diff --git a/HISTORY.rst b/HISTORY.rst index 4fc1aae..748296c 100644 --- a/HISTORY.rst +++ b/HISTORY.rst @@ -1,6 +1,8 @@ ======= History ======= +2024.3.22 -- Updated for new scheme for running background jobs. + 2024.1.5 -- Bugfix: Thermal conductivity * If the Helfand moments fit in the thermal conductivity step failed it stopped the entire job. This is correct, as well as some of the undelying causes for diff --git a/thermal_conductivity_step/thermal_conductivity.py b/thermal_conductivity_step/thermal_conductivity.py index aad55ea..f95d9dc 100644 --- a/thermal_conductivity_step/thermal_conductivity.py +++ b/thermal_conductivity_step/thermal_conductivity.py @@ -317,6 +317,9 @@ def run(self): node.all_options = self.all_options node = node.next() + # And the subflowchart has the executor + self.subflowchart.executor = self.flowchart.executor + # Loop over the runs nruns = P["nruns"] fmt = f"0{len(str(nruns))}" diff --git a/versioneer.py b/versioneer.py index 2b54540..3aa5da3 100644 --- a/versioneer.py +++ b/versioneer.py @@ -1,3 +1,4 @@ + # Version: 0.18 """The Versioneer - like a rocketeer, but for versions. @@ -276,7 +277,6 @@ """ from __future__ import print_function - try: import configparser except ImportError: @@ -308,13 +308,11 @@ def get_root(): setup_py = os.path.join(root, "setup.py") versioneer_py = os.path.join(root, "versioneer.py") if not (os.path.exists(setup_py) or os.path.exists(versioneer_py)): - err = ( - "Versioneer was unable to run the project root directory. " - "Versioneer requires setup.py to be executed from " - "its immediate directory (like 'python setup.py COMMAND'), " - "or in a way that lets it use sys.argv[0] to find the root " - "(like 'python path/to/setup.py COMMAND')." - ) + err = ("Versioneer was unable to run the project root directory. " + "Versioneer requires setup.py to be executed from " + "its immediate directory (like 'python setup.py COMMAND'), " + "or in a way that lets it use sys.argv[0] to find the root " + "(like 'python path/to/setup.py COMMAND').") raise VersioneerBadRootError(err) try: # Certain runtime workflows (setup.py install/develop in a setuptools @@ -327,10 +325,8 @@ def get_root(): me_dir = os.path.normcase(os.path.splitext(me)[0]) vsr_dir = os.path.normcase(os.path.splitext(versioneer_py)[0]) if me_dir != vsr_dir: - print( - "Warning: build in %s is using versioneer.py from %s" - % (os.path.dirname(me), versioneer_py) - ) + print("Warning: build in %s is using versioneer.py from %s" + % (os.path.dirname(me), versioneer_py)) except NameError: pass return root @@ -343,16 +339,15 @@ def get_config_from_root(root): # configparser.NoOptionError (if it lacks "VCS="). See the docstring at # the top of versioneer.py for instructions on writing your setup.cfg . setup_cfg = os.path.join(root, "setup.cfg") - parser = configparser.SafeConfigParser() + parser = configparser.ConfigParser() with open(setup_cfg, "r") as f: - parser.readfp(f) + parser.read_file(f) VCS = parser.get("versioneer", "VCS") # mandatory def get(parser, name): if parser.has_option("versioneer", name): return parser.get("versioneer", name) return None - cfg = VersioneerConfig() cfg.VCS = VCS cfg.style = get(parser, "style") or "" @@ -377,18 +372,17 @@ 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 -def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False, env=None): +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 @@ -396,13 +390,10 @@ def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False, env= 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), - ) + 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] @@ -427,9 +418,7 @@ def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False, env= return stdout, p.returncode -LONG_VERSION_PY[ - "git" -] = ''' +LONG_VERSION_PY['git'] = ''' # 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 @@ -1004,7 +993,7 @@ 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 @@ -1013,7 +1002,7 @@ 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)) if verbose: @@ -1021,26 +1010,19 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose): 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, - "date": date, - } + 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, - } + return {"version": "0+unknown", + "full-revisionid": keywords["full"].strip(), + "dirty": False, "error": "no suitable tags", "date": None} @register_vcs_handler("git", "pieces_from_vcs") @@ -1055,7 +1037,8 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command): if sys.platform == "win32": GITS = ["git.cmd", "git.exe"] - out, rc = run_command(GITS, ["rev-parse", "--git-dir"], cwd=root, hide_stderr=True) + 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) @@ -1063,19 +1046,10 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command): # 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, - ) + 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") @@ -1098,16 +1072,17 @@ 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 @@ -1116,12 +1091,10 @@ 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)) @@ -1132,13 +1105,13 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command): else: # HEX: no tags pieces["closest-tag"] = None - count_out, rc = run_command(GITS, ["rev-list", "HEAD", "--count"], cwd=root) + 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() + date = run_command(GITS, ["show", "-s", "--format=%ci", "HEAD"], + cwd=root)[0].strip() pieces["date"] = date.strip().replace(" ", "T", 1).replace(" ", "", 1) return pieces @@ -1194,22 +1167,16 @@ def versions_from_parentdir(parentdir_prefix, root, verbose): 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, - } + 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) - ) + print("Tried directories %s but none started with prefix %s" % + (str(rootdirs), parentdir_prefix)) raise NotThisMethod("rootdir doesn't start with parentdir_prefix") @@ -1238,13 +1205,11 @@ def versions_from_file(filename): contents = f.read() except EnvironmentError: raise NotThisMethod("unable to read _version.py") - mo = re.search( - r"version_json = '''\n(.*)''' # END VERSION_JSON", contents, re.M | re.S - ) + mo = re.search(r"version_json = '''\n(.*)''' # END VERSION_JSON", + contents, re.M | re.S) if not mo: - mo = re.search( - r"version_json = '''\r\n(.*)''' # END VERSION_JSON", contents, re.M | re.S - ) + mo = re.search(r"version_json = '''\r\n(.*)''' # END VERSION_JSON", + contents, re.M | re.S) if not mo: raise NotThisMethod("no version_json in _version.py") return json.loads(mo.group(1)) @@ -1253,7 +1218,8 @@ def versions_from_file(filename): def write_to_version_file(filename, versions): """Write the given version number to the given _version.py file.""" os.unlink(filename) - contents = json.dumps(versions, sort_keys=True, indent=1, separators=(",", ": ")) + contents = json.dumps(versions, sort_keys=True, + indent=1, separators=(",", ": ")) with open(filename, "w") as f: f.write(SHORT_VERSION_PY % contents) @@ -1285,7 +1251,8 @@ 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 @@ -1399,13 +1366,11 @@ 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"], - "date": None, - } + 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 @@ -1425,13 +1390,9 @@ def render(pieces, style): else: raise ValueError("unknown style '%s'" % style) - return { - "version": rendered, - "full-revisionid": pieces["long"], - "dirty": pieces["dirty"], - "error": None, - "date": pieces.get("date"), - } + return {"version": rendered, "full-revisionid": pieces["long"], + "dirty": pieces["dirty"], "error": None, + "date": pieces.get("date")} class VersioneerBadRootError(Exception): @@ -1454,9 +1415,8 @@ def get_versions(verbose=False): handlers = HANDLERS.get(cfg.VCS) assert handlers, "unrecognized VCS '%s'" % cfg.VCS verbose = verbose or cfg.verbose - assert ( - cfg.versionfile_source is not None - ), "please set versioneer.versionfile_source" + assert cfg.versionfile_source is not None, \ + "please set versioneer.versionfile_source" assert cfg.tag_prefix is not None, "please set versioneer.tag_prefix" versionfile_abs = os.path.join(root, cfg.versionfile_source) @@ -1510,13 +1470,9 @@ def get_versions(verbose=False): if verbose: print("unable to compute version") - return { - "version": "0+unknown", - "full-revisionid": None, - "dirty": None, - "error": "unable to compute version", - "date": None, - } + return {"version": "0+unknown", "full-revisionid": None, + "dirty": None, "error": "unable to compute version", + "date": None} def get_version(): @@ -1565,7 +1521,6 @@ def run(self): print(" date: %s" % vers.get("date")) if vers["error"]: print(" error: %s" % vers["error"]) - cmds["version"] = cmd_version # we override "build_py" in both distutils and setuptools @@ -1598,15 +1553,14 @@ def run(self): # now locate _version.py in the new build/ directory and replace # it with an updated value if cfg.versionfile_build: - target_versionfile = os.path.join(self.build_lib, cfg.versionfile_build) + target_versionfile = os.path.join(self.build_lib, + cfg.versionfile_build) print("UPDATING %s" % target_versionfile) write_to_version_file(target_versionfile, versions) - cmds["build_py"] = cmd_build_py if "cx_Freeze" in sys.modules: # cx_freeze enabled? from cx_Freeze.dist import build_exe as _build_exe - # nczeczulin reports that py2exe won't like the pep440-style string # as FILEVERSION, but it can be used for PRODUCTVERSION, e.g. # setup(console=[{ @@ -1627,21 +1581,17 @@ def run(self): os.unlink(target_versionfile) with open(cfg.versionfile_source, "w") as f: LONG = LONG_VERSION_PY[cfg.VCS] - f.write( - LONG - % { - "DOLLAR": "$", - "STYLE": cfg.style, - "TAG_PREFIX": cfg.tag_prefix, - "PARENTDIR_PREFIX": cfg.parentdir_prefix, - "VERSIONFILE_SOURCE": cfg.versionfile_source, - } - ) - + f.write(LONG % + {"DOLLAR": "$", + "STYLE": cfg.style, + "TAG_PREFIX": cfg.tag_prefix, + "PARENTDIR_PREFIX": cfg.parentdir_prefix, + "VERSIONFILE_SOURCE": cfg.versionfile_source, + }) cmds["build_exe"] = cmd_build_exe del cmds["build_py"] - if "py2exe" in sys.modules: # py2exe enabled? + if 'py2exe' in sys.modules: # py2exe enabled? try: from py2exe.distutils_buildexe import py2exe as _py2exe # py3 except ImportError: @@ -1660,17 +1610,13 @@ def run(self): os.unlink(target_versionfile) with open(cfg.versionfile_source, "w") as f: LONG = LONG_VERSION_PY[cfg.VCS] - f.write( - LONG - % { - "DOLLAR": "$", - "STYLE": cfg.style, - "TAG_PREFIX": cfg.tag_prefix, - "PARENTDIR_PREFIX": cfg.parentdir_prefix, - "VERSIONFILE_SOURCE": cfg.versionfile_source, - } - ) - + f.write(LONG % + {"DOLLAR": "$", + "STYLE": cfg.style, + "TAG_PREFIX": cfg.tag_prefix, + "PARENTDIR_PREFIX": cfg.parentdir_prefix, + "VERSIONFILE_SOURCE": cfg.versionfile_source, + }) cmds["py2exe"] = cmd_py2exe # we override different "sdist" commands for both environments @@ -1697,10 +1643,8 @@ def make_release_tree(self, base_dir, files): # updated value target_versionfile = os.path.join(base_dir, cfg.versionfile_source) print("UPDATING %s" % target_versionfile) - write_to_version_file( - target_versionfile, self._versioneer_generated_versions - ) - + write_to_version_file(target_versionfile, + self._versioneer_generated_versions) cmds["sdist"] = cmd_sdist return cmds @@ -1755,13 +1699,11 @@ def do_setup(): root = get_root() try: cfg = get_config_from_root(root) - except ( - EnvironmentError, - configparser.NoSectionError, - configparser.NoOptionError, - ) as e: + except (EnvironmentError, configparser.NoSectionError, + configparser.NoOptionError) as e: if isinstance(e, (EnvironmentError, configparser.NoSectionError)): - print("Adding sample versioneer config to setup.cfg", file=sys.stderr) + print("Adding sample versioneer config to setup.cfg", + file=sys.stderr) with open(os.path.join(root, "setup.cfg"), "a") as f: f.write(SAMPLE_CONFIG) print(CONFIG_ERROR, file=sys.stderr) @@ -1770,18 +1712,15 @@ def do_setup(): print(" creating %s" % cfg.versionfile_source) with open(cfg.versionfile_source, "w") as f: LONG = LONG_VERSION_PY[cfg.VCS] - f.write( - LONG - % { - "DOLLAR": "$", - "STYLE": cfg.style, - "TAG_PREFIX": cfg.tag_prefix, - "PARENTDIR_PREFIX": cfg.parentdir_prefix, - "VERSIONFILE_SOURCE": cfg.versionfile_source, - } - ) - - ipy = os.path.join(os.path.dirname(cfg.versionfile_source), "__init__.py") + f.write(LONG % {"DOLLAR": "$", + "STYLE": cfg.style, + "TAG_PREFIX": cfg.tag_prefix, + "PARENTDIR_PREFIX": cfg.parentdir_prefix, + "VERSIONFILE_SOURCE": cfg.versionfile_source, + }) + + ipy = os.path.join(os.path.dirname(cfg.versionfile_source), + "__init__.py") if os.path.exists(ipy): try: with open(ipy, "r") as f: @@ -1823,10 +1762,8 @@ def do_setup(): else: print(" 'versioneer.py' already in MANIFEST.in") if cfg.versionfile_source not in simple_includes: - print( - " appending versionfile_source ('%s') to MANIFEST.in" - % cfg.versionfile_source - ) + print(" appending versionfile_source ('%s') to MANIFEST.in" % + cfg.versionfile_source) with open(manifest_in, "a") as f: f.write("include %s\n" % cfg.versionfile_source) else: