Git-Bob

Installation as GitHub action

There is a detailed tutorial on how to install git-bob as GitHub action to your repository. In very short, to use git-bob in your GitHub repository, you need to Copy the git-bob GitHub workflow in folder .github/workflows/ to your repository. Make sure to replace pip install -e . with a specific git-bob version such as pip install git-bob==0.16.0. If your project does not contain a requirements.txt file, remove the line pip install -r requirements.txt. Configure the LLM you want to use in the workflow files by specifying the GIT_BOB_LLM_NAME GitHub repository secret. These were tested: anthropic:claude-3-5-sonnet-20241022 openai:gpt-4o-2024-08-06 github_models:gpt-4o github_models:meta-llama-3.1-405b-instruct google:gemini-1.5-pro-002 mistral:mistral-large-2411 (uses pixtral-12b-2409 for vision tasks) deepseek:deepseek-chat e-infra_cz:llama3.3:latest configure a GitHub secret with the corresponding key from the LLM provider depending on the above configured LLM: OPENAI_API_KEY: OpenAI (gpt) ANTHROPIC_API_KEY: Anthropic (claude) GH_MODELS_API_KEY: GitHub Models Marketplace GOOGLE_API_KEY: Google AI MISTRAL_API_KEY: Mistral DEEPSEEK_API_KEY: DeepSeek KISSKI_API_KEY: KISSKI BLABLADOR_API_KEY: BLABLADOR E_INFRA_CZ_API_KEY chat.ai.e-infra.cz docs * configure GitHub actions to run the workflow on issues and pull requests. Also give write-access to the Workflow using the GITHUB_TOKEN.

When using it in your repository, you can also set a custom system message, for example for: General Data Science / Python Programming Bio-Image Analysis Giving advice on a specific repository / library Manuscript writing

Furthermore, to guide discussions, you may want to setup issue templates, e.g. General Python Programming Questions Bio-Image Analysis * Statistics and Plotting

Installation as gitlab pipeline

Since version 0.10.1 git-bob has experimental support for gitlab. You find detailed instructions how to install it here.

Installation for development

git clone https://github.com/haesleinhuepf/git-bob.git
cd git-bob

Usage: Trigger words

To trigger git-bob, you need to comment on an issue or pull request with the comment trigger word (or aliases think about, review, respond):

git-bob comment

If you want to ask git-bob for a review of a pull-request, you can use the review trigger word. Also make sure mention explictly what you want to be reviewed.

git-bob review this PR. Check code quality and comments.

After some back-and-forth discussion, you can also use the solve trigger word (or aliases implement, apply) make git-bob solve an issue and send a pull-request. This trigger can also be used to modify code in pull requests.

git-bob solve

You can ask git-bob to implement a solution for testing, without sending a pull-request, using the try trigger:

git-bob try

If you have multiple API-Key for different LLMs configured, you can specify the LLM in the command using the ask <LLM-Name> to trigger command:

git-bob ask claude-3-5-sonnet-20241022 to solve this issue.

If the issue is complex and should be split into sub-issues, you can use the following command:

git-bob split

If you have two GitHub secrets TWINE_USERNAME and TWINE_PASSWORD configured, you can also use the following command to publish a new version of your library to PyPI:

git-bob deploy

All trigger words can be combined with please and/or ,, which will make no difference to calling git-bob without these words:

git-bob, please ask gemini-1.5-pro-002 to solve this issue.

Use-case examples

A huge variety of use-cases for git-bob are thinkable. Here are some examples. Many serve purely demonstrative purposes. Some were parts of real scientific data analysis projects.

• Question answering
• About specific Python libraries
• The capital of France
• Asking for git-bob's capabilities
• Translation
• Translating text in Jupyter notebooks in other Languages
• Translating PowerPoint files
• Image Analysis
• Nuclei segmentation
• Cell segmentation
• Resizing images
• Natural image classification
• Programming
• Caching
• Fixing bugs in notebooks
• Summarize code of a file
• Summarize code in a repository
• Programming Google Search
• Implementing a generic Factory patters
• Generating a QR-Code
• Caching LLM prompt responses
• Interactive bash inside a program
• Prompting
• Prompting for SVG files
• Continuous Integration and Deployment
• Configuring Github workflows
• Configuring a Jupyter Book
• Data & Code Management
• Write a Data Management Plan (DMP)
• Research Data Management & Folder Structures
• Documenting source code
• Determining licenses of dependencies
• Assisting scientific manuscript writing
• Deleting files
• Converting tables to key-value pairs
• Exporting Google Scholar profile as bibtex
• Deciding for file formats: JSON versus YAML
• Generating Galaxy workflows
• Count citations of given DOIs
• Convert PDF documents to PNG images
• Convert PDF documents to animated GIFs
• Split PDFs
• Convert SVG files to PNG images
• Querying the arxiv
• Retrieving meta-data of arxiv articles
• Counting PowerPoint slides in Zenodo records
• Search for duplicate entries in a yml file
• Running multiple notebooks and trace failures
• Graphical User Interfaces
• Interactive drawing on an ipcanvas
• Statistics
• Filtering data and counting records
• Selecting ranges of columns
• Summarizing data and plotting
• Writing text about well-known statistical methods
• Drawing a decision tree for statistial tests
• Converting Dice and Jaccard indices
• Generating personal profile data of random scientists
• Plotting
• Violing plots with simulated data
• UMAPs with simulated data
• Plotting a circle of triangles (in gitlab)
• Pairplots with simulated data
• Word clouds
• Plot simulated income data
• Ploting the Dunning Kruger effect
• Reproducing a plot
• Animated zooming into an image
• Science Communication
• Making slides for Deep Learning training
• Making slides for Research Data Management training
• Visualizing how Fourier-Transform works
• Making Jupyter Notebooks for training
• Making slides about text
• Visualizing processes using CPUs and GPUs
• Fun
• Playing Tic-Tac-Toe
• Story Telling for kids
• PowerPoint Karaoke
• Solving Advent of Code 2024 puzzles
• Drawing a Christmas tree as SVG
• Asking for the Meaning of Life
• Creating audio files (also in German and French)
• git-bob refusing to help
• Changing the working directory of the parent shell
• Solving the Halting Problem [2nd attempt]
• Things that didn't work well
• How to use aider from python
• How to use the atproto API
• Executing code in a sandbox
• Summarize code in a repository
• Drawing multiple trees in a SVG file
• Drawing relationships between agents in a multi-agent system
• Complex code refactoring
• Debugging OpenCL error
• Signing PDFs with visual signature AND cryptographic signing
• Extending cell types in Jupyter notebooks

Usage as command-line tool (for development)

You can also install git-bob locally and run it from the terminal. In this case, create a GitHub token and store it in an environment variable named GITHUB_API_KEY. Also create an environment variable GIT_BOB_LLM_NAME with the name of the LLM you want to use, e.g. "gpt-4o-2024-05-13" or "claude-3-5-sonnet-20241022" or "github_models:gpt-4o". Then you can install git-bob using pip:

pip install git-bob

You can then use git-bob from the terminal on repositories you have read/write access to. It is recommended to call it from the root folder of the repository you want to interact with.

git clone https://github.com/<organization>/<repository>
cd <repository>
git-bob <action> <organization>/<repository> <issue-number>

Available actions: review-pull-request comment-on-issue solve-issue split-issue

Recommended Workflow

Here's the recommended workflow for using git-bob:

1. Create an issue describing the problem or task.
2. Comment on the issue with git-bob comment, or git-bob think about this (an alias for comment) to trigger git-bob making a plan.
3. Respond to git-bob with any clarifications or additional information it requests.
4. Comment on the issue with git-bob solve or git-bob implement this (an alias for solve) to trigger git-bob.
5. Wait for git-bob to create a pull request (PR) addressing the issue.
6. Review the PR and comment on the PR or on the original issue if changes are needed.
7. Wait for git-bob to create new PR or modifying the existing PR with the requested changes.
8. Repeat steps 3-5 as necessary until the issue is resolved satisfactorily.

Filtering extensions

If you wish to extend git-bob with custom triggers or prompt handlers, but avoid default triggers and prompt handlers, you can configure a filter in the git-bob.yml workflow file. Just overwrite this default regular expression accepting all extensions:

GIT_BOB_EXTENSIONS_FILTER_REGEXP: ".*"

If you want to only accept extensions starting with my_library, you can configure the filter like this:

GIT_BOB_EXTENSIONS_FILTER_REGEXP: "^my_library.*"

If you want to accept all extensions but not git-bob`s defaults, you can configure the filter like this:

GIT_BOB_EXTENSIONS_FILTER_REGEXP: "^(?!git_bob).*"