Add tool library.

autogen/agentchat/contrib/captainagent.py

@@ -230,7 +230,7 @@ class CaptainUserProxyAgent(ConversableAgent):
 
     CONVERSATION_REVIEW_PROMPT = """# Your task
 Briefly summarize the conversation history derived from an experts' group chat by following the answer format.
-If you found non-trivial errors or issues in the conversation, point it out with a detailed reason and mark the "Need double-check" as "Yes." if you think it is worth further verification.
+If you found non-trivial errors or issues in the conversation, point it out with a detailed reason, if you think it is worth further verification, mark the "Need double-check" as "Yes"
 
 # Conversation history:
 {chat_history}
@@ -373,7 +373,7 @@ def _run_autobuild(self, group_name: str, execution_task: str, building_task: st
                 tool_root_dir = self.tool_root_dir
                 tool_builder = ToolBuilder(
                     corpus_path=os.path.join(tool_root_dir, "tool_description.tsv"),
-                    retriever=self._nested_config["autobuild_tool_config"]["retriever"],
+                    retriever=self._nested_config["autobuild_tool_config"].get("retriever", "all-mpnet-base-v2"),
                 )
                 for idx, agent in enumerate(agent_list):
                     if idx == len(self.tool_history[group_name]):
@@ -404,7 +404,7 @@ def _run_autobuild(self, group_name: str, execution_task: str, building_task: st
                     # Retrieve and build tools based on the smilarities between the skills and the tool description
                     tool_builder = ToolBuilder(
                         corpus_path=os.path.join(tool_root_dir, "tool_description.tsv"),
-                        retriever=self._nested_config["autobuild_tool_config"]["retriever"],
+                        retriever=self._nested_config["autobuild_tool_config"].get("retriever", "all-mpnet-base-v2"),
                     )
                     for idx, skill in enumerate(skills):
                         tools = tool_builder.retrieve(skill)

autogen/agentchat/contrib/captainagent/tools/README.md

@@ -0,0 +1,44 @@
+# Introduction
+
+This directory contains a library of manually created python tools. These tools have three categories: math, data_analysis and information_retrieval.
+
+# Directory Layout
+```
+tools
+├── README.md
+├── data_analysis
+│   ├── calculate_correlation.py
+│   └── ...
+├── information_retrieval
+│   ├── arxiv_download.py
+│   ├── arxiv_search.py
+│   └── ...
+├── math
+│   ├── calculate_circle_area_from_diameter.py
+│   └── ...
+└── tool_description.tsv
+```
+
+Tools can be imported from `tools/{category}/{tool_name}.py` with exactly the same function name.
+
+`tool_description.tsv` contains descriptions of tools for retrieval.
+
+# How to use
+Some tools require Bing Search API key and RapidAPI key. For Bing API, you can read more about how to get an API on the [Bing Web Search API](https://www.microsoft.com/en-us/bing/apis/bing-web-search-api) page. For RapidAPI, you can [sign up](https://rapidapi.com/auth/sign-up) and subscribe to these two links([link1](https://rapidapi.com/solid-api-solid-api-default/api/youtube-transcript3), [link2](https://rapidapi.com/420vijay47/api/youtube-mp3-downloader2)). These apis have free billing options and there is no need to worry about extra costs.
+
+To install the requirements for running tools, use pip install.
+```bash
+pip install -r autogen/agentchat/contrib/captainagent/tools/requirements.txt
+```
+
+Whenever you run the tool-related code, remember to export the api keys to system variables.
+```bash
+export BING_API_KEY=""
+export RAPID_API_KEY=""
+```
+or
+```python
+import os
+os.environ["BING_API_KEY"] = ""
+os.environ["RAPID_API_KEY"] = ""
+```

autogen/agentchat/contrib/captainagent/tools/data_analysis/calculate_correlation.py

@@ -0,0 +1,38 @@
+def calculate_correlation(csv_path: str, column1: str, column2: str, method: str = "pearson") -> float:
+    """
+    Calculate the correlation between two columns in a CSV file.
+
+    Args:
+    csv_path (str): The path to the CSV file.
+    column1 (str): The name of the first column.
+    column2 (str): The name of the second column.
+    method (str or callable, optional): The method used to calculate the correlation.
+        - 'pearson' (default): Pearson correlation coefficient.
+        - 'kendall': Kendall Tau correlation coefficient.
+        - 'spearman': Spearman rank correlation coefficient.
+        - callable: A custom correlation function that takes two arrays and returns a scalar.
+
+    Returns:
+    float: The correlation coefficient between the two columns.
+    """
+    import pandas as pd
+
+    # Read the CSV file into a pandas DataFrame
+    df = pd.read_csv(csv_path)
+
+    # Select the specified columns
+    selected_columns = df[[column1, column2]]
+
+    # Calculate the correlation based on the specified method
+    if method == "pearson":
+        correlation = selected_columns.corr().iloc[0, 1]
+    elif method == "kendall":
+        correlation = selected_columns.corr(method="kendall").iloc[0, 1]
+    elif method == "spearman":
+        correlation = selected_columns.corr(method="spearman").iloc[0, 1]
+    elif callable(method):
+        correlation = selected_columns.corr(method=method).iloc[0, 1]
+    else:
+        raise ValueError("Invalid correlation method. Please choose 'pearson', 'kendall', 'spearman', or a callable.")
+
+    return correlation

autogen/agentchat/contrib/captainagent/tools/data_analysis/calculate_skewness_and_kurtosis.py

@@ -0,0 +1,26 @@
+def calculate_skewness_and_kurtosis(csv_file: str, column_name: str) -> tuple:
+    """
+    Calculate the skewness and kurtosis of a specified column in a CSV file. The kurtosis is calculated using the Fisher definition.
+    The two metrics are computed using scipy.stats functions.
+
+    Args:
+    csv_file (str): The path to the CSV file.
+    column_name (str): The name of the column to calculate skewness and kurtosis for.
+
+    Returns:
+    tuple: (skewness, kurtosis)
+    """
+    import pandas as pd
+    from scipy.stats import kurtosis, skew
+
+    # Read the CSV file into a pandas DataFrame
+    df = pd.read_csv(csv_file)
+
+    # Extract the specified column
+    column = df[column_name]
+
+    # Calculate the skewness and kurtosis
+    skewness = skew(column)
+    kurt = kurtosis(column)
+
+    return skewness, kurt

autogen/agentchat/contrib/captainagent/tools/data_analysis/detect_outlier_iqr.py

@@ -0,0 +1,26 @@
+def detect_outlier_iqr(csv_file: str, column_name: str):
+    """
+    Detect outliers in a specified column of a CSV file using the IQR method.
+
+    Args:
+    csv_file (str): The path to the CSV file.
+    column_name (str): The name of the column to detect outliers in.
+
+    Returns:
+    list: A list of row indices that correspond to the outliers.
+    """
+    import pandas as pd
+
+    # Read the CSV file into a pandas DataFrame
+    df = pd.read_csv(csv_file)
+
+    # Calculate the quartiles and IQR for the specified column
+    q1 = df[column_name].quantile(0.25)
+    q3 = df[column_name].quantile(0.75)
+    iqr = q3 - q1
+
+    # Find the outliers based on the defined criteria
+    outliers = df[(df[column_name] < q1 - 1.5 * iqr) | (df[column_name] > q3 + 1.5 * iqr)]
+
+    # Return the row indices of the outliers
+    return outliers.index.tolist()

autogen/agentchat/contrib/captainagent/tools/data_analysis/detect_outlier_zscore.py

@@ -0,0 +1,26 @@
+def detect_outlier_zscore(csv_file, column_name, threshold=3):
+    """
+    Detect outliers in a CSV file based on a specified column. The outliers are determined by calculating the z-score of the data points in the column.
+
+    Args:
+    csv_file (str): The path to the CSV file.
+    column_name (str): The name of the column to calculate z-scores for.
+    threshold (float, optional): The threshold value for determining outliers. By default set to 3.
+
+    Returns:
+    list: A list of row indices where the z-score is above the threshold.
+    """
+    import numpy as np
+    import pandas as pd
+
+    # Read the CSV file into a pandas DataFrame
+    df = pd.read_csv(csv_file)
+
+    # Calculate the z-score for the specified column
+    z_scores = np.abs((df[column_name] - df[column_name].mean()) / df[column_name].std())
+
+    # Find the row indices where the z-score is above the threshold
+    outlier_indices = np.where(z_scores > threshold)[0]
+
+    # Return the row indices of the outliers
+    return outlier_indices

autogen/agentchat/contrib/captainagent/tools/data_analysis/explore_csv.py

@@ -0,0 +1,19 @@
+def explore_csv(file_path, num_lines=5):
+    """
+    Reads a CSV file and prints the column names, shape, data types, and the first few lines of data.
+
+    Args:
+        file_path (str): The path to the CSV file.
+        num_lines (int, optional): The number of lines to print. Defaults to 5.
+    """
+    import pandas as pd
+
+    df = pd.read_csv(file_path)
+    header = df.columns
+    print("Columns:")
+    print(", ".join(header))
+    print("Shape:", df.shape)
+    print("Data Types:")
+    print(df.dtypes)
+    print("First", num_lines, "lines:")
+    print(df.head(num_lines))

autogen/agentchat/contrib/captainagent/tools/data_analysis/shapiro_wilk_test.py

@@ -0,0 +1,28 @@
+from autogen.coding.func_with_reqs import with_requirements
+
+
+@with_requirements(["pandas", "scipy"])
+def shapiro_wilk_test(csv_file, column_name):
+    """
+    Perform the Shapiro-Wilk test on a specified column of a CSV file.
+
+    Args:
+    csv_file (str): The path to the CSV file.
+    column_name (str): The name of the column to perform the test on.
+
+    Returns:
+    float: The p-value resulting from the Shapiro-Wilk test.
+    """
+    import pandas as pd
+    from scipy.stats import shapiro
+
+    # Read the CSV file into a pandas DataFrame
+    df = pd.read_csv(csv_file)
+
+    # Extract the specified column as a numpy array
+    column_data = df[column_name].values
+
+    # Perform the Shapiro-Wilk test
+    _, p_value = shapiro(column_data)
+
+    return p_value

autogen/agentchat/contrib/captainagent/tools/information_retrieval/arxiv_download.py

@@ -0,0 +1,23 @@
+import arxiv
+
+from autogen.coding.func_with_reqs import with_requirements
+
+
+@with_requirements(["arxiv"], ["arxiv"])
+def arxiv_download(id_list: list, download_dir="./"):
+    """
+    Downloads PDF files from ArXiv based on a list of arxiv paper IDs.
+
+    Args:
+        id_list (list): A list of paper IDs to download. e.g. [2302.00006v1]
+        download_dir (str, optional): The directory to save the downloaded PDF files. Defaults to './'.
+
+    Returns:
+        list: A list of paths to the downloaded PDF files.
+    """
+    paths = []
+    for paper in arxiv.Client().results(arxiv.Search(id_list=id_list)):
+        path = paper.download_pdf(download_dir, filename=paper.get_short_id() + ".pdf")
+        paths.append(path)
+        print("Paper id:", paper.get_short_id(), "Downloaded to:", path)
+    return paths

autogen/agentchat/contrib/captainagent/tools/information_retrieval/arxiv_search.py

@@ -0,0 +1,52 @@
+import arxiv
+
+from autogen.coding.func_with_reqs import with_requirements
+
+
+@with_requirements(["arxiv"], ["arxiv"])
+def arxiv_search(query, max_results=10, sortby="relevance"):
+    """
+    Search for articles on arXiv based on the given query.
+
+    Args:
+        query (str): The search query.
+        max_results (int, optional): The maximum number of results to retrieve. Defaults to 10.
+        sortby (str, optional): The sorting criterion for the search results. Can be 'relevance' or 'submittedDate'. Defaults to 'relevance'.
+
+    Returns:
+        list: A list of dictionaries containing information about the search results. Each dictionary contains the following keys:
+            - 'title': The title of the article.
+            - 'authors': The authors of the article.
+            - 'summary': The summary of the article.
+            - 'entry_id': The entry ID of the article.
+            - 'doi': The DOI of the article (If applicable).
+            - 'published': The publication date of the article in the format 'Y-M'.
+    """
+
+    def get_author(r):
+        return ", ".join(a.name for a in r.authors)
+
+    criterion = {"relevance": arxiv.SortCriterion.Relevance, "submittedDate": arxiv.SortCriterion.SubmittedDate}[sortby]
+
+    client = arxiv.Client()
+    search = arxiv.Search(query=query, max_results=max_results, sort_by=criterion)
+    res = []
+    results = client.results(search)
+    for r in results:
+        print("Entry id:", r.entry_id)
+        print("Title:", r.title)
+        print("Authors:", get_author(r))
+        print("DOI:", r.doi)
+        print("Published:", r.published.strftime("%Y-%m"))
+        # print("Summary:", r.summary)
+        res.append(
+            {
+                "title": r.title,
+                "authors": get_author(r),
+                "summary": r.summary,
+                "entry_id": r.entry_id,
+                "doi": r.doi,
+                "published": r.published.strftime("%Y-%m"),
+            }
+        )
+    return res

autogen/agentchat/contrib/captainagent/tools/information_retrieval/extract_pdf_image.py

@@ -0,0 +1,51 @@
+import os
+
+from autogen.coding.func_with_reqs import with_requirements
+
+
+@with_requirements(["PyMuPDF"], ["os"])
+def extract_pdf_image(pdf_path: str, output_dir: str, page_number=None):
+    """
+    Extracts images from a PDF file and saves them to the specified output directory.
+
+    Args:
+        pdf_path (str): The path to the PDF file.
+        output_dir (str): The directory to save the extracted images.
+        page_number (int, optional): The page number to extract images from. If not provided, extract images from all pages.
+    """
+    import fitz  # PyMuPDF library
+
+    # Open the PDF file
+    doc = fitz.open(pdf_path)
+
+    # Create the output directory if it doesn't exist
+    os.makedirs(output_dir, exist_ok=True)
+
+    # Extract images from the PDF file
+    images = []
+    if page_number is not None:
+        page = doc[page_number - 1]  # Adjust page number to 0-based index
+        for img in page.get_images():
+            xref = img[0]
+            base_image = doc.extract_image(xref)
+            image_bytes = base_image["image"]
+            images.append(image_bytes)
+    else:
+        for page in doc:
+            for img in page.get_images():
+                xref = img[0]
+                base_image = doc.extract_image(xref)
+                image_bytes = base_image["image"]
+                images.append(image_bytes)
+
+    # Save the extracted images
+    for i, image_bytes in enumerate(images):
+        image_path = os.path.join(output_dir, f"image_{i}.png")
+        with open(image_path, "wb") as f:
+            f.write(image_bytes)
+
+    # Print the total number of images saved
+    print(f"Saved a total of {len(images)} images")
+
+    # Close the PDF file
+    doc.close()