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git-diff-to-commit-gemma-3-270m

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diff --git a/rhaptos/cnxmlutils/odt2cnxml.py b/rhaptos/cnxmlutils/odt2cnxml.py index <HASH>..<HASH> 100644 --- a/rhaptos/cnxmlutils/odt2cnxml.py +++ b/rhaptos/cnxmlutils/odt2cnxml.py @@ -144,7 +144,7 @@ def transform(odtfile, debug=False, outputdir=None): try: xml = etree.fromstring(etree.tostring(result)) except etree.XMLSyntaxError, e: - xml = makeXsl('pass1_odt2red-failed.xsl')(xml, message="'%s'" % e.msg) + xml = makeXsl('pass1_odt2red-failed.xsl')(xml, message="'%s'" % str(e)) xml = xml.getroot() return xml
In python<I> apparently etree.XMLSyntaxError.msg is always the empty string
py
diff --git a/benchexec/tools/veriabs.py b/benchexec/tools/veriabs.py index <HASH>..<HASH> 100644 --- a/benchexec/tools/veriabs.py +++ b/benchexec/tools/veriabs.py @@ -38,15 +38,15 @@ class Tool(benchexec.tools.template.BaseTool): def executable(self): return util.find_executable('scripts/veriabs') - + def name(self): return 'VeriAbs' - + def cmdline(self, executable, options, tasks, propertyfile, rlimits): if propertyfile: - options += ['--property-file', propertyfile] + options = options + ['--property-file', propertyfile] return [executable] + options + tasks - + def determine_result(self, returncode, returnsignal, output, isTimeout): lines = " ".join(output[-10:]) if isTimeout:
Fix bug in tool-info module for Veriabs, it must not change the passed list options.
py
diff --git a/src/_pytest/main.py b/src/_pytest/main.py index <HASH>..<HASH> 100644 --- a/src/_pytest/main.py +++ b/src/_pytest/main.py @@ -542,7 +542,15 @@ class Session(nodes.FSCollector): col = root._collectfile(argpath) if col: self._node_cache[argpath] = col - for y in self.matchnodes(col, names): + m = self.matchnodes(col, names) + # If __init__.py was the only file requested, then the matched node will be + # the corresponding Package, and the first yielded item will be the __init__ + # Module itself, so just use that. If this special case isn't taken, then all + # the files in the package will be yielded. + if argpath.basename == "__init__.py": + yield next(m[0].collect()) + return + for y in m: yield y def _collectfile(self, path):
Fix __init__.py as argument also including other package files
py
diff --git a/scripts/experiments/scrape_expout.py b/scripts/experiments/scrape_expout.py index <HASH>..<HASH> 100644 --- a/scripts/experiments/scrape_expout.py +++ b/scripts/experiments/scrape_expout.py @@ -63,6 +63,7 @@ class DPScraper(Scraper): exp.update(relaxTime = get_following_literal(stdout_lines, "relaxTime(ms): ", -1)) exp.update(relaxBound = get_following_literal(stdout_lines, "relaxBound: ", -1)) exp.update(relative = get_following_literal(stdout_lines, "relative: ", -1)) + exp.update(projLogLikelihood = get_following_literal(stdout_lines, "projLogLikelihood: ", -1)) else: exp.update(trainAccuracy = get_following_literal(stdout_lines, "Accuracy on train: ", -1)) exp.update(trainLogLikelihood = get_following_literal(stdout_lines, "LogLikelihood on train: ", -1))
scraping projected likelihood git-svn-id: svn+ssh://external.hltcoe.jhu.edu/home/hltcoe/mgormley/public/repos/dep_parse_filtered/trunk@<I> <I>f-cb4b-<I>-8b<I>-c<I>bcb<I>
py
diff --git a/mapchete/__init__.py b/mapchete/__init__.py index <HASH>..<HASH> 100644 --- a/mapchete/__init__.py +++ b/mapchete/__init__.py @@ -547,12 +547,11 @@ class Mapchete(object): elif isinstance(process_data, (list, types.GeneratorType)): return list(process_data) # for data, metadata tuples - elif isinstance(process_data, tuple): - if not all([ - len(process_data) == 2, - isinstance(process_data[1], dict), - ]): - raise MapcheteProcessOutputError("malformed process output") + elif all([ + isinstance(process_data, tuple), + len(process_data) == 2, + isinstance(process_data[1], dict) + ]): data, metadata = process_data return self._streamline_output(data), metadata elif not process_data:
better capture data, metadata tuples
py
diff --git a/cloudvolume/secrets.py b/cloudvolume/secrets.py index <HASH>..<HASH> 100644 --- a/cloudvolume/secrets.py +++ b/cloudvolume/secrets.py @@ -80,10 +80,11 @@ def google_credentials(bucket = ''): project_name = json.loads(f.read())['project_id'] break - GOOGLE_CREDENTIALS_CACHE[bucket] = (project_name, google_credentials) - if google_credentials == None: print(colorize('yellow', 'Using default Google credentials. There is no ~/.cloudvolume/secrets/google-secret.json set.')) + else: + GOOGLE_CREDENTIALS_CACHE[bucket] = (project_name, google_credentials) + return project_name, google_credentials AWS_CREDENTIALS_CACHE = defaultdict(dict) @@ -106,7 +107,7 @@ def aws_credentials(bucket = '', service = 'aws'): if bucket: paths = [ secretpath('secrets/{}-{}-secret.json'.format(bucket, service)) ] + paths - aws_credentials = '' + aws_credentials = {} aws_credentials_path = secretpath(default_file_path) for aws_credentials_path in paths: if os.path.exists(aws_credentials_path):
misc enhancements (#<I>)
py
diff --git a/cassandra/cluster.py b/cassandra/cluster.py index <HASH>..<HASH> 100644 --- a/cassandra/cluster.py +++ b/cassandra/cluster.py @@ -837,8 +837,12 @@ class Session(object): self._load_balancer = cluster.load_balancing_policy self._metrics = cluster.metrics + # create connection pools in parallel + futures = [] for host in hosts: - future = self.add_or_renew_pool(host, is_host_addition=False) + futures.append(self.add_or_renew_pool(host, is_host_addition=False)) + + for future in futures: future.result() def execute(self, query, parameters=None, trace=False):
Create conn pools in parallel when creating sesssions
py
diff --git a/setup.py b/setup.py index <HASH>..<HASH> 100644 --- a/setup.py +++ b/setup.py @@ -112,11 +112,18 @@ def find_package_data( out.setdefault(package, []).append(prefix+name) return out +try: + import pypandoc + description = pypandoc.convert('README.md', 'rst') +except ImportError: + description = '' + setup( name="django-graphos", version=get_version(), description="Django app to provide a JS agnostic way to work with charts.", - long_description=read("README.md"), + #long_description=read("README.md"), + long_description=description, author="Agiliq", author_email="hello@agiliq.com", license="BSD",
Convert md to rst
py
diff --git a/psyplot/data.py b/psyplot/data.py index <HASH>..<HASH> 100755 --- a/psyplot/data.py +++ b/psyplot/data.py @@ -782,7 +782,10 @@ class CFDecoder(object): elif nans == 'skip': dims = [dim for dim in set(var.dims) - set(bounds.dims)] mask = var.notnull().all(list(dims)) if dims else var.notnull() - bounds = bounds[mask.values] + try: + bounds = bounds[mask.values] + except IndexError: # 3D bounds + bounds = bounds.where(mask) elif nans == 'only': dims = [dim for dim in set(var.dims) - set(bounds.dims)] mask = var.isnull().all(list(dims)) if dims else var.isnull()
Minor bug fix for 3D bounds
py
diff --git a/openquake/calculators/hazard/classical/core.py b/openquake/calculators/hazard/classical/core.py index <HASH>..<HASH> 100644 --- a/openquake/calculators/hazard/classical/core.py +++ b/openquake/calculators/hazard/classical/core.py @@ -226,7 +226,6 @@ class ClassicalHazardCalculator(haz_general.BaseHazardCalculatorNext): is_complete=False, lt_realization=lt_rlz).order_by('id') source_ids = source_progress.values_list('parsed_source_id', flat=True) - self.progress['total'] += len(source_ids) for offset in xrange(0, len(source_ids), block_size): task_args = ( @@ -260,10 +259,17 @@ class ClassicalHazardCalculator(haz_general.BaseHazardCalculatorNext): # work is complete. self.initialize_realizations( rlz_callbacks=[self.initialize_hazard_curve_progress]) - self.initialize_pr_data() self.record_init_stats() + # Set the progress counters: + num_sources = models.SourceProgress.objects.filter( + is_complete=False, + lt_realization__hazard_calculation=self.hc).count() + self.progress['total'] = num_sources + + self.initialize_pr_data() + def post_execute(self): """ Create the final output records for hazard curves. This is done by
calcs/hazard/classical/core: Cleaned up classical progress counter initialization code, to be more consistent with the approach in disagg. Former-commit-id: fd5be<I>c1b9addc<I>c7c3da6be<I>ce<I>fbb1
py
diff --git a/src/jsonlogger.py b/src/jsonlogger.py index <HASH>..<HASH> 100644 --- a/src/jsonlogger.py +++ b/src/jsonlogger.py @@ -2,6 +2,11 @@ import logging import json import re +#Support order in python 2.7 and 3 +try: + from collections import OrderedDict +except: + pass class JsonFormatter(logging.Formatter): """A custom formatter to format logging records as json objects""" @@ -21,8 +26,6 @@ class JsonFormatter(logging.Formatter): record.asctime = self.formatTime(record, self.datefmt) try: - #Support order in python 2.7 and 3 - from collections import OrderedDict log_record = OrderedDict() except: log_record = {}
Took advice to not import during log event
py
diff --git a/python/ray/worker.py b/python/ray/worker.py index <HASH>..<HASH> 100644 --- a/python/ray/worker.py +++ b/python/ray/worker.py @@ -494,6 +494,12 @@ def get_gpu_ids(): worker = global_worker worker.check_connected() + if worker.mode != WORKER_MODE: + logger.warning( + "`ray.get_gpu_ids()` will always return the empty list when " + "called from the driver. This is because Ray does not manage " + "GPU allocations to the driver process.") + # TODO(ilr) Handle inserting resources in local mode all_resource_ids = global_worker.core_worker.resource_ids() assigned_ids = set()
Add warning if get_gpu_ids() is called on the driver. (#<I>)
py
diff --git a/setup.py b/setup.py index <HASH>..<HASH> 100644 --- a/setup.py +++ b/setup.py @@ -29,7 +29,7 @@ reqs = [str(req.req) for req in install_reqs] setup( name="astrocats", - version="0.1.6", + version=version, author="James Guillochon", author_email="guillochon@gmail.com", description=("Package for downloading, analyzing, and constructing open "
BUG: wasn't passing version to setup
py
diff --git a/holoviews/plotting/plotly/__init__.py b/holoviews/plotting/plotly/__init__.py index <HASH>..<HASH> 100644 --- a/holoviews/plotting/plotly/__init__.py +++ b/holoviews/plotting/plotly/__init__.py @@ -126,6 +126,11 @@ options.Raster = Options('style', cmap=dflt_cmap) options.QuadMesh = Options('style', cmap=dflt_cmap) options.HeatMap = Options('style', cmap='RdBu_r') +# Disable padding for image-like elements +options.Image = Options("plot", padding=0) +options.Raster = Options("plot", padding=0) +options.RGB = Options("plot", padding=0) + # 3D options.Scatter3D = Options('style', color=Cycle(), size=6)
Fix datashader instability by disabling plot padding for Plotly RGB elements. (#<I>) * Disable plot padding for plotly RGB, Raster, and Image elements.
py
diff --git a/sortedm2m_filter_horizontal_widget/forms.py b/sortedm2m_filter_horizontal_widget/forms.py index <HASH>..<HASH> 100644 --- a/sortedm2m_filter_horizontal_widget/forms.py +++ b/sortedm2m_filter_horizontal_widget/forms.py @@ -7,7 +7,12 @@ from django.db.models.query import QuerySet from django.utils.encoding import force_text from django.utils.html import conditional_escape, escape from django.utils.safestring import mark_safe -from django.forms.util import flatatt + +try: + from django.forms.utils import flatatt +except ImportError: + from django.forms.util import flatatt + from django.utils.translation import ugettext_lazy as _
Fix Django <I> warning This patch fix Django <I> warning: lib/python<I>/site-packages/sortedm2m_filter_horizontal_widget/forms.py:<I>: RemovedInDjango<I>Warning: The django.forms.util module has been renamed. Use django.forms.utils instead. from django.forms.util import flatatt
py
diff --git a/salt/modules/boto_ec2.py b/salt/modules/boto_ec2.py index <HASH>..<HASH> 100644 --- a/salt/modules/boto_ec2.py +++ b/salt/modules/boto_ec2.py @@ -81,9 +81,9 @@ def __virtual__(): # which was added in boto 2.8.0 # https://github.com/boto/boto/commit/33ac26b416fbb48a60602542b4ce15dcc7029f12 if not HAS_BOTO: - return False + return (False, "The boto_ec2 module cannot be loaded: boto library not found") elif _LooseVersion(boto.__version__) < _LooseVersion(required_boto_version): - return False + return (False, "The boto_ec2 module cannot be loaded: boto library verion incorrect ") return True
Add return messages on boto library load failure lines for library not avalible and wrong version added.
py
diff --git a/ros_buildfarm/sourcedeb_job.py b/ros_buildfarm/sourcedeb_job.py index <HASH>..<HASH> 100644 --- a/ros_buildfarm/sourcedeb_job.py +++ b/ros_buildfarm/sourcedeb_job.py @@ -116,6 +116,11 @@ def build_sourcedeb(sources_dir, os_name=None, os_code_name=None): cmd += [ # dpkg-buildpackage args '-us', '-uc', + # set the option for dpkg-source to auto-commit upstream changes + # This is needed for Debian increments where the upstream has changed. + # It's not the best practice but we have people doing it a bunch. + '--hook-source=\'bash -c "echo >> debian/source/options' + ' && echo auto-commit >> debian/source/options"\'', # debuild args for lintian '--lintian-opts', '--suppress-tags', 'newer-standards-version']
add support for changing upstream content (#<I>) * add support for changing tarballs. This will auto commit changes to the upstream tarball as diffs for the debian increment. Addresses issue in #<I> * fix spelling * Change to append * making sure there's a new line * wrap
py
diff --git a/claripy/vsa/strided_interval.py b/claripy/vsa/strided_interval.py index <HASH>..<HASH> 100644 --- a/claripy/vsa/strided_interval.py +++ b/claripy/vsa/strided_interval.py @@ -411,7 +411,12 @@ class StridedInterval(object): stride = fractions.gcd(self.stride, b.stride) if overflow: - return self.top(new_bits) + if b.is_integer() and b.lower_bound >> (new_bits - 1) == 1: + # Treat it as a minus then + operand = - ((0 - b.lower_bound) & ((1 << new_bits) - 1)) + return self.__add__(operand) + else: + return self.top(new_bits) else: # new_lb = self.lower(new_bits, lb_, stride) if lb_underflow_ else lb_ # new_ub = self.upper(new_bits, ub_, stride) if ub_overflow_ else ub_
more intelligently performing additions between BIs when there is an overflow.
py
diff --git a/KCOJ_api/api.py b/KCOJ_api/api.py index <HASH>..<HASH> 100644 --- a/KCOJ_api/api.py +++ b/KCOJ_api/api.py @@ -63,7 +63,7 @@ class KCOJ: except requests.exceptions.Timeout: return None - def get_question(self) -> dict: + def get_question(self, number: str=None) -> dict: """ 取得課程中的所有題目資訊 """ @@ -79,10 +79,8 @@ class KCOJ: if tag.find('a') == None: continue - # 取得題號 - number = tag.find('a').get_text().strip() # 儲存題目資訊 - questions[number] = { + questions[tag.find('a').get_text().strip()] = { # 繳交期限 'deadline': tag.find_all('td')[3].get_text().strip(), # 是否已經過期限 @@ -93,7 +91,10 @@ class KCOJ: 'language': tag.find_all('td')[5].get_text().strip(), } # 回傳結果 - return questions + if number != None: + return questions.get(number) + else: + return questions except requests.exceptions.Timeout: return {
Use get_question(number) to get specific question info
py
diff --git a/src/pybel/manager/models.py b/src/pybel/manager/models.py index <HASH>..<HASH> 100644 --- a/src/pybel/manager/models.py +++ b/src/pybel/manager/models.py @@ -651,15 +651,15 @@ class Evidence(Base): def __str__(self): return '{}:{}'.format(self.citation, self.sha512[:8]) - def to_json(self, include_id=False): + def to_json(self, include_id: bool = False): """Create a dictionary that is used to recreate the edge data dictionary for a :class:`BELGraph`. - :param bool include_id: If true, includes the model identifier + :param include_id: If true, includes the model identifier :return: Dictionary containing citation and evidence for a :class:`BELGraph` edge. :rtype: dict """ result = { - CITATION: self.citation.to_json(), + CITATION: self.citation.to_json(include_id=include_id), EVIDENCE: self.text }
Propgate inclusion of id's to citation
py
diff --git a/claripy/frontends/replacement_frontend.py b/claripy/frontends/replacement_frontend.py index <HASH>..<HASH> 100644 --- a/claripy/frontends/replacement_frontend.py +++ b/claripy/frontends/replacement_frontend.py @@ -78,6 +78,14 @@ class ReplacementFrontend(ConstrainedFrontend): self._replacements[old.cache_key] = new self._replacement_cache[old.cache_key] = new + def remove_replacements(self, old_entries): + self._replacements = {k: v for k, v in self._replacements if k not in old_entries} + self._replacement_cache = weakref.WeakKeyDictionary(self._replacements) + + def clear_replacements(self): + self._replacements = dict() + self._replacement_cache = weakref.WeakKeyDictionary(self._replacements) + def _replacement(self, old): if not isinstance(old, Base): return old
Added methods to safely allow removing replacements
py
diff --git a/umis/umis.py b/umis/umis.py index <HASH>..<HASH> 100644 --- a/umis/umis.py +++ b/umis/umis.py @@ -101,6 +101,8 @@ def tagcount(genemap, sam, out, output_evidence_table, positional, cb_filter): if cb_filter: with open(cb_filter) as fh: cb_filter = set(cb.strip() for cb in fh) + else: + cb_filter = type('universe', (object,), {'__contains__' : lambda self, other: True})() sam_file = Reader(sam) @@ -114,9 +116,8 @@ def tagcount(genemap, sam, out, output_evidence_table, positional, cb_filter): CB = match['CB'] MB = match['MB'] - if cb_filter: - if CB not in cb_filter: - continue + if CB not in cb_filter: + continue if gene_map: target_name = gene_map[aln.rname]
using universal set type for default cb_filter Because I'm bored
py
diff --git a/bananas/admin/api/router.py b/bananas/admin/api/router.py index <HASH>..<HASH> 100644 --- a/bananas/admin/api/router.py +++ b/bananas/admin/api/router.py @@ -1,12 +1,14 @@ -from typing import Type - -from .mixins import BananasAPI from .schemas import BananasRouter __all__ = ["register"] -def register(view: Type[BananasAPI]): +def register(view): # Type[BananasAPI] + """ + Register the API view class in the bananas router. + + :param BananasAPI view: + """ meta = view.get_admin_meta() prefix = meta.basename.replace(".", "/") router.register(prefix, view, meta.basename)
Remove typing for py<I>
py
diff --git a/instaloader/__main__.py b/instaloader/__main__.py index <HASH>..<HASH> 100644 --- a/instaloader/__main__.py +++ b/instaloader/__main__.py @@ -93,6 +93,7 @@ def _main(instaloader: Instaloader, targetlist: List[str], latest_stamps = None if latest_stamps_file is not None: latest_stamps = LatestStamps(latest_stamps_file) + instaloader.context.log(f"Using latest stamps from {latest_stamps_file}.") # Login, if desired if username is not None: if not re.match(r"^[A-Za-z0-9._]+$", username):
Log "Using latest stamps from ..." message Instaloader always logs which files are loaded and considered in the current run (such as session files or resume files). This commit adds a log message "Using latest stamps from ..." when using --latest-stamps, to be consistent.
py
diff --git a/test/feedforward_test.py b/test/feedforward_test.py index <HASH>..<HASH> 100644 --- a/test/feedforward_test.py +++ b/test/feedforward_test.py @@ -82,9 +82,8 @@ class TestWeightedClassifier(TestClassifier): def test_score_onelayer(self): net = self._build(13) - z = net.score(self.images, - self.labels, - np.random.randint(0, 2, size=self.labels.shape)) + z = net.score( + self.images, self.labels, 0.5 * np.ones(self.labels.shape, 'f')) assert 0 < z < 1
Make weights for test deterministic.
py
diff --git a/lib/svtplay/output.py b/lib/svtplay/output.py index <HASH>..<HASH> 100644 --- a/lib/svtplay/output.py +++ b/lib/svtplay/output.py @@ -1,7 +1,30 @@ import sys +import os from svtplay.log import log +progress_stream = sys.stderr + +def progress(byte, total, extra = ""): + """ Print some info about how much we have downloaded """ + ratio = float(byte) / total + percent = round(ratio*100, 2) + tlen = str(len(str(total))) + fmt = "Downloaded %"+tlen+"dkB of %dkB bytes (% 3.2f%%)" + progresstr = fmt % (byte >> 10, total >> 10, percent) + + columns = int(os.getenv("COLUMNS", "80")) + if len(progresstr) < columns - 13: + p = int((columns - len(progresstr) - 3) * ratio) + q = int((columns - len(progresstr) - 3) * (1 - ratio)) + progresstr = "[" + ("#" * p) + (" " * q) + "] " + progresstr + progress_stream.write(progresstr + ' ' + extra + '\r') + + if byte >= total: + progress_stream.write('\n') + + progress_stream.flush() + def progressbar(total, pos, msg=""): """ Given a total and a progress position, output a progress bar
Break out progress() to svtplay.output module Now it is very clear that progressbar() duplicates an existing function. But obsoleting one or the other is work for the future.
py
diff --git a/anyconfig/backend/bson.py b/anyconfig/backend/bson.py index <HASH>..<HASH> 100644 --- a/anyconfig/backend/bson.py +++ b/anyconfig/backend/bson.py @@ -68,7 +68,7 @@ class Parser(anyconfig.backend.base.FromStringLoader, _load_opts = [] if bson.has_c() else ["codec_options"] _dump_opts = [] if bson.has_c() else ["check_keys", "codec_options"] _open_flags = ('rb', 'wb') - _ordered = True + _ordered = not bson.has_c() def _load_options(self, container, **options): """
fix: [bson] order of items are not kept if C implemetation is used
py
diff --git a/tests/ignite/contrib/metrics/regression/test_fractional_bias.py b/tests/ignite/contrib/metrics/regression/test_fractional_bias.py index <HASH>..<HASH> 100644 --- a/tests/ignite/contrib/metrics/regression/test_fractional_bias.py +++ b/tests/ignite/contrib/metrics/regression/test_fractional_bias.py @@ -115,7 +115,7 @@ def test_error_is_not_nan(): assert not (torch.isnan(m._sum_of_errors).any() or torch.isinf(m._sum_of_errors).any()), m._sum_of_errors -def _test_distrib_compute(device, tol=1e-6): +def _test_distrib_compute(device, tol=1e-5): rank = idist.get_rank() def _test(metric_device): @@ -149,7 +149,7 @@ def _test_distrib_compute(device, tol=1e-6): _test(idist.device()) -def _test_distrib_integration(device, tol=1e-6): +def _test_distrib_integration(device, tol=1e-5): rank = idist.get_rank() torch.manual_seed(12)
reduce tolerence (#<I>) (#<I>)
py
diff --git a/app/preparation/mzidtsv/quant.py b/app/preparation/mzidtsv/quant.py index <HASH>..<HASH> 100644 --- a/app/preparation/mzidtsv/quant.py +++ b/app/preparation/mzidtsv/quant.py @@ -16,6 +16,13 @@ def generate_psms_quanted(quantdbfn, tsvfn, quantheader, oldheader): yield outpsm +def get_full_and_quant_headers(oldheader, quantdbfn): + quantdb = sqlite.QuantDB(quantdbfn) + quantmap = quantdb.get_all_quantmaps() + qheader = sorted([x[0] for x in quantmap]) + return oldheader + qheader, qheader + + def get_quant_header(oldheader, quantdbfn): quantdb = sqlite.QuantDB(quantdbfn) quantmap = quantdb.get_all_quantmaps() @@ -40,4 +47,4 @@ def get_quant_NAs(quantdata, quantheader): def lookup_quant(spectrafile, psm_scan_nr, quantdb): """Outputs dict with keys == quantname, values == quantintensity.""" dbquants = quantdb.lookup_quant(spectrafile, psm_scan_nr) - return {x[0]: x[1] for x in dbquants} + return {x[0]: str(x[1]) for x in dbquants}
Quant prep header maker disappeared. Also return strings to tsv writer
py
diff --git a/tests/test_Optimiser.py b/tests/test_Optimiser.py index <HASH>..<HASH> 100644 --- a/tests/test_Optimiser.py +++ b/tests/test_Optimiser.py @@ -31,7 +31,7 @@ class OptimiserTest(unittest.TestCase): self.optimiser.move_nodes(partition, fixed_nodes=fixed_nodes, consider_comms=leidenalg.ALL_NEIGH_COMMS); self.assertListEqual( partition.sizes(), [1, 1, 1], - msg="CPMVertexPartition(resolution_parameter=0.5) of complete graph after move nodes incorrect."); + msg="CPMVertexPartition(resolution_parameter=0.1) of one edge plus singleton after move nodes with fixed nodes is incorrect."); def test_merge_nodes(self): G = ig.Graph.Full(100); @@ -71,10 +71,9 @@ class OptimiserTest(unittest.TestCase): partition = leidenalg.CPMVertexPartition( G, resolution_parameter=0.01, - initial_membership=[2, 1, 2]) + initial_membership=[2, 1, 0]) # Equivalent to setting initial membership #partition.set_membership([2, 1, 2]) - print(partition.membership) opt = leidenalg.Optimiser() fixed_nodes = [True, False, False] opt.optimise_partition(partition, fixed_nodes=fixed_nodes)
Changed some text in test, and using a different initial membership.
py
diff --git a/zipline/pipeline/loaders/blaze.py b/zipline/pipeline/loaders/blaze.py index <HASH>..<HASH> 100644 --- a/zipline/pipeline/loaders/blaze.py +++ b/zipline/pipeline/loaders/blaze.py @@ -39,6 +39,7 @@ valid_deltas_node_types = ( bz.expr.ReLabel, bz.expr.Symbol, ) +is_invalid_deltas_node = complement(flip(isinstance, valid_deltas_node_types)) getname = attrgetter('__name__') @@ -328,10 +329,7 @@ def from_blaze(expr, """ deltas = _get_deltas(expr, deltas, no_deltas_rule) if deltas is not None: - invalid_nodes = tuple(filter( - complement(flip(isinstance, valid_deltas_node_types)), - expr._subterms(), - )) + invalid_nodes = tuple(filter(is_invalid_deltas_node, expr._subterms())) if invalid_nodes: raise TypeError( 'expression with deltas may only contain (%s) nodes,'
MAINT: name filter predicate
py
diff --git a/arctic/_compression.py b/arctic/_compression.py index <HASH>..<HASH> 100644 --- a/arctic/_compression.py +++ b/arctic/_compression.py @@ -1,5 +1,10 @@ from .logging import logger -import _compress as clz4 + +try: + from . import _compress as clz4 +except ImportError: + logger.warn("Couldn't import cython lz4") + import lz4 as clz4 USE_LZ4HC = True # switch to use LZ4HC. Default True
Fallback to using the lz4 package if we can't import / build the cythonized lz4
py
diff --git a/cosmic_ray/cli.py b/cosmic_ray/cli.py index <HASH>..<HASH> 100644 --- a/cosmic_ray/cli.py +++ b/cosmic_ray/cli.py @@ -99,7 +99,10 @@ options: def _get_db_name(session_name): - return '{}.json'.format(session_name) + if session_name.endswith('.json'): + return session_name + else: + return '{}.json'.format(session_name) def handle_init(configuration):
Allow session-name.json to be passed on the command line this makes it easier to use bash tab completion
py
diff --git a/indra/sources/cwms/processor.py b/indra/sources/cwms/processor.py index <HASH>..<HASH> 100644 --- a/indra/sources/cwms/processor.py +++ b/indra/sources/cwms/processor.py @@ -148,11 +148,14 @@ class CWMSProcessor(object): if event_id in self.relation_subj_obj_ids: continue # Make an Event statement if it is a standalone event + ev_type = event_entry.find('type').text + polarity = POLARITY_DICT['EVENT'][ev_type] evidence = self._get_evidence(event_entry, context=None) event = self._get_event(event_entry, "*[@role=':AFFECTED']", evidence=[evidence]) if event is None: continue + event.delta['polarity'] = polarity self.statements.append(event) self._remove_multi_extraction_artifacts()
Add polarity to Event in CWMS
py
diff --git a/keyring/backends/kwallet.py b/keyring/backends/kwallet.py index <HASH>..<HASH> 100644 --- a/keyring/backends/kwallet.py +++ b/keyring/backends/kwallet.py @@ -30,7 +30,7 @@ class DBusKeyring(KeyringBackend): bus.get_object('org.kde.kwalletd5', '/modules/kwalletd5') except dbus.DBusException: raise RuntimeError('cannot connect to org.kde.kwalletd5') - return 5.1 + return 4.9 def __init__(self, *arg, **kw): super(DBusKeyring, self).__init__(*arg, **kw)
Make KWallet backend have lower priority than Secret Service backend Secret Service is an XDG standard and thus should be preferred on systems where both protocols are available.
py
diff --git a/ELiDE/ELiDE/screen.py b/ELiDE/ELiDE/screen.py index <HASH>..<HASH> 100644 --- a/ELiDE/ELiDE/screen.py +++ b/ELiDE/ELiDE/screen.py @@ -294,6 +294,7 @@ class MainScreen(Screen): if not self.dialog_todo: return self._update_dialog(self.dialog_todo.pop(0)) + self.app.engine.universal['last_result_idx'] += 1 def _update_dialog(self, diargs, **kwargs): if diargs is None: @@ -335,7 +336,6 @@ class MainScreen(Screen): else: raise TypeError("Don't know how to turn {} into a dialog".format(type(diargs))) self.ids.dialoglayout.add_widget(dia) - self.app.engine.universal['last_result_idx'] += 1 def ok(self, cb=None, *args): self.ids.dialoglayout.clear_widgets()
Don't increment the last_result_idx until you've advanced the dialog
py
diff --git a/passwords/validators.py b/passwords/validators.py index <HASH>..<HASH> 100644 --- a/passwords/validators.py +++ b/passwords/validators.py @@ -26,6 +26,9 @@ COMMON_SEQUENCES = [ "qwertzuiopü*asdfghjklöä'>yxcvbnm;:_", "qaywsxedcrfvtgbzhnujmikolp", ] +DICT_CACHE = [] +DICT_FILESIZE = -1 +DICT_MAX_CACHE = 1000000 # Settings PASSWORD_MIN_LENGTH = getattr( @@ -179,6 +182,17 @@ class DictionaryValidator(BaseSimilarityValidator): threshold=threshold) def get_dictionary_words(self, dictionary): + if DICT_CACHE: + return DICT_CACHE + if DICT_FILESIZE is -1: + f = open(dictionary) + f.seek(0,2) + DICT_FILESIZE = f.tell() + f.close() + if DICT_FILESIZE < 1000000: + with open(dictionary) as dictionary: + DICT_CACHE = [smart_text(x.strip()) for x in dictionary.readlines()] + return DICT_CACHE with open(dictionary) as dictionary: return [smart_text(x.strip()) for x in dictionary.readlines()]
Add simple dict cacheing for small dict sizes
py
diff --git a/backend/tests/fixtures/base.py b/backend/tests/fixtures/base.py index <HASH>..<HASH> 100644 --- a/backend/tests/fixtures/base.py +++ b/backend/tests/fixtures/base.py @@ -66,9 +66,8 @@ def client(app): def testdb(session_app): """Establish an application context before running the tests.""" app = session_app - # app.db.create_all() + app.db.create_all() yield app.db - app.db.session.remove() engine = app.db.get_engine(app) metadata = app.db.Model.metadata @@ -83,14 +82,12 @@ def testdb(session_app): @pytest.fixture(scope="function") -def db(app): +def db(app, testdb): """ SetUp before each test is run: push a context and use subtransactions. """ - app.db.session.begin(subtransactions=True) yield app.db app.db.session.rollback() - app.db.session.close()
[#<I>] Refactor Model.
py
diff --git a/galpy/orbit/integrateLinearOrbit.py b/galpy/orbit/integrateLinearOrbit.py index <HASH>..<HASH> 100644 --- a/galpy/orbit/integrateLinearOrbit.py +++ b/galpy/orbit/integrateLinearOrbit.py @@ -25,8 +25,13 @@ if PY3: else: #pragma: no cover _ext_suffix= '.so' for path in sys.path: + if not os.path.isdir(path): continue try: - _lib = ctypes.CDLL(os.path.join(path,'galpy_integrate_c%s' % _ext_suffix)) + if sys.platform == 'win32' and sys.version_info >= (3,8): # pragma: no cover + # winmode=0x008 is easy-going way to call LoadLibraryExA + _lib = ctypes.CDLL(os.path.join(path,'galpy_integrate_c%s' % _ext_suffix),winmode=0x008) + else: + _lib = ctypes.CDLL(os.path.join(path,'galpy_integrate_c%s' % _ext_suffix)) except OSError as e: if os.path.exists(os.path.join(path,'galpy_integrate_c%s' % _ext_suffix)): #pragma: no cover outerr= e
Also use winmode to load DLL in integrateLinearOrbit
py
diff --git a/flask_appbuilder/tests/test_api.py b/flask_appbuilder/tests/test_api.py index <HASH>..<HASH> 100644 --- a/flask_appbuilder/tests/test_api.py +++ b/flask_appbuilder/tests/test_api.py @@ -2537,7 +2537,7 @@ class APITestCase(FABTestCase): """ client = self.app.test_client() self.browser_login(client, USERNAME_ADMIN, PASSWORD_ADMIN) - uri = "swaggerview/v1" + uri = "swagger/v1" rv = client.get(uri) self.assertEqual(rv.status_code, 200)
fix: swagger test (#<I>)
py
diff --git a/dwave/cloud/testing/mocks.py b/dwave/cloud/testing/mocks.py index <HASH>..<HASH> 100644 --- a/dwave/cloud/testing/mocks.py +++ b/dwave/cloud/testing/mocks.py @@ -78,7 +78,7 @@ def structured_solver_data(id: str = None, "h_range": [-2.0, 2.0], "j_range": [-1.0, 1.0], "num_reads_range": [1, 10000], - "annealing_time_range": [1, 2000], + "annealing_time_range": [1.0, 2000.0], "extended_j_range": [-2.0, 1.0], "quota_conversion_rate": 1, "parameters": {
Update mocks for SAPI timing params type change (#<I>)
py
diff --git a/pipenv/cli.py b/pipenv/cli.py index <HASH>..<HASH> 100644 --- a/pipenv/cli.py +++ b/pipenv/cli.py @@ -1390,6 +1390,7 @@ def uninstall( ) ) package_names = project.parsed_pipfile['dev-packages'] + package_names = package_names.keys() pipfile_remove = False else: puts(
fix: uninstall dev expecting tuple, not dict
py
diff --git a/subscriptions/tasks.py b/subscriptions/tasks.py index <HASH>..<HASH> 100644 --- a/subscriptions/tasks.py +++ b/subscriptions/tasks.py @@ -580,12 +580,17 @@ class FireWeekEstimateLast(Task): '*' in schedule.day_of_week): totals[day] = totals[day] + schedule.total_subs + # Django's datetime's weekday method has Monday = 0 + # whereas the cron format used in the schedules has Sunday = 0 + sunday = totals.pop(0) + totals[7] = sunday + totals = {(k-1): v for k, v in totals.items()} + today = now() for dow, total in totals.items(): # Only fire the metric for today or days in the future so that # estimates for the week don't get updated after the day in - # question. Django's datetime's weekday method has Monday = 0 - # whereas the cron format used in the schedules has Sunday = 0 + # question. if dow >= (today.weekday() - 1): fire_metric.apply_async(kwargs={ "metric_name": 'subscriptions.send.estimate.%s.last' % dow,
Changed weekday order of estimate metrics
py
diff --git a/tests/test_meta.py b/tests/test_meta.py index <HASH>..<HASH> 100644 --- a/tests/test_meta.py +++ b/tests/test_meta.py @@ -1,3 +1,5 @@ +from __future__ import unicode_literals, absolute_import, division + import re import pytest @@ -13,3 +15,13 @@ def test_meta_for_this_package(): dist = meta.load('.') assert re.match(r'[\d.]+', dist.version) assert dist.metadata['Name'] == 'pep517' + + +def test_classic_package(tmpdir): + (tmpdir / 'setup.py').write_text( + 'from distutils.core import setup; setup(name="foo", version="1.0")', + encoding='utf-8', + ) + dist = meta.load(str(tmpdir)) + assert dist.version == '1.0' + assert dist.metadata['Name'] == 'foo'
Add another test demonstrating support for classic packages.
py
diff --git a/safe/messaging/item/brand.py b/safe/messaging/item/brand.py index <HASH>..<HASH> 100644 --- a/safe/messaging/item/brand.py +++ b/safe/messaging/item/brand.py @@ -23,7 +23,11 @@ from safe.utilities.resources import ( resource_url) class Brand(Text): - """A class to model the inasafe brand.""" + """A class to model the inasafe brand. + + .. versionadded: 3.2 + + """ def __init__(self, **kwargs): """Creates a brand element.
Annotated brand class to indicate which version it was added in.
py
diff --git a/salt/states/service.py b/salt/states/service.py index <HASH>..<HASH> 100644 --- a/salt/states/service.py +++ b/salt/states/service.py @@ -93,6 +93,7 @@ def _enable(name, started, result=True, **kwargs): if __salt__['service.enabled'](name): # Service is enabled if started is True: + ret['changes'][name] = True ret['comment'] = ('Service {0} is already enabled,' ' and is running').format(name) return ret
Change output of states.service to reflect changes If a service is started, but already enabled, changes are now reflected to the user.
py
diff --git a/lmj/nn/flags.py b/lmj/nn/flags.py index <HASH>..<HASH> 100644 --- a/lmj/nn/flags.py +++ b/lmj/nn/flags.py @@ -84,6 +84,8 @@ g.add_argument('-C', '--cg-batches', type=int, metavar='N', help='use at most N batches for CG computation') g.add_argument('--initial-lambda', type=float, default=1., metavar='K', help='start the HF method with Tikhonov damping of K') +g.add_argument('--global-backtracking', action='store_true', + help='backtrack to lowest cost parameters during CG') g.add_argument('--preconditioner', action='store_true', help='precondition the system during CG') g.add_argument('--save-progress', metavar='FILE',
Add a flag for controlling backtracking strategy during CG in the HF optimizer.
py
diff --git a/abilian/services/indexing/service.py b/abilian/services/indexing/service.py index <HASH>..<HASH> 100644 --- a/abilian/services/indexing/service.py +++ b/abilian/services/indexing/service.py @@ -303,7 +303,7 @@ def index_update(index, items): adapted = service.adapted session = Session(bind=db.session.get_bind(None, None), autocommit=True) - + updated = set() with AsyncWriter(index) as writer: for op, cls_name, pk, data in items: if pk is None: @@ -319,6 +319,12 @@ def index_update(index, items): # FIXME: log to sentry? continue + if object_key in updated: + # don't add twice the same document in same transaction. The writer will + # not delete previous records, ending in duplicate records for same + # document. + continue + if op in ("new", "changed"): with session.begin(): obj = adapter.retrieve(pk, _session=session, **data) @@ -335,5 +341,6 @@ def index_update(index, items): document = adapter.get_document(obj) writer.add_document(**document) + updated.add(object_key) session.close()
index update: don't add twice the same document during a single transaction
py
diff --git a/bulbs/content/forms.py b/bulbs/content/forms.py index <HASH>..<HASH> 100644 --- a/bulbs/content/forms.py +++ b/bulbs/content/forms.py @@ -1,19 +1,23 @@ from django import forms +from django.utils.functional import lazy from .models import Content -class DoctypeChoiceField(forms.ChoiceField): - """Field for choosing amongst the doctypes of a given polymorphic model.""" - def __init__(self, model, exclude_base=False, *args, **kwargs): +def mapping_type_choices(model, exclude_base=True): + def get_choices(): mapping_type_models = model.get_mapping_type_models(exclude_base=exclude_base) choices = [] for mapping_type_name, content_type in mapping_type_models: choices.append((mapping_type_name, content_type.name)) - super(DoctypeChoiceField, self).__init__(choices=choices, *args, **kwargs) + return choices + return get_choices class ContentDoctypeForm(forms.Form): """Form for choosing a Content subclass doctype.""" - doctype = DoctypeChoiceField(Content, exclude_base=True, label='Type') + doctype = forms.ChoiceField( + choices=lazy(mapping_type_choices(Content, exclude_base=True), list)(), + label='Type' + )
Replaced DoctypeChoiceField with a lazily evaluated function
py
diff --git a/glue/ligolw/lsctables.py b/glue/ligolw/lsctables.py index <HASH>..<HASH> 100644 --- a/glue/ligolw/lsctables.py +++ b/glue/ligolw/lsctables.py @@ -681,7 +681,7 @@ class SnglInspiralTable(table.Table): "bank_chisq": "real_4", "bank_chisq_dof": "int_4s", "cont_chisq": "real_4", - "cont_chisq_dof": "int_4", + "cont_chisq_dof": "int_4s", "sigmasq": "real_8", "rsqveto_duration": "real_4", "Gamma0": "real_4",
I committed a typo that I am fixing there is no int_4 type
py
diff --git a/tests/test_common.py b/tests/test_common.py index <HASH>..<HASH> 100644 --- a/tests/test_common.py +++ b/tests/test_common.py @@ -31,11 +31,13 @@ class TestClasses(object): assert _class is not eval(repr(_class)) def test_equality(self, _class, _copy): - _copy.foo = 'bar' - assert not _class == _copy + copy_ = _copy(_class) + copy_.foo = 'bar' + assert not _class == copy_ assert not _class == "not a class instance" def test_inequality(self, _class, _copy): - _copy.foo = 'bar' - assert not _class != _copy + copy_ = _copy(_class) + copy_.foo = 'bar' + assert not _class != copy_ assert _class != "not a class instance"
Fix original not passed to deepcopy fixture
py
diff --git a/tests/build/test_build_request.py b/tests/build/test_build_request.py index <HASH>..<HASH> 100644 --- a/tests/build/test_build_request.py +++ b/tests/build/test_build_request.py @@ -1156,6 +1156,8 @@ class TestBuildRequest(object): build_request.set_params(**kwargs) build_json = build_request.render() + assert build_json["metadata"]["labels"]["git-branch"] is not None + # Verify the triggers are now disabled assert "triggers" not in build_json["spec"]
tests: make sure that git-branch is not being set to None
py
diff --git a/src/SALib/sample/saltelli.py b/src/SALib/sample/saltelli.py index <HASH>..<HASH> 100644 --- a/src/SALib/sample/saltelli.py +++ b/src/SALib/sample/saltelli.py @@ -1,5 +1,6 @@ from __future__ import division +import warnings import numpy as np from . import common_args @@ -28,7 +29,11 @@ def sample(problem, N, calc_second_order=True, seed=None, skip_values=1000): Calculate second-order sensitivities (default True) """ if seed: - np.random.seed(seed) + msg = "The seed value is ignored for the Saltelli sampler\n" + msg += "as it uses the (deterministic) Sobol sequence.\n" + msg += "Different samples can be obtained by setting the\n" + msg += "`skip_values` parameter (defaults to 1000)." + warnings.warn(msg) D = problem['num_vars'] groups = problem.get('groups')
Display warning if seed value is set
py
diff --git a/yabt/utils.py b/yabt/utils.py index <HASH>..<HASH> 100644 --- a/yabt/utils.py +++ b/yabt/utils.py @@ -79,7 +79,7 @@ def rmtree(path: str): pass -def link_func(src: str, dst: str, force: bool=False): +def link_func(src: str, dst: str, force: bool=True): if force: try: os.remove(dst) @@ -91,7 +91,7 @@ def link_func(src: str, dst: str, force: bool=False): pass -def link_node(abs_src: str, abs_dest: str, force: bool=False): +def link_node(abs_src: str, abs_dest: str, force: bool=True): """Sync source node (file / dir) to destination path using hard links.""" dest_parent_dir = split(abs_dest)[0] if not isdir(dest_parent_dir):
Allways force hard link. We encountered a bug when a python test depends on a cpp binary, in such cases once the binary was linked into the yabtwork workspace of the py test it will never be updated. After think about it a file can always be deleted in the origin and re-created thus links always should be forced.
py
diff --git a/script/bootstrap.py b/script/bootstrap.py index <HASH>..<HASH> 100755 --- a/script/bootstrap.py +++ b/script/bootstrap.py @@ -70,10 +70,10 @@ def update_win32_python(): def touch_config_gypi(): config_gypi = os.path.join(SOURCE_ROOT, 'vendor', 'node', 'config.gypi') - if not os.path.exists(config_gypi): - with open(config_gypi, 'w+') as f: - f.truncate(0) - f.write('{}') + with open(config_gypi, 'w+') as f: + content = '\n{}' + if f.read() != content: + f.write(content) def update_atom_shell():
Make sure the fake config.gypi can be parsed by node.js.
py
diff --git a/astroid/bases.py b/astroid/bases.py index <HASH>..<HASH> 100644 --- a/astroid/bases.py +++ b/astroid/bases.py @@ -43,7 +43,7 @@ PROPERTIES = {BUILTINS + '.property', 'abc.abstractproperty'} POSSIBLE_PROPERTIES = {"cached_property", "cachedproperty", "lazyproperty", "lazy_property", "reify", "lazyattribute", "lazy_attribute", - "LazyProperty", "lazy"} + "LazyProperty", "lazy", "cache_readonly"} def _is_property(meth):
Add cache_readonly to POSSIBLE_PROPERTIES for pandas
py
diff --git a/satpy/tests/writer_tests/test_ninjotiff.py b/satpy/tests/writer_tests/test_ninjotiff.py index <HASH>..<HASH> 100644 --- a/satpy/tests/writer_tests/test_ninjotiff.py +++ b/satpy/tests/writer_tests/test_ninjotiff.py @@ -37,8 +37,11 @@ class FakeImage: self.mode = mode -modules = {'pyninjotiff.ninjotiff': mock.Mock()} -@mock.patch.dict(sys.modules) +modules = {'pyninjotiff': mock.Mock(), + 'pyninjotiff.ninjotiff': mock.Mock()} + + +@mock.patch.dict(sys.modules, modules) class TestNinjoTIFFWriter(unittest.TestCase): """The ninjo tiff writer tests."""
Fix import mocking for ninjotiff writer tests
py
diff --git a/aprslib/inet.py b/aprslib/inet.py index <HASH>..<HASH> 100644 --- a/aprslib/inet.py +++ b/aprslib/inet.py @@ -111,7 +111,7 @@ class IS(object): while True: try: self._connect() - if self.skip_login: + if not self.skip_login: self._send_login() break except (LoginError, ConnectionError):
fix skip_login check being reversed
py
diff --git a/sacad/recurse.py b/sacad/recurse.py index <HASH>..<HASH> 100755 --- a/sacad/recurse.py +++ b/sacad/recurse.py @@ -222,22 +222,23 @@ def get_covers(work, args): except Exception as exception: stats["errors"] += 1 errors.append((path, artist, album, exception)) - if status: - if args.filename == EMBEDDED_ALBUM_ART_SYMBOL: - try: - embed_album_art(cover_filepath, path) - except Exception as exception: - stats["errors"] += 1 - errors.append((path, artist, album, exception)) + else: + if status: + if args.filename == EMBEDDED_ALBUM_ART_SYMBOL: + try: + embed_album_art(cover_filepath, path) + except Exception as exception: + stats["errors"] += 1 + errors.append((path, artist, album, exception)) + else: + stats["ok"] += 1 + finally: + os.remove(cover_filepath) else: stats["ok"] += 1 - finally: - os.remove(cover_filepath) else: - stats["ok"] += 1 - else: - stats["no result found"] += 1 - not_found.append((path, artist, album)) + stats["no result found"] += 1 + not_found.append((path, artist, album)) progress.set_postfix(stats) progress.update(1)
sacad_r: Fix error reporting
py
diff --git a/steam/sim.py b/steam/sim.py index <HASH>..<HASH> 100644 --- a/steam/sim.py +++ b/steam/sim.py @@ -201,7 +201,7 @@ class item(base.items.item): return self.get_name() def is_untradable(self): - return bool(not self._item["tradable"]) + return bool(not self._item.get("tradable")) def get_quantity(self): return int(self._item["amount"]) @@ -234,7 +234,7 @@ class item(base.items.item): return self._item.get("type", "") def get_image(self, size): - smallicon = self._item["icon_url"] + smallicon = self._item.get("icon_url") if not smallicon: return ""
Fix errors from sim items without tradable flags or icons attached
py
diff --git a/xerox/darwin.py b/xerox/darwin.py index <HASH>..<HASH> 100644 --- a/xerox/darwin.py +++ b/xerox/darwin.py @@ -5,7 +5,6 @@ import subprocess -import commands from .base import * @@ -23,7 +22,7 @@ def copy(string): def paste(): """Returns system clipboard contents.""" try: - return unicode(commands.getoutput('pbpaste')) + return unicode(subprocess.check_output('pbpaste')) except OSError as why: raise XcodeNotFound
Use `subprocess.check_output` rather than `commands.getoutput`. `commands` is deprecated.
py
diff --git a/libarchive/constants/archive_entry.py b/libarchive/constants/archive_entry.py index <HASH>..<HASH> 100644 --- a/libarchive/constants/archive_entry.py +++ b/libarchive/constants/archive_entry.py @@ -1,11 +1,11 @@ -AE_IFMT = 0170000 -AE_IFREG = 0100000 -AE_IFLNK = 0120000 -AE_IFSOCK = 0140000 -AE_IFCHR = 0020000 -AE_IFBLK = 0060000 -AE_IFDIR = 0040000 -AE_IFIFO = 0010000 +AE_IFMT = 0o170000 +AE_IFREG = 0o100000 +AE_IFLNK = 0o120000 +AE_IFSOCK = 0o140000 +AE_IFCHR = 0o020000 +AE_IFBLK = 0o060000 +AE_IFDIR = 0o040000 +AE_IFIFO = 0o010000 FILETYPES = { 'IFREG': AE_IFREG,
Added octal specifier to archive entry fields to prevent Python 3 errors.
py
diff --git a/gifi/queue.py b/gifi/queue.py index <HASH>..<HASH> 100644 --- a/gifi/queue.py +++ b/gifi/queue.py @@ -1,5 +1,6 @@ from command import Command, AggregatedCommand, CommandException from utils.git_utils import get_repo, check_repo_is_clean +import feature def _pop(): @@ -22,8 +23,10 @@ def _pop_finish(repo=None): def _push(): repo = get_repo() check_repo_is_clean(repo) - if repo.head.commit == repo.commit('origin/master'): - raise CommandException('You are currently at origin/master, there is nothing to push') + feature_config = feature.configuration(repo) + base = '%s/%s' % (feature_config.working_remote, feature_config.target_branch) + if repo.head.commit == repo.commit(base): + raise CommandException('You are currently at %s, there is nothing to push' % base) commit_message = repo.head.commit.message repo.git.reset('--soft', 'HEAD^') repo.git.stash('save', _escape_new_lines(commit_message))
queue: do not push when you are at working_remote/target_branch
py
diff --git a/setup.py b/setup.py index <HASH>..<HASH> 100644 --- a/setup.py +++ b/setup.py @@ -32,9 +32,11 @@ setup(name='instana', traces to your Instana dashboard.", zip_safe=False, install_requires=['autowrapt>=1.0', + 'basictracer>=3.0.0', + 'certifi>=2018.4.16', 'fysom>=2.1.2', 'opentracing>=2.0.0', - 'basictracer>=3.0.0'], + 'urllib3>=1.18.1'], entry_points={ 'instana': ['string = instana:load'], 'flask': ['flask = instana.flaskana:hook'], @@ -49,6 +51,7 @@ traces to your Instana dashboard.", 'flask>=0.12.2', 'lxml>=3.4', 'MySQL-python>=1.2.5;python_version<="2.7"', + 'pyOpenSSL>=16.1.0;python_version<="2.7"', 'requests>=2.17.1', 'urllib3[secure]>=1.15', 'spyne>=2.9',
Add dependencies for the REST API client (#<I>) * Add dependencies for the REST API client * Add pyOpenSSL for Python <I>.x
py
diff --git a/setup.py b/setup.py index <HASH>..<HASH> 100644 --- a/setup.py +++ b/setup.py @@ -72,7 +72,7 @@ setup( "eth-hash[pycryptodome]>=0.2.0,<1.0.0", "eth-typing>=2.0.0,<3.0.0", "eth-utils>=1.4.0,<2.0.0", - "ethpm==0.1.4a15", + "ethpm>=0.1.4a19,<2.0.0", "hexbytes>=0.1.0,<1.0.0", "lru-dict>=1.1.6,<2.0.0", "requests>=2.16.0,<3.0.0",
Update ethpm dep to latest alpha
py
diff --git a/packages/vaex-core/vaex/expression.py b/packages/vaex-core/vaex/expression.py index <HASH>..<HASH> 100644 --- a/packages/vaex-core/vaex/expression.py +++ b/packages/vaex-core/vaex/expression.py @@ -177,6 +177,10 @@ class Expression(with_metaclass(Meta)): def __getitem__(self, slice): return self.ds[slice][self.expression] + def __abs__(self): + """Returns the absolute value of the expression""" + return self.abs() + @property def dt(self): return DateTime(self)
feat: np.abs(df.x) and abs(df.x) now works, since it calls Expression.__abs__
py
diff --git a/setup.py b/setup.py index <HASH>..<HASH> 100755 --- a/setup.py +++ b/setup.py @@ -7,14 +7,14 @@ from setuptools import setup setup( name = 'easyhid', - version = '0.0.0', + version = '0.0.1', description = "A simple interface to the HIDAPI library.", url = "http://github.com/ahtn/python-easyhid", author = "jem", author_email = "jem@seethis.link", license = 'MIT', packages = ['easyhid'], - install_requires = ['cffi', 'ctypes'], + install_requires = ['cffi'], keywords = ['hidapi', 'usb', 'hid'], zip_safe = False )
remove ctypes from dependencies
py
diff --git a/aioxmpp/utils.py b/aioxmpp/utils.py index <HASH>..<HASH> 100644 --- a/aioxmpp/utils.py +++ b/aioxmpp/utils.py @@ -174,7 +174,7 @@ class LazyTask(asyncio.Future): def __iter__(self): self.__start_task() - return super().__iter__() + return iter(self.__task) if hasattr(asyncio.Future, "__await__"): def __await__(self):
utils: fix python<I> incompatibility I have no idea why the old way doesn’t work though. I presume this is some internals of asyncio which changed.
py
diff --git a/h5netcdf/tests/test_h5netcdf.py b/h5netcdf/tests/test_h5netcdf.py index <HASH>..<HASH> 100644 --- a/h5netcdf/tests/test_h5netcdf.py +++ b/h5netcdf/tests/test_h5netcdf.py @@ -576,6 +576,9 @@ def test_failed_read_open_and_clean_delete(tmpdir): def test_create_variable_matching_saved_dimension(tmp_local_or_remote_netcdf): h5 = get_hdf5_module(tmp_local_or_remote_netcdf) + if h5 is not h5py: + pytest.xfail('https://github.com/shoyer/h5netcdf/issues/48') + with h5netcdf.File(tmp_local_or_remote_netcdf) as f: f.dimensions['x'] = 2 f.create_variable('y', data=[1, 2], dimensions=('x',))
xfail failing h5pyd test
py
diff --git a/openupgradelib/openupgrade_120.py b/openupgradelib/openupgrade_120.py index <HASH>..<HASH> 100644 --- a/openupgradelib/openupgrade_120.py +++ b/openupgradelib/openupgrade_120.py @@ -362,7 +362,7 @@ def _convert_field_bootstrap_3to4_orm(env, model_name, field_name, update_field_multilang( records, field_name, - lambda old, *a, **k: convert_field_bootstrap_3to4(old), + lambda old, *a, **k: convert_string_bootstrap_3to4(old), )
[FIX] typo in <I> tools Fix typo in openupgrade_<I> in `_convert_field_bootstrap_3to4_orm` method. it have to call string conversion.
py
diff --git a/docido_sdk/index/processor/es_api.py b/docido_sdk/index/processor/es_api.py index <HASH>..<HASH> 100644 --- a/docido_sdk/index/processor/es_api.py +++ b/docido_sdk/index/processor/es_api.py @@ -148,6 +148,10 @@ class ElasticsearchProcessor(IndexAPIProcessor): '_id': _id } }) + + if len(body) == 0: + return error_docs + params = { 'body': body, 'refresh': True, @@ -185,6 +189,10 @@ class ElasticsearchProcessor(IndexAPIProcessor): '_id': _id } }) + + if len(body) == 0: + return error_docs + params = { 'body': body, 'refresh': True, @@ -215,6 +223,10 @@ class ElasticsearchProcessor(IndexAPIProcessor): } body.append(action) body.append(doc) + + if len(body) == 0: + return error_docs + params = { 'body': body, 'refresh': True,
es_api: don't even talk to the API if we have nothing to say
py
diff --git a/jsmin/test.py b/jsmin/test.py index <HASH>..<HASH> 100644 --- a/jsmin/test.py +++ b/jsmin/test.py @@ -317,5 +317,10 @@ var foo = "hey"; original = '/(NaN| {2}|^$)/.test(a)&&(a="M 0 0");' self.assertMinified(original, original) # there should be nothing jsmin can do here + def test_space_with_regex_repeats_not_at_start(self): + original = 'aaa;/(NaN| {2}|^$)/.test(a)&&(a="M 0 0");' + self.assertMinified(original, original) # there should be nothing jsmin can do here + + if __name__ == '__main__': unittest.main()
Testing issue #<I> also when the regex is not at the start of the script.
py
diff --git a/tests/test_recommendation_manager.py b/tests/test_recommendation_manager.py index <HASH>..<HASH> 100644 --- a/tests/test_recommendation_manager.py +++ b/tests/test_recommendation_manager.py @@ -58,3 +58,29 @@ def test_recommendation_strategy(): 10, extra_data={'branch': 'linear'}) assert results == EXPECTED_ADDONS + + +def test_recommendation_ensemble(): + """The recommendation manager support an ensemble + method. We want to verify that at least the dispatch + to the stub ensemble recommendation is correctly executing. + """ + EXPECTED_ADDONS = [("ensemble_guid1", 0.1), + ("ensemble_guid2", 0.2), + ("ensemble_guid3", 0.3)] + + # Create a stub ProfileFetcher that always returns the same + # client data. + class StubFetcher: + def get(self, client_id): + return {'client_id': '00000'} + + # Configure the recommender so that only the second model + # can recommend and return the expected addons. + + # Make sure the recommender returns the expected addons. + manager = RecommendationManager(StubFetcher()) + results = manager.recommend("client-id", + 10, + extra_data={'branch': 'ensemble'}) + assert results == EXPECTED_ADDONS
Added a testcase to verify that ensemble recommendations are dispatching correctly.
py
diff --git a/test/test_cluster_spec.py b/test/test_cluster_spec.py index <HASH>..<HASH> 100644 --- a/test/test_cluster_spec.py +++ b/test/test_cluster_spec.py @@ -118,6 +118,14 @@ class TestAllScenarios(unittest.TestCase): pass +def cluster_type_name(cluster_type): + return CLUSTER_TYPE._fields[cluster_type] + + +def server_type_name(server_type): + return SERVER_TYPE._fields[server_type] + + def check_outcome(self, cluster, outcome): expected_servers = outcome['servers'] @@ -144,8 +152,8 @@ def check_outcome(self, cluster, outcome): SERVER_TYPE, expected_server['type']) self.assertEqual( - expected_server_type, - actual_server_description.server_type) + server_type_name(expected_server_type), + server_type_name(actual_server_description.server_type)) self.assertEqual( expected_server['setName'], @@ -153,7 +161,8 @@ def check_outcome(self, cluster, outcome): self.assertEqual(outcome['setName'], cluster.description.set_name) expected_cluster_type = getattr(CLUSTER_TYPE, outcome['clusterType']) - self.assertEqual(expected_cluster_type, cluster.description.cluster_type) + self.assertEqual(cluster_type_name(expected_cluster_type), + cluster_type_name(cluster.description.cluster_type)) def create_test(scenario_def):
PYTHON-<I> Better test_cluster_spec messages. If a server or cluster is the wrong type at the end of a test, print the type's name, not its number.
py
diff --git a/ccxt/exchanges.py b/ccxt/exchanges.py index <HASH>..<HASH> 100644 --- a/ccxt/exchanges.py +++ b/ccxt/exchanges.py @@ -116,6 +116,7 @@ import calendar import datetime import hashlib import json +import math import sys import time import decimal
added missing import math to ./ccxt/exchanges.py
py
diff --git a/shap/explainers/_partition.py b/shap/explainers/_partition.py index <HASH>..<HASH> 100644 --- a/shap/explainers/_partition.py +++ b/shap/explainers/_partition.py @@ -83,7 +83,7 @@ class Partition(Explainer): self.input_shape = masker.shape[1:] if hasattr(masker, "shape") and not callable(masker.shape) else None # self.output_names = output_names - self.model = lambda x: np.array(model(*x)) + self.model = lambda *args: np.array(model(*args)) self.elemental_model = model self.expected_value = None self._curr_base_value = None
Changed variable naming from x->args and unpacking of args when passed to the model
py
diff --git a/bika/lims/browser/analysisrequest/view.py b/bika/lims/browser/analysisrequest/view.py index <HASH>..<HASH> 100644 --- a/bika/lims/browser/analysisrequest/view.py +++ b/bika/lims/browser/analysisrequest/view.py @@ -104,6 +104,19 @@ class AnalysisRequestViewView(BrowserView): {'id': 'retract'}, {'id': 'verify'}] self.qctable = qcview.contents_table() + # If a general retracted is done, rise a waring + if workflow.getInfoFor(ar, 'review_state') == 'sample_received': + allstatus = list() + for analysis in ar.getAnalyses(): + status = workflow.getInfoFor(analysis.getObject(), 'review_state') + if status not in ['retracted','to_be_verified','verified']: + allstatus = [] + break + else: + allstatus.append(status) + if len(allstatus) > 0: + self.addMessage("General Retract Done", 'warning') + # If is a retracted AR, show the link to child AR and show a warn msg if workflow.getInfoFor(ar, 'review_state') == 'invalid': childar = hasattr(ar, 'getChildAnalysisRequest') \
Warning missage when you do a "full" retract on ARview
py
diff --git a/src/vistir/spin.py b/src/vistir/spin.py index <HASH>..<HASH> 100644 --- a/src/vistir/spin.py +++ b/src/vistir/spin.py @@ -112,6 +112,8 @@ class VistirSpinner(base_obj): """ self.handler = handler + import colorama + colorama.init() sigmap = {} if handler: sigmap.update({
make sure to init colorama in spinner
py
diff --git a/setup.py b/setup.py index <HASH>..<HASH> 100644 --- a/setup.py +++ b/setup.py @@ -4,7 +4,7 @@ from setuptools import setup setup(name='dtw', - version='1.1', + version='1.2', description='Python DTW Module', author='Pierre Rouanet', author_email='pierre.rouanet@gmail.com',
Bump to version <I>
py
diff --git a/arviz/rcparams.py b/arviz/rcparams.py index <HASH>..<HASH> 100644 --- a/arviz/rcparams.py +++ b/arviz/rcparams.py @@ -234,15 +234,19 @@ class rc_context: # pylint: disable=invalid-name Examples -------- This allows one to do:: + with az.rc_context(fname='pystan.rc'): idata = az.load_arviz_data("radon") az.plot_posterior(idata, var_names=["gamma"]) + The plot would have settings from 'screen.rc' A dictionary can also be passed to the context manager:: + with az.rc_context(rc={'plot.max_subplots': None}, fname='pystan.rc'): idata = az.load_arviz_data("radon") az.plot_posterior(idata, var_names=["gamma"]) + The 'rc' dictionary takes precedence over the settings loaded from 'fname'. Passing a dictionary only is also valid. """
fix code example in rc_context (#<I>)
py
diff --git a/MAVProxy/mavproxy.py b/MAVProxy/mavproxy.py index <HASH>..<HASH> 100755 --- a/MAVProxy/mavproxy.py +++ b/MAVProxy/mavproxy.py @@ -2278,10 +2278,11 @@ Auto-detected serial ports are: else: print("no script %s" % start_script) - # some core functionality is in modules - standard_modules = ['log'] - for m in standard_modules: - process_stdin('module load %s' % m) + if not opts.setup: + # some core functionality is in modules + standard_modules = ['log'] + for m in standard_modules: + process_stdin('module load %s' % m) if opts.console: process_stdin('module load console')
don't load log module in setup mode
py
diff --git a/angr/analyses/decompiler/structured_codegen.py b/angr/analyses/decompiler/structured_codegen.py index <HASH>..<HASH> 100644 --- a/angr/analyses/decompiler/structured_codegen.py +++ b/angr/analyses/decompiler/structured_codegen.py @@ -188,6 +188,8 @@ class CFunction(CConstruct): # pylint:disable=abstract-method yield " ", None if variable.name: yield variable.name, cvariable + elif isinstance(variable, SimTemporaryVariable): + yield "tmp_%d" % variable.tmp_id, cvariable else: yield str(variable), cvariable yield ";\n", None @@ -748,6 +750,8 @@ class CVariable(CExpression): if isinstance(self.variable, SimVariable): if self.variable.name: yield self.variable.name, self + elif isinstance(self.variable, SimTemporaryVariable): + yield "tmp_%d" % self.variable.tmp_id, self else: yield str(self.variable), self elif isinstance(self.variable, CExpression):
StructuredCodeGen: Pretty print temporary variables. (#<I>)
py
diff --git a/salt/modules/network.py b/salt/modules/network.py index <HASH>..<HASH> 100644 --- a/salt/modules/network.py +++ b/salt/modules/network.py @@ -125,15 +125,15 @@ def subnets(): salt '*' network.subnets ''' ifaces = interfaces() - subnets = [] + subnetworks = [] for ipv4_info in ifaces.values(): for ipv4 in ipv4_info.get('inet', []): if ipv4['address'] == '127.0.0.1': continue network = _calculate_subnet(ipv4['address'], ipv4['netmask']) - subnets.append(network) - return subnets + subnetworks.append(network) + return subnetworks def in_subnet(cidr):
network mod: rename subnets -> subnetworks, to avoid shadowing func
py
diff --git a/setup.py b/setup.py index <HASH>..<HASH> 100644 --- a/setup.py +++ b/setup.py @@ -16,9 +16,13 @@ setup( version='1.0.5', packages=[ 'ntlm_auth' ], install_requires=[ - "six", - "ordereddict ; python_version<'2.7'" + 'six' ], + extras_require={ + ':python_version<"2.7"': [ + 'ordereddict' + ] + }, author='Jordan Borean', author_email='jborean93@gmail.com', url='https://github.com/jborean93/ntlm-auth',
Fix environment markers being stripped when building python wheels (#<I>)
py
diff --git a/bcbio/structural/manta.py b/bcbio/structural/manta.py index <HASH>..<HASH> 100644 --- a/bcbio/structural/manta.py +++ b/bcbio/structural/manta.py @@ -105,6 +105,9 @@ def _prep_config(items, paired, work_dir): cmd += ["--exome"] for region in _maybe_limit_chromosomes(data): cmd += ["--region", region] + resources = config_utils.get_resources("manta", data["config"]) + if resources.get("options"): + cmd += [str(x) for x in resources["options"]] # If we are removing polyX, avoid calling on small indels which require # excessively long runtimes on noisy WGS runs if "polyx" in dd.get_exclude_regions(data):
Manta: configManta command line tweaks with resources/options
py
diff --git a/tests/pytests/unit/states/test_makeconf.py b/tests/pytests/unit/states/test_makeconf.py index <HASH>..<HASH> 100644 --- a/tests/pytests/unit/states/test_makeconf.py +++ b/tests/pytests/unit/states/test_makeconf.py @@ -28,9 +28,6 @@ def test_present(): assert makeconf.present(name) == ret -# 'absent' function tests: 1 - - def test_absent(): """ Test to verify that the variable is not in the ``make.conf``.
Move makeconf state tests to pytest
py
diff --git a/bika/lims/browser/analyses.py b/bika/lims/browser/analyses.py index <HASH>..<HASH> 100644 --- a/bika/lims/browser/analyses.py +++ b/bika/lims/browser/analyses.py @@ -43,7 +43,6 @@ class AnalysesView(BikaListingView): self.show_column_toggles = False self.pagesize = 0 self.form_id = 'analyses_form' - self.categories = [] self.portal = getToolByName(context, 'portal_url').getPortalObject() self.portal_url = self.portal.absolute_url() @@ -303,6 +302,7 @@ class AnalysesView(BikaListingView): self.show_select_column = self.allow_edit context_active = isActive(self.context) + self.categories = [] items = super(AnalysesView, self).folderitems(full_objects = True) # manually skim retracted analyses from the list
LIMS-<I>: Prevent merging of field/lab categories This was causing empty categories to display, also.
py
diff --git a/selectable/tests/views.py b/selectable/tests/views.py index <HASH>..<HASH> 100644 --- a/selectable/tests/views.py +++ b/selectable/tests/views.py @@ -1,9 +1,9 @@ from django.http import HttpResponseNotFound, HttpResponseServerError -def test_404(request): +def test_404(request, *args, **kwargs): return HttpResponseNotFound() -def test_500(request): +def test_500(request, *args, **kwargs): return HttpResponseServerError()
<I> added another argument to the error handler views.
py
diff --git a/salt/version.py b/salt/version.py index <HASH>..<HASH> 100644 --- a/salt/version.py +++ b/salt/version.py @@ -574,7 +574,7 @@ def dependency_information(include_salt_cloud=False): ('msgpack-python', 'msgpack', 'version'), ('msgpack-pure', 'msgpack_pure', 'version'), ('pycrypto', 'Crypto', '__version__'), - ('pycryptodome', 'Cryptodome', '__version__'), + ('pycryptodome', 'Cryptodome', 'version_info'), ('libnacl', 'libnacl', '__version__'), ('PyYAML', 'yaml', '__version__'), ('ioflo', 'ioflo', '__version__'),
fix the cryptodome version lookup for the versions report
py
diff --git a/tests/unit/utils/test_templates.py b/tests/unit/utils/test_templates.py index <HASH>..<HASH> 100644 --- a/tests/unit/utils/test_templates.py +++ b/tests/unit/utils/test_templates.py @@ -109,7 +109,7 @@ class RenderTestCase(TestCase): ctx = dict(context) ctx['var'] = 'OK' res = salt.utils.templates.render_wempy_tmpl(tmpl, ctx) - self.assertEqual(res, '<RU>OK</RU>') + self.assertEqual(res, 'OK') ### Tests for genshi template (xml-based) def test_render_genshi_sanity(self):
Re-fixed the copy-pasta error in the wempy_variable test from unit.utils.test_templates so it doesn't check for xml that wasn't defined in the template.
py
diff --git a/webssh/handler.py b/webssh/handler.py index <HASH>..<HASH> 100644 --- a/webssh/handler.py +++ b/webssh/handler.py @@ -48,6 +48,10 @@ class MixinHandler(object): raise InvalidValueError('Missing value {}'.format(name)) return value + def get_client_addr(self): + return self.get_real_client_addr() or self.request.connection.context.\ + address + def get_real_client_addr(self): ip = self.request.remote_ip @@ -194,10 +198,6 @@ class IndexHandler(MixinHandler, tornado.web.RequestHandler): logging.debug(args) return args - def get_client_addr(self): - return self.get_real_client_addr() or self.request.connection.stream.\ - socket.getpeername() - def get_default_encoding(self, ssh): try: _, stdout, _ = ssh.exec_command('locale charmap') @@ -277,9 +277,6 @@ class WsockHandler(MixinHandler, tornado.websocket.WebSocketHandler): self.loop = loop self.worker_ref = None - def get_client_addr(self): - return self.get_real_client_addr() or self.stream.socket.getpeername() - def open(self): self.src_addr = self.get_client_addr() logging.info('Connected from {}:{}'.format(*self.src_addr))
Move get_client_addr to MixinHandler
py
diff --git a/dynesty/nestedsamplers.py b/dynesty/nestedsamplers.py index <HASH>..<HASH> 100644 --- a/dynesty/nestedsamplers.py +++ b/dynesty/nestedsamplers.py @@ -547,6 +547,11 @@ class MultiEllipsoidSampler(Sampler): self.fmove = self.kwargs.get('fmove', 0.9) self.max_move = self.kwargs.get('max_move', 100) + def __getstate__(self): + state = self.__dict__.copy() + del state['rstate'] + return state + def update(self, pointvol): """Update the bounding ellipsoids using the current set of live points."""
for pickling, remove 'rstate' from dictionary
py
diff --git a/livelossplot/plot_losses.py b/livelossplot/plot_losses.py index <HASH>..<HASH> 100644 --- a/livelossplot/plot_losses.py +++ b/livelossplot/plot_losses.py @@ -1,12 +1,12 @@ import warnings from typing import Type, Tuple, List, Optional, TypeVar - from livelossplot.main_logger import MainLogger from livelossplot.outputs import BaseOutput, MatplotlibPlot, ExtremaPrinter BO = TypeVar('BO', bound=BaseOutput) + class PlotLosses: """ Class collect metrics from the training engine and send it to plugins, when send is called
fix(yapf) misc
py
diff --git a/ontquery/plugins/services/rdflib.py b/ontquery/plugins/services/rdflib.py index <HASH>..<HASH> 100644 --- a/ontquery/plugins/services/rdflib.py +++ b/ontquery/plugins/services/rdflib.py @@ -130,7 +130,7 @@ class rdflibLocal(OntService): # reccomended for local default implementation #print(red.format('WARNING:'), 'untranslated predicate', p) else: c = pn - if c in out: + if c in out and o not in out[c]: if not isinstance(out[c], tuple): out[c] = out.pop(c), o else:
rdflib service dont add duplicate objects to query result under some circumstances both "asdf" and "asdf"^^xsd:string may be present in a graph, therefore skip cases where the python object is identical
py
diff --git a/fundamentals/__version__.py b/fundamentals/__version__.py index <HASH>..<HASH> 100644 --- a/fundamentals/__version__.py +++ b/fundamentals/__version__.py @@ -1 +1 @@ -__version__ = '2.1.7' +__version__ = '2.2.0'
added a dbConn to the directory script runner and a execute_mysql_script function
py
diff --git a/custodian/vasp/handlers.py b/custodian/vasp/handlers.py index <HASH>..<HASH> 100644 --- a/custodian/vasp/handlers.py +++ b/custodian/vasp/handlers.py @@ -396,8 +396,13 @@ class VaspErrorHandler(ErrorHandler): actions.append({"dict": "INCAR", "action": {"_set": {"ALGO": "All"}}}) if "grad_not_orth" in self.errors: - if vi["INCAR"].get("ISMEAR", 1) < 0: - actions.append({"dict": "INCAR", "action": {"_set": {"ISMEAR": 0, "SIGMA": 0.05}}}) + if ( + (vi["INCAR"].get("Algo", "Normal") == "All" + and not vi["INCAR"].get("METAGGA", False) + and not vi["INCAR"].get("LHFCALC", False)) + or vi["INCAR"].get("ALGO", "Normal") == "Damped" + ): + actions.append({"dict": "INCAR", "action": {"_set": {"Algo": "Normal"}}}) if "zheev" in self.errors: if vi["INCAR"].get("ALGO", "Fast").lower() != "exact":
More appropriate grad_not_orth fix grad_not_orth is primarily an issue related to how VASP is compiled. Instead of changing ISMEAR, Custodian now checks to see if Algo = All or Algo = Damped is set, in which case Algo = Normal is the new algorithm. Algo = All is *not* modified if METAGGA = True or LHFCALC = True.
py
diff --git a/src/anyconfig/globals/datatypes.py b/src/anyconfig/globals/datatypes.py index <HASH>..<HASH> 100644 --- a/src/anyconfig/globals/datatypes.py +++ b/src/anyconfig/globals/datatypes.py @@ -27,6 +27,6 @@ class IOInfo(typing.NamedTuple): extension: str -IOI_KEYS: typing.Tuple[typing.Optional[typing.Any]] = IOInfo._fields +IOI_KEYS: typing.Tuple[str, ...] = IOInfo._fields # vim:sw=4:ts=4:et:
fix: correct an wrong type hint to .globals.IOI_KEYS
py
diff --git a/test/integration/007_graph_selection_tests/test_graph_selection.py b/test/integration/007_graph_selection_tests/test_graph_selection.py index <HASH>..<HASH> 100644 --- a/test/integration/007_graph_selection_tests/test_graph_selection.py +++ b/test/integration/007_graph_selection_tests/test_graph_selection.py @@ -234,6 +234,6 @@ class TestGraphSelection(DBTIntegrationTest): user_last_end = users.timing[1]['completed_at'] dep_first_start = dep.timing[0]['started_at'] self.assertTrue( - user_last_end < dep_first_start, + user_last_end <= dep_first_start, 'dependency started before its transitive parent ({} > {})'.format(user_last_end, dep_first_start) )
fix a test bug dbt doing two things in the same second incorrectly failed the test
py
diff --git a/pinax/invitations/models.py b/pinax/invitations/models.py index <HASH>..<HASH> 100644 --- a/pinax/invitations/models.py +++ b/pinax/invitations/models.py @@ -39,7 +39,7 @@ class JoinInvitation(models.Model): message = models.TextField(null=True) sent = models.DateTimeField(default=timezone.now) status = models.IntegerField(choices=INVITE_STATUS_CHOICES) - signup_code = models.OneToOneField(SignupCode) + signup_code = models.OneToOneField(SignupCode, on_delete=models.CASCADE) def to_user_email(self): return self.signup_code.email
Add another `on_delete`
py
diff --git a/src/hamster/overview_activities.py b/src/hamster/overview_activities.py index <HASH>..<HASH> 100644 --- a/src/hamster/overview_activities.py +++ b/src/hamster/overview_activities.py @@ -140,7 +140,7 @@ class OverviewBox(gtk.VBox): self.delete_selected() return True elif (event.keyval == gtk.keysyms.Insert): - dialogs.edit.show() + self.launch_edit(self.fact_tree.get_selected_fact()) return True elif event.keyval == gtk.keysyms.c and event.state & gtk.gdk.CONTROL_MASK: self.copy_selected()
keyboard shortcut points should point to same launch edit action (so that the fact gets passed in and such)
py