opsci-toolbox 0.0.13__py3-none-any.whl → 0.0.15__py3-none-any.whl

opsci_toolbox/helpers/common.py

@@ -383,6 +383,8 @@ def write_json(json_dict: dict, path: str, name: str) -> str:
     return file_path
 
 
+
+
 def write_dataframe_to_json(df: pd.DataFrame, path: str, name: str, orient: str = 'records') -> str:
     """
     Write a DataFrame to a JSON file.
@@ -603,7 +605,7 @@ def list_files_in_subdirectories(path: str, filetype: str = '*.json') -> list:
 
     return files
 
-def copy_file(source_path: str, destination_path: str, new_filename: str = '') -> str:
+def copy_file(source_path: str, destination_path: str, new_filename: str = None) -> str:
     """
     Copy a file from a source path to a destination path.
 

opsci_toolbox/helpers/dates.py

@@ -58,7 +58,7 @@ def number_of_days(start_date: datetime, end_date: datetime) -> int:
         days_difference (int): The number of days between the start and end dates.
     """
     # Calculate the difference
-    time_difference = start_date - end_date
+    time_difference = end_date -  start_date
     # Extract the number of days from the timedelta object
     days_difference = time_difference.days
     return days_difference

opsci_toolbox/helpers/nlp.py

@@ -7,7 +7,7 @@ import os
 from sklearn.decomposition import TruncatedSVD
 from sklearn.feature_extraction.text import TfidfVectorizer, CountVectorizer
 from sklearn.manifold import TSNE
-from sklearn.preprocessing import StandardScaler, MinMaxScaler
+from sklearn.preprocessing import StandardScaler, MinMaxScaler, LabelEncoder, OneHotEncoder
 from sklearn.cluster import AgglomerativeClustering
 from sentence_transformers import SentenceTransformer
 from tqdm import tqdm
@@ -94,7 +94,7 @@ def filter_by_query(df: pd.DataFrame, col_text: str, query: str, ignore_case: bo
             The filtered DataFrame.
     """
     eldar_query=Query(query, ignore_case = ignore_case, ignore_accent=ignore_accent, match_word=match_word)
-    df[col_text] = df[df[col_text].apply(eldar_query)]
+    df = df[df[col_text].apply(eldar_query)]
     df=df.reset_index(drop=True)
     return df
 
@@ -126,7 +126,7 @@ def TM_clean_text(df: pd.DataFrame, col: str, col_clean: str) -> pd.DataFrame:
     df[col_clean] = df[col_clean].apply(lambda x : brackets(x))
     df[col_clean] = df[col_clean].apply(lambda x : urls(x, repl= ''))
     df[col_clean] = df.apply(lambda row: " ".join(filter(lambda x: x[0] != "@", row[col_clean].split())), 1)
-    df[col_clean] = df[col_clean].apply(remove_multiple_hashtags)
+    # df[col_clean] = df[col_clean].apply(remove_multiple_hashtags)
     df[col_clean] = df[col_clean].apply(remove_extra_spaces)
     # df = df.loc[(df[col_clean] != ""), :]
     return df
@@ -541,7 +541,7 @@ def substitute_punctuations_with_white_space(text : str) -> str:
     text = re.sub(r"[%s]" % re.escape('!"#$%&\()*+,-./:;<=>?@[\\]^_`{|}~“…”’'), " ", text)
     return text
 
-def translate_wt_libre(text: str, source: str, target: str, filename: str, dir_json: str, url: str = "http://127.0.0.1:5000/translate") -> dict:
+def translate_wt_libre(text: str, source: str, target: str, filename: str, dir_json: str, url: str = "http://127.0.0.1:5000/translate", format_payload="html") -> dict:
     """
     Translate text using LibreTranslate service.
 
@@ -558,6 +558,8 @@ def translate_wt_libre(text: str, source: str, target: str, filename: str, dir_j
             The directory to save the translation result JSON file.
         url : str, optional
             The URL of the WT Libre translation service. Default is "http://127.0.0.1:5000/translate".
+        format_payload : str, optional
+            Possible values are html or text.
 
     Returns:
         json_data : dict
@@ -568,7 +570,7 @@ def translate_wt_libre(text: str, source: str, target: str, filename: str, dir_j
         "q": text,
         "source": source,
         "target": target,
-        "format": "text",
+        "format": format_payload,
         "api_key": ""
     }
 
@@ -580,7 +582,7 @@ def translate_wt_libre(text: str, source: str, target: str, filename: str, dir_j
         write_json(json_data, dir_json , str(filename))
         return json_data
     
-def translate_batch(batch_text: list, source: str, target: str, filename: str, dir_json: str, url: str = "http://127.0.0.1:5000/translate") -> list:
+def translate_batch(batch_text: list, source: str, target: str, filename: str, dir_json: str, url: str = "http://127.0.0.1:5000/translate", format_payload="html") -> list:
     """
     Translate a batch of texts using LibreTranslate service.
 
@@ -597,6 +599,8 @@ def translate_batch(batch_text: list, source: str, target: str, filename: str, d
             The directory to save the translation result JSONL file.
         url : str, optional
             The URL of the WT Libre translation service. Default is "http://127.0.0.1:5000/translate".
+        format_payload : str, optional
+            Possible values are html or text.
 
     Returns:
         json_results : list of dict
@@ -607,7 +611,7 @@ def translate_batch(batch_text: list, source: str, target: str, filename: str, d
         "q": batch_text,
         "source": source,
         "target": target,
-        "format": "text",
+        "format": format_payload,
         "api_key": ""
     }
 
@@ -623,7 +627,7 @@ def translate_batch(batch_text: list, source: str, target: str, filename: str, d
         write_jsonl(json_results, dir_json , str(filename))
         return json_results
 
-def translate(text: str, source: str, target: str, url: str = "http://127.0.0.1:5000/translate") -> str:
+def translate(text: str, source: str, target: str, url: str = "http://127.0.0.1:5000/translate", format_payload="html") -> str:
     """
     Translate text using LibreTranslate service.
 
@@ -636,6 +640,8 @@ def translate(text: str, source: str, target: str, url: str = "http://127.0.0.1:
             The target language code.
         url : str, optional
             The URL of the translation service. Default is "http://127.0.0.1:5000/translate".
+        format_payload : str, optional
+            Possible values are html or text.
 
     Returns:
         translatedText : str
@@ -646,7 +652,7 @@ def translate(text: str, source: str, target: str, url: str = "http://127.0.0.1:
         "q": text,
         "source": source,
         "target": target,
-        "format": "text",
+        "format": format_payload,
         "api_key": ""
     }
 
@@ -905,6 +911,8 @@ def topic_aggregate_chunks(df: pd.DataFrame, col_id: str, col_topic : str, col_c
     """
     metrics_dict = dict()
     # metrics_dict[col_id]=(col_id,'first')
+    # if col_id != col_chunk_id:
+    #     metrics_dict[col_chunk_id]=(col_chunk_id,"nunique")
     metrics_dict[col_chunk_id]=(col_chunk_id,"nunique")
     metrics_dict[col_engagement]=(col_engagement,'first')
 
@@ -1280,10 +1288,12 @@ def PRarmy_nlp_process(nlp, df: pd.DataFrame, col_text: str, col_lemma: str = "l
                 NER_type.append(ent.label_)
                 NER_text.append(ent.text)
 
+        
         record = (NER_type, NER_text, ' '.join(map(str, lemmas_list)))
         all_records.append(record)
 
 
+
     df[['NER_type', 'NER_text', col_lemma]] = pd.DataFrame(all_records, index=df.index)
 
     return df
@@ -1570,10 +1580,10 @@ def extract_emojis(nlp, df: pd.DataFrame, col_text: str, batch_size: int = 100,
     
     return df
 
-def split_n_sentences(nlp, df: pd.DataFrame, col_text: str, n_sentences: int = 1, batch_size: int = 100, n_process: int = 1, stats: bool = False) -> pd.DataFrame:
+def split_n_sentences(nlp, df: pd.DataFrame, col_text: str, n_sentences: int = 1, batch_size: int = 100, n_process: int = 1, stats: bool = False, threshold: int = None) -> pd.DataFrame:
     """
-    Split a text into chunks of n sentences
-    
+    Split a text into chunks of n sentences, returning their start and end indexes in separate columns.
+
     Parameters:
         nlp : spacy.language.Language
             The spaCy language processing pipeline.
@@ -1589,41 +1599,64 @@ def split_n_sentences(nlp, df: pd.DataFrame, col_text: str, n_sentences: int = 1
             The number of processes to use for text processing. Default is 1.
         stats : bool, optional
             Flag indicating whether to compute statistics about the splitting process. Default is False.
-    
+        threshold : int, optional
+            Maximum number of sentence batches to return per text. If None, all batches are returned. Default is None.
+
     Returns:
         pd.DataFrame
-            DataFrame containing the split sentences.
+            DataFrame containing the split sentences with their start and end indexes in separate columns.
 
-    Description:
-        This function splits text in a DataFrame into chunks of n sentences. It returns a DataFrame containing the split sentences.
-        Optionally, it can compute statistics such as the count of sentences and batches if the 'stats' parameter is set to True.
     """
+    text = list(df[col_text].astype('unicode').values)
+
+    count_sentences = []
+    count_batches = []
+    results = []
+    start_indexes = []
+    end_indexes = []
+
+    for doc in tqdm(nlp.pipe(text, batch_size=batch_size, n_process=n_process), total=len(text), desc="Sentence splitting"):
+        sentences = []
+
+
+        # Extract sentences and their positions
+        for sent in doc.sents:
+            sentences.append((sent.text, sent.start_char, sent.end_char))
 
-    text=list(df[col_text].astype('unicode').values)
-    
-    count_sentences=[]
-    count_batches=[]
-    results=[]
-    for doc in tqdm(nlp.pipe(text, batch_size=batch_size, n_process=n_process), total= len(text), desc = "Sentence splitting"):
-        # Split the text into sentences
-        sentences = [sent.text for sent in doc.sents]
         if stats:
             count_sentences.append(len(sentences))
-        if n_sentences>1:
-            # Split the sentences into batches of size n
+
+        if n_sentences > 1:
+            # # Split sentences into batches of size n_sentences
             batches = [sentences[i:i + n_sentences] for i in range(0, len(sentences), n_sentences)]
-            concatenate_batches=[" ".join(sublist) for sublist in batches]
+
+            # Concatenate batches of sentences and adjust spans accordingly
+            concatenate_batches = [" ".join([sub[0] for sub in sublist]) for sublist in batches]
+            concatenate_spans = [(sublist[0][1], sublist[-1][2]) for sublist in batches]
+
+            if threshold is not None:
+                concatenate_batches = concatenate_batches[:threshold]
+                concatenate_spans = concatenate_spans[:threshold]
+
             results.append(concatenate_batches)
+            start_indexes.append([span[0] for span in concatenate_spans])
+            end_indexes.append([span[1] for span in concatenate_spans])
+
             if stats:
                 count_batches.append(len(concatenate_batches))
-            
         else:
-            results.append(sentences)
+            sentences = sentences[:threshold] if threshold is not None else sentences
+
+            results.append([sub[0] for sub in sentences])
+            start_indexes.append([sub[1] for sub in sentences])
+            end_indexes.append([sub[2] for sub in sentences])
 
     df['sentences'] = results
-    if stats:
-        df['sentences_count']=count_sentences
-        df['batch_sentences_count']=count_batches
+    df['start_indexes'] = start_indexes
+    df['end_indexes'] = end_indexes
+
+    df = df.explode(['sentences','start_indexes', 'end_indexes']).reset_index(drop=True)
+
     return df
 
 
@@ -1998,6 +2031,75 @@ def encode_chunked_files(chunk_files_paths: list,
 
     return new_file_paths
 
+####################################################################
+# ENCODING FEATURES
+####################################################################
+
+def encode_labels(data_to_encode: np.ndarray) -> tuple:
+    """
+    Encodes a list of labels using a LabelEncoder.
+
+    Args:
+    - data_to_encode (List[Union[str, int]]): The list of labels to encode. Labels can be of any hashable type, 
+      but strings or integers are typical.
+
+    Returns:
+    - Tuple[LabelEncoder, np.ndarray]: A tuple containing the fitted LabelEncoder instance and a numpy array 
+      of encoded labels.
+    """
+    label_encoder = LabelEncoder()
+    label_encoder.fit(data_to_encode)
+    encoded_labels = label_encoder.transform(data_to_encode)
+    return label_encoder, encoded_labels
+
+
+def encode_new_labels(label_encoder : LabelEncoder, data_to_encode : np.ndarray) -> np.ndarray:
+    """
+    Encodes a list of new labels using an already fitted LabelEncoder.
+
+    Args:
+    - label_encoder (LabelEncoder): A pre-fitted LabelEncoder instance.
+    - data_to_encode (List[Union[str, int]]): The list of new labels to encode using the pre-fitted encoder.
+
+    Returns:
+    - np.ndarray: A numpy array of encoded labels.
+    """
+    encoded_labels = label_encoder.transform(data_to_encode)
+    return encoded_labels
+
+def one_hot_encode(data_to_encode:np.ndarray) -> tuple:
+    """
+    One-hot encodes a list of categorical values using OneHotEncoder.
+
+    Args:
+    - data_to_encode (List[Union[str, int]]): The list of categorical values to encode. The values can be of 
+      any hashable type, typically strings or integers.
+
+    Returns:
+    - Tuple[OneHotEncoder, np.ndarray]: A tuple containing the fitted OneHotEncoder instance and a numpy array 
+      of one-hot encoded values.
+    """
+    one_hot_encoder = OneHotEncoder(sparse=False)
+    data_to_encode_reshaped = np.array(data_to_encode).reshape(-1, 1)  # Reshape for OneHotEncoder
+    one_hot_encoder.fit(data_to_encode_reshaped)
+    encoded_array = one_hot_encoder.transform(data_to_encode_reshaped)
+    return one_hot_encoder, encoded_array
+
+
+def one_hot_encode_new_data(one_hot_encoder: OneHotEncoder, data_to_encode: np.ndarray) -> np.ndarray:
+    """
+    One-hot encodes a list of new categorical values using an already fitted OneHotEncoder.
+
+    Args:
+    - one_hot_encoder (OneHotEncoder): A pre-fitted OneHotEncoder instance.
+    - data_to_encode (List[Union[str, int]]): The list of new categorical values to encode using the pre-fitted encoder.
+
+    Returns:
+    - np.ndarray: A numpy array of one-hot encoded values.
+    """
+    data_to_encode_reshaped = np.array(data_to_encode).reshape(-1, 1)  # Reshape for OneHotEncoder
+    encoded_array = one_hot_encoder.transform(data_to_encode_reshaped)
+    return encoded_array
 
 ####################################################################
 # SCALING FEATURES
@@ -2327,3 +2429,46 @@ def HF_sentiment_classifier(tokenizer, model, text, col_text, filename, dir_json
             write_json(results, dir_json , str(filename))
             
     return results
+
+
+def add_tag_libretranslate_not_translate(text):
+    """
+    This function add fake html tag around words such as mentions, hashtags, urls and emojis to avoid translation of those tokens.
+
+    Args:
+    text (str): The text to process
+
+    Returns:
+    str: The text with the fake html tags
+    """
+    # This regex finds words starting with # and followed by alphanumeric characters or underscores
+    mention_pattern = r"(?:RT\s|QT\s)?(?<=^|(?<=[^a-zA-Z0-9-_\.]))(@[A-Za-z0-9_]{4,15})"
+    hashtag_pattern = r"(\B#\w+)"
+    url_pattern = r"(https?://[^ ]+)"
+    emoji_pattern = r':[a-zA-Z_]+:'
+
+    pattern = re.compile(emoji_pattern+ "|" + mention_pattern + "|" + hashtag_pattern + "|" + url_pattern)
+    
+    # This function replaces the hashtag with an HTML link tag
+    def replace_with_link(match):
+        matcher_group = match.group(0)
+        return f'<a href="{matcher_group}"></a>'
+    
+    # Use re.sub to substitute the hashtags with the HTML link tags
+    text_no_emojis = emoji.demojize(text)
+    result = re.sub(pattern, replace_with_link, text_no_emojis)
+    
+    return result
+
+def clean_libre_translate_tags(text):
+    """
+    This function remove fake tags added by add_tag_libretranslate_not_translate() function.
+    
+    Args:
+    text (str): The text to process
+
+    Returns:
+    str: The text with the fake html tags
+    """
+    cleaned_string = text.replace('<a href="', '').replace('"></a>', '')
+    return cleaned_string

opsci_toolbox/helpers/nlp_cuml.py

@@ -18,7 +18,8 @@ def reduce_with_cuml_UMAP(embeddings: np.ndarray,
                           metric: str = "cosine", 
                           spread: float = 1.0,
                           learning_rate: float = 1.0, 
-                          n_epochs:int = 300
+                          n_epochs:int = 300,
+                          random_state:int = None
                            ) -> tuple:
     """
     Reduces the dimensionality of embeddings using UMAP with cuML library.
@@ -41,7 +42,48 @@ def reduce_with_cuml_UMAP(embeddings: np.ndarray,
                    metric=metric,
                    spread = spread,
                    n_epochs=n_epochs, 
-                   learning_rate=learning_rate).fit(embeddings)
+                   learning_rate=learning_rate,
+                   random_state=random_state).fit(embeddings)
+    
+    reduced_embeddings = reducer.transform(embeddings)
+    return reducer, reduced_embeddings
+
+
+def supervised_reduce_with_cuml_UMAP(embeddings: np.ndarray, 
+                          n_neighbors: int = 5, 
+                          n_components: int = 3, 
+                          min_dist: float = 0.0, 
+                          metric: str = "cosine", 
+                          spread: float = 1.0,
+                          learning_rate: float = 1.0, 
+                          n_epochs:int = 300,
+                          y: np.ndarray = None,
+                          convert_dtype: bool = False,
+                          random_state:int=None
+                           ) -> tuple:
+    """
+    Reduces the dimensionality of embeddings using UMAP with cuML library.
+
+    Args:
+        embeddings (np.ndarray): The input embeddings to be reduced.
+        n_neighbors (int, optional): The number of nearest neighbors to consider. Defaults to 5.
+        n_components (int, optional): The number of dimensions of the embedded space. Defaults to 3.
+        min_dist (float, optional): The minimum distance between embedded points. Defaults to 0.0.
+        metric (str, optional): The metric to use for distance computation. Defaults to "cosine".
+        spread (float, optional): The effective scale of embedded points. Defaults to 1.0.
+
+    Returns:
+        reducer (UMAP): The UMAP reducer object.
+        reduced_embeddings (np.ndarray): The reduced embeddings.
+    """    
+    reducer = UMAP(n_neighbors=n_neighbors, 
+                   n_components=n_components, 
+                   min_dist=min_dist, 
+                   metric=metric,
+                   spread = spread,
+                   n_epochs=n_epochs, 
+                   learning_rate=learning_rate,
+                   random_state=random_state).fit(X = embeddings, y = y, convert_dtype = convert_dtype)
     
     reduced_embeddings = reducer.transform(embeddings)
     return reducer, reduced_embeddings
@@ -409,6 +451,9 @@ def cuml_word_frequency_per_categorie(gdf: pd.DataFrame, col_text: str, col_cat:
     # Convert the result back to pandas DataFrame
     return df_count.to_pandas()
 
+
+
+
 # def cuml_chi2_per_category(lst_text: list, lst_categorie: list, col_cat: str, n_words: int = 10, p_value_limit: float = 0.95, min_freq: int = 3) -> pd.DataFrame:
 
 #     # Convert input lists to cuDF Series

opsci_toolbox/helpers/sna.py

@@ -11,6 +11,40 @@ from collections import Counter
 from opsci_toolbox.helpers.dataviz import boxplot
 from fa2_modified import ForceAtlas2
 
+def create_subgraph_min_metric(G: nx.Graph, metric: str = "degree", min_value: float = 2) -> nx.Graph:
+    """
+    Creates a subgraph containing only the nodes that have at least the specified minimum value for a given metric.
+
+    Args:
+        G (nx.Graph): The input graph.
+        metric (str, optional): The node metric to filter nodes by (e.g., "degree", "in_degree", "out_degree", "degree_centrality"). Default is "degree".
+        min_value (float, optional): The minimum value required for nodes to be included in the subgraph. Default is 2.
+
+    Returns:
+        subgraph (nx.Graph): A subgraph containing only the nodes with at least the specified minimum metric value.
+    """
+    
+    if metric == "degree":
+        nodes_with_min_metric = [node for node, value in G.degree() if value >= min_value]
+    elif metric == "in_degree" and G.is_directed():
+        nodes_with_min_metric = [node for node, value in G.in_degree() if value >= min_value]
+    elif metric == "out_degree" and G.is_directed():
+        nodes_with_min_metric = [node for node, value in G.out_degree() if value >= min_value]
+    elif metric == "degree_centrality":
+        centrality = nx.degree_centrality(G)
+        nodes_with_min_metric = [node for node, value in centrality.items() if value >= min_value]
+    elif metric == "betweenness_centrality":
+        centrality = nx.betweenness_centrality(G)
+        nodes_with_min_metric = [node for node, value in centrality.items() if value >= min_value]
+    elif metric == "closeness_centrality":
+        centrality = nx.closeness_centrality(G)
+        nodes_with_min_metric = [node for node, value in centrality.items() if value >= min_value]
+    else:
+        raise ValueError(f"Unsupported metric: {metric}")
+    
+    subgraph = G.subgraph(nodes_with_min_metric).copy()
+    return subgraph
+
 def group_nodes_by_values(dictionnary : dict) -> dict:
     """
     Group nodes by their values from a dictionary.

{opsci_toolbox-0.0.13.dist-info → opsci_toolbox-0.0.15.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: opsci-toolbox
-Version: 0.0.13
+Version: 0.0.15
 Summary: a complete toolbox
 Home-page: UNKNOWN
 Author: Erwan Le Nagard
@@ -41,7 +41,7 @@ Requires-Dist: spacy-language-detection ==0.2.1
 Requires-Dist: spacymoji ==3.1.0
 Requires-Dist: supervision ==0.21.0
 Requires-Dist: textacy ==0.13.0
-Requires-Dist: torch ==2.0.1
+Requires-Dist: torch >=2.4.0
 Requires-Dist: tqdm >=4.66.2
 Requires-Dist: trafilatura ==1.7.0
 Requires-Dist: transformers ==4.38.2

{opsci_toolbox-0.0.13.dist-info → opsci_toolbox-0.0.15.dist-info}/RECORD

@@ -1,25 +1,26 @@
 opsci_toolbox/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 opsci_toolbox/apis/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-opsci_toolbox/apis/rapidapi_helpers.py,sha256=k_hYcRNww5noNkX7zyz5Htggxb15BPoKSlbY7NLuQXI,26696
-opsci_toolbox/apis/reddit.py,sha256=zhK2CY9CkCezNcekQFdv1So3NmHHYxB7-tgMVErHOGI,15763
-opsci_toolbox/apis/telegram.py,sha256=GKDLpZg1fc9D_PGCgi9pfTaW7Jjm_2luQ-2trXTr38A,42208
+opsci_toolbox/apis/rapidapi_helpers.py,sha256=plX0uoGXWBEmeRqK7QfB_CVYJnW15kVUWtitESxPLNw,26669
+opsci_toolbox/apis/reddit.py,sha256=b_dJFZ_bOB9LLugGBBw5bCbUZdq8VnwtVCGaTYljIIg,21096
+opsci_toolbox/apis/telegram.py,sha256=JjmAk6tKvpnFIYpZDKthxS_mgqhWQpDPUOvyC7SiWPA,60920
 opsci_toolbox/apis/webscraping.py,sha256=1DAIYbywZoPwTSyoqFGxyF0-q_nUsGg_VK51zLL_bB0,21465
 opsci_toolbox/apis/youtube_helpers.py,sha256=j4hwCS2BEWRJjd9Q5XBN9FeCrL3lqteyz5dqbtfypdo,17418
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 opsci_toolbox/lexicons/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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opsci_toolbox-0.0.15.dist-info/dependency_links.txt

@@ -0,0 +1 @@
+https://download.pytorch.org/whl/cu124