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train
get_root_resource
Returns the root resource.
nefertari/resource.py
def get_root_resource(config): """Returns the root resource.""" app_package_name = get_app_package_name(config) return config.registry._root_resources.setdefault( app_package_name, Resource(config))
def get_root_resource(config): """Returns the root resource.""" app_package_name = get_app_package_name(config) return config.registry._root_resources.setdefault( app_package_name, Resource(config))
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ramses-tech/nefertari
python
https://github.com/ramses-tech/nefertari/blob/c7caffe11576c11aa111adbdbadeff70ce66b1dd/nefertari/resource.py#L46-L50
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c7caffe11576c11aa111adbdbadeff70ce66b1dd
train
add_resource_routes
``view`` is a dotted name of (or direct reference to) a Python view class, e.g. ``'my.package.views.MyView'``. ``member_name`` should be the appropriate singular version of the resource given your locale and used with members of the collection. ``collection_name`` will be used to refer to the reso...
nefertari/resource.py
def add_resource_routes(config, view, member_name, collection_name, **kwargs): """ ``view`` is a dotted name of (or direct reference to) a Python view class, e.g. ``'my.package.views.MyView'``. ``member_name`` should be the appropriate singular version of the resource given your locale and used...
def add_resource_routes(config, view, member_name, collection_name, **kwargs): """ ``view`` is a dotted name of (or direct reference to) a Python view class, e.g. ``'my.package.views.MyView'``. ``member_name`` should be the appropriate singular version of the resource given your locale and used...
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ramses-tech/nefertari
python
https://github.com/ramses-tech/nefertari/blob/c7caffe11576c11aa111adbdbadeff70ce66b1dd/nefertari/resource.py#L57-L190
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c7caffe11576c11aa111adbdbadeff70ce66b1dd
train
get_default_view_path
Returns the dotted path to the default view class.
nefertari/resource.py
def get_default_view_path(resource): "Returns the dotted path to the default view class." parts = [a.member_name for a in resource.ancestors] +\ [resource.collection_name or resource.member_name] if resource.prefix: parts.insert(-1, resource.prefix) view_file = '%s' % '_'.join(par...
def get_default_view_path(resource): "Returns the dotted path to the default view class." parts = [a.member_name for a in resource.ancestors] +\ [resource.collection_name or resource.member_name] if resource.prefix: parts.insert(-1, resource.prefix) view_file = '%s' % '_'.join(par...
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ramses-tech/nefertari
python
https://github.com/ramses-tech/nefertari/blob/c7caffe11576c11aa111adbdbadeff70ce66b1dd/nefertari/resource.py#L193-L206
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c7caffe11576c11aa111adbdbadeff70ce66b1dd
train
Resource.get_ancestors
Returns the list of ancestor resources.
nefertari/resource.py
def get_ancestors(self): "Returns the list of ancestor resources." if self._ancestors: return self._ancestors if not self.parent: return [] obj = self.resource_map.get(self.parent.uid) while obj and obj.member_name: self._ancestors.append(o...
def get_ancestors(self): "Returns the list of ancestor resources." if self._ancestors: return self._ancestors if not self.parent: return [] obj = self.resource_map.get(self.parent.uid) while obj and obj.member_name: self._ancestors.append(o...
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ramses-tech/nefertari
python
https://github.com/ramses-tech/nefertari/blob/c7caffe11576c11aa111adbdbadeff70ce66b1dd/nefertari/resource.py#L231-L247
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c7caffe11576c11aa111adbdbadeff70ce66b1dd
train
Resource.add
:param member_name: singular name of the resource. It should be the appropriate singular version of the resource given your locale and used with members of the collection. :param collection_name: plural name of the resource. It will be used to refer to the resource collectio...
nefertari/resource.py
def add(self, member_name, collection_name='', parent=None, uid='', **kwargs): """ :param member_name: singular name of the resource. It should be the appropriate singular version of the resource given your locale and used with members of the collection. :par...
def add(self, member_name, collection_name='', parent=None, uid='', **kwargs): """ :param member_name: singular name of the resource. It should be the appropriate singular version of the resource given your locale and used with members of the collection. :par...
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ramses-tech/nefertari
python
https://github.com/ramses-tech/nefertari/blob/c7caffe11576c11aa111adbdbadeff70ce66b1dd/nefertari/resource.py#L257-L379
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c7caffe11576c11aa111adbdbadeff70ce66b1dd
train
Resource.add_from_child
Add a resource with its all children resources to the current resource.
nefertari/resource.py
def add_from_child(self, resource, **kwargs): """ Add a resource with its all children resources to the current resource. """ new_resource = self.add( resource.member_name, resource.collection_name, **kwargs) for child in resource.children: new_resource.a...
def add_from_child(self, resource, **kwargs): """ Add a resource with its all children resources to the current resource. """ new_resource = self.add( resource.member_name, resource.collection_name, **kwargs) for child in resource.children: new_resource.a...
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ramses-tech/nefertari
python
https://github.com/ramses-tech/nefertari/blob/c7caffe11576c11aa111adbdbadeff70ce66b1dd/nefertari/resource.py#L381-L389
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c7caffe11576c11aa111adbdbadeff70ce66b1dd
train
DatasetContainer.add
Add the path of a data set to the list of available sets NOTE: a data set is assumed to be a pickled and gzip compressed Pandas DataFrame Parameters ---------- path : str
opengrid/datasets/datasets.py
def add(self, path): """ Add the path of a data set to the list of available sets NOTE: a data set is assumed to be a pickled and gzip compressed Pandas DataFrame Parameters ---------- path : str """ name_with_ext = os.path.split(path)[1] # spli...
def add(self, path): """ Add the path of a data set to the list of available sets NOTE: a data set is assumed to be a pickled and gzip compressed Pandas DataFrame Parameters ---------- path : str """ name_with_ext = os.path.split(path)[1] # spli...
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opengridcc/opengrid
python
https://github.com/opengridcc/opengrid/blob/69b8da3c8fcea9300226c45ef0628cd6d4307651/opengrid/datasets/datasets.py#L27-L40
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69b8da3c8fcea9300226c45ef0628cd6d4307651
train
DatasetContainer.unpack
Unpacks a data set to a Pandas DataFrame Parameters ---------- name : str call `.list` to see all availble datasets Returns ------- pd.DataFrame
opengrid/datasets/datasets.py
def unpack(self, name): """ Unpacks a data set to a Pandas DataFrame Parameters ---------- name : str call `.list` to see all availble datasets Returns ------- pd.DataFrame """ path = self.list[name] df = pd.read_pickl...
def unpack(self, name): """ Unpacks a data set to a Pandas DataFrame Parameters ---------- name : str call `.list` to see all availble datasets Returns ------- pd.DataFrame """ path = self.list[name] df = pd.read_pickl...
[ "Unpacks", "a", "data", "set", "to", "a", "Pandas", "DataFrame" ]
opengridcc/opengrid
python
https://github.com/opengridcc/opengrid/blob/69b8da3c8fcea9300226c45ef0628cd6d4307651/opengrid/datasets/datasets.py#L42-L57
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69b8da3c8fcea9300226c45ef0628cd6d4307651
train
six_frame
translate each sequence into six reading frames
ctbBio/sixframe.py
def six_frame(genome, table, minimum = 10): """ translate each sequence into six reading frames """ for seq in parse_fasta(genome): dna = Seq(seq[1].upper().replace('U', 'T'), IUPAC.ambiguous_dna) counter = 0 for sequence in ['f', dna], ['rc', dna.reverse_complement()]: ...
def six_frame(genome, table, minimum = 10): """ translate each sequence into six reading frames """ for seq in parse_fasta(genome): dna = Seq(seq[1].upper().replace('U', 'T'), IUPAC.ambiguous_dna) counter = 0 for sequence in ['f', dna], ['rc', dna.reverse_complement()]: ...
[ "translate", "each", "sequence", "into", "six", "reading", "frames" ]
christophertbrown/bioscripts
python
https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/sixframe.py#L13-L32
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83b2566b3a5745437ec651cd6cafddd056846240
train
publish_processed_network_packets
# Redis/RabbitMQ/SQS messaging endpoints for pub-sub routing_key = ev("PUBLISH_EXCHANGE", "reporting.accounts") queue_name = ev("PUBLISH_QUEUE", "reporting.accounts") auth_url = ev("PUB_BROKER_URL", "redis://localhost:6379/15") serializer = "jso...
network_pipeline/scripts/network_agent.py
def publish_processed_network_packets( name="not-set", task_queue=None, result_queue=None, need_response=False, shutdown_msg="SHUTDOWN"): """ # Redis/RabbitMQ/SQS messaging endpoints for pub-sub routing_key = ev("PUBLISH_EXCHANGE", "reporting.acc...
def publish_processed_network_packets( name="not-set", task_queue=None, result_queue=None, need_response=False, shutdown_msg="SHUTDOWN"): """ # Redis/RabbitMQ/SQS messaging endpoints for pub-sub routing_key = ev("PUBLISH_EXCHANGE", "reporting.acc...
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jay-johnson/network-pipeline
python
https://github.com/jay-johnson/network-pipeline/blob/4e53ae13fe12085e0cf2e5e1aff947368f4f1ffa/network_pipeline/scripts/network_agent.py#L35-L244
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4e53ae13fe12085e0cf2e5e1aff947368f4f1ffa
train
run_main
run_main start the packet consumers and the packet processors :param need_response: should send response back to publisher :param callback: handler method
network_pipeline/scripts/network_agent.py
def run_main( need_response=False, callback=None): """run_main start the packet consumers and the packet processors :param need_response: should send response back to publisher :param callback: handler method """ stop_file = ev("STOP_FILE", "/opt/stop_record...
def run_main( need_response=False, callback=None): """run_main start the packet consumers and the packet processors :param need_response: should send response back to publisher :param callback: handler method """ stop_file = ev("STOP_FILE", "/opt/stop_record...
[ "run_main" ]
jay-johnson/network-pipeline
python
https://github.com/jay-johnson/network-pipeline/blob/4e53ae13fe12085e0cf2e5e1aff947368f4f1ffa/network_pipeline/scripts/network_agent.py#L248-L341
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4e53ae13fe12085e0cf2e5e1aff947368f4f1ffa
train
best_model
determine the best model: archaea, bacteria, eukarya (best score)
ctbBio/16SfromHMM.py
def best_model(seq2hmm): """ determine the best model: archaea, bacteria, eukarya (best score) """ for seq in seq2hmm: best = [] for model in seq2hmm[seq]: best.append([model, sorted([i[-1] for i in seq2hmm[seq][model]], reverse = True)[0]]) best_model = sorted(best, ...
def best_model(seq2hmm): """ determine the best model: archaea, bacteria, eukarya (best score) """ for seq in seq2hmm: best = [] for model in seq2hmm[seq]: best.append([model, sorted([i[-1] for i in seq2hmm[seq][model]], reverse = True)[0]]) best_model = sorted(best, ...
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christophertbrown/bioscripts
python
https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/16SfromHMM.py#L21-L31
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83b2566b3a5745437ec651cd6cafddd056846240
train
check_gaps
check for large gaps between alignment windows
ctbBio/16SfromHMM.py
def check_gaps(matches, gap_threshold = 0): """ check for large gaps between alignment windows """ gaps = [] prev = None for match in sorted(matches, key = itemgetter(0)): if prev is None: prev = match continue if match[0] - prev[1] >= gap_threshold: ...
def check_gaps(matches, gap_threshold = 0): """ check for large gaps between alignment windows """ gaps = [] prev = None for match in sorted(matches, key = itemgetter(0)): if prev is None: prev = match continue if match[0] - prev[1] >= gap_threshold: ...
[ "check", "for", "large", "gaps", "between", "alignment", "windows" ]
christophertbrown/bioscripts
python
https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/16SfromHMM.py#L33-L46
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83b2566b3a5745437ec651cd6cafddd056846240
train
check_overlap
determine if sequence has already hit the same part of the model, indicating that this hit is for another 16S rRNA gene
ctbBio/16SfromHMM.py
def check_overlap(current, hit, overlap = 200): """ determine if sequence has already hit the same part of the model, indicating that this hit is for another 16S rRNA gene """ for prev in current: p_coords = prev[2:4] coords = hit[2:4] if get_overlap(coords, p_coords) >= over...
def check_overlap(current, hit, overlap = 200): """ determine if sequence has already hit the same part of the model, indicating that this hit is for another 16S rRNA gene """ for prev in current: p_coords = prev[2:4] coords = hit[2:4] if get_overlap(coords, p_coords) >= over...
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christophertbrown/bioscripts
python
https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/16SfromHMM.py#L51-L61
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83b2566b3a5745437ec651cd6cafddd056846240
train
check_order
determine if hits are sequential on model and on the same strand * if not, they should be split into different groups
ctbBio/16SfromHMM.py
def check_order(current, hit, overlap = 200): """ determine if hits are sequential on model and on the same strand * if not, they should be split into different groups """ prev_model = current[-1][2:4] prev_strand = current[-1][-2] hit_model = hit[2:4] hit_strand = hit[-2] # ...
def check_order(current, hit, overlap = 200): """ determine if hits are sequential on model and on the same strand * if not, they should be split into different groups """ prev_model = current[-1][2:4] prev_strand = current[-1][-2] hit_model = hit[2:4] hit_strand = hit[-2] # ...
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christophertbrown/bioscripts
python
https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/16SfromHMM.py#L63-L83
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83b2566b3a5745437ec651cd6cafddd056846240
train
hit_groups
* each sequence may have more than one 16S rRNA gene * group hits for each gene
ctbBio/16SfromHMM.py
def hit_groups(hits): """ * each sequence may have more than one 16S rRNA gene * group hits for each gene """ groups = [] current = False for hit in sorted(hits, key = itemgetter(0)): if current is False: current = [hit] elif check_overlap(current, hit) is True or...
def hit_groups(hits): """ * each sequence may have more than one 16S rRNA gene * group hits for each gene """ groups = [] current = False for hit in sorted(hits, key = itemgetter(0)): if current is False: current = [hit] elif check_overlap(current, hit) is True or...
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christophertbrown/bioscripts
python
https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/16SfromHMM.py#L85-L101
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83b2566b3a5745437ec651cd6cafddd056846240
train
find_coordinates
find 16S rRNA gene sequence coordinates
ctbBio/16SfromHMM.py
def find_coordinates(hmms, bit_thresh): """ find 16S rRNA gene sequence coordinates """ # get coordinates from cmsearch output seq2hmm = parse_hmm(hmms, bit_thresh) seq2hmm = best_model(seq2hmm) group2hmm = {} # group2hmm[seq][group] = [model, strand, coordinates, matches, gaps] for seq,...
def find_coordinates(hmms, bit_thresh): """ find 16S rRNA gene sequence coordinates """ # get coordinates from cmsearch output seq2hmm = parse_hmm(hmms, bit_thresh) seq2hmm = best_model(seq2hmm) group2hmm = {} # group2hmm[seq][group] = [model, strand, coordinates, matches, gaps] for seq,...
[ "find", "16S", "rRNA", "gene", "sequence", "coordinates" ]
christophertbrown/bioscripts
python
https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/16SfromHMM.py#L103-L126
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83b2566b3a5745437ec651cd6cafddd056846240
train
get_info
get info from either ssu-cmsearch or cmsearch output
ctbBio/16SfromHMM.py
def get_info(line, bit_thresh): """ get info from either ssu-cmsearch or cmsearch output """ if len(line) >= 18: # output is from cmsearch id, model, bit, inc = line[0].split()[0], line[2], float(line[14]), line[16] sstart, send, strand = int(line[7]), int(line[8]), line[9] mstar...
def get_info(line, bit_thresh): """ get info from either ssu-cmsearch or cmsearch output """ if len(line) >= 18: # output is from cmsearch id, model, bit, inc = line[0].split()[0], line[2], float(line[14]), line[16] sstart, send, strand = int(line[7]), int(line[8]), line[9] mstar...
[ "get", "info", "from", "either", "ssu", "-", "cmsearch", "or", "cmsearch", "output" ]
christophertbrown/bioscripts
python
https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/16SfromHMM.py#L128-L157
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83b2566b3a5745437ec651cd6cafddd056846240
train
check_buffer
check to see how much of the buffer is being used
ctbBio/16SfromHMM.py
def check_buffer(coords, length, buffer): """ check to see how much of the buffer is being used """ s = min(coords[0], buffer) e = min(length - coords[1], buffer) return [s, e]
def check_buffer(coords, length, buffer): """ check to see how much of the buffer is being used """ s = min(coords[0], buffer) e = min(length - coords[1], buffer) return [s, e]
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christophertbrown/bioscripts
python
https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/16SfromHMM.py#L189-L195
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83b2566b3a5745437ec651cd6cafddd056846240
train
convert_parser_to
:return: a parser of type parser_or_type, initialized with the properties of parser. If parser_or_type is a type, an instance of it must contain a update method. The update method must also process the set of properties supported by MetadataParser for the conversion to have any affect. :param parser: the pa...
gis_metadata/metadata_parser.py
def convert_parser_to(parser, parser_or_type, metadata_props=None): """ :return: a parser of type parser_or_type, initialized with the properties of parser. If parser_or_type is a type, an instance of it must contain a update method. The update method must also process the set of properties supported by...
def convert_parser_to(parser, parser_or_type, metadata_props=None): """ :return: a parser of type parser_or_type, initialized with the properties of parser. If parser_or_type is a type, an instance of it must contain a update method. The update method must also process the set of properties supported by...
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consbio/gis-metadata-parser
python
https://github.com/consbio/gis-metadata-parser/blob/59eefb2e51cd4d8cc3e94623a2167499ca9ef70f/gis_metadata/metadata_parser.py#L30-L48
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59eefb2e51cd4d8cc3e94623a2167499ca9ef70f
train
get_metadata_parser
Takes a metadata_container, which may be a type or instance of a parser, a dict, string, or file. :return: a new instance of a parser corresponding to the standard represented by metadata_container :see: get_parsed_content(metdata_content) for more on types of content that can be parsed
gis_metadata/metadata_parser.py
def get_metadata_parser(metadata_container, **metadata_defaults): """ Takes a metadata_container, which may be a type or instance of a parser, a dict, string, or file. :return: a new instance of a parser corresponding to the standard represented by metadata_container :see: get_parsed_content(metdata_con...
def get_metadata_parser(metadata_container, **metadata_defaults): """ Takes a metadata_container, which may be a type or instance of a parser, a dict, string, or file. :return: a new instance of a parser corresponding to the standard represented by metadata_container :see: get_parsed_content(metdata_con...
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consbio/gis-metadata-parser
python
https://github.com/consbio/gis-metadata-parser/blob/59eefb2e51cd4d8cc3e94623a2167499ca9ef70f/gis_metadata/metadata_parser.py#L51-L85
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59eefb2e51cd4d8cc3e94623a2167499ca9ef70f
train
get_parsed_content
Parses any of the following types of content: 1. XML string or file object: parses XML content 2. MetadataParser instance: deep copies xml_tree 3. Dictionary with nested objects containing: - name (required): the name of the element tag - text: the text contained by element - tail: t...
gis_metadata/metadata_parser.py
def get_parsed_content(metadata_content): """ Parses any of the following types of content: 1. XML string or file object: parses XML content 2. MetadataParser instance: deep copies xml_tree 3. Dictionary with nested objects containing: - name (required): the name of the element tag -...
def get_parsed_content(metadata_content): """ Parses any of the following types of content: 1. XML string or file object: parses XML content 2. MetadataParser instance: deep copies xml_tree 3. Dictionary with nested objects containing: - name (required): the name of the element tag -...
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consbio/gis-metadata-parser
python
https://github.com/consbio/gis-metadata-parser/blob/59eefb2e51cd4d8cc3e94623a2167499ca9ef70f/gis_metadata/metadata_parser.py#L88-L138
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59eefb2e51cd4d8cc3e94623a2167499ca9ef70f
train
_import_parsers
Lazy imports to prevent circular dependencies between this module and utils
gis_metadata/metadata_parser.py
def _import_parsers(): """ Lazy imports to prevent circular dependencies between this module and utils """ global ARCGIS_NODES global ARCGIS_ROOTS global ArcGISParser global FGDC_ROOT global FgdcParser global ISO_ROOTS global IsoParser global VALID_ROOTS if ARCGIS_NODES is N...
def _import_parsers(): """ Lazy imports to prevent circular dependencies between this module and utils """ global ARCGIS_NODES global ARCGIS_ROOTS global ArcGISParser global FGDC_ROOT global FgdcParser global ISO_ROOTS global IsoParser global VALID_ROOTS if ARCGIS_NODES is N...
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consbio/gis-metadata-parser
python
https://github.com/consbio/gis-metadata-parser/blob/59eefb2e51cd4d8cc3e94623a2167499ca9ef70f/gis_metadata/metadata_parser.py#L141-L170
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59eefb2e51cd4d8cc3e94623a2167499ca9ef70f
train
MetadataParser._init_metadata
Dynamically sets attributes from a Dictionary passed in by children. The Dictionary will contain the name of each attribute as keys, and either an XPATH mapping to a text value in _xml_tree, or a function that takes no parameters and returns the intended value.
gis_metadata/metadata_parser.py
def _init_metadata(self): """ Dynamically sets attributes from a Dictionary passed in by children. The Dictionary will contain the name of each attribute as keys, and either an XPATH mapping to a text value in _xml_tree, or a function that takes no parameters and returns the inte...
def _init_metadata(self): """ Dynamically sets attributes from a Dictionary passed in by children. The Dictionary will contain the name of each attribute as keys, and either an XPATH mapping to a text value in _xml_tree, or a function that takes no parameters and returns the inte...
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consbio/gis-metadata-parser
python
https://github.com/consbio/gis-metadata-parser/blob/59eefb2e51cd4d8cc3e94623a2167499ca9ef70f/gis_metadata/metadata_parser.py#L236-L254
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59eefb2e51cd4d8cc3e94623a2167499ca9ef70f
train
MetadataParser._init_data_map
Default data map initialization: MUST be overridden in children
gis_metadata/metadata_parser.py
def _init_data_map(self): """ Default data map initialization: MUST be overridden in children """ if self._data_map is None: self._data_map = {'_root': None} self._data_map.update({}.fromkeys(self._metadata_props))
def _init_data_map(self): """ Default data map initialization: MUST be overridden in children """ if self._data_map is None: self._data_map = {'_root': None} self._data_map.update({}.fromkeys(self._metadata_props))
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consbio/gis-metadata-parser
python
https://github.com/consbio/gis-metadata-parser/blob/59eefb2e51cd4d8cc3e94623a2167499ca9ef70f/gis_metadata/metadata_parser.py#L256-L261
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59eefb2e51cd4d8cc3e94623a2167499ca9ef70f
train
MetadataParser._get_template
Iterate over items metadata_defaults {prop: val, ...} to populate template
gis_metadata/metadata_parser.py
def _get_template(self, root=None, **metadata_defaults): """ Iterate over items metadata_defaults {prop: val, ...} to populate template """ if root is None: if self._data_map is None: self._init_data_map() root = self._xml_root = self._data_map['_root'] ...
def _get_template(self, root=None, **metadata_defaults): """ Iterate over items metadata_defaults {prop: val, ...} to populate template """ if root is None: if self._data_map is None: self._init_data_map() root = self._xml_root = self._data_map['_root'] ...
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consbio/gis-metadata-parser
python
https://github.com/consbio/gis-metadata-parser/blob/59eefb2e51cd4d8cc3e94623a2167499ca9ef70f/gis_metadata/metadata_parser.py#L263-L280
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59eefb2e51cd4d8cc3e94623a2167499ca9ef70f
train
MetadataParser._get_xpath_for
:return: the configured xpath for a given property
gis_metadata/metadata_parser.py
def _get_xpath_for(self, prop): """ :return: the configured xpath for a given property """ xpath = self._data_map.get(prop) return getattr(xpath, 'xpath', xpath)
def _get_xpath_for(self, prop): """ :return: the configured xpath for a given property """ xpath = self._data_map.get(prop) return getattr(xpath, 'xpath', xpath)
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consbio/gis-metadata-parser
python
https://github.com/consbio/gis-metadata-parser/blob/59eefb2e51cd4d8cc3e94623a2167499ca9ef70f/gis_metadata/metadata_parser.py#L282-L286
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59eefb2e51cd4d8cc3e94623a2167499ca9ef70f
train
MetadataParser._parse_complex
Default parsing operation for a complex struct
gis_metadata/metadata_parser.py
def _parse_complex(self, prop): """ Default parsing operation for a complex struct """ xpath_root = None xpath_map = self._data_structures[prop] return parse_complex(self._xml_tree, xpath_root, xpath_map, prop)
def _parse_complex(self, prop): """ Default parsing operation for a complex struct """ xpath_root = None xpath_map = self._data_structures[prop] return parse_complex(self._xml_tree, xpath_root, xpath_map, prop)
[ "Default", "parsing", "operation", "for", "a", "complex", "struct" ]
consbio/gis-metadata-parser
python
https://github.com/consbio/gis-metadata-parser/blob/59eefb2e51cd4d8cc3e94623a2167499ca9ef70f/gis_metadata/metadata_parser.py#L293-L299
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59eefb2e51cd4d8cc3e94623a2167499ca9ef70f
train
MetadataParser._parse_complex_list
Default parsing operation for lists of complex structs
gis_metadata/metadata_parser.py
def _parse_complex_list(self, prop): """ Default parsing operation for lists of complex structs """ xpath_root = self._get_xroot_for(prop) xpath_map = self._data_structures[prop] return parse_complex_list(self._xml_tree, xpath_root, xpath_map, prop)
def _parse_complex_list(self, prop): """ Default parsing operation for lists of complex structs """ xpath_root = self._get_xroot_for(prop) xpath_map = self._data_structures[prop] return parse_complex_list(self._xml_tree, xpath_root, xpath_map, prop)
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consbio/gis-metadata-parser
python
https://github.com/consbio/gis-metadata-parser/blob/59eefb2e51cd4d8cc3e94623a2167499ca9ef70f/gis_metadata/metadata_parser.py#L301-L307
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59eefb2e51cd4d8cc3e94623a2167499ca9ef70f
train
MetadataParser._parse_dates
Creates and returns a Date Types data structure parsed from the metadata
gis_metadata/metadata_parser.py
def _parse_dates(self, prop=DATES): """ Creates and returns a Date Types data structure parsed from the metadata """ return parse_dates(self._xml_tree, self._data_structures[prop])
def _parse_dates(self, prop=DATES): """ Creates and returns a Date Types data structure parsed from the metadata """ return parse_dates(self._xml_tree, self._data_structures[prop])
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consbio/gis-metadata-parser
python
https://github.com/consbio/gis-metadata-parser/blob/59eefb2e51cd4d8cc3e94623a2167499ca9ef70f/gis_metadata/metadata_parser.py#L309-L312
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59eefb2e51cd4d8cc3e94623a2167499ca9ef70f
train
MetadataParser._update_complex
Default update operation for a complex struct
gis_metadata/metadata_parser.py
def _update_complex(self, **update_props): """ Default update operation for a complex struct """ prop = update_props['prop'] xpath_root = self._get_xroot_for(prop) xpath_map = self._data_structures[prop] return update_complex(xpath_root=xpath_root, xpath_map=xpath_map, **update...
def _update_complex(self, **update_props): """ Default update operation for a complex struct """ prop = update_props['prop'] xpath_root = self._get_xroot_for(prop) xpath_map = self._data_structures[prop] return update_complex(xpath_root=xpath_root, xpath_map=xpath_map, **update...
[ "Default", "update", "operation", "for", "a", "complex", "struct" ]
consbio/gis-metadata-parser
python
https://github.com/consbio/gis-metadata-parser/blob/59eefb2e51cd4d8cc3e94623a2167499ca9ef70f/gis_metadata/metadata_parser.py#L314-L321
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59eefb2e51cd4d8cc3e94623a2167499ca9ef70f
train
MetadataParser._update_complex_list
Default update operation for lists of complex structs
gis_metadata/metadata_parser.py
def _update_complex_list(self, **update_props): """ Default update operation for lists of complex structs """ prop = update_props['prop'] xpath_root = self._get_xroot_for(prop) xpath_map = self._data_structures[prop] return update_complex_list(xpath_root=xpath_root, xpath_map=x...
def _update_complex_list(self, **update_props): """ Default update operation for lists of complex structs """ prop = update_props['prop'] xpath_root = self._get_xroot_for(prop) xpath_map = self._data_structures[prop] return update_complex_list(xpath_root=xpath_root, xpath_map=x...
[ "Default", "update", "operation", "for", "lists", "of", "complex", "structs" ]
consbio/gis-metadata-parser
python
https://github.com/consbio/gis-metadata-parser/blob/59eefb2e51cd4d8cc3e94623a2167499ca9ef70f/gis_metadata/metadata_parser.py#L323-L330
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59eefb2e51cd4d8cc3e94623a2167499ca9ef70f
train
MetadataParser._update_dates
Default update operation for Dates metadata :see: gis_metadata.utils._complex_definitions[DATES]
gis_metadata/metadata_parser.py
def _update_dates(self, xpath_root=None, **update_props): """ Default update operation for Dates metadata :see: gis_metadata.utils._complex_definitions[DATES] """ tree_to_update = update_props['tree_to_update'] prop = update_props['prop'] values = (update_props['...
def _update_dates(self, xpath_root=None, **update_props): """ Default update operation for Dates metadata :see: gis_metadata.utils._complex_definitions[DATES] """ tree_to_update = update_props['tree_to_update'] prop = update_props['prop'] values = (update_props['...
[ "Default", "update", "operation", "for", "Dates", "metadata", ":", "see", ":", "gis_metadata", ".", "utils", ".", "_complex_definitions", "[", "DATES", "]" ]
consbio/gis-metadata-parser
python
https://github.com/consbio/gis-metadata-parser/blob/59eefb2e51cd4d8cc3e94623a2167499ca9ef70f/gis_metadata/metadata_parser.py#L332-L356
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59eefb2e51cd4d8cc3e94623a2167499ca9ef70f
train
MetadataParser.write
Validates instance properties, updates an XML tree with them, and writes the content to a file. :param use_template: if True, updates a new template XML tree; otherwise the original XML tree :param out_file_or_path: optionally override self.out_file_or_path with a custom file path :param encodin...
gis_metadata/metadata_parser.py
def write(self, use_template=False, out_file_or_path=None, encoding=DEFAULT_ENCODING): """ Validates instance properties, updates an XML tree with them, and writes the content to a file. :param use_template: if True, updates a new template XML tree; otherwise the original XML tree :param...
def write(self, use_template=False, out_file_or_path=None, encoding=DEFAULT_ENCODING): """ Validates instance properties, updates an XML tree with them, and writes the content to a file. :param use_template: if True, updates a new template XML tree; otherwise the original XML tree :param...
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consbio/gis-metadata-parser
python
https://github.com/consbio/gis-metadata-parser/blob/59eefb2e51cd4d8cc3e94623a2167499ca9ef70f/gis_metadata/metadata_parser.py#L373-L388
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59eefb2e51cd4d8cc3e94623a2167499ca9ef70f
train
MetadataParser.validate
Default validation for updated properties: MAY be overridden in children
gis_metadata/metadata_parser.py
def validate(self): """ Default validation for updated properties: MAY be overridden in children """ validate_properties(self._data_map, self._metadata_props) for prop in self._data_map: validate_any(prop, getattr(self, prop), self._data_structures.get(prop)) return self
def validate(self): """ Default validation for updated properties: MAY be overridden in children """ validate_properties(self._data_map, self._metadata_props) for prop in self._data_map: validate_any(prop, getattr(self, prop), self._data_structures.get(prop)) return self
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consbio/gis-metadata-parser
python
https://github.com/consbio/gis-metadata-parser/blob/59eefb2e51cd4d8cc3e94623a2167499ca9ef70f/gis_metadata/metadata_parser.py#L410-L418
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59eefb2e51cd4d8cc3e94623a2167499ca9ef70f
train
_search_regex
Search order: * specified regexps * operators sorted from longer to shorter
sugartex/sugartex_filter.py
def _search_regex(ops: dict, regex_pat: str): """ Search order: * specified regexps * operators sorted from longer to shorter """ custom_regexps = list(filter(None, [dic['regex'] for op, dic in ops.items() if 'regex' in dic])) op_names = [op for op, dic in ops.items() if 'regex' not in d...
def _search_regex(ops: dict, regex_pat: str): """ Search order: * specified regexps * operators sorted from longer to shorter """ custom_regexps = list(filter(None, [dic['regex'] for op, dic in ops.items() if 'regex' in dic])) op_names = [op for op, dic in ops.items() if 'regex' not in d...
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kiwi0fruit/sugartex
python
https://github.com/kiwi0fruit/sugartex/blob/9eb13703cb02d3e2163c9c5f29df280f6bf49cec/sugartex/sugartex_filter.py#L165-L174
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9eb13703cb02d3e2163c9c5f29df280f6bf49cec
train
Styles.spec
Return prefix unary operators list
sugartex/sugartex_filter.py
def spec(self, postf_un_ops: str) -> list: """Return prefix unary operators list""" spec = [(l + op, {'pat': self.pat(pat), 'postf': self.postf(r, postf_un_ops), 'regex': None}) for op, pat in self.styles.items() for l, ...
def spec(self, postf_un_ops: str) -> list: """Return prefix unary operators list""" spec = [(l + op, {'pat': self.pat(pat), 'postf': self.postf(r, postf_un_ops), 'regex': None}) for op, pat in self.styles.items() for l, ...
[ "Return", "prefix", "unary", "operators", "list" ]
kiwi0fruit/sugartex
python
https://github.com/kiwi0fruit/sugartex/blob/9eb13703cb02d3e2163c9c5f29df280f6bf49cec/sugartex/sugartex_filter.py#L216-L227
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9eb13703cb02d3e2163c9c5f29df280f6bf49cec
train
PrefUnGreedy.spec
Returns prefix unary operators list. Sets only one regex for all items in the dict.
sugartex/sugartex_filter.py
def spec(self) -> list: """Returns prefix unary operators list. Sets only one regex for all items in the dict.""" spec = [item for op, pat in self.ops.items() for item in [('{' + op, {'pat': pat, 'postf': self.postf, 'regex': None}), (...
def spec(self) -> list: """Returns prefix unary operators list. Sets only one regex for all items in the dict.""" spec = [item for op, pat in self.ops.items() for item in [('{' + op, {'pat': pat, 'postf': self.postf, 'regex': None}), (...
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kiwi0fruit/sugartex
python
https://github.com/kiwi0fruit/sugartex/blob/9eb13703cb02d3e2163c9c5f29df280f6bf49cec/sugartex/sugartex_filter.py#L242-L251
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9eb13703cb02d3e2163c9c5f29df280f6bf49cec
train
PrefUnOps.fill
Insert: * math styles * other styles * unary prefix operators without brackets * defaults
sugartex/sugartex_filter.py
def fill(self, postf_un_ops: str): """ Insert: * math styles * other styles * unary prefix operators without brackets * defaults """ for op, dic in self.ops.items(): if 'postf' not in dic: dic['postf'] = self.postf ...
def fill(self, postf_un_ops: str): """ Insert: * math styles * other styles * unary prefix operators without brackets * defaults """ for op, dic in self.ops.items(): if 'postf' not in dic: dic['postf'] = self.postf ...
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kiwi0fruit/sugartex
python
https://github.com/kiwi0fruit/sugartex/blob/9eb13703cb02d3e2163c9c5f29df280f6bf49cec/sugartex/sugartex_filter.py#L325-L344
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9eb13703cb02d3e2163c9c5f29df280f6bf49cec
train
PostfUnOps.one_symbol_ops_str
Regex-escaped string with all one-symbol operators
sugartex/sugartex_filter.py
def one_symbol_ops_str(self) -> str: """Regex-escaped string with all one-symbol operators""" return re.escape(''.join((key for key in self.ops.keys() if len(key) == 1)))
def one_symbol_ops_str(self) -> str: """Regex-escaped string with all one-symbol operators""" return re.escape(''.join((key for key in self.ops.keys() if len(key) == 1)))
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kiwi0fruit/sugartex
python
https://github.com/kiwi0fruit/sugartex/blob/9eb13703cb02d3e2163c9c5f29df280f6bf49cec/sugartex/sugartex_filter.py#L389-L391
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9eb13703cb02d3e2163c9c5f29df280f6bf49cec
train
SugarTeX._su_scripts_regex
:return: [compiled regex, function]
sugartex/sugartex_filter.py
def _su_scripts_regex(self): """ :return: [compiled regex, function] """ sups = re.escape(''.join([k for k in self.superscripts.keys()])) subs = re.escape(''.join([k for k in self.subscripts.keys()])) # language=PythonRegExp su_regex = (r'\\([{su_}])|([{sub}]...
def _su_scripts_regex(self): """ :return: [compiled regex, function] """ sups = re.escape(''.join([k for k in self.superscripts.keys()])) subs = re.escape(''.join([k for k in self.subscripts.keys()])) # language=PythonRegExp su_regex = (r'\\([{su_}])|([{sub}]...
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kiwi0fruit/sugartex
python
https://github.com/kiwi0fruit/sugartex/blob/9eb13703cb02d3e2163c9c5f29df280f6bf49cec/sugartex/sugartex_filter.py#L671-L696
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9eb13703cb02d3e2163c9c5f29df280f6bf49cec
train
SugarTeX._local_map
:param match: :param loc: str "l" or "r" or "lr" turns on/off left/right local area calculation :return: list list of the same size as the string + 2 it's the local map that counted { and } list can contain: None or int>=0 from the ...
sugartex/sugartex_filter.py
def _local_map(match, loc: str = 'lr') -> list: """ :param match: :param loc: str "l" or "r" or "lr" turns on/off left/right local area calculation :return: list list of the same size as the string + 2 it's the local map that counted { and ...
def _local_map(match, loc: str = 'lr') -> list: """ :param match: :param loc: str "l" or "r" or "lr" turns on/off left/right local area calculation :return: list list of the same size as the string + 2 it's the local map that counted { and ...
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kiwi0fruit/sugartex
python
https://github.com/kiwi0fruit/sugartex/blob/9eb13703cb02d3e2163c9c5f29df280f6bf49cec/sugartex/sugartex_filter.py#L708-L753
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9eb13703cb02d3e2163c9c5f29df280f6bf49cec
train
SugarTeX._operators_replace
Searches for first unary or binary operator (via self.op_regex that has only one group that contain operator) then replaces it (or escapes it if brackets do not match). Everything until: * space ' ' * begin/end of the string * bracket from outer scope (like '{a/b}':...
sugartex/sugartex_filter.py
def _operators_replace(self, string: str) -> str: """ Searches for first unary or binary operator (via self.op_regex that has only one group that contain operator) then replaces it (or escapes it if brackets do not match). Everything until: * space ' ' * begin...
def _operators_replace(self, string: str) -> str: """ Searches for first unary or binary operator (via self.op_regex that has only one group that contain operator) then replaces it (or escapes it if brackets do not match). Everything until: * space ' ' * begin...
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kiwi0fruit/sugartex
python
https://github.com/kiwi0fruit/sugartex/blob/9eb13703cb02d3e2163c9c5f29df280f6bf49cec/sugartex/sugartex_filter.py#L755-L849
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9eb13703cb02d3e2163c9c5f29df280f6bf49cec
train
SugarTeX.replace
Extends LaTeX syntax via regex preprocess :param src: str LaTeX string :return: str New LaTeX string
sugartex/sugartex_filter.py
def replace(self, src: str) -> str: """ Extends LaTeX syntax via regex preprocess :param src: str LaTeX string :return: str New LaTeX string """ if not self.readied: self.ready() # Brackets + simple pre replacements: sr...
def replace(self, src: str) -> str: """ Extends LaTeX syntax via regex preprocess :param src: str LaTeX string :return: str New LaTeX string """ if not self.readied: self.ready() # Brackets + simple pre replacements: sr...
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kiwi0fruit/sugartex
python
https://github.com/kiwi0fruit/sugartex/blob/9eb13703cb02d3e2163c9c5f29df280f6bf49cec/sugartex/sugartex_filter.py#L863-L904
[ "def", "replace", "(", "self", ",", "src", ":", "str", ")", "->", "str", ":", "if", "not", "self", ".", "readied", ":", "self", ".", "ready", "(", ")", "# Brackets + simple pre replacements:", "src", "=", "self", ".", "_dict_replace", "(", "self", ".", ...
9eb13703cb02d3e2163c9c5f29df280f6bf49cec
train
plot_gaps
plot % of gaps at each position
ctbBio/strip_align.py
def plot_gaps(plot, columns): """ plot % of gaps at each position """ from plot_window import window_plot_convolve as plot_window # plot_window([columns], len(columns)*.01, plot) plot_window([[100 - i for i in columns]], len(columns)*.01, plot)
def plot_gaps(plot, columns): """ plot % of gaps at each position """ from plot_window import window_plot_convolve as plot_window # plot_window([columns], len(columns)*.01, plot) plot_window([[100 - i for i in columns]], len(columns)*.01, plot)
[ "plot", "%", "of", "gaps", "at", "each", "position" ]
christophertbrown/bioscripts
python
https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/strip_align.py#L11-L17
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83b2566b3a5745437ec651cd6cafddd056846240
train
strip_msa_100
strip out columns of a MSA that represent gaps for X percent (threshold) of sequences
ctbBio/strip_align.py
def strip_msa_100(msa, threshold, plot = False): """ strip out columns of a MSA that represent gaps for X percent (threshold) of sequences """ msa = [seq for seq in parse_fasta(msa)] columns = [[0, 0] for pos in msa[0][1]] # [[#bases, #gaps], [#bases, #gaps], ...] for seq in msa: for position, base in enumerate...
def strip_msa_100(msa, threshold, plot = False): """ strip out columns of a MSA that represent gaps for X percent (threshold) of sequences """ msa = [seq for seq in parse_fasta(msa)] columns = [[0, 0] for pos in msa[0][1]] # [[#bases, #gaps], [#bases, #gaps], ...] for seq in msa: for position, base in enumerate...
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christophertbrown/bioscripts
python
https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/strip_align.py#L19-L39
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83b2566b3a5745437ec651cd6cafddd056846240
train
sample_group
Iterate through all categories in an OrderedDict and return category name if SampleID present in that category. :type sid: str :param sid: SampleID from dataset. :type groups: OrderedDict :param groups: Returned dict from phylotoast.util.gather_categories() function. :return type: str :re...
bin/extract_shared_or_unique_otuids.py
def sample_group(sid, groups): """ Iterate through all categories in an OrderedDict and return category name if SampleID present in that category. :type sid: str :param sid: SampleID from dataset. :type groups: OrderedDict :param groups: Returned dict from phylotoast.util.gather_categories...
def sample_group(sid, groups): """ Iterate through all categories in an OrderedDict and return category name if SampleID present in that category. :type sid: str :param sid: SampleID from dataset. :type groups: OrderedDict :param groups: Returned dict from phylotoast.util.gather_categories...
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smdabdoub/phylotoast
python
https://github.com/smdabdoub/phylotoast/blob/0b74ef171e6a84761710548501dfac71285a58a3/bin/extract_shared_or_unique_otuids.py#L22-L38
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0b74ef171e6a84761710548501dfac71285a58a3
train
combine_sets
Combine multiple sets to create a single larger set.
bin/extract_shared_or_unique_otuids.py
def combine_sets(*sets): """ Combine multiple sets to create a single larger set. """ combined = set() for s in sets: combined.update(s) return combined
def combine_sets(*sets): """ Combine multiple sets to create a single larger set. """ combined = set() for s in sets: combined.update(s) return combined
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smdabdoub/phylotoast
python
https://github.com/smdabdoub/phylotoast/blob/0b74ef171e6a84761710548501dfac71285a58a3/bin/extract_shared_or_unique_otuids.py#L41-L48
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0b74ef171e6a84761710548501dfac71285a58a3
train
unique_otuids
Get unique OTUIDs of each category. :type groups: Dict :param groups: {Category name: OTUIDs in category} :return type: dict :return: Dict keyed on category name and unique OTUIDs as values.
bin/extract_shared_or_unique_otuids.py
def unique_otuids(groups): """ Get unique OTUIDs of each category. :type groups: Dict :param groups: {Category name: OTUIDs in category} :return type: dict :return: Dict keyed on category name and unique OTUIDs as values. """ uniques = {key: set() for key in groups} for i, group in...
def unique_otuids(groups): """ Get unique OTUIDs of each category. :type groups: Dict :param groups: {Category name: OTUIDs in category} :return type: dict :return: Dict keyed on category name and unique OTUIDs as values. """ uniques = {key: set() for key in groups} for i, group in...
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smdabdoub/phylotoast
python
https://github.com/smdabdoub/phylotoast/blob/0b74ef171e6a84761710548501dfac71285a58a3/bin/extract_shared_or_unique_otuids.py#L51-L66
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0b74ef171e6a84761710548501dfac71285a58a3
train
shared_otuids
Get shared OTUIDs between all unique combinations of groups. :type groups: Dict :param groups: {Category name: OTUIDs in category} :return type: dict :return: Dict keyed on group combination and their shared OTUIDs as values.
bin/extract_shared_or_unique_otuids.py
def shared_otuids(groups): """ Get shared OTUIDs between all unique combinations of groups. :type groups: Dict :param groups: {Category name: OTUIDs in category} :return type: dict :return: Dict keyed on group combination and their shared OTUIDs as values. """ for g in sorted(groups): ...
def shared_otuids(groups): """ Get shared OTUIDs between all unique combinations of groups. :type groups: Dict :param groups: {Category name: OTUIDs in category} :return type: dict :return: Dict keyed on group combination and their shared OTUIDs as values. """ for g in sorted(groups): ...
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smdabdoub/phylotoast
python
https://github.com/smdabdoub/phylotoast/blob/0b74ef171e6a84761710548501dfac71285a58a3/bin/extract_shared_or_unique_otuids.py#L69-L93
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0b74ef171e6a84761710548501dfac71285a58a3
train
write_uniques
Given a path, the method writes out one file for each group name in the uniques dictionary with the file name in the pattern PATH/prefix_group.txt with each file containing the unique OTUIDs found when comparing that group to all the other groups in uniques. :type path: str :param path: O...
bin/extract_shared_or_unique_otuids.py
def write_uniques(path, prefix, uniques): """ Given a path, the method writes out one file for each group name in the uniques dictionary with the file name in the pattern PATH/prefix_group.txt with each file containing the unique OTUIDs found when comparing that group to all the other grou...
def write_uniques(path, prefix, uniques): """ Given a path, the method writes out one file for each group name in the uniques dictionary with the file name in the pattern PATH/prefix_group.txt with each file containing the unique OTUIDs found when comparing that group to all the other grou...
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smdabdoub/phylotoast
python
https://github.com/smdabdoub/phylotoast/blob/0b74ef171e6a84761710548501dfac71285a58a3/bin/extract_shared_or_unique_otuids.py#L96-L118
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0b74ef171e6a84761710548501dfac71285a58a3
train
storeFASTA
Parse the records in a FASTA-format file by first reading the entire file into memory. :type source: path to FAST file or open file handle :param source: The data source from which to parse the FASTA records. Expects the input to resolve to a collection that can be iterated through, such as ...
phylotoast/util.py
def storeFASTA(fastaFNH): """ Parse the records in a FASTA-format file by first reading the entire file into memory. :type source: path to FAST file or open file handle :param source: The data source from which to parse the FASTA records. Expects the input to resolve to a collection ...
def storeFASTA(fastaFNH): """ Parse the records in a FASTA-format file by first reading the entire file into memory. :type source: path to FAST file or open file handle :param source: The data source from which to parse the FASTA records. Expects the input to resolve to a collection ...
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smdabdoub/phylotoast
python
https://github.com/smdabdoub/phylotoast/blob/0b74ef171e6a84761710548501dfac71285a58a3/phylotoast/util.py#L20-L34
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0b74ef171e6a84761710548501dfac71285a58a3
train
parseFASTA
Parse the records in a FASTA-format file keeping the file open, and reading through one line at a time. :type source: path to FAST file or open file handle :param source: The data source from which to parse the FASTA records. Expects the input to resolve to a collection that can be itera...
phylotoast/util.py
def parseFASTA(fastaFNH): """ Parse the records in a FASTA-format file keeping the file open, and reading through one line at a time. :type source: path to FAST file or open file handle :param source: The data source from which to parse the FASTA records. Expects the input to res...
def parseFASTA(fastaFNH): """ Parse the records in a FASTA-format file keeping the file open, and reading through one line at a time. :type source: path to FAST file or open file handle :param source: The data source from which to parse the FASTA records. Expects the input to res...
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smdabdoub/phylotoast
python
https://github.com/smdabdoub/phylotoast/blob/0b74ef171e6a84761710548501dfac71285a58a3/phylotoast/util.py#L37-L73
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0b74ef171e6a84761710548501dfac71285a58a3
train
parse_map_file
Opens a QIIME mapping file and stores the contents in a dictionary keyed on SampleID (default) or a user-supplied one. The only required fields are SampleID, BarcodeSequence, LinkerPrimerSequence (in that order), and Description (which must be the final field). :type mapFNH: str :param mapFNH: Eith...
phylotoast/util.py
def parse_map_file(mapFNH): """ Opens a QIIME mapping file and stores the contents in a dictionary keyed on SampleID (default) or a user-supplied one. The only required fields are SampleID, BarcodeSequence, LinkerPrimerSequence (in that order), and Description (which must be the final field). :...
def parse_map_file(mapFNH): """ Opens a QIIME mapping file and stores the contents in a dictionary keyed on SampleID (default) or a user-supplied one. The only required fields are SampleID, BarcodeSequence, LinkerPrimerSequence (in that order), and Description (which must be the final field). :...
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smdabdoub/phylotoast
python
https://github.com/smdabdoub/phylotoast/blob/0b74ef171e6a84761710548501dfac71285a58a3/phylotoast/util.py#L76-L108
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0b74ef171e6a84761710548501dfac71285a58a3
valid
learn
Train a deepq model. Parameters ------- env: gym.Env environment to train on network: string or a function neural network to use as a q function approximator. If string, has to be one of the names of registered models in baselines.common.models (mlp, cnn, conv_only). If a functi...
baselines/deepq/deepq.py
def learn(env, network, seed=None, lr=5e-4, total_timesteps=100000, buffer_size=50000, exploration_fraction=0.1, exploration_final_eps=0.02, train_freq=1, batch_size=32, print_freq=100, checkpoint_freq=10000, ...
def learn(env, network, seed=None, lr=5e-4, total_timesteps=100000, buffer_size=50000, exploration_fraction=0.1, exploration_final_eps=0.02, train_freq=1, batch_size=32, print_freq=100, checkpoint_freq=10000, ...
[ "Train", "a", "deepq", "model", "." ]
openai/baselines
python
https://github.com/openai/baselines/blob/3301089b48c42b87b396e246ea3f56fa4bfc9678/baselines/deepq/deepq.py#L95-L333
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3301089b48c42b87b396e246ea3f56fa4bfc9678
valid
ActWrapper.save_act
Save model to a pickle located at `path`
baselines/deepq/deepq.py
def save_act(self, path=None): """Save model to a pickle located at `path`""" if path is None: path = os.path.join(logger.get_dir(), "model.pkl") with tempfile.TemporaryDirectory() as td: save_variables(os.path.join(td, "model")) arc_name = os.path.join(td, "...
def save_act(self, path=None): """Save model to a pickle located at `path`""" if path is None: path = os.path.join(logger.get_dir(), "model.pkl") with tempfile.TemporaryDirectory() as td: save_variables(os.path.join(td, "model")) arc_name = os.path.join(td, "...
[ "Save", "model", "to", "a", "pickle", "located", "at", "path" ]
openai/baselines
python
https://github.com/openai/baselines/blob/3301089b48c42b87b396e246ea3f56fa4bfc9678/baselines/deepq/deepq.py#L55-L72
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3301089b48c42b87b396e246ea3f56fa4bfc9678
valid
nature_cnn
CNN from Nature paper.
baselines/common/models.py
def nature_cnn(unscaled_images, **conv_kwargs): """ CNN from Nature paper. """ scaled_images = tf.cast(unscaled_images, tf.float32) / 255. activ = tf.nn.relu h = activ(conv(scaled_images, 'c1', nf=32, rf=8, stride=4, init_scale=np.sqrt(2), **conv_kwargs)) h2 = activ(conv(h...
def nature_cnn(unscaled_images, **conv_kwargs): """ CNN from Nature paper. """ scaled_images = tf.cast(unscaled_images, tf.float32) / 255. activ = tf.nn.relu h = activ(conv(scaled_images, 'c1', nf=32, rf=8, stride=4, init_scale=np.sqrt(2), **conv_kwargs)) h2 = activ(conv(h...
[ "CNN", "from", "Nature", "paper", "." ]
openai/baselines
python
https://github.com/openai/baselines/blob/3301089b48c42b87b396e246ea3f56fa4bfc9678/baselines/common/models.py#L16-L27
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3301089b48c42b87b396e246ea3f56fa4bfc9678
valid
mlp
Stack of fully-connected layers to be used in a policy / q-function approximator Parameters: ---------- num_layers: int number of fully-connected layers (default: 2) num_hidden: int size of fully-connected layers (default: 64) activation: activ...
baselines/common/models.py
def mlp(num_layers=2, num_hidden=64, activation=tf.tanh, layer_norm=False): """ Stack of fully-connected layers to be used in a policy / q-function approximator Parameters: ---------- num_layers: int number of fully-connected layers (default: 2) num_hidden: int ...
def mlp(num_layers=2, num_hidden=64, activation=tf.tanh, layer_norm=False): """ Stack of fully-connected layers to be used in a policy / q-function approximator Parameters: ---------- num_layers: int number of fully-connected layers (default: 2) num_hidden: int ...
[ "Stack", "of", "fully", "-", "connected", "layers", "to", "be", "used", "in", "a", "policy", "/", "q", "-", "function", "approximator" ]
openai/baselines
python
https://github.com/openai/baselines/blob/3301089b48c42b87b396e246ea3f56fa4bfc9678/baselines/common/models.py#L31-L59
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3301089b48c42b87b396e246ea3f56fa4bfc9678
valid
lstm
Builds LSTM (Long-Short Term Memory) network to be used in a policy. Note that the resulting function returns not only the output of the LSTM (i.e. hidden state of lstm for each step in the sequence), but also a dictionary with auxiliary tensors to be set as policy attributes. Specifically, S i...
baselines/common/models.py
def lstm(nlstm=128, layer_norm=False): """ Builds LSTM (Long-Short Term Memory) network to be used in a policy. Note that the resulting function returns not only the output of the LSTM (i.e. hidden state of lstm for each step in the sequence), but also a dictionary with auxiliary tensors to be set a...
def lstm(nlstm=128, layer_norm=False): """ Builds LSTM (Long-Short Term Memory) network to be used in a policy. Note that the resulting function returns not only the output of the LSTM (i.e. hidden state of lstm for each step in the sequence), but also a dictionary with auxiliary tensors to be set a...
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openai/baselines
python
https://github.com/openai/baselines/blob/3301089b48c42b87b396e246ea3f56fa4bfc9678/baselines/common/models.py#L84-L135
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3301089b48c42b87b396e246ea3f56fa4bfc9678
valid
conv_only
convolutions-only net Parameters: ---------- conv: list of triples (filter_number, filter_size, stride) specifying parameters for each layer. Returns: function that takes tensorflow tensor as input and returns the output of the last convolutional layer
baselines/common/models.py
def conv_only(convs=[(32, 8, 4), (64, 4, 2), (64, 3, 1)], **conv_kwargs): ''' convolutions-only net Parameters: ---------- conv: list of triples (filter_number, filter_size, stride) specifying parameters for each layer. Returns: function that takes tensorflow tensor as input and re...
def conv_only(convs=[(32, 8, 4), (64, 4, 2), (64, 3, 1)], **conv_kwargs): ''' convolutions-only net Parameters: ---------- conv: list of triples (filter_number, filter_size, stride) specifying parameters for each layer. Returns: function that takes tensorflow tensor as input and re...
[ "convolutions", "-", "only", "net" ]
openai/baselines
python
https://github.com/openai/baselines/blob/3301089b48c42b87b396e246ea3f56fa4bfc9678/baselines/common/models.py#L171-L198
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3301089b48c42b87b396e246ea3f56fa4bfc9678
valid
get_network_builder
If you want to register your own network outside models.py, you just need: Usage Example: ------------- from baselines.common.models import register @register("your_network_name") def your_network_define(**net_kwargs): ... return network_fn
baselines/common/models.py
def get_network_builder(name): """ If you want to register your own network outside models.py, you just need: Usage Example: ------------- from baselines.common.models import register @register("your_network_name") def your_network_define(**net_kwargs): ... return network_fn...
def get_network_builder(name): """ If you want to register your own network outside models.py, you just need: Usage Example: ------------- from baselines.common.models import register @register("your_network_name") def your_network_define(**net_kwargs): ... return network_fn...
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openai/baselines
python
https://github.com/openai/baselines/blob/3301089b48c42b87b396e246ea3f56fa4bfc9678/baselines/common/models.py#L206-L224
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3301089b48c42b87b396e246ea3f56fa4bfc9678
valid
mlp
This model takes as input an observation and returns values of all actions. Parameters ---------- hiddens: [int] list of sizes of hidden layers layer_norm: bool if true applies layer normalization for every layer as described in https://arxiv.org/abs/1607.06450 Returns ...
baselines/deepq/models.py
def mlp(hiddens=[], layer_norm=False): """This model takes as input an observation and returns values of all actions. Parameters ---------- hiddens: [int] list of sizes of hidden layers layer_norm: bool if true applies layer normalization for every layer as described in http...
def mlp(hiddens=[], layer_norm=False): """This model takes as input an observation and returns values of all actions. Parameters ---------- hiddens: [int] list of sizes of hidden layers layer_norm: bool if true applies layer normalization for every layer as described in http...
[ "This", "model", "takes", "as", "input", "an", "observation", "and", "returns", "values", "of", "all", "actions", "." ]
openai/baselines
python
https://github.com/openai/baselines/blob/3301089b48c42b87b396e246ea3f56fa4bfc9678/baselines/deepq/models.py#L17-L33
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3301089b48c42b87b396e246ea3f56fa4bfc9678
valid
cnn_to_mlp
This model takes as input an observation and returns values of all actions. Parameters ---------- convs: [(int, int, int)] list of convolutional layers in form of (num_outputs, kernel_size, stride) hiddens: [int] list of sizes of hidden layers dueling: bool if true d...
baselines/deepq/models.py
def cnn_to_mlp(convs, hiddens, dueling=False, layer_norm=False): """This model takes as input an observation and returns values of all actions. Parameters ---------- convs: [(int, int, int)] list of convolutional layers in form of (num_outputs, kernel_size, stride) hiddens: [int] ...
def cnn_to_mlp(convs, hiddens, dueling=False, layer_norm=False): """This model takes as input an observation and returns values of all actions. Parameters ---------- convs: [(int, int, int)] list of convolutional layers in form of (num_outputs, kernel_size, stride) hiddens: [int] ...
[ "This", "model", "takes", "as", "input", "an", "observation", "and", "returns", "values", "of", "all", "actions", "." ]
openai/baselines
python
https://github.com/openai/baselines/blob/3301089b48c42b87b396e246ea3f56fa4bfc9678/baselines/deepq/models.py#L73-L96
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3301089b48c42b87b396e246ea3f56fa4bfc9678
valid
make_vec_env
Create a wrapped, monitored SubprocVecEnv for Atari and MuJoCo.
baselines/common/cmd_util.py
def make_vec_env(env_id, env_type, num_env, seed, wrapper_kwargs=None, start_index=0, reward_scale=1.0, flatten_dict_observations=True, gamestate=None): """ Create a wrapped, monitored SubprocVecEnv for Atari and MuJoCo. ""...
def make_vec_env(env_id, env_type, num_env, seed, wrapper_kwargs=None, start_index=0, reward_scale=1.0, flatten_dict_observations=True, gamestate=None): """ Create a wrapped, monitored SubprocVecEnv for Atari and MuJoCo. ""...
[ "Create", "a", "wrapped", "monitored", "SubprocVecEnv", "for", "Atari", "and", "MuJoCo", "." ]
openai/baselines
python
https://github.com/openai/baselines/blob/3301089b48c42b87b396e246ea3f56fa4bfc9678/baselines/common/cmd_util.py#L21-L52
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3301089b48c42b87b396e246ea3f56fa4bfc9678
valid
make_mujoco_env
Create a wrapped, monitored gym.Env for MuJoCo.
baselines/common/cmd_util.py
def make_mujoco_env(env_id, seed, reward_scale=1.0): """ Create a wrapped, monitored gym.Env for MuJoCo. """ rank = MPI.COMM_WORLD.Get_rank() myseed = seed + 1000 * rank if seed is not None else None set_global_seeds(myseed) env = gym.make(env_id) logger_path = None if logger.get_dir() ...
def make_mujoco_env(env_id, seed, reward_scale=1.0): """ Create a wrapped, monitored gym.Env for MuJoCo. """ rank = MPI.COMM_WORLD.Get_rank() myseed = seed + 1000 * rank if seed is not None else None set_global_seeds(myseed) env = gym.make(env_id) logger_path = None if logger.get_dir() ...
[ "Create", "a", "wrapped", "monitored", "gym", ".", "Env", "for", "MuJoCo", "." ]
openai/baselines
python
https://github.com/openai/baselines/blob/3301089b48c42b87b396e246ea3f56fa4bfc9678/baselines/common/cmd_util.py#L88-L102
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3301089b48c42b87b396e246ea3f56fa4bfc9678
valid
make_robotics_env
Create a wrapped, monitored gym.Env for MuJoCo.
baselines/common/cmd_util.py
def make_robotics_env(env_id, seed, rank=0): """ Create a wrapped, monitored gym.Env for MuJoCo. """ set_global_seeds(seed) env = gym.make(env_id) env = FlattenDictWrapper(env, ['observation', 'desired_goal']) env = Monitor( env, logger.get_dir() and os.path.join(logger.get_dir(), st...
def make_robotics_env(env_id, seed, rank=0): """ Create a wrapped, monitored gym.Env for MuJoCo. """ set_global_seeds(seed) env = gym.make(env_id) env = FlattenDictWrapper(env, ['observation', 'desired_goal']) env = Monitor( env, logger.get_dir() and os.path.join(logger.get_dir(), st...
[ "Create", "a", "wrapped", "monitored", "gym", ".", "Env", "for", "MuJoCo", "." ]
openai/baselines
python
https://github.com/openai/baselines/blob/3301089b48c42b87b396e246ea3f56fa4bfc9678/baselines/common/cmd_util.py#L104-L115
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3301089b48c42b87b396e246ea3f56fa4bfc9678
valid
common_arg_parser
Create an argparse.ArgumentParser for run_mujoco.py.
baselines/common/cmd_util.py
def common_arg_parser(): """ Create an argparse.ArgumentParser for run_mujoco.py. """ parser = arg_parser() parser.add_argument('--env', help='environment ID', type=str, default='Reacher-v2') parser.add_argument('--env_type', help='type of environment, used when the environment type cannot be au...
def common_arg_parser(): """ Create an argparse.ArgumentParser for run_mujoco.py. """ parser = arg_parser() parser.add_argument('--env', help='environment ID', type=str, default='Reacher-v2') parser.add_argument('--env_type', help='type of environment, used when the environment type cannot be au...
[ "Create", "an", "argparse", ".", "ArgumentParser", "for", "run_mujoco", ".", "py", "." ]
openai/baselines
python
https://github.com/openai/baselines/blob/3301089b48c42b87b396e246ea3f56fa4bfc9678/baselines/common/cmd_util.py#L135-L153
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3301089b48c42b87b396e246ea3f56fa4bfc9678
valid
robotics_arg_parser
Create an argparse.ArgumentParser for run_mujoco.py.
baselines/common/cmd_util.py
def robotics_arg_parser(): """ Create an argparse.ArgumentParser for run_mujoco.py. """ parser = arg_parser() parser.add_argument('--env', help='environment ID', type=str, default='FetchReach-v0') parser.add_argument('--seed', help='RNG seed', type=int, default=None) parser.add_argument('--n...
def robotics_arg_parser(): """ Create an argparse.ArgumentParser for run_mujoco.py. """ parser = arg_parser() parser.add_argument('--env', help='environment ID', type=str, default='FetchReach-v0') parser.add_argument('--seed', help='RNG seed', type=int, default=None) parser.add_argument('--n...
[ "Create", "an", "argparse", ".", "ArgumentParser", "for", "run_mujoco", ".", "py", "." ]
openai/baselines
python
https://github.com/openai/baselines/blob/3301089b48c42b87b396e246ea3f56fa4bfc9678/baselines/common/cmd_util.py#L155-L163
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3301089b48c42b87b396e246ea3f56fa4bfc9678
valid
parse_unknown_args
Parse arguments not consumed by arg parser into a dicitonary
baselines/common/cmd_util.py
def parse_unknown_args(args): """ Parse arguments not consumed by arg parser into a dicitonary """ retval = {} preceded_by_key = False for arg in args: if arg.startswith('--'): if '=' in arg: key = arg.split('=')[0][2:] value = arg.split('=')[1...
def parse_unknown_args(args): """ Parse arguments not consumed by arg parser into a dicitonary """ retval = {} preceded_by_key = False for arg in args: if arg.startswith('--'): if '=' in arg: key = arg.split('=')[0][2:] value = arg.split('=')[1...
[ "Parse", "arguments", "not", "consumed", "by", "arg", "parser", "into", "a", "dicitonary" ]
openai/baselines
python
https://github.com/openai/baselines/blob/3301089b48c42b87b396e246ea3f56fa4bfc9678/baselines/common/cmd_util.py#L166-L185
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3301089b48c42b87b396e246ea3f56fa4bfc9678
valid
clear_mpi_env_vars
from mpi4py import MPI will call MPI_Init by default. If the child process has MPI environment variables, MPI will think that the child process is an MPI process just like the parent and do bad things such as hang. This context manager is a hacky way to clear those environment variables temporarily such as when we...
baselines/common/vec_env/vec_env.py
def clear_mpi_env_vars(): """ from mpi4py import MPI will call MPI_Init by default. If the child process has MPI environment variables, MPI will think that the child process is an MPI process just like the parent and do bad things such as hang. This context manager is a hacky way to clear those environment...
def clear_mpi_env_vars(): """ from mpi4py import MPI will call MPI_Init by default. If the child process has MPI environment variables, MPI will think that the child process is an MPI process just like the parent and do bad things such as hang. This context manager is a hacky way to clear those environment...
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openai/baselines
python
https://github.com/openai/baselines/blob/3301089b48c42b87b396e246ea3f56fa4bfc9678/baselines/common/vec_env/vec_env.py#L204-L219
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3301089b48c42b87b396e246ea3f56fa4bfc9678
valid
learn
Learn policy using PPO algorithm (https://arxiv.org/abs/1707.06347) Parameters: ---------- network: policy network architecture. Either string (mlp, lstm, lnlstm, cnn_lstm, cnn, cnn_small, conv_only - see baselines.common/models.py for full list) ...
baselines/ppo2/ppo2.py
def learn(*, network, env, total_timesteps, eval_env = None, seed=None, nsteps=2048, ent_coef=0.0, lr=3e-4, vf_coef=0.5, max_grad_norm=0.5, gamma=0.99, lam=0.95, log_interval=10, nminibatches=4, noptepochs=4, cliprange=0.2, save_interval=0, load_path=None, model_fn=None, **network_k...
def learn(*, network, env, total_timesteps, eval_env = None, seed=None, nsteps=2048, ent_coef=0.0, lr=3e-4, vf_coef=0.5, max_grad_norm=0.5, gamma=0.99, lam=0.95, log_interval=10, nminibatches=4, noptepochs=4, cliprange=0.2, save_interval=0, load_path=None, model_fn=None, **network_k...
[ "Learn", "policy", "using", "PPO", "algorithm", "(", "https", ":", "//", "arxiv", ".", "org", "/", "abs", "/", "1707", ".", "06347", ")" ]
openai/baselines
python
https://github.com/openai/baselines/blob/3301089b48c42b87b396e246ea3f56fa4bfc9678/baselines/ppo2/ppo2.py#L21-L204
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3301089b48c42b87b396e246ea3f56fa4bfc9678
valid
cg
Demmel p 312
baselines/common/cg.py
def cg(f_Ax, b, cg_iters=10, callback=None, verbose=False, residual_tol=1e-10): """ Demmel p 312 """ p = b.copy() r = b.copy() x = np.zeros_like(b) rdotr = r.dot(r) fmtstr = "%10i %10.3g %10.3g" titlestr = "%10s %10s %10s" if verbose: print(titlestr % ("iter", "residual norm",...
def cg(f_Ax, b, cg_iters=10, callback=None, verbose=False, residual_tol=1e-10): """ Demmel p 312 """ p = b.copy() r = b.copy() x = np.zeros_like(b) rdotr = r.dot(r) fmtstr = "%10i %10.3g %10.3g" titlestr = "%10s %10s %10s" if verbose: print(titlestr % ("iter", "residual norm",...
[ "Demmel", "p", "312" ]
openai/baselines
python
https://github.com/openai/baselines/blob/3301089b48c42b87b396e246ea3f56fa4bfc9678/baselines/common/cg.py#L2-L34
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3301089b48c42b87b396e246ea3f56fa4bfc9678
valid
observation_placeholder
Create placeholder to feed observations into of the size appropriate to the observation space Parameters: ---------- ob_space: gym.Space observation space batch_size: int size of the batch to be fed into input. Can be left None in most cases. name: str name of the place...
baselines/common/input.py
def observation_placeholder(ob_space, batch_size=None, name='Ob'): ''' Create placeholder to feed observations into of the size appropriate to the observation space Parameters: ---------- ob_space: gym.Space observation space batch_size: int size of the batch to be fed into input....
def observation_placeholder(ob_space, batch_size=None, name='Ob'): ''' Create placeholder to feed observations into of the size appropriate to the observation space Parameters: ---------- ob_space: gym.Space observation space batch_size: int size of the batch to be fed into input....
[ "Create", "placeholder", "to", "feed", "observations", "into", "of", "the", "size", "appropriate", "to", "the", "observation", "space" ]
openai/baselines
python
https://github.com/openai/baselines/blob/3301089b48c42b87b396e246ea3f56fa4bfc9678/baselines/common/input.py#L5-L31
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3301089b48c42b87b396e246ea3f56fa4bfc9678
valid
observation_input
Create placeholder to feed observations into of the size appropriate to the observation space, and add input encoder of the appropriate type.
baselines/common/input.py
def observation_input(ob_space, batch_size=None, name='Ob'): ''' Create placeholder to feed observations into of the size appropriate to the observation space, and add input encoder of the appropriate type. ''' placeholder = observation_placeholder(ob_space, batch_size, name) return placeholder...
def observation_input(ob_space, batch_size=None, name='Ob'): ''' Create placeholder to feed observations into of the size appropriate to the observation space, and add input encoder of the appropriate type. ''' placeholder = observation_placeholder(ob_space, batch_size, name) return placeholder...
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openai/baselines
python
https://github.com/openai/baselines/blob/3301089b48c42b87b396e246ea3f56fa4bfc9678/baselines/common/input.py#L34-L41
[ "def", "observation_input", "(", "ob_space", ",", "batch_size", "=", "None", ",", "name", "=", "'Ob'", ")", ":", "placeholder", "=", "observation_placeholder", "(", "ob_space", ",", "batch_size", ",", "name", ")", "return", "placeholder", ",", "encode_observatio...
3301089b48c42b87b396e246ea3f56fa4bfc9678
valid
encode_observation
Encode input in the way that is appropriate to the observation space Parameters: ---------- ob_space: gym.Space observation space placeholder: tf.placeholder observation input placeholder
baselines/common/input.py
def encode_observation(ob_space, placeholder): ''' Encode input in the way that is appropriate to the observation space Parameters: ---------- ob_space: gym.Space observation space placeholder: tf.placeholder observation input placeholder ''' if isinstance(ob_space, Di...
def encode_observation(ob_space, placeholder): ''' Encode input in the way that is appropriate to the observation space Parameters: ---------- ob_space: gym.Space observation space placeholder: tf.placeholder observation input placeholder ''' if isinstance(ob_space, Di...
[ "Encode", "input", "in", "the", "way", "that", "is", "appropriate", "to", "the", "observation", "space" ]
openai/baselines
python
https://github.com/openai/baselines/blob/3301089b48c42b87b396e246ea3f56fa4bfc9678/baselines/common/input.py#L43-L63
[ "def", "encode_observation", "(", "ob_space", ",", "placeholder", ")", ":", "if", "isinstance", "(", "ob_space", ",", "Discrete", ")", ":", "return", "tf", ".", "to_float", "(", "tf", ".", "one_hot", "(", "placeholder", ",", "ob_space", ".", "n", ")", ")...
3301089b48c42b87b396e246ea3f56fa4bfc9678
valid
RolloutWorker.generate_rollouts
Performs `rollout_batch_size` rollouts in parallel for time horizon `T` with the current policy acting on it accordingly.
baselines/her/rollout.py
def generate_rollouts(self): """Performs `rollout_batch_size` rollouts in parallel for time horizon `T` with the current policy acting on it accordingly. """ self.reset_all_rollouts() # compute observations o = np.empty((self.rollout_batch_size, self.dims['o']), np.float...
def generate_rollouts(self): """Performs `rollout_batch_size` rollouts in parallel for time horizon `T` with the current policy acting on it accordingly. """ self.reset_all_rollouts() # compute observations o = np.empty((self.rollout_batch_size, self.dims['o']), np.float...
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openai/baselines
python
https://github.com/openai/baselines/blob/3301089b48c42b87b396e246ea3f56fa4bfc9678/baselines/her/rollout.py#L51-L137
[ "def", "generate_rollouts", "(", "self", ")", ":", "self", ".", "reset_all_rollouts", "(", ")", "# compute observations", "o", "=", "np", ".", "empty", "(", "(", "self", ".", "rollout_batch_size", ",", "self", ".", "dims", "[", "'o'", "]", ")", ",", "np"...
3301089b48c42b87b396e246ea3f56fa4bfc9678
valid
RolloutWorker.save_policy
Pickles the current policy for later inspection.
baselines/her/rollout.py
def save_policy(self, path): """Pickles the current policy for later inspection. """ with open(path, 'wb') as f: pickle.dump(self.policy, f)
def save_policy(self, path): """Pickles the current policy for later inspection. """ with open(path, 'wb') as f: pickle.dump(self.policy, f)
[ "Pickles", "the", "current", "policy", "for", "later", "inspection", "." ]
openai/baselines
python
https://github.com/openai/baselines/blob/3301089b48c42b87b396e246ea3f56fa4bfc9678/baselines/her/rollout.py#L151-L155
[ "def", "save_policy", "(", "self", ",", "path", ")", ":", "with", "open", "(", "path", ",", "'wb'", ")", "as", "f", ":", "pickle", ".", "dump", "(", "self", ".", "policy", ",", "f", ")" ]
3301089b48c42b87b396e246ea3f56fa4bfc9678
valid
RolloutWorker.logs
Generates a dictionary that contains all collected statistics.
baselines/her/rollout.py
def logs(self, prefix='worker'): """Generates a dictionary that contains all collected statistics. """ logs = [] logs += [('success_rate', np.mean(self.success_history))] if self.compute_Q: logs += [('mean_Q', np.mean(self.Q_history))] logs += [('episode', sel...
def logs(self, prefix='worker'): """Generates a dictionary that contains all collected statistics. """ logs = [] logs += [('success_rate', np.mean(self.success_history))] if self.compute_Q: logs += [('mean_Q', np.mean(self.Q_history))] logs += [('episode', sel...
[ "Generates", "a", "dictionary", "that", "contains", "all", "collected", "statistics", "." ]
openai/baselines
python
https://github.com/openai/baselines/blob/3301089b48c42b87b396e246ea3f56fa4bfc9678/baselines/her/rollout.py#L157-L169
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3301089b48c42b87b396e246ea3f56fa4bfc9678
valid
smooth
Smooth signal y, where radius is determines the size of the window mode='twosided': average over the window [max(index - radius, 0), min(index + radius, len(y)-1)] mode='causal': average over the window [max(index - radius, 0), index] valid_only: put nan in entries where the full-sized win...
baselines/common/plot_util.py
def smooth(y, radius, mode='two_sided', valid_only=False): ''' Smooth signal y, where radius is determines the size of the window mode='twosided': average over the window [max(index - radius, 0), min(index + radius, len(y)-1)] mode='causal': average over the window [max(index - radius, ...
def smooth(y, radius, mode='two_sided', valid_only=False): ''' Smooth signal y, where radius is determines the size of the window mode='twosided': average over the window [max(index - radius, 0), min(index + radius, len(y)-1)] mode='causal': average over the window [max(index - radius, ...
[ "Smooth", "signal", "y", "where", "radius", "is", "determines", "the", "size", "of", "the", "window" ]
openai/baselines
python
https://github.com/openai/baselines/blob/3301089b48c42b87b396e246ea3f56fa4bfc9678/baselines/common/plot_util.py#L11-L37
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3301089b48c42b87b396e246ea3f56fa4bfc9678
valid
one_sided_ema
perform one-sided (causal) EMA (exponential moving average) smoothing and resampling to an even grid with n points. Does not do extrapolation, so we assume xolds[0] <= low && high <= xolds[-1] Arguments: xolds: array or list - x values of data. Needs to be sorted in ascending order yolds: arr...
baselines/common/plot_util.py
def one_sided_ema(xolds, yolds, low=None, high=None, n=512, decay_steps=1., low_counts_threshold=1e-8): ''' perform one-sided (causal) EMA (exponential moving average) smoothing and resampling to an even grid with n points. Does not do extrapolation, so we assume xolds[0] <= low && high <= xolds[-1]...
def one_sided_ema(xolds, yolds, low=None, high=None, n=512, decay_steps=1., low_counts_threshold=1e-8): ''' perform one-sided (causal) EMA (exponential moving average) smoothing and resampling to an even grid with n points. Does not do extrapolation, so we assume xolds[0] <= low && high <= xolds[-1]...
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openai/baselines
python
https://github.com/openai/baselines/blob/3301089b48c42b87b396e246ea3f56fa4bfc9678/baselines/common/plot_util.py#L39-L109
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3301089b48c42b87b396e246ea3f56fa4bfc9678
valid
symmetric_ema
perform symmetric EMA (exponential moving average) smoothing and resampling to an even grid with n points. Does not do extrapolation, so we assume xolds[0] <= low && high <= xolds[-1] Arguments: xolds: array or list - x values of data. Needs to be sorted in ascending order yolds: array of lis...
baselines/common/plot_util.py
def symmetric_ema(xolds, yolds, low=None, high=None, n=512, decay_steps=1., low_counts_threshold=1e-8): ''' perform symmetric EMA (exponential moving average) smoothing and resampling to an even grid with n points. Does not do extrapolation, so we assume xolds[0] <= low && high <= xolds[-1] Arg...
def symmetric_ema(xolds, yolds, low=None, high=None, n=512, decay_steps=1., low_counts_threshold=1e-8): ''' perform symmetric EMA (exponential moving average) smoothing and resampling to an even grid with n points. Does not do extrapolation, so we assume xolds[0] <= low && high <= xolds[-1] Arg...
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openai/baselines
python
https://github.com/openai/baselines/blob/3301089b48c42b87b396e246ea3f56fa4bfc9678/baselines/common/plot_util.py#L111-L147
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3301089b48c42b87b396e246ea3f56fa4bfc9678
valid
load_results
load summaries of runs from a list of directories (including subdirectories) Arguments: enable_progress: bool - if True, will attempt to load data from progress.csv files (data saved by logger). Default: True enable_monitor: bool - if True, will attempt to load data from monitor.csv files (data saved by M...
baselines/common/plot_util.py
def load_results(root_dir_or_dirs, enable_progress=True, enable_monitor=True, verbose=False): ''' load summaries of runs from a list of directories (including subdirectories) Arguments: enable_progress: bool - if True, will attempt to load data from progress.csv files (data saved by logger). Default: T...
def load_results(root_dir_or_dirs, enable_progress=True, enable_monitor=True, verbose=False): ''' load summaries of runs from a list of directories (including subdirectories) Arguments: enable_progress: bool - if True, will attempt to load data from progress.csv files (data saved by logger). Default: T...
[ "load", "summaries", "of", "runs", "from", "a", "list", "of", "directories", "(", "including", "subdirectories", ")", "Arguments", ":" ]
openai/baselines
python
https://github.com/openai/baselines/blob/3301089b48c42b87b396e246ea3f56fa4bfc9678/baselines/common/plot_util.py#L152-L220
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3301089b48c42b87b396e246ea3f56fa4bfc9678
valid
plot_results
Plot multiple Results objects xy_fn: function Result -> x,y - function that converts results objects into tuple of x and y values. By default, x is cumsum of episode lengths, and y is episode rewards split_fn: function Result -> hashable - function tha...
baselines/common/plot_util.py
def plot_results( allresults, *, xy_fn=default_xy_fn, split_fn=default_split_fn, group_fn=default_split_fn, average_group=False, shaded_std=True, shaded_err=True, figsize=None, legend_outside=False, resample=0, smooth_step=1.0 ): ''' Plot multiple Results objects ...
def plot_results( allresults, *, xy_fn=default_xy_fn, split_fn=default_split_fn, group_fn=default_split_fn, average_group=False, shaded_std=True, shaded_err=True, figsize=None, legend_outside=False, resample=0, smooth_step=1.0 ): ''' Plot multiple Results objects ...
[ "Plot", "multiple", "Results", "objects" ]
openai/baselines
python
https://github.com/openai/baselines/blob/3301089b48c42b87b396e246ea3f56fa4bfc9678/baselines/common/plot_util.py#L240-L375
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3301089b48c42b87b396e246ea3f56fa4bfc9678
valid
check_synced
It's common to forget to initialize your variables to the same values, or (less commonly) if you update them in some other way than adam, to get them out of sync. This function checks that variables on all MPI workers are the same, and raises an AssertionError otherwise Arguments: comm: MPI com...
baselines/common/mpi_adam_optimizer.py
def check_synced(localval, comm=None): """ It's common to forget to initialize your variables to the same values, or (less commonly) if you update them in some other way than adam, to get them out of sync. This function checks that variables on all MPI workers are the same, and raises an AssertionEr...
def check_synced(localval, comm=None): """ It's common to forget to initialize your variables to the same values, or (less commonly) if you update them in some other way than adam, to get them out of sync. This function checks that variables on all MPI workers are the same, and raises an AssertionEr...
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openai/baselines
python
https://github.com/openai/baselines/blob/3301089b48c42b87b396e246ea3f56fa4bfc9678/baselines/common/mpi_adam_optimizer.py#L40-L54
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3301089b48c42b87b396e246ea3f56fa4bfc9678
valid
copy_obs_dict
Deep-copy an observation dict.
baselines/common/vec_env/util.py
def copy_obs_dict(obs): """ Deep-copy an observation dict. """ return {k: np.copy(v) for k, v in obs.items()}
def copy_obs_dict(obs): """ Deep-copy an observation dict. """ return {k: np.copy(v) for k, v in obs.items()}
[ "Deep", "-", "copy", "an", "observation", "dict", "." ]
openai/baselines
python
https://github.com/openai/baselines/blob/3301089b48c42b87b396e246ea3f56fa4bfc9678/baselines/common/vec_env/util.py#L11-L15
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3301089b48c42b87b396e246ea3f56fa4bfc9678
valid
obs_space_info
Get dict-structured information about a gym.Space. Returns: A tuple (keys, shapes, dtypes): keys: a list of dict keys. shapes: a dict mapping keys to shapes. dtypes: a dict mapping keys to dtypes.
baselines/common/vec_env/util.py
def obs_space_info(obs_space): """ Get dict-structured information about a gym.Space. Returns: A tuple (keys, shapes, dtypes): keys: a list of dict keys. shapes: a dict mapping keys to shapes. dtypes: a dict mapping keys to dtypes. """ if isinstance(obs_space, gym.spac...
def obs_space_info(obs_space): """ Get dict-structured information about a gym.Space. Returns: A tuple (keys, shapes, dtypes): keys: a list of dict keys. shapes: a dict mapping keys to shapes. dtypes: a dict mapping keys to dtypes. """ if isinstance(obs_space, gym.spac...
[ "Get", "dict", "-", "structured", "information", "about", "a", "gym", ".", "Space", "." ]
openai/baselines
python
https://github.com/openai/baselines/blob/3301089b48c42b87b396e246ea3f56fa4bfc9678/baselines/common/vec_env/util.py#L28-L50
[ "def", "obs_space_info", "(", "obs_space", ")", ":", "if", "isinstance", "(", "obs_space", ",", "gym", ".", "spaces", ".", "Dict", ")", ":", "assert", "isinstance", "(", "obs_space", ".", "spaces", ",", "OrderedDict", ")", "subspaces", "=", "obs_space", "....
3301089b48c42b87b396e246ea3f56fa4bfc9678
valid
q_retrace
Calculates q_retrace targets :param R: Rewards :param D: Dones :param q_i: Q values for actions taken :param v: V values :param rho_i: Importance weight for each action :return: Q_retrace values
baselines/acer/acer.py
def q_retrace(R, D, q_i, v, rho_i, nenvs, nsteps, gamma): """ Calculates q_retrace targets :param R: Rewards :param D: Dones :param q_i: Q values for actions taken :param v: V values :param rho_i: Importance weight for each action :return: Q_retrace values """ rho_bar = batch_to...
def q_retrace(R, D, q_i, v, rho_i, nenvs, nsteps, gamma): """ Calculates q_retrace targets :param R: Rewards :param D: Dones :param q_i: Q values for actions taken :param v: V values :param rho_i: Importance weight for each action :return: Q_retrace values """ rho_bar = batch_to...
[ "Calculates", "q_retrace", "targets" ]
openai/baselines
python
https://github.com/openai/baselines/blob/3301089b48c42b87b396e246ea3f56fa4bfc9678/baselines/acer/acer.py#L25-L51
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3301089b48c42b87b396e246ea3f56fa4bfc9678
valid
learn
Main entrypoint for ACER (Actor-Critic with Experience Replay) algorithm (https://arxiv.org/pdf/1611.01224.pdf) Train an agent with given network architecture on a given environment using ACER. Parameters: ---------- network: policy network architecture. Either string (mlp, lstm, lnlstm, cn...
baselines/acer/acer.py
def learn(network, env, seed=None, nsteps=20, total_timesteps=int(80e6), q_coef=0.5, ent_coef=0.01, max_grad_norm=10, lr=7e-4, lrschedule='linear', rprop_epsilon=1e-5, rprop_alpha=0.99, gamma=0.99, log_interval=100, buffer_size=50000, replay_ratio=4, replay_start=10000, c=10.0, trust_regio...
def learn(network, env, seed=None, nsteps=20, total_timesteps=int(80e6), q_coef=0.5, ent_coef=0.01, max_grad_norm=10, lr=7e-4, lrschedule='linear', rprop_epsilon=1e-5, rprop_alpha=0.99, gamma=0.99, log_interval=100, buffer_size=50000, replay_ratio=4, replay_start=10000, c=10.0, trust_regio...
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openai/baselines
python
https://github.com/openai/baselines/blob/3301089b48c42b87b396e246ea3f56fa4bfc9678/baselines/acer/acer.py#L274-L377
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3301089b48c42b87b396e246ea3f56fa4bfc9678
valid
KfacOptimizer.apply_stats
compute stats and update/apply the new stats to the running average
baselines/acktr/kfac.py
def apply_stats(self, statsUpdates): """ compute stats and update/apply the new stats to the running average """ def updateAccumStats(): if self._full_stats_init: return tf.cond(tf.greater(self.sgd_step, self._cold_iter), lambda: tf.group(*self._apply_stats(statsUpda...
def apply_stats(self, statsUpdates): """ compute stats and update/apply the new stats to the running average """ def updateAccumStats(): if self._full_stats_init: return tf.cond(tf.greater(self.sgd_step, self._cold_iter), lambda: tf.group(*self._apply_stats(statsUpda...
[ "compute", "stats", "and", "update", "/", "apply", "the", "new", "stats", "to", "the", "running", "average" ]
openai/baselines
python
https://github.com/openai/baselines/blob/3301089b48c42b87b396e246ea3f56fa4bfc9678/baselines/acktr/kfac.py#L440-L474
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3301089b48c42b87b396e246ea3f56fa4bfc9678
valid
tile_images
Tile N images into one big PxQ image (P,Q) are chosen to be as close as possible, and if N is square, then P=Q. input: img_nhwc, list or array of images, ndim=4 once turned into array n = batch index, h = height, w = width, c = channel returns: bigim_HWc, ndarray with ndim=3
baselines/common/tile_images.py
def tile_images(img_nhwc): """ Tile N images into one big PxQ image (P,Q) are chosen to be as close as possible, and if N is square, then P=Q. input: img_nhwc, list or array of images, ndim=4 once turned into array n = batch index, h = height, w = width, c = channel returns: big...
def tile_images(img_nhwc): """ Tile N images into one big PxQ image (P,Q) are chosen to be as close as possible, and if N is square, then P=Q. input: img_nhwc, list or array of images, ndim=4 once turned into array n = batch index, h = height, w = width, c = channel returns: big...
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openai/baselines
python
https://github.com/openai/baselines/blob/3301089b48c42b87b396e246ea3f56fa4bfc9678/baselines/common/tile_images.py#L3-L22
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3301089b48c42b87b396e246ea3f56fa4bfc9678
valid
SumSegmentTree.sum
Returns arr[start] + ... + arr[end]
baselines/common/segment_tree.py
def sum(self, start=0, end=None): """Returns arr[start] + ... + arr[end]""" return super(SumSegmentTree, self).reduce(start, end)
def sum(self, start=0, end=None): """Returns arr[start] + ... + arr[end]""" return super(SumSegmentTree, self).reduce(start, end)
[ "Returns", "arr", "[", "start", "]", "+", "...", "+", "arr", "[", "end", "]" ]
openai/baselines
python
https://github.com/openai/baselines/blob/3301089b48c42b87b396e246ea3f56fa4bfc9678/baselines/common/segment_tree.py#L101-L103
[ "def", "sum", "(", "self", ",", "start", "=", "0", ",", "end", "=", "None", ")", ":", "return", "super", "(", "SumSegmentTree", ",", "self", ")", ".", "reduce", "(", "start", ",", "end", ")" ]
3301089b48c42b87b396e246ea3f56fa4bfc9678
valid
SumSegmentTree.find_prefixsum_idx
Find the highest index `i` in the array such that sum(arr[0] + arr[1] + ... + arr[i - i]) <= prefixsum if array values are probabilities, this function allows to sample indexes according to the discrete probability efficiently. Parameters ---------- perfixsu...
baselines/common/segment_tree.py
def find_prefixsum_idx(self, prefixsum): """Find the highest index `i` in the array such that sum(arr[0] + arr[1] + ... + arr[i - i]) <= prefixsum if array values are probabilities, this function allows to sample indexes according to the discrete probability efficiently. ...
def find_prefixsum_idx(self, prefixsum): """Find the highest index `i` in the array such that sum(arr[0] + arr[1] + ... + arr[i - i]) <= prefixsum if array values are probabilities, this function allows to sample indexes according to the discrete probability efficiently. ...
[ "Find", "the", "highest", "index", "i", "in", "the", "array", "such", "that", "sum", "(", "arr", "[", "0", "]", "+", "arr", "[", "1", "]", "+", "...", "+", "arr", "[", "i", "-", "i", "]", ")", "<", "=", "prefixsum" ]
openai/baselines
python
https://github.com/openai/baselines/blob/3301089b48c42b87b396e246ea3f56fa4bfc9678/baselines/common/segment_tree.py#L105-L131
[ "def", "find_prefixsum_idx", "(", "self", ",", "prefixsum", ")", ":", "assert", "0", "<=", "prefixsum", "<=", "self", ".", "sum", "(", ")", "+", "1e-5", "idx", "=", "1", "while", "idx", "<", "self", ".", "_capacity", ":", "# while non-leaf", "if", "sel...
3301089b48c42b87b396e246ea3f56fa4bfc9678
valid
MinSegmentTree.min
Returns min(arr[start], ..., arr[end])
baselines/common/segment_tree.py
def min(self, start=0, end=None): """Returns min(arr[start], ..., arr[end])""" return super(MinSegmentTree, self).reduce(start, end)
def min(self, start=0, end=None): """Returns min(arr[start], ..., arr[end])""" return super(MinSegmentTree, self).reduce(start, end)
[ "Returns", "min", "(", "arr", "[", "start", "]", "...", "arr", "[", "end", "]", ")" ]
openai/baselines
python
https://github.com/openai/baselines/blob/3301089b48c42b87b396e246ea3f56fa4bfc9678/baselines/common/segment_tree.py#L142-L145
[ "def", "min", "(", "self", ",", "start", "=", "0", ",", "end", "=", "None", ")", ":", "return", "super", "(", "MinSegmentTree", ",", "self", ")", ".", "reduce", "(", "start", ",", "end", ")" ]
3301089b48c42b87b396e246ea3f56fa4bfc9678
valid
PiecewiseSchedule.value
See Schedule.value
baselines/common/schedules.py
def value(self, t): """See Schedule.value""" for (l_t, l), (r_t, r) in zip(self._endpoints[:-1], self._endpoints[1:]): if l_t <= t and t < r_t: alpha = float(t - l_t) / (r_t - l_t) return self._interpolation(l, r, alpha) # t does not belong to any of ...
def value(self, t): """See Schedule.value""" for (l_t, l), (r_t, r) in zip(self._endpoints[:-1], self._endpoints[1:]): if l_t <= t and t < r_t: alpha = float(t - l_t) / (r_t - l_t) return self._interpolation(l, r, alpha) # t does not belong to any of ...
[ "See", "Schedule", ".", "value" ]
openai/baselines
python
https://github.com/openai/baselines/blob/3301089b48c42b87b396e246ea3f56fa4bfc9678/baselines/common/schedules.py#L64-L73
[ "def", "value", "(", "self", ",", "t", ")", ":", "for", "(", "l_t", ",", "l", ")", ",", "(", "r_t", ",", "r", ")", "in", "zip", "(", "self", ".", "_endpoints", "[", ":", "-", "1", "]", ",", "self", ".", "_endpoints", "[", "1", ":", "]", "...
3301089b48c42b87b396e246ea3f56fa4bfc9678
valid
_subproc_worker
Control a single environment instance using IPC and shared memory.
baselines/common/vec_env/shmem_vec_env.py
def _subproc_worker(pipe, parent_pipe, env_fn_wrapper, obs_bufs, obs_shapes, obs_dtypes, keys): """ Control a single environment instance using IPC and shared memory. """ def _write_obs(maybe_dict_obs): flatdict = obs_to_dict(maybe_dict_obs) for k in keys: dst = obs_bufs[...
def _subproc_worker(pipe, parent_pipe, env_fn_wrapper, obs_bufs, obs_shapes, obs_dtypes, keys): """ Control a single environment instance using IPC and shared memory. """ def _write_obs(maybe_dict_obs): flatdict = obs_to_dict(maybe_dict_obs) for k in keys: dst = obs_bufs[...
[ "Control", "a", "single", "environment", "instance", "using", "IPC", "and", "shared", "memory", "." ]
openai/baselines
python
https://github.com/openai/baselines/blob/3301089b48c42b87b396e246ea3f56fa4bfc9678/baselines/common/vec_env/shmem_vec_env.py#L105-L139
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3301089b48c42b87b396e246ea3f56fa4bfc9678
valid
learn
Main entrypoint for A2C algorithm. Train a policy with given network architecture on a given environment using a2c algorithm. Parameters: ----------- network: policy network architecture. Either string (mlp, lstm, lnlstm, cnn_lstm, cnn, cnn_small, conv_only - see baselines.common/models.py for ...
baselines/a2c/a2c.py
def learn( network, env, seed=None, nsteps=5, total_timesteps=int(80e6), vf_coef=0.5, ent_coef=0.01, max_grad_norm=0.5, lr=7e-4, lrschedule='linear', epsilon=1e-5, alpha=0.99, gamma=0.99, log_interval=100, load_path=None, **network_kwargs): ''' Ma...
def learn( network, env, seed=None, nsteps=5, total_timesteps=int(80e6), vf_coef=0.5, ent_coef=0.01, max_grad_norm=0.5, lr=7e-4, lrschedule='linear', epsilon=1e-5, alpha=0.99, gamma=0.99, log_interval=100, load_path=None, **network_kwargs): ''' Ma...
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openai/baselines
python
https://github.com/openai/baselines/blob/3301089b48c42b87b396e246ea3f56fa4bfc9678/baselines/a2c/a2c.py#L119-L231
[ "def", "learn", "(", "network", ",", "env", ",", "seed", "=", "None", ",", "nsteps", "=", "5", ",", "total_timesteps", "=", "int", "(", "80e6", ")", ",", "vf_coef", "=", "0.5", ",", "ent_coef", "=", "0.01", ",", "max_grad_norm", "=", "0.5", ",", "l...
3301089b48c42b87b396e246ea3f56fa4bfc9678
valid
sf01
swap and then flatten axes 0 and 1
baselines/ppo2/runner.py
def sf01(arr): """ swap and then flatten axes 0 and 1 """ s = arr.shape return arr.swapaxes(0, 1).reshape(s[0] * s[1], *s[2:])
def sf01(arr): """ swap and then flatten axes 0 and 1 """ s = arr.shape return arr.swapaxes(0, 1).reshape(s[0] * s[1], *s[2:])
[ "swap", "and", "then", "flatten", "axes", "0", "and", "1" ]
openai/baselines
python
https://github.com/openai/baselines/blob/3301089b48c42b87b396e246ea3f56fa4bfc9678/baselines/ppo2/runner.py#L69-L74
[ "def", "sf01", "(", "arr", ")", ":", "s", "=", "arr", ".", "shape", "return", "arr", ".", "swapaxes", "(", "0", ",", "1", ")", ".", "reshape", "(", "s", "[", "0", "]", "*", "s", "[", "1", "]", ",", "*", "s", "[", "2", ":", "]", ")" ]
3301089b48c42b87b396e246ea3f56fa4bfc9678
valid
PolicyWithValue.step
Compute next action(s) given the observation(s) Parameters: ---------- observation observation data (either single or a batch) **extra_feed additional data such as state or mask (names of the arguments should match the ones in constructor, see __init__) Returns: ...
baselines/common/policies.py
def step(self, observation, **extra_feed): """ Compute next action(s) given the observation(s) Parameters: ---------- observation observation data (either single or a batch) **extra_feed additional data such as state or mask (names of the arguments should match ...
def step(self, observation, **extra_feed): """ Compute next action(s) given the observation(s) Parameters: ---------- observation observation data (either single or a batch) **extra_feed additional data such as state or mask (names of the arguments should match ...
[ "Compute", "next", "action", "(", "s", ")", "given", "the", "observation", "(", "s", ")" ]
openai/baselines
python
https://github.com/openai/baselines/blob/3301089b48c42b87b396e246ea3f56fa4bfc9678/baselines/common/policies.py#L77-L96
[ "def", "step", "(", "self", ",", "observation", ",", "*", "*", "extra_feed", ")", ":", "a", ",", "v", ",", "state", ",", "neglogp", "=", "self", ".", "_evaluate", "(", "[", "self", ".", "action", ",", "self", ".", "vf", ",", "self", ".", "state",...
3301089b48c42b87b396e246ea3f56fa4bfc9678
valid
PolicyWithValue.value
Compute value estimate(s) given the observation(s) Parameters: ---------- observation observation data (either single or a batch) **extra_feed additional data such as state or mask (names of the arguments should match the ones in constructor, see __init__) Returns: ...
baselines/common/policies.py
def value(self, ob, *args, **kwargs): """ Compute value estimate(s) given the observation(s) Parameters: ---------- observation observation data (either single or a batch) **extra_feed additional data such as state or mask (names of the arguments should match th...
def value(self, ob, *args, **kwargs): """ Compute value estimate(s) given the observation(s) Parameters: ---------- observation observation data (either single or a batch) **extra_feed additional data such as state or mask (names of the arguments should match th...
[ "Compute", "value", "estimate", "(", "s", ")", "given", "the", "observation", "(", "s", ")" ]
openai/baselines
python
https://github.com/openai/baselines/blob/3301089b48c42b87b396e246ea3f56fa4bfc9678/baselines/common/policies.py#L98-L113
[ "def", "value", "(", "self", ",", "ob", ",", "*", "args", ",", "*", "*", "kwargs", ")", ":", "return", "self", ".", "_evaluate", "(", "self", ".", "vf", ",", "ob", ",", "*", "args", ",", "*", "*", "kwargs", ")" ]
3301089b48c42b87b396e246ea3f56fa4bfc9678
valid
pretty_eta
Print the number of seconds in human readable format. Examples: 2 days 2 hours and 37 minutes less than a minute Paramters --------- seconds_left: int Number of seconds to be converted to the ETA Returns ------- eta: str String representing the pretty ETA.
baselines/common/misc_util.py
def pretty_eta(seconds_left): """Print the number of seconds in human readable format. Examples: 2 days 2 hours and 37 minutes less than a minute Paramters --------- seconds_left: int Number of seconds to be converted to the ETA Returns ------- eta: str Stri...
def pretty_eta(seconds_left): """Print the number of seconds in human readable format. Examples: 2 days 2 hours and 37 minutes less than a minute Paramters --------- seconds_left: int Number of seconds to be converted to the ETA Returns ------- eta: str Stri...
[ "Print", "the", "number", "of", "seconds", "in", "human", "readable", "format", "." ]
openai/baselines
python
https://github.com/openai/baselines/blob/3301089b48c42b87b396e246ea3f56fa4bfc9678/baselines/common/misc_util.py#L65-L104
[ "def", "pretty_eta", "(", "seconds_left", ")", ":", "minutes_left", "=", "seconds_left", "//", "60", "seconds_left", "%=", "60", "hours_left", "=", "minutes_left", "//", "60", "minutes_left", "%=", "60", "days_left", "=", "hours_left", "//", "24", "hours_left", ...
3301089b48c42b87b396e246ea3f56fa4bfc9678