent some specific + # subpackage(s) from being added, if needed + packages=find_packages(), + + # Optional include package data to ship with your package + # Customize MANIFEST.in if the general case does not suit your needs + # Comment out this line to prevent the files from being packaged with your software + include_package_data=True, + + # Allows `setup.py test` to work correctly with pytest + setup_requires=[] + pytest_runner, + + # Additional entries you may want simply uncomment the lines you want and fill in the data + url='https://github.com/choderalab/openmmtools', # Website + # install_requires=[], # Required packages, pulls from pip if needed; do not use for Conda deployment + platforms=['Linux', + 'Mac OS-X', + 'Unix', + 'Windows'], # Valid platforms your code works on, adjust to your flavor classifiers=CLASSIFIERS.splitlines(), - packages=['openmmtools', 'openmmtools.tests', 'openmmtools.scripts', 'openmmtools.storage','openmmtools.multistate', 'openmmtools.multistate.mixing'], - package_dir={'openmmtools': 'openmmtools'}, - package_data={'openmmtools': find_package_data('openmmtools/data', 'openmmtools')}, + python_requires=">=3.6", # Python version restrictions + + # Manual control if final package is compressible or not, set False to prevent the .egg from being made zip_safe=False, - scripts=[], + ext_modules=cythonize(extensions), entry_points={'console_scripts': [ 'test-openmm-platforms = openmmtools.scripts.test_openmm_platforms:main', 'benchmark-alchemy = openmmtools.tests.test_alchemy:benchmark_alchemy_from_pdb', ]}, ) -check_dependencies() From 54dded24ff10563ed0fe7926972005ad533987ea Mon Sep 17 00:00:00 2001 From: Andrea Rizzi Date: Wed, 29 May 2019 10:39:48 +0200 Subject: [PATCH 2/9] Create _version.py --- openmmtools/_version.py | 520 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 520 insertions(+) create mode 100644 openmmtools/_version.py diff --git a/openmmtools/_version.py b/openmmtools/_version.py new file mode 100644 index 000000000..d9171440d --- /dev/null +++ b/openmmtools/_version.py @@ -0,0 +1,520 @@ + +# 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 = "None" + cfg.versionfile_source = "{{cookiecutter.repo_name}}/_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} From a4b62e4b6afacf2fb9e666498e90ef3e4210ce90 Mon Sep 17 00:00:00 2001 From: Andrea Rizzi Date: Wed, 29 May 2019 10:43:43 +0200 Subject: [PATCH 3/9] Update releasehistory.rst --- docs/releasehistory.rst | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/docs/releasehistory.rst b/docs/releasehistory.rst index 83d10ffe0..a21e0d534 100644 --- a/docs/releasehistory.rst +++ b/docs/releasehistory.rst @@ -1,16 +1,16 @@ Release History *************** -0.19.0 -====== - -New features ------------- +0.18.2 - Bugfix release +======================= Bugfixes -------- -- Update build infrastructure to match `MolSSI cookiecutter `_. -- A bug in the multistate samplers where``logsumexp`` was imported from ``scipy.misc`` (now in ``scipy.special``) was fixed +- A bug in the multistate samplers where``logsumexp`` was imported from ``scipy.misc`` (now in ``scipy.special``) was fixed (`#423 `_). + +Other +----- +- Update build infrastructure to match `MolSSI cookiecutter `_ (`#424 `_, `#426 `_). 0.18.1 - Bugfix release ======================= From 030cc13bce3b8a6759fbb8f0a6d2b5fb9063e4c6 Mon Sep 17 00:00:00 2001 From: Andrea Rizzi Date: Wed, 29 May 2019 11:26:40 +0200 Subject: [PATCH 4/9] Let versioneer set the version --- openmmtools/__init__.py | 4 ---- 1 file changed, 4 deletions(-) diff --git a/openmmtools/__init__.py b/openmmtools/__init__.py index 8511b4d2f..85e6e9dc6 100644 --- a/openmmtools/__init__.py +++ b/openmmtools/__init__.py @@ -5,8 +5,4 @@ """ -# Define global version. -from openmmtools import version -__version__ = version.version - from openmmtools import testsystems, integrators, alchemy, mcmc, states, cache, utils, constants, forces, forcefactories, storage, multistate From 1e14040341c38bda3d5c253644ba9534895a0a75 Mon Sep 17 00:00:00 2001 From: Andrea Rizzi Date: Wed, 29 May 2019 11:30:43 +0200 Subject: [PATCH 5/9] Determine version in __init__ with versioneer --- openmmtools/__init__.py | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/openmmtools/__init__.py b/openmmtools/__init__.py index 85e6e9dc6..fb273c6da 100644 --- a/openmmtools/__init__.py +++ b/openmmtools/__init__.py @@ -6,3 +6,10 @@ """ from openmmtools import testsystems, integrators, alchemy, mcmc, states, cache, utils, constants, forces, forcefactories, storage, multistate + +# Handle versioneer +from ._version import get_versions +versions = get_versions() +__version__ = versions['version'] +__git_revision__ = versions['full-revisionid'] +del get_versions, versions From d827d20f5820f50ec835646c1ab61d7569f4cc12 Mon Sep 17 00:00:00 2001 From: Andrea Rizzi Date: Wed, 29 May 2019 11:34:07 +0200 Subject: [PATCH 6/9] Use versioneer version when initializing netcdf --- openmmtools/multistate/multistatereporter.py | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/openmmtools/multistate/multistatereporter.py b/openmmtools/multistate/multistatereporter.py index 72cfb8000..f562610a1 100644 --- a/openmmtools/multistate/multistatereporter.py +++ b/openmmtools/multistate/multistatereporter.py @@ -46,7 +46,7 @@ from simtk import unit from openmmtools.utils import deserialize, with_timer, serialize, quantity_from_string -from openmmtools import version,states +from openmmtools import states logger = logging.getLogger(__name__) @@ -385,6 +385,8 @@ def _initialize_storage_file(self, ncfile, nc_name, convention): If the dataset has been initialized before, nothing happens. Return True if the file has been initialized before and False otherwise. """ + from openmmtools import versions + if 'scalar' not in ncfile.dimensions: # Create common dimensions. ncfile.createDimension('scalar', 1) # Scalar dimension. @@ -394,7 +396,7 @@ def _initialize_storage_file(self, ncfile, nc_name, convention): # Set global attributes. ncfile.application = 'YANK' ncfile.program = 'yank.py' - ncfile.programVersion = version.short_version + ncfile.programVersion = versions['version'] ncfile.Conventions = convention ncfile.ConventionVersion = '0.2' ncfile.DataUsedFor = nc_name From 727e6a5b19b444ee55135a972f71911567692657 Mon Sep 17 00:00:00 2001 From: Andrea Rizzi Date: Wed, 29 May 2019 12:01:06 +0200 Subject: [PATCH 7/9] Fix version reference --- openmmtools/multistate/multistatereporter.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/openmmtools/multistate/multistatereporter.py b/openmmtools/multistate/multistatereporter.py index f562610a1..4f231c9c5 100644 --- a/openmmtools/multistate/multistatereporter.py +++ b/openmmtools/multistate/multistatereporter.py @@ -385,7 +385,7 @@ def _initialize_storage_file(self, ncfile, nc_name, convention): If the dataset has been initialized before, nothing happens. Return True if the file has been initialized before and False otherwise. """ - from openmmtools import versions + from openmmtools import __version__ if 'scalar' not in ncfile.dimensions: # Create common dimensions. @@ -396,7 +396,7 @@ def _initialize_storage_file(self, ncfile, nc_name, convention): # Set global attributes. ncfile.application = 'YANK' ncfile.program = 'yank.py' - ncfile.programVersion = versions['version'] + ncfile.programVersion = __version__ ncfile.Conventions = convention ncfile.ConventionVersion = '0.2' ncfile.DataUsedFor = nc_name From 53170a1c325868d2be872760c3aa2b07982c9ae2 Mon Sep 17 00:00:00 2001 From: Andrea Rizzi Date: Thu, 30 May 2019 12:40:46 +0200 Subject: [PATCH 8/9] Fix error handling --- openmmtools/multistate/multistatereporter.py | 2 +- openmmtools/multistate/replicaexchange.py | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/openmmtools/multistate/multistatereporter.py b/openmmtools/multistate/multistatereporter.py index 4f231c9c5..d6109dcce 100644 --- a/openmmtools/multistate/multistatereporter.py +++ b/openmmtools/multistate/multistatereporter.py @@ -372,7 +372,7 @@ def _open_dataset_robustly(self, *args, n_attempts=5, sleep_time=2, raise e except: logger.debug('Attempt {}/{} to open {} failed. Retrying ' - 'in {} seconds'.format(i+1, n_attempts, sleep_time)) + 'in {} seconds'.format(attempt+1, n_attempts, sleep_time)) time.sleep(sleep_time) diff --git a/openmmtools/multistate/replicaexchange.py b/openmmtools/multistate/replicaexchange.py index e017ef3d9..7c846f00a 100644 --- a/openmmtools/multistate/replicaexchange.py +++ b/openmmtools/multistate/replicaexchange.py @@ -269,8 +269,8 @@ def _mix_replicas(self): # otherwise fall back to Python-accelerated code. try: self._mix_all_replicas_cython() - except ValueError as e: - logger.warning(e.message) + except (ValueError, ImportError) as e: + logger.warning(str(e)) self._mix_all_replicas() else: assert self.replica_mixing_scheme is None From 27c43ce5908e6cd1ccefd81e11ae60eda226f560 Mon Sep 17 00:00:00 2001 From: Andrea Rizzi Date: Thu, 30 May 2019 12:41:54 +0200 Subject: [PATCH 9/9] Attempt setting env var HDF5_USE_FILE_LOCKING to false when opening netcdf file on failure --- openmmtools/multistate/multistatereporter.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/openmmtools/multistate/multistatereporter.py b/openmmtools/multistate/multistatereporter.py index d6109dcce..b1ee7d4af 100644 --- a/openmmtools/multistate/multistatereporter.py +++ b/openmmtools/multistate/multistatereporter.py @@ -375,6 +375,10 @@ def _open_dataset_robustly(self, *args, n_attempts=5, sleep_time=2, 'in {} seconds'.format(attempt+1, n_attempts, sleep_time)) time.sleep(sleep_time) + # At the very last attempt, we try setting the environment variable + # controlling the locking mechanism of HDF5 (see choderalab/yank#1165). + if n_attempts > 1: + os.environ['HDF5_USE_FILE_LOCKING'] = 'FALSE' # Last attempt finally raises any error. return netcdf.Dataset(*args, **kwargs)