_id
stringlengths
2
7
title
stringlengths
1
88
partition
stringclasses
3 values
text
stringlengths
75
19.8k
language
stringclasses
1 value
meta_information
dict
q10500
compute_objective_value
train
def compute_objective_value(objective_func, parameters, data=None, cl_runtime_info=None): """Calculate and return the objective function value of the given model for the given parameters. Args: objective_func (mot.lib.cl_function.CLFunction): A CL function with the signature: .. code-block:: c double <func_name>(local const mot_float_type* const x, void* data, local mot_float_type* objective_list); parameters (ndarray): The parameters to use in the evaluation of the model, an (d, p) matrix with d problems and p parameters. data (mot.lib.kernel_data.KernelData): the user provided data for the ``void* data`` pointer. cl_runtime_info (mot.configuration.CLRuntimeInfo): the runtime information Returns: ndarray: vector matrix with per problem the objective function value """ return objective_func.evaluate({'data': data, 'parameters': Array(parameters, 'mot_float_type', mode='r')}, parameters.shape[0], use_local_reduction=True, cl_runtime_info=cl_runtime_info)
python
{ "resource": "" }
q10501
get_log
train
def get_log(username): """ Return a list of page views. Each item is a dict with `datetime`, `method`, `path` and `code` keys. """ redis = get_redis_client() log_key = 'log:{}'.format(username) raw_log = redis.lrange(log_key, 0, -1) log = [] for raw_item in raw_log: item = json.loads(raw_item.decode()) item['datetime'] = convert_timestamp(item.pop('time')) log.append(item) return log
python
{ "resource": "" }
q10502
get_token
train
def get_token(username, length=20, timeout=20): """ Obtain an access token that can be passed to a websocket client. """ redis = get_redis_client() token = get_random_string(length) token_key = 'token:{}'.format(token) redis.set(token_key, username) redis.expire(token_key, timeout) return token
python
{ "resource": "" }
q10503
UserLogMiddleware.get_log
train
def get_log(self, request, response): """ Return a dict of data to log for a given request and response. Override this method if you need to log a different set of values. """ return { 'method': request.method, 'path': request.get_full_path(), 'code': response.status_code, 'time': time.time(), }
python
{ "resource": "" }
q10504
MusicManager.download
train
def download(self, song): """Download a song from a Google Music library. Parameters: song (dict): A song dict. Returns: tuple: Song content as bytestring, suggested filename. """ song_id = song['id'] response = self._call( mm_calls.Export, self.uploader_id, song_id) audio = response.body suggested_filename = unquote( response.headers['Content-Disposition'].split("filename*=UTF-8''")[-1] ) return (audio, suggested_filename)
python
{ "resource": "" }
q10505
MusicManager.quota
train
def quota(self): """Get the uploaded track count and allowance. Returns: tuple: Number of uploaded tracks, number of tracks allowed. """ response = self._call( mm_calls.ClientState, self.uploader_id ) client_state = response.body.clientstate_response return (client_state.total_track_count, client_state.locker_track_limit)
python
{ "resource": "" }
q10506
MusicManager.songs
train
def songs(self, *, uploaded=True, purchased=True): """Get a listing of Music Library songs. Returns: list: Song dicts. """ if not uploaded and not purchased: raise ValueError("'uploaded' and 'purchased' cannot both be False.") if purchased and uploaded: song_list = [] for chunk in self.songs_iter(export_type=1): song_list.extend(chunk) elif purchased: song_list = [] for chunk in self.songs_iter(export_type=2): song_list.extend(chunk) elif uploaded: purchased_songs = [] for chunk in self.songs_iter(export_type=2): purchased_songs.extend(chunk) song_list = [ song for chunk in self.songs_iter(export_type=1) for song in chunk if song not in purchased_songs ] return song_list
python
{ "resource": "" }
q10507
MusicManager.songs_iter
train
def songs_iter(self, *, continuation_token=None, export_type=1): """Get a paged iterator of Music Library songs. Parameters: continuation_token (str, Optional): The token of the page to return. Default: Not sent to get first page. export_type (int, Optional): The type of tracks to return. 1 for all tracks, 2 for promotional and purchased. Default: ``1`` Yields: list: Song dicts. """ def track_info_to_dict(track_info): return dict( (field.name, value) for field, value in track_info.ListFields() ) while True: response = self._call( mm_calls.ExportIDs, self.uploader_id, continuation_token=continuation_token, export_type=export_type ) items = [ track_info_to_dict(track_info) for track_info in response.body.download_track_info ] if items: yield items continuation_token = response.body.continuation_token if not continuation_token: break
python
{ "resource": "" }
q10508
GoogleMusicClient.login
train
def login(self, username, *, token=None): """Log in to Google Music. Parameters: username (str, Optional): Your Google Music username. Used for keeping stored OAuth tokens for multiple accounts separate. device_id (str, Optional): A mobile device ID or music manager uploader ID. Default: MAC address is used. token (dict, Optional): An OAuth token compatible with ``requests-oauthlib``. Returns: bool: ``True`` if successfully authenticated, ``False`` if not. """ self._username = username self._oauth(username, token=token) return self.is_authenticated
python
{ "resource": "" }
q10509
GoogleMusicClient.switch_user
train
def switch_user(self, username='', *, token=None): """Log in to Google Music with a different user. Parameters: username (str, Optional): Your Google Music username. Used for keeping stored OAuth tokens for multiple accounts separate. token (dict, Optional): An OAuth token compatible with ``requests-oauthlib``. Returns: bool: ``True`` if successfully authenticated, ``False`` if not. """ if self.logout(): return self.login(username, token=token) return False
python
{ "resource": "" }
q10510
gen_tau
train
def gen_tau(S, K, delta): """The Robust part of the RSD, we precompute an array for speed """ pivot = floor(K/S) return [S/K * 1/d for d in range(1, pivot)] \ + [S/K * log(S/delta)] \ + [0 for d in range(pivot, K)]
python
{ "resource": "" }
q10511
gen_mu
train
def gen_mu(K, delta, c): """The Robust Soliton Distribution on the degree of transmitted blocks """ S = c * log(K/delta) * sqrt(K) tau = gen_tau(S, K, delta) rho = gen_rho(K) normalizer = sum(rho) + sum(tau) return [(rho[d] + tau[d])/normalizer for d in range(K)]
python
{ "resource": "" }
q10512
gen_rsd_cdf
train
def gen_rsd_cdf(K, delta, c): """The CDF of the RSD on block degree, precomputed for sampling speed""" mu = gen_mu(K, delta, c) return [sum(mu[:d+1]) for d in range(K)]
python
{ "resource": "" }
q10513
PRNG._get_next
train
def _get_next(self): """Executes the next iteration of the PRNG evolution process, and returns the result """ self.state = PRNG_A * self.state % PRNG_M return self.state
python
{ "resource": "" }
q10514
PRNG._sample_d
train
def _sample_d(self): """Samples degree given the precomputed distributions above and the linear PRNG output """ p = self._get_next() / PRNG_MAX_RAND for ix, v in enumerate(self.cdf): if v > p: return ix + 1 return ix + 1
python
{ "resource": "" }
q10515
PRNG.get_src_blocks
train
def get_src_blocks(self, seed=None): """Returns the indices of a set of `d` source blocks sampled from indices i = 1, ..., K-1 uniformly, where `d` is sampled from the RSD described above. """ if seed: self.state = seed blockseed = self.state d = self._sample_d() have = 0 nums = set() while have < d: num = self._get_next() % self.K if num not in nums: nums.add(num) have += 1 return blockseed, d, nums
python
{ "resource": "" }
q10516
run
train
def run(fn, blocksize, seed, c, delta): """Run the encoder until the channel is broken, signalling that the receiver has successfully reconstructed the file """ with open(fn, 'rb') as f: for block in encode.encoder(f, blocksize, seed, c, delta): sys.stdout.buffer.write(block)
python
{ "resource": "" }
q10517
MobileClient.album
train
def album(self, album_id, *, include_description=True, include_songs=True): """Get information about an album. Parameters: album_id (str): An album ID. Album IDs start with a 'B'. include_description (bool, Optional): Include description of the album in the returned dict. include_songs (bool, Optional): Include songs from the album in the returned dict. Default: ``True``. Returns: dict: Album information. """ response = self._call( mc_calls.FetchAlbum, album_id, include_description=include_description, include_tracks=include_songs ) album_info = response.body return album_info
python
{ "resource": "" }
q10518
MobileClient.artist
train
def artist( self, artist_id, *, include_albums=True, num_related_artists=5, num_top_tracks=5 ): """Get information about an artist. Parameters: artist_id (str): An artist ID. Artist IDs start with an 'A'. include_albums (bool, Optional): Include albums by the artist in returned dict. Default: ``True``. num_related_artists (int, Optional): Include up to given number of related artists in returned dict. Default: ``5``. num_top_tracks (int, Optional): Include up to given number of top tracks in returned dict. Default: ``5``. Returns: dict: Artist information. """ response = self._call( mc_calls.FetchArtist, artist_id, include_albums=include_albums, num_related_artists=num_related_artists, num_top_tracks=num_top_tracks ) artist_info = response.body return artist_info
python
{ "resource": "" }
q10519
MobileClient.browse_podcasts
train
def browse_podcasts(self, podcast_genre_id='JZCpodcasttopchartall'): """Get the podcasts for a genre from the Podcasts browse tab. Parameters: podcast_genre_id (str, Optional): A podcast genre ID as found in :meth:`browse_podcasts_genres`. Default: ``'JZCpodcasttopchartall'``. Returns: list: Podcast dicts. """ response = self._call( mc_calls.PodcastBrowse, podcast_genre_id=podcast_genre_id ) podcast_series_list = response.body.get('series', []) return podcast_series_list
python
{ "resource": "" }
q10520
MobileClient.browse_podcasts_genres
train
def browse_podcasts_genres(self): """Get the genres from the Podcasts browse tab dropdown. Returns: list: Genre groups that contain sub groups. """ response = self._call( mc_calls.PodcastBrowseHierarchy ) genres = response.body.get('groups', []) return genres
python
{ "resource": "" }
q10521
MobileClient.browse_stations
train
def browse_stations(self, station_category_id): """Get the stations for a category from Browse Stations. Parameters: station_category_id (str): A station category ID as found with :meth:`browse_stations_categories`. Returns: list: Station dicts. """ response = self._call( mc_calls.BrowseStations, station_category_id ) stations = response.body.get('stations', []) return stations
python
{ "resource": "" }
q10522
MobileClient.browse_stations_categories
train
def browse_stations_categories(self): """Get the categories from Browse Stations. Returns: list: Station categories that can contain subcategories. """ response = self._call( mc_calls.BrowseStationCategories ) station_categories = response.body.get('root', {}).get('subcategories', []) return station_categories
python
{ "resource": "" }
q10523
MobileClient.config
train
def config(self): """Get a listing of mobile client configuration settings.""" response = self._call( mc_calls.Config ) config_list = response.body.get('data', {}).get('entries', []) return config_list
python
{ "resource": "" }
q10524
MobileClient.devices
train
def devices(self): """Get a listing of devices registered to the Google Music account.""" response = self._call( mc_calls.DeviceManagementInfo ) registered_devices = response.body.get('data', {}).get('items', []) return registered_devices
python
{ "resource": "" }
q10525
MobileClient.explore_genres
train
def explore_genres(self, parent_genre_id=None): """Get a listing of song genres. Parameters: parent_genre_id (str, Optional): A genre ID. If given, a listing of this genre's sub-genres is returned. Returns: list: Genre dicts. """ response = self._call( mc_calls.ExploreGenres, parent_genre_id ) genre_list = response.body.get('genres', []) return genre_list
python
{ "resource": "" }
q10526
MobileClient.explore_tabs
train
def explore_tabs(self, *, num_items=100, genre_id=None): """Get a listing of explore tabs. Parameters: num_items (int, Optional): Number of items per tab to return. Default: ``100`` genre_id (genre_id, Optional): Genre ID from :meth:`explore_genres` to explore. Default: ``None``. Returns: dict: Explore tabs content. """ response = self._call( mc_calls.ExploreTabs, num_items=num_items, genre_id=genre_id ) tab_list = response.body.get('tabs', []) explore_tabs = {} for tab in tab_list: explore_tabs[tab['tab_type'].lower()] = tab return explore_tabs
python
{ "resource": "" }
q10527
MobileClient.listen_now_dismissed_items
train
def listen_now_dismissed_items(self): """Get a listing of items dismissed from Listen Now tab.""" response = self._call( mc_calls.ListenNowGetDismissedItems ) dismissed_items = response.body.get('items', []) return dismissed_items
python
{ "resource": "" }
q10528
MobileClient.listen_now_items
train
def listen_now_items(self): """Get a listing of Listen Now items. Note: This does not include situations; use the :meth:`situations` method instead. Returns: dict: With ``albums`` and ``stations`` keys of listen now items. """ response = self._call( mc_calls.ListenNowGetListenNowItems ) listen_now_item_list = response.body.get('listennow_items', []) listen_now_items = defaultdict(list) for item in listen_now_item_list: type_ = f"{ListenNowItemType(item['type']).name}s" listen_now_items[type_].append(item) return dict(listen_now_items)
python
{ "resource": "" }
q10529
MobileClient.playlist_song
train
def playlist_song(self, playlist_song_id): """Get information about a playlist song. Note: This returns the playlist entry information only. For full song metadata, use :meth:`song` with the ``'trackId'`` field. Parameters: playlist_song_id (str): A playlist song ID. Returns: dict: Playlist song information. """ playlist_song_info = next( ( playlist_song for playlist in self.playlists(include_songs=True) for playlist_song in playlist['tracks'] if playlist_song['id'] == playlist_song_id ), None ) return playlist_song_info
python
{ "resource": "" }
q10530
MobileClient.playlist_song_add
train
def playlist_song_add( self, song, playlist, *, after=None, before=None, index=None, position=None ): """Add a song to a playlist. Note: * Provide no optional arguments to add to end. * Provide playlist song dicts for ``after`` and/or ``before``. * Provide a zero-based ``index``. * Provide a one-based ``position``. Songs are inserted *at* given index or position. It's also possible to add to the end by using ``len(songs)`` for index or ``len(songs) + 1`` for position. Parameters: song (dict): A song dict. playlist (dict): A playlist dict. after (dict, Optional): A playlist song dict ``songs`` will follow. before (dict, Optional): A playlist song dict ``songs`` will precede. index (int, Optional): The zero-based index position to insert ``song``. position (int, Optional): The one-based position to insert ``song``. Returns: dict: Playlist dict including songs. """ prev, next_ = get_ple_prev_next( self.playlist_songs(playlist), after=after, before=before, index=index, position=position ) if 'storeId' in song: song_id = song['storeId'] elif 'trackId' in song: song_id = song['trackId'] else: song_id = song['id'] mutation = mc_calls.PlaylistEntriesBatch.create( song_id, playlist['id'], preceding_entry_id=prev.get('id'), following_entry_id=next_.get('id') ) self._call(mc_calls.PlaylistEntriesBatch, mutation) return self.playlist(playlist['id'], include_songs=True)
python
{ "resource": "" }
q10531
MobileClient.playlist_songs_add
train
def playlist_songs_add( self, songs, playlist, *, after=None, before=None, index=None, position=None ): """Add songs to a playlist. Note: * Provide no optional arguments to add to end. * Provide playlist song dicts for ``after`` and/or ``before``. * Provide a zero-based ``index``. * Provide a one-based ``position``. Songs are inserted *at* given index or position. It's also possible to add to the end by using ``len(songs)`` for index or ``len(songs) + 1`` for position. Parameters: songs (list): A list of song dicts. playlist (dict): A playlist dict. after (dict, Optional): A playlist song dict ``songs`` will follow. before (dict, Optional): A playlist song dict ``songs`` will precede. index (int, Optional): The zero-based index position to insert ``songs``. position (int, Optional): The one-based position to insert ``songs``. Returns: dict: Playlist dict including songs. """ playlist_songs = self.playlist_songs(playlist) prev, next_ = get_ple_prev_next( playlist_songs, after=after, before=before, index=index, position=position ) songs_len = len(songs) for i, song in enumerate(songs): if 'storeId' in song: song_id = song['storeId'] elif 'trackId' in song: song_id = song['trackId'] else: song_id = song['id'] mutation = mc_calls.PlaylistEntriesBatch.create( song_id, playlist['id'], preceding_entry_id=prev.get('id'), following_entry_id=next_.get('id') ) response = self._call(mc_calls.PlaylistEntriesBatch, mutation) result = response.body['mutate_response'][0] # TODO: Proper exception on failure. if result['response_code'] != 'OK': break if i < songs_len - 1: while True: prev = self.playlist_song(result['id']) if prev: break return self.playlist(playlist['id'], include_songs=True)
python
{ "resource": "" }
q10532
MobileClient.playlist_song_delete
train
def playlist_song_delete(self, playlist_song): """Delete song from playlist. Parameters: playlist_song (str): A playlist song dict. Returns: dict: Playlist dict including songs. """ self.playlist_songs_delete([playlist_song]) return self.playlist(playlist_song['playlistId'], include_songs=True)
python
{ "resource": "" }
q10533
MobileClient.playlist_songs_delete
train
def playlist_songs_delete(self, playlist_songs): """Delete songs from playlist. Parameters: playlist_songs (list): A list of playlist song dicts. Returns: dict: Playlist dict including songs. """ if not more_itertools.all_equal( playlist_song['playlistId'] for playlist_song in playlist_songs ): raise ValueError( "All 'playlist_songs' must be from the same playlist." ) mutations = [mc_calls.PlaylistEntriesBatch.delete(playlist_song['id']) for playlist_song in playlist_songs] self._call(mc_calls.PlaylistEntriesBatch, mutations) return self.playlist(playlist_songs[0]['playlistId'], include_songs=True)
python
{ "resource": "" }
q10534
MobileClient.playlist_song_move
train
def playlist_song_move( self, playlist_song, *, after=None, before=None, index=None, position=None ): """Move a song in a playlist. Note: * Provide no optional arguments to move to end. * Provide playlist song dicts for ``after`` and/or ``before``. * Provide a zero-based ``index``. * Provide a one-based ``position``. Songs are inserted *at* given index or position. It's also possible to move to the end by using ``len(songs)`` for index or ``len(songs) + 1`` for position. Parameters: playlist_song (dict): A playlist song dict. after (dict, Optional): A playlist song dict ``songs`` will follow. before (dict, Optional): A playlist song dict ``songs`` will precede. index (int, Optional): The zero-based index position to insert ``song``. position (int, Optional): The one-based position to insert ``song``. Returns: dict: Playlist dict including songs. """ playlist_songs = self.playlist( playlist_song['playlistId'], include_songs=True )['tracks'] prev, next_ = get_ple_prev_next( playlist_songs, after=after, before=before, index=index, position=position ) mutation = mc_calls.PlaylistEntriesBatch.update( playlist_song, preceding_entry_id=prev.get('id'), following_entry_id=next_.get('id') ) self._call(mc_calls.PlaylistEntriesBatch, mutation) return self.playlist(playlist_song['playlistId'], include_songs=True)
python
{ "resource": "" }
q10535
MobileClient.playlist_songs_move
train
def playlist_songs_move( self, playlist_songs, *, after=None, before=None, index=None, position=None ): """Move songs in a playlist. Note: * Provide no optional arguments to move to end. * Provide playlist song dicts for ``after`` and/or ``before``. * Provide a zero-based ``index``. * Provide a one-based ``position``. Songs are inserted *at* given index or position. It's also possible to move to the end by using ``len(songs)`` for index or ``len(songs) + 1`` for position. Parameters: playlist_songs (list): A list of playlist song dicts. after (dict, Optional): A playlist song dict ``songs`` will follow. before (dict, Optional): A playlist song dict ``songs`` will precede. index (int, Optional): The zero-based index position to insert ``songs``. position (int, Optional): The one-based position to insert ``songs``. Returns: dict: Playlist dict including songs. """ if not more_itertools.all_equal( playlist_song['playlistId'] for playlist_song in playlist_songs ): raise ValueError( "All 'playlist_songs' must be from the same playlist." ) playlist = self.playlist( playlist_songs[0]['playlistId'], include_songs=True ) prev, next_ = get_ple_prev_next( playlist['tracks'], after=after, before=before, index=index, position=position ) playlist_songs_len = len(playlist_songs) for i, playlist_song in enumerate(playlist_songs): mutation = mc_calls.PlaylistEntriesBatch.update( playlist_song, preceding_entry_id=prev.get('id'), following_entry_id=next_.get('id') ) response = self._call(mc_calls.PlaylistEntriesBatch, mutation) result = response.body['mutate_response'][0] # TODO: Proper exception on failure. if result['response_code'] != 'OK': break if i < playlist_songs_len - 1: while True: prev = self.playlist_song(result['id']) if prev: break return self.playlist(playlist_songs[0]['playlistId'], include_songs=True)
python
{ "resource": "" }
q10536
MobileClient.playlist_songs
train
def playlist_songs(self, playlist): """Get a listing of songs from a playlist. Paramters: playlist (dict): A playlist dict. Returns: list: Playlist song dicts. """ playlist_type = playlist.get('type') playlist_song_list = [] if playlist_type in ('USER_GENERATED', None): start_token = None playlist_song_list = [] while True: response = self._call( mc_calls.PlaylistEntryFeed, max_results=49995, start_token=start_token ) items = response.body.get('data', {}).get('items', []) if items: playlist_song_list.extend(items) start_token = response.body.get('nextPageToken') if start_token is None: break elif playlist_type == 'SHARED': playlist_share_token = playlist['shareToken'] start_token = None playlist_song_list = [] while True: response = self._call( mc_calls.PlaylistEntriesShared, playlist_share_token, max_results=49995, start_token=start_token ) entry = response.body['entries'][0] items = entry.get('playlistEntry', []) if items: playlist_song_list.extend(items) start_token = entry.get('nextPageToken') if start_token is None: break playlist_song_list.sort(key=itemgetter('absolutePosition')) return playlist_song_list
python
{ "resource": "" }
q10537
MobileClient.playlist
train
def playlist(self, playlist_id, *, include_songs=False): """Get information about a playlist. Parameters: playlist_id (str): A playlist ID. include_songs (bool, Optional): Include songs from the playlist in the returned dict. Default: ``False`` Returns: dict: Playlist information. """ playlist_info = next( ( playlist for playlist in self.playlists(include_songs=include_songs) if playlist['id'] == playlist_id ), None ) return playlist_info
python
{ "resource": "" }
q10538
MobileClient.playlist_create
train
def playlist_create( self, name, description='', *, make_public=False, songs=None ): """Create a playlist. Parameters: name (str): Name to give the playlist. description (str): Description to give the playlist. make_public (bool, Optional): If ``True`` and account has a subscription, make playlist public. Default: ``False`` songs (list, Optional): A list of song dicts to add to the playlist. Returns: dict: Playlist information. """ share_state = 'PUBLIC' if make_public else 'PRIVATE' playlist = self._call( mc_calls.PlaylistsCreate, name, description, share_state ).body if songs: playlist = self.playlist_songs_add(songs, playlist) return playlist
python
{ "resource": "" }
q10539
MobileClient.playlist_subscribe
train
def playlist_subscribe(self, playlist): """Subscribe to a public playlist. Parameters: playlist (dict): A public playlist dict. Returns: dict: Playlist information. """ mutation = mc_calls.PlaylistBatch.create( playlist['name'], playlist['description'], 'SHARED', owner_name=playlist.get('ownerName', ''), share_token=playlist['shareToken'] ) response_body = self._call( mc_calls.PlaylistBatch, mutation ).body playlist_id = response_body['mutate_response'][0]['id'] return self.playlist(playlist_id)
python
{ "resource": "" }
q10540
MobileClient.playlists
train
def playlists(self, *, include_songs=False): """Get a listing of library playlists. Parameters: include_songs (bool, Optional): Include songs in the returned playlist dicts. Default: ``False``. Returns: list: A list of playlist dicts. """ playlist_list = [] for chunk in self.playlists_iter(page_size=49995): for playlist in chunk: if include_songs: playlist['tracks'] = self.playlist_songs(playlist) playlist_list.append(playlist) return playlist_list
python
{ "resource": "" }
q10541
MobileClient.playlists_iter
train
def playlists_iter(self, *, start_token=None, page_size=250): """Get a paged iterator of library playlists. Parameters: start_token (str): The token of the page to return. Default: Not sent to get first page. page_size (int, Optional): The maximum number of results per returned page. Max allowed is ``49995``. Default: ``250`` Yields: list: Playlist dicts. """ start_token = None while True: response = self._call( mc_calls.PlaylistFeed, max_results=page_size, start_token=start_token ) items = response.body.get('data', {}).get('items', []) if items: yield items start_token = response.body.get('nextPageToken') if start_token is None: break
python
{ "resource": "" }
q10542
MobileClient.podcast
train
def podcast(self, podcast_series_id, *, max_episodes=50): """Get information about a podcast series. Parameters: podcast_series_id (str): A podcast series ID. max_episodes (int, Optional): Include up to given number of episodes in returned dict. Default: ``50`` Returns: dict: Podcast series information. """ podcast_info = self._call( mc_calls.PodcastFetchSeries, podcast_series_id, max_episodes=max_episodes ).body return podcast_info
python
{ "resource": "" }
q10543
MobileClient.podcasts
train
def podcasts(self, *, device_id=None): """Get a listing of subsribed podcast series. Paramaters: device_id (str, Optional): A mobile device ID. Default: Use ``device_id`` of the :class:`MobileClient` instance. Returns: list: Podcast series dict. """ if device_id is None: device_id = self.device_id podcast_list = [] for chunk in self.podcasts_iter(device_id=device_id, page_size=49995): podcast_list.extend(chunk) return podcast_list
python
{ "resource": "" }
q10544
MobileClient.podcasts_iter
train
def podcasts_iter(self, *, device_id=None, page_size=250): """Get a paged iterator of subscribed podcast series. Parameters: device_id (str, Optional): A mobile device ID. Default: Use ``device_id`` of the :class:`MobileClient` instance. page_size (int, Optional): The maximum number of results per returned page. Max allowed is ``49995``. Default: ``250`` Yields: list: Podcast series dicts. """ if device_id is None: device_id = self.device_id start_token = None prev_items = None while True: response = self._call( mc_calls.PodcastSeries, device_id, max_results=page_size, start_token=start_token ) items = response.body.get('data', {}).get('items', []) # Google does some weird shit. if items != prev_items: subscribed_podcasts = [ item for item in items if item.get('userPreferences', {}).get('subscribed') ] yield subscribed_podcasts prev_items = items else: break start_token = response.body.get('nextPageToken') if start_token is None: break
python
{ "resource": "" }
q10545
MobileClient.podcast_episode
train
def podcast_episode(self, podcast_episode_id): """Get information about a podcast_episode. Parameters: podcast_episode_id (str): A podcast episode ID. Returns: dict: Podcast episode information. """ response = self._call( mc_calls.PodcastFetchEpisode, podcast_episode_id ) podcast_episode_info = [ podcast_episode for podcast_episode in response.body if not podcast_episode['deleted'] ] return podcast_episode_info
python
{ "resource": "" }
q10546
MobileClient.podcast_episodes
train
def podcast_episodes(self, *, device_id=None): """Get a listing of podcast episodes for all subscribed podcasts. Paramaters: device_id (str, Optional): A mobile device ID. Default: Use ``device_id`` of the :class:`MobileClient` instance. Returns: list: Podcast episode dicts. """ if device_id is None: device_id = self.device_id podcast_episode_list = [] for chunk in self.podcast_episodes_iter( device_id=device_id, page_size=49995 ): podcast_episode_list.extend(chunk) return podcast_episode_list
python
{ "resource": "" }
q10547
MobileClient.podcast_episodes_iter
train
def podcast_episodes_iter(self, *, device_id=None, page_size=250): """Get a paged iterator of podcast episode for all subscribed podcasts. Parameters: device_id (str, Optional): A mobile device ID. Default: Use ``device_id`` of the :class:`MobileClient` instance. page_size (int, Optional): The maximum number of results per returned page. Max allowed is ``49995``. Default: ``250`` Yields: list: Podcast episode dicts. """ if device_id is None: device_id = self.device_id start_token = None prev_items = None while True: response = self._call( mc_calls.PodcastEpisode, device_id, max_results=page_size, start_token=start_token ) items = response.body.get('data', {}).get('items', []) # Google does some weird shit. if items != prev_items: yield items prev_items = items else: break start_token = response.body.get('nextPageToken') if start_token is None: break
python
{ "resource": "" }
q10548
MobileClient.search
train
def search(self, query, *, max_results=100, **kwargs): """Search Google Music and library for content. Parameters: query (str): Search text. max_results (int, Optional): Maximum number of results per type per location to retrieve. I.e up to 100 Google and 100 library for a total of 200 for the default value. Google only accepts values up to 100. Default: ``100`` kwargs (bool, Optional): Any of ``albums``, ``artists``, ``genres``, ``playlists``, ``podcasts``, ``situations``, ``songs``, ``stations``, ``videos`` set to ``True`` will include that result type in the returned dict. Setting none of them will include all result types in the returned dict. Returns: dict: A dict of results separated into keys: ``'albums'``, ``'artists'``, ``'genres'``, ``'playlists'``, ```'podcasts'``, ``'situations'``, ``'songs'``, ``'stations'``, ``'videos'``. Note: Free account search is restricted so may not contain hits for all result types. """ results = defaultdict(list) for type_, results_ in self.search_library( query, max_results=max_results, **kwargs ).items(): results[type_].extend(results_) for type_, results_ in self.search_google( query, max_results=max_results, **kwargs ).items(): results[type_].extend(results_) return dict(results)
python
{ "resource": "" }
q10549
MobileClient.search_suggestion
train
def search_suggestion(self, query): """Get search query suggestions for query. Parameters: query (str): Search text. Returns: list: Suggested query strings. """ response = self._call( mc_calls.QuerySuggestion, query ) suggested_queries = response.body.get('suggested_queries', []) return [ suggested_query['suggestion_string'] for suggested_query in suggested_queries ]
python
{ "resource": "" }
q10550
MobileClient.situations
train
def situations(self, *, tz_offset=None): """Get a listing of situations. Parameters: tz_offset (int, Optional): A time zone offset from UTC in seconds. """ response = self._call( mc_calls.ListenNowSituations, tz_offset ) situation_list = response.body.get('situations', []) return situation_list
python
{ "resource": "" }
q10551
MobileClient.song
train
def song(self, song_id): """Get information about a song. Parameters: song_id (str): A song ID. Returns: dict: Song information. """ if song_id.startswith('T'): song_info = self._call( mc_calls.FetchTrack, song_id ).body else: song_info = next( ( song for song in self.songs() if song['id'] == song_id ), None ) return song_info
python
{ "resource": "" }
q10552
MobileClient.songs_add
train
def songs_add(self, songs): """Add store songs to your library. Parameters: songs (list): A list of store song dicts. Returns: list: Songs' library IDs. """ mutations = [mc_calls.TrackBatch.add(song) for song in songs] response = self._call( mc_calls.TrackBatch, mutations ) success_ids = [ res['id'] for res in response.body['mutate_response'] if res['response_code'] == 'OK' ] return success_ids
python
{ "resource": "" }
q10553
MobileClient.songs_delete
train
def songs_delete(self, songs): """Delete songs from library. Parameters: song (list): A list of song dicts. Returns: list: Successfully deleted song IDs. """ mutations = [mc_calls.TrackBatch.delete(song['id']) for song in songs] response = self._call( mc_calls.TrackBatch, mutations ) success_ids = [ res['id'] for res in response.body['mutate_response'] if res['response_code'] == 'OK' ] # TODO: Report failures. # failure_ids = [ # res['id'] # for res in response.body['mutate_response'] # if res['response_code'] != 'OK' # ] return success_ids
python
{ "resource": "" }
q10554
MobileClient.song_play
train
def song_play(self, song): """Add play to song play count. Parameters: song (dict): A song dict. Returns: bool: ``True`` if successful, ``False`` if not. """ if 'storeId' in song: song_id = song['storeId'] elif 'trackId' in song: song_id = song['trackId'] else: song_id = song['id'] song_duration = song['durationMillis'] event = mc_calls.ActivityRecordRealtime.play(song_id, song_duration) response = self._call( mc_calls.ActivityRecordRealtime, event ) return True if response.body['eventResults'][0]['code'] == 'OK' else False
python
{ "resource": "" }
q10555
MobileClient.song_rate
train
def song_rate(self, song, rating): """Rate song. Parameters: song (dict): A song dict. rating (int): 0 (not rated), 1 (thumbs down), or 5 (thumbs up). Returns: bool: ``True`` if successful, ``False`` if not. """ if 'storeId' in song: song_id = song['storeId'] elif 'trackId' in song: song_id = song['trackId'] else: song_id = song['id'] event = mc_calls.ActivityRecordRealtime.rate(song_id, rating) response = self._call( mc_calls.ActivityRecordRealtime, event ) return True if response.body['eventResults'][0]['code'] == 'OK' else False
python
{ "resource": "" }
q10556
MobileClient.songs
train
def songs(self): """Get a listing of library songs. Returns: list: Song dicts. """ song_list = [] for chunk in self.songs_iter(page_size=49995): song_list.extend(chunk) return song_list
python
{ "resource": "" }
q10557
MobileClient.songs_iter
train
def songs_iter(self, *, page_size=250): """Get a paged iterator of library songs. Parameters: page_size (int, Optional): The maximum number of results per returned page. Max allowed is ``49995``. Default: ``250`` Yields: list: Song dicts. """ start_token = None while True: response = self._call( mc_calls.TrackFeed, max_results=page_size, start_token=start_token ) items = response.body.get('data', {}).get('items', []) if items: yield items start_token = response.body.get('nextPageToken') if start_token is None: break
python
{ "resource": "" }
q10558
MobileClient.station
train
def station(self, station_id, *, num_songs=25, recently_played=None): """Get information about a station. Parameters: station_id (str): A station ID. Use 'IFL' for I'm Feeling Lucky. num_songs (int, Optional): The maximum number of songs to return from the station. Default: ``25`` recently_played (list, Optional): A list of dicts in the form of {'id': '', 'type'} where ``id`` is a song ID and ``type`` is 0 for a library song and 1 for a store song. Returns: dict: Station information. """ station_info = { 'station_id': station_id, 'num_entries': num_songs, 'library_content_only': False } if recently_played is not None: station_info['recently_played'] = recently_played response = self._call( mc_calls.RadioStationFeed, station_infos=[station_info] ) station_feed = response.body.get('data', {}).get('stations', []) try: station = station_feed[0] except IndexError: station = {} return station
python
{ "resource": "" }
q10559
MobileClient.station_feed
train
def station_feed(self, *, num_songs=25, num_stations=4): """Generate stations. Note: A Google Music subscription is required. Parameters: num_songs (int, Optional): The total number of songs to return. Default: ``25`` num_stations (int, Optional): The number of stations to return when no station_infos is provided. Default: ``5`` Returns: list: Station information dicts. """ response = self._call( mc_calls.RadioStationFeed, num_entries=num_songs, num_stations=num_stations ) station_feed = response.body.get('data', {}).get('stations', []) return station_feed
python
{ "resource": "" }
q10560
MobileClient.station_songs
train
def station_songs(self, station, *, num_songs=25, recently_played=None): """Get a listing of songs from a station. Parameters: station (str): A station dict. num_songs (int, Optional): The maximum number of songs to return from the station. Default: ``25`` recently_played (list, Optional): A list of dicts in the form of {'id': '', 'type'} where ``id`` is a song ID and ``type`` is 0 for a library song and 1 for a store song. Returns: list: Station song dicts. """ station_id = station['id'] station = self.station( station_id, num_songs=num_songs, recently_played=recently_played ) return station.get('tracks', [])
python
{ "resource": "" }
q10561
MobileClient.stations
train
def stations(self, *, generated=True, library=True): """Get a listing of library stations. The listing can contain stations added to the library and generated from the library. Parameters: generated (bool, Optional): Include generated stations. Default: True library (bool, Optional): Include library stations. Default: True Returns: list: Station information dicts. """ station_list = [] for chunk in self.stations_iter(page_size=49995): for station in chunk: if ( (generated and not station.get('inLibrary')) or (library and station.get('inLibrary')) ): station_list.append(station) return station_list
python
{ "resource": "" }
q10562
MobileClient.stations_iter
train
def stations_iter(self, *, page_size=250): """Get a paged iterator of library stations. Parameters: page_size (int, Optional): The maximum number of results per returned page. Max allowed is ``49995``. Default: ``250`` Yields: list: Station dicts. """ start_token = None while True: response = self._call( mc_calls.RadioStation, max_results=page_size, start_token=start_token ) yield response.body.get('data', {}).get('items', []) start_token = response.body.get('nextPageToken') if start_token is None: break
python
{ "resource": "" }
q10563
MobileClient.stream
train
def stream(self, item, *, device_id=None, quality='hi', session_token=None): """Get MP3 stream of a podcast episode, library song, station_song, or store song. Note: Streaming requires a ``device_id`` from a valid, linked mobile device. Parameters: item (str): A podcast episode, library song, station_song, or store song. A Google Music subscription is required to stream store songs. device_id (str, Optional): A mobile device ID. Default: Use ``device_id`` of the :class:`MobileClient` instance. quality (str, Optional): Stream quality is one of ``'hi'`` (320Kbps), ``'med'`` (160Kbps), or ``'low'`` (128Kbps). Default: ``'hi'``. session_token (str): Session token from a station dict required for unsubscribed users to stream a station song. station['sessionToken'] as returend by :meth:`station` only exists for free accounts. Returns: bytes: An MP3 file. """ if device_id is None: device_id = self.device_id stream_url = self.stream_url( item, device_id=device_id, quality=quality, session_token=session_token ) response = self.session.get(stream_url) audio = response.content return audio
python
{ "resource": "" }
q10564
MobileClient.stream_url
train
def stream_url(self, item, *, device_id=None, quality='hi', session_token=None): """Get a URL to stream a podcast episode, library song, station_song, or store song. Note: Streaming requires a ``device_id`` from a valid, linked mobile device. Parameters: item (str): A podcast episode, library song, station_song, or store song. A Google Music subscription is required to stream store songs. device_id (str, Optional): A mobile device ID. Default: Use ``device_id`` of the :class:`MobileClient` instance. quality (str, Optional): Stream quality is one of ``'hi'`` (320Kbps), ``'med'`` (160Kbps), or ``'low'`` (128Kbps). Default: ``'hi'``. session_token (str): Session token from a station dict required for unsubscribed users to stream a station song. station['sessionToken'] as returend by :meth:`station` only exists for free accounts. Returns: str: A URL to an MP3 file. """ if device_id is None: device_id = self.device_id if 'episodeId' in item: # Podcast episode. response = self._call( mc_calls.PodcastEpisodeStreamURL, item['episodeId'], quality=quality, device_id=device_id ) elif 'wentryid' in item: # Free account station song. response = self._call( mc_calls.RadioStationTrackStreamURL, item['storeId'], item['wentryid'], session_token, quality=quality, device_id=device_id ) elif 'trackId' in item: # Playlist song. response = self._call( mc_calls.TrackStreamURL, item['trackId'], quality=quality, device_id=device_id ) elif 'storeId' in item and self.is_subscribed: # Store song. response = self._call( mc_calls.TrackStreamURL, item['storeId'], quality=quality, device_id=device_id ) elif 'id' in item: # Library song. response = self._call( mc_calls.TrackStreamURL, item['id'], quality=quality, device_id=device_id ) else: # TODO: Create an exception for not being subscribed or use a better builtin exception for this case. if 'storeId' in item and not self.is_subscribed: msg = "Can't stream a store song without a subscription." else: msg = "Item does not contain an ID field." raise ValueError(msg) try: stream_url = response.headers['Location'] except KeyError: stream_url = response.body['url'] return stream_url
python
{ "resource": "" }
q10565
MobileClient.thumbs_up_songs
train
def thumbs_up_songs(self, *, library=True, store=True): """Get a listing of 'Thumbs Up' store songs. Parameters: library (bool, Optional): Include 'Thumbs Up' songs from library. Default: True generated (bool, Optional): Include 'Thumbs Up' songs from store. Default: True Returns: list: Dicts of 'Thumbs Up' songs. """ thumbs_up_songs = [] if library is True: thumbs_up_songs.extend( song for song in self.songs() if song.get('rating', '0') == '5' ) if store is True: response = self._call(mc_calls.EphemeralTop) thumbs_up_songs.extend(response.body.get('data', {}).get('items', [])) return thumbs_up_songs
python
{ "resource": "" }
q10566
MobileClient.top_charts
train
def top_charts(self): """Get a listing of the default top charts.""" response = self._call(mc_calls.BrowseTopChart) top_charts = response.body return top_charts
python
{ "resource": "" }
q10567
MobileClient.top_charts_for_genre
train
def top_charts_for_genre(self, genre_id): """Get a listing of top charts for a top chart genre. Parameters: genre_id (str): A top chart genre ID as found with :meth:`top_charts_genres`. """ response = self._call(mc_calls.BrowseTopChartForGenre, genre_id) top_chart_for_genre = response.body return top_chart_for_genre
python
{ "resource": "" }
q10568
MobileClient.top_charts_genres
train
def top_charts_genres(self): """Get a listing of genres from the browse top charts tab.""" response = self._call(mc_calls.BrowseTopChartGenres) top_chart_genres = response.body.get('genres', []) return top_chart_genres
python
{ "resource": "" }
q10569
run
train
def run(stream=sys.stdin.buffer): """Reads from stream, applying the LT decoding algorithm to incoming encoded blocks until sufficiently many blocks have been received to reconstruct the entire file. """ payload = decode.decode(stream) sys.stdout.write(payload.decode('utf8'))
python
{ "resource": "" }
q10570
_split_file
train
def _split_file(f, blocksize): """Block file byte contents into blocksize chunks, padding last one if necessary """ f_bytes = f.read() blocks = [int.from_bytes(f_bytes[i:i+blocksize].ljust(blocksize, b'0'), sys.byteorder) for i in range(0, len(f_bytes), blocksize)] return len(f_bytes), blocks
python
{ "resource": "" }
q10571
encoder
train
def encoder(f, blocksize, seed=None, c=sampler.DEFAULT_C, delta=sampler.DEFAULT_DELTA): """Generates an infinite sequence of blocks to transmit to the receiver """ # Generate seed if not provided if seed is None: seed = randint(0, 1 << 31 - 1) # get file blocks filesize, blocks = _split_file(f, blocksize) # init stream vars K = len(blocks) prng = sampler.PRNG(params=(K, delta, c)) prng.set_seed(seed) # block generation loop while True: blockseed, d, ix_samples = prng.get_src_blocks() block_data = 0 for ix in ix_samples: block_data ^= blocks[ix] # Generate blocks of XORed data in network byte order block = (filesize, blocksize, blockseed, int.to_bytes(block_data, blocksize, sys.byteorder)) yield pack('!III%ss'%blocksize, *block)
python
{ "resource": "" }
q10572
_read_block
train
def _read_block(blocksize, stream): """Read block data from network into integer type """ blockdata = stream.read(blocksize) return int.from_bytes(blockdata, 'big')
python
{ "resource": "" }
q10573
read_blocks
train
def read_blocks(stream): """Generate parsed blocks from input stream """ while True: header = _read_header(stream) block = _read_block(header[1], stream) yield (header, block)
python
{ "resource": "" }
q10574
BlockGraph.add_block
train
def add_block(self, nodes, data): """Adds a new check node and edges between that node and all source nodes it connects, resolving all message passes that become possible as a result. """ # We can eliminate this source node if len(nodes) == 1: to_eliminate = list(self.eliminate(next(iter(nodes)), data)) # Recursively eliminate all nodes that can now be resolved while len(to_eliminate): other, check = to_eliminate.pop() to_eliminate.extend(self.eliminate(other, check)) else: # Pass messages from already-resolved source nodes for node in list(nodes): if node in self.eliminated: nodes.remove(node) data ^= self.eliminated[node] # Resolve if we are left with a single non-resolved source node if len(nodes) == 1: return self.add_block(nodes, data) else: # Add edges for all remaining nodes to this check check = CheckNode(nodes, data) for node in nodes: self.checks[node].append(check) # Are we done yet? return len(self.eliminated) >= self.num_blocks
python
{ "resource": "" }
q10575
BlockGraph.eliminate
train
def eliminate(self, node, data): """Resolves a source node, passing the message to all associated checks """ # Cache resolved value self.eliminated[node] = data others = self.checks[node] del self.checks[node] # Pass messages to all associated checks for check in others: check.check ^= data check.src_nodes.remove(node) # Yield all nodes that can now be resolved if len(check.src_nodes) == 1: yield (next(iter(check.src_nodes)), check.check)
python
{ "resource": "" }
q10576
mobileclient
train
def mobileclient(username=None, device_id=None, *, token=None, locale='en_US'): """Create and authenticate a Google Music mobile client. >>> import google_music >>> mc = google_music.mobileclient('username') Parameters: username (str, Optional): Your Google Music username. This is used to store OAuth credentials for different accounts separately. device_id (str, Optional): A mobile device ID. Default: MAC address is used. token (dict, Optional): An OAuth token compatible with ``requests-oauthlib``. locale (str, Optional): `ICU <http://www.localeplanet.com/icu/>`__ locale used to localize some responses. This must be a locale supported by Android. Default: `'en_US'``. Returns: MobileClient: An authenticated :class:`~google_music.MobileClient` instance. """ return MobileClient( username, device_id, token=token, locale=locale )
python
{ "resource": "" }
q10577
_dendropy_to_dataframe
train
def _dendropy_to_dataframe( tree, add_node_labels=True, use_uids=True): """Convert Dendropy tree to Pandas dataframe.""" # Maximum distance from root. tree.max_distance_from_root() # Initialize the data object. idx = [] data = { 'type': [], 'id': [], 'parent': [], 'length': [], 'label': [], 'distance': []} if use_uids: data['uid'] = [] # Add labels to internal nodes if set to true. if add_node_labels: for i, node in enumerate(tree.internal_nodes()): node.label = str(i) for node in tree.nodes(): # Get node type if node.is_leaf(): type_ = 'leaf' label = str(node.taxon.label).replace(' ', '_') elif node.is_internal(): type_ = 'node' label = str(node.label) # Set node label and parent. id_ = label parent_node = node.parent_node length = node.edge_length distance = node.distance_from_root() # Is this node a root? if parent_node is None and length is None: parent_label = None parent_node = None length = 0 distance = 0 type_ = 'root' # Set parent node label elif parent_node.is_internal(): parent_label = str(parent_node.label) else: raise Exception("Subtree is not attached to tree?") # Add this node to the data. data['type'].append(type_) data['id'].append(id_) data['parent'].append(parent_label) data['length'].append(length) data['label'].append(label) data['distance'].append(distance) if use_uids: data['uid'].append(get_random_id(10)) # Construct dataframe. df = pandas.DataFrame(data) return df
python
{ "resource": "" }
q10578
_read
train
def _read( filename=None, data=None, schema=None, add_node_labels=True, use_uids=True ): """Read a phylogenetic tree into a phylopandas.DataFrame. The resulting DataFrame has the following columns: - name: label for each taxa or node. - id: unique id (created by phylopandas) given to each node. - type: type of node (leaf, internal, or root). - parent: parent id. necessary for constructing trees. - length: length of branch from parent to node. - distance: distance from root. Parameters ---------- filename: str (default is None) newick file to read into DataFrame. data: str (default is None) newick string to parse and read into DataFrame. add_node_labels: bool If true, labels the internal nodes with numbers. Returns ------- df: phylopandas.DataFrame. """ if filename is not None: # Use Dendropy to parse tree. tree = dendropy.Tree.get( path=filename, schema=schema, preserve_underscores=True) elif data is not None: tree = dendropy.Tree.get( data=data, schema=schema, preserve_underscores=True) else: raise Exception('No tree given?') df = _dendropy_to_dataframe( tree, add_node_labels=add_node_labels, use_uids=use_uids ) return df
python
{ "resource": "" }
q10579
pandas_df_to_biopython_seqrecord
train
def pandas_df_to_biopython_seqrecord( df, id_col='uid', sequence_col='sequence', extra_data=None, alphabet=None, ): """Convert pandas dataframe to biopython seqrecord for easy writing. Parameters ---------- df : Dataframe Pandas dataframe to convert id_col : str column in dataframe to use as sequence label sequence_col str: column in dataframe to use as sequence data extra_data : list extra columns to use in sequence description line alphabet : biopython Alphabet object Returns ------- seq_records : List of biopython seqrecords. """ seq_records = [] for i, row in df.iterrows(): # Tries getting sequence data. If a TypeError at the seqrecord # creation is thrown, it is assumed that this row does not contain # sequence data and therefore the row is ignored. try: # Get sequence seq = Seq(row[sequence_col], alphabet=alphabet) # Get id id = row[id_col] # Build a description description = "" if extra_data is not None: description = " ".join([row[key] for key in extra_data]) # Build a record record = SeqRecord( seq=seq, id=id, description=description, ) seq_records.append(record) except TypeError: pass return seq_records
python
{ "resource": "" }
q10580
pandas_series_to_biopython_seqrecord
train
def pandas_series_to_biopython_seqrecord( series, id_col='uid', sequence_col='sequence', extra_data=None, alphabet=None ): """Convert pandas series to biopython seqrecord for easy writing. Parameters ---------- series : Series Pandas series to convert id_col : str column in dataframe to use as sequence label sequence_col : str column in dataframe to use as sequence data extra_data : list extra columns to use in sequence description line Returns ------- seq_records : List of biopython seqrecords. """ # Get sequence seq = Seq(series[sequence_col], alphabet=alphabet) # Get id id = series[id_col] # Build a description description = "" if extra_data is not None: description = " ".join([series[key] for key in extra_data]) # Build a record record = SeqRecord( seq=seq, id=id, description=description, ) seq_records = [record] return seq_records
python
{ "resource": "" }
q10581
_write
train
def _write( data, filename=None, schema='fasta', id_col='uid', sequence_col='sequence', extra_data=None, alphabet=None, **kwargs): """General write function. Write phylopanda data to biopython format. Parameters ---------- filename : str File to write string to. If no filename is given, a string will be returned. sequence_col : str (default='sequence') Sequence column name in DataFrame. id_col : str (default='id') ID column name in DataFrame id_only : bool (default=False) If True, use only the ID column to label sequences in fasta. """ # Check Alphabet if given if alphabet is None: alphabet = Bio.Alphabet.Alphabet() elif alphabet in ['dna', 'rna', 'protein', 'nucleotide']: alphabet = getattr(Bio.Alphabet, 'generic_{}'.format(alphabet)) else: raise Exception( "The alphabet is not recognized. Must be 'dna', 'rna', " "'nucleotide', or 'protein'.") # Build a list of records from a pandas DataFrame if type(data) is pd.DataFrame: seq_records = pandas_df_to_biopython_seqrecord( data, id_col=id_col, sequence_col=sequence_col, extra_data=extra_data, alphabet=alphabet, ) # Build a record from a pandas Series elif type(data) is pd.Series: seq_records = pandas_series_to_biopython_seqrecord( data, id_col=id_col, sequence_col=sequence_col, extra_data=extra_data, alphabet=alphabet, ) # Write to disk or return string if filename is not None: SeqIO.write(seq_records, filename, format=schema, **kwargs) else: return "".join([s.format(schema) for s in seq_records])
python
{ "resource": "" }
q10582
_read
train
def _read( filename, schema, seq_label='sequence', alphabet=None, use_uids=True, **kwargs): """Use BioPython's sequence parsing module to convert any file format to a Pandas DataFrame. The resulting DataFrame has the following columns: - name - id - description - sequence """ # Check Alphabet if given if alphabet is None: alphabet = Bio.Alphabet.Alphabet() elif alphabet in ['dna', 'rna', 'protein', 'nucleotide']: alphabet = getattr(Bio.Alphabet, 'generic_{}'.format(alphabet)) else: raise Exception( "The alphabet is not recognized. Must be 'dna', 'rna', " "'nucleotide', or 'protein'.") kwargs.update(alphabet=alphabet) # Prepare DataFrame fields. data = { 'id': [], seq_label: [], 'description': [], 'label': [] } if use_uids: data['uid'] = [] # Parse Fasta file. for i, s in enumerate(SeqIO.parse(filename, format=schema, **kwargs)): data['id'].append(s.id) data[seq_label].append(str(s.seq)) data['description'].append(s.description) data['label'].append(s.name) if use_uids: data['uid'].append(get_random_id(10)) # Port to DataFrame. return pd.DataFrame(data)
python
{ "resource": "" }
q10583
read_blast_xml
train
def read_blast_xml(filename, **kwargs): """Read BLAST XML format.""" # Read file. with open(filename, 'r') as f: blast_record = NCBIXML.read(f) # Prepare DataFrame fields. data = {'accession': [], 'hit_def': [], 'hit_id': [], 'title': [], 'length': [], 'e_value': [], 'sequence': []} # Get alignments from blast result. for i, s in enumerate(blast_record.alignments): data['accession'] = s.accession data['hit_def'] = s.hit_def data['hit_id'] = s.hit_id data['title'] = s.title data['length'] = s.length data['e_value'] = s.hsps[0].expect data['sequence'] = s.hsps[0].sbjct # Port to DataFrame. return pd.DataFrame(data)
python
{ "resource": "" }
q10584
_pandas_df_to_dendropy_tree
train
def _pandas_df_to_dendropy_tree( df, taxon_col='uid', taxon_annotations=[], node_col='uid', node_annotations=[], branch_lengths=True, ): """Turn a phylopandas dataframe into a dendropy tree. Parameters ---------- df : DataFrame DataFrame containing tree data. taxon_col : str (optional) Column in dataframe to label the taxon. If None, the index will be used. taxon_annotations : str List of columns to annotation in the tree taxon. node_col : str (optional) Column in dataframe to label the nodes. If None, the index will be used. node_annotations : str List of columns to annotation in the node taxon. branch_lengths : bool If True, inclues branch lengths. """ if isinstance(taxon_col, str) is False: raise Exception("taxon_col must be a string.") if isinstance(node_col, str) is False: raise Exception("taxon_col must be a string.") # Construct a list of nodes from dataframe. taxon_namespace = dendropy.TaxonNamespace() nodes = {} for idx in df.index: # Get node data. data = df.loc[idx] # Get taxon for node (if leaf node). taxon = None if data['type'] == 'leaf': taxon = dendropy.Taxon(label=data[taxon_col]) # Add annotations data. for ann in taxon_annotations: taxon.annotations.add_new(ann, data[ann]) taxon_namespace.add_taxon(taxon) # Get label for node. label = data[node_col] # Get edge length. edge_length = None if branch_lengths is True: edge_length = data['length'] # Build a node n = dendropy.Node( taxon=taxon, label=label, edge_length=edge_length ) # Add node annotations for ann in node_annotations: n.annotations.add_new(ann, data[ann]) nodes[idx] = n # Build branching pattern for nodes. root = None for idx, node in nodes.items(): # Get node data. data = df.loc[idx] # Get children nodes children_idx = df[df['parent'] == data['id']].index children_nodes = [nodes[i] for i in children_idx] # Set child nodes nodes[idx].set_child_nodes(children_nodes) # Check if this is root. if data['parent'] is None: root = nodes[idx] # Build tree. tree = dendropy.Tree( seed_node=root, taxon_namespace=taxon_namespace ) return tree
python
{ "resource": "" }
q10585
_write
train
def _write( df, filename=None, schema='newick', taxon_col='uid', taxon_annotations=[], node_col='uid', node_annotations=[], branch_lengths=True, **kwargs ): """Write a phylopandas tree DataFrame to various formats. Parameters ---------- df : DataFrame DataFrame containing tree data. filename : str filepath to write out tree. If None, will return string. schema : str tree format to write out. taxon_col : str (optional) Column in dataframe to label the taxon. If None, the index will be used. taxon_annotations : str List of columns to annotation in the tree taxon. node_col : str (optional) Column in dataframe to label the nodes. If None, the index will be used. node_annotations : str List of columns to annotation in the node taxon. branch_lengths : bool If True, inclues branch lengths. """ tree = _pandas_df_to_dendropy_tree( df, taxon_col=taxon_col, taxon_annotations=taxon_annotations, node_col=node_col, node_annotations=node_annotations, branch_lengths=branch_lengths, ) # Write out format print(schema) if filename is not None: tree.write(path=filename, schema=schema, suppress_annotations=False, **kwargs) else: return tree.as_string(schema=schema)
python
{ "resource": "" }
q10586
get_random_id
train
def get_random_id(length): """Generate a random, alpha-numerical id.""" alphabet = string.ascii_uppercase + string.ascii_lowercase + string.digits return ''.join(random.choice(alphabet) for _ in range(length))
python
{ "resource": "" }
q10587
PyGreen.set_folder
train
def set_folder(self, folder): """ Sets the folder where the files to serve are located. """ self.folder = folder self.templates.directories[0] = folder self.app.root_path = folder
python
{ "resource": "" }
q10588
PyGreen.run
train
def run(self, host='0.0.0.0', port=8080): """ Launch a development web server. """ waitress.serve(self.app, host=host, port=port)
python
{ "resource": "" }
q10589
PyGreen.get
train
def get(self, path): """ Get the content of a file, indentified by its path relative to the folder configured in PyGreen. If the file extension is one of the extensions that should be processed through Mako, it will be processed. """ data = self.app.test_client().get("/%s" % path).data return data
python
{ "resource": "" }
q10590
PyGreen.gen_static
train
def gen_static(self, output_folder): """ Generates a complete static version of the web site. It will stored in output_folder. """ files = [] for l in self.file_listers: files += l() for f in files: _logger.info("generating %s" % f) content = self.get(f) loc = os.path.join(output_folder, f) d = os.path.dirname(loc) if not os.path.exists(d): os.makedirs(d) with open(loc, "wb") as file_: file_.write(content)
python
{ "resource": "" }
q10591
PyGreen.cli
train
def cli(self, cmd_args=None): """ The command line interface of PyGreen. """ logging.basicConfig(level=logging.INFO, format='%(message)s') parser = argparse.ArgumentParser(description='PyGreen, micro web framework/static web site generator') subparsers = parser.add_subparsers(dest='action') parser_serve = subparsers.add_parser('serve', help='serve the web site') parser_serve.add_argument('-p', '--port', type=int, default=8080, help='port to serve on') parser_serve.add_argument('-f', '--folder', default=".", help='folder containg files to serve') parser_serve.add_argument('-d', '--disable-templates', action='store_true', default=False, help='just serve static files, do not use Mako') def serve(): if args.disable_templates: self.template_exts = set([]) self.run(port=args.port) parser_serve.set_defaults(func=serve) parser_gen = subparsers.add_parser('gen', help='generate a static version of the site') parser_gen.add_argument('output', help='folder to store the files') parser_gen.add_argument('-f', '--folder', default=".", help='folder containing files to generate') def gen(): self.gen_static(args.output) parser_gen.set_defaults(func=gen) args = parser.parse_args(cmd_args) self.set_folder(args.folder) print(parser.description) print("") args.func()
python
{ "resource": "" }
q10592
WSGIMimeRender
train
def WSGIMimeRender(*args, **kwargs): ''' A wrapper for _WSGIMimeRender that wrapps the inner callable with wsgi_wrap first. ''' def wrapper(*args2, **kwargs2): # take the function def wrapped(f): return _WSGIMimeRender(*args, **kwargs)(*args2, **kwargs2)(wsgi_wrap(f)) return wrapped return wrapper
python
{ "resource": "" }
q10593
URI.relative
train
def relative(self): """Identify if this URI is relative to some "current context". For example, if the protocol is missing, it's protocol-relative. If the host is missing, it's host-relative, etc. """ scheme = self.scheme if not scheme: return True return scheme.is_relative(self)
python
{ "resource": "" }
q10594
URI.resolve
train
def resolve(self, uri=None, **parts): """Attempt to resolve a new URI given an updated URI, partial or complete.""" if uri: result = self.__class__(urljoin(str(self), str(uri))) else: result = self.__class__(self) for part, value in parts.items(): if part not in self.__all_parts__: raise TypeError("Unknown URI component: " + part) setattr(result, part, value) return result
python
{ "resource": "" }
q10595
JalaliDate.replace
train
def replace(self, year=None, month=None, day=None): """ Replaces the given arguments on this instance, and return a new instance. :param year: :param month: :param day: :return: A :py:class:`khayyam.JalaliDate` with the same attributes, except for those attributes given new values by which keyword arguments are specified. """ return JalaliDate( year if year else self.year, month if month else self.month, day if day else self.day )
python
{ "resource": "" }
q10596
JalaliDate.todate
train
def todate(self): """ Calculates the corresponding day in the gregorian calendar. this is the main use case of this library. :return: Corresponding date in gregorian calendar. :rtype: :py:class:`datetime.date` """ arr = get_gregorian_date_from_julian_day(self.tojulianday()) return datetime.date(int(arr[0]), int(arr[1]), int(arr[2]))
python
{ "resource": "" }
q10597
JalaliDatetime.date
train
def date(self): """ Return date object with same year, month and day. :rtype: :py:class:`khayyam.JalaliDate` """ return khayyam.JalaliDate(self.year, self.month, self.day)
python
{ "resource": "" }
q10598
levinson_1d
train
def levinson_1d(r, order): """Levinson-Durbin recursion, to efficiently solve symmetric linear systems with toeplitz structure. Parameters --------- r : array-like input array to invert (since the matrix is symmetric Toeplitz, the corresponding pxp matrix is defined by p items only). Generally the autocorrelation of the signal for linear prediction coefficients estimation. The first item must be a non zero real. Notes ---- This implementation is in python, hence unsuitable for any serious computation. Use it as educational and reference purpose only. Levinson is a well-known algorithm to solve the Hermitian toeplitz equation: _ _ -R[1] = R[0] R[1] ... R[p-1] a[1] : : : : * : : : : _ * : -R[p] = R[p-1] R[p-2] ... R[0] a[p] _ with respect to a ( is the complex conjugate). Using the special symmetry in the matrix, the inversion can be done in O(p^2) instead of O(p^3). """ r = np.atleast_1d(r) if r.ndim > 1: raise ValueError("Only rank 1 are supported for now.") n = r.size if n < 1: raise ValueError("Cannot operate on empty array !") elif order > n - 1: raise ValueError("Order should be <= size-1") if not np.isreal(r[0]): raise ValueError("First item of input must be real.") elif not np.isfinite(1 / r[0]): raise ValueError("First item should be != 0") # Estimated coefficients a = np.empty(order + 1, 'float32') # temporary array t = np.empty(order + 1, 'float32') # Reflection coefficients k = np.empty(order, 'float32') a[0] = 1. e = r[0] for i in range(1, order + 1): acc = r[i] for j in range(1, i): acc += a[j] * r[i - j] k[i - 1] = -acc / e a[i] = k[i - 1] for j in range(order): t[j] = a[j] for j in range(1, i): a[j] += k[i - 1] * np.conj(t[i - j]) e *= 1 - k[i - 1] * np.conj(k[i - 1]) return a, e, k
python
{ "resource": "" }
q10599
acorr_lpc
train
def acorr_lpc(x, axis=-1): """Compute autocorrelation of x along the given axis. This compute the biased autocorrelation estimator (divided by the size of input signal) Notes ----- The reason why we do not use acorr directly is for speed issue.""" if not np.isrealobj(x): raise ValueError("Complex input not supported yet") maxlag = x.shape[axis] nfft = int(2 ** nextpow2(2 * maxlag - 1)) if axis != -1: x = np.swapaxes(x, -1, axis) a = _acorr_last_axis(x, nfft, maxlag) if axis != -1: a = np.swapaxes(a, -1, axis) return a
python
{ "resource": "" }