From e4968888ac666233fd4ebdc1dcc2de8c5c3c75fc Mon Sep 17 00:00:00 2001 From: Matthew Evans Date: Mon, 7 Oct 2024 17:50:55 +0100 Subject: [PATCH 1/7] Add initial project stubs --- .python-version | 1 + README.md | 34 + pyproject.toml | 36 + src/yellowhammer/__init__.py | 8 + uv.lock | 3089 ++++++++++++++++++++++++++++++++++ 5 files changed, 3168 insertions(+) create mode 100644 .python-version create mode 100644 pyproject.toml create mode 100644 src/yellowhammer/__init__.py create mode 100644 uv.lock diff --git a/.python-version b/.python-version new file mode 100644 index 0000000..c8cfe39 --- /dev/null +++ b/.python-version @@ -0,0 +1 @@ +3.10 diff --git a/README.md b/README.md index 09b1b0f..297e66b 100644 --- a/README.md +++ b/README.md @@ -4,3 +4,37 @@ # yeLLowhaMmer + +A continuation of the [LLM hackathon](https://www.eventbrite.com/e/llm-hackathon-for-applications-in-materials-and-chemistry-tickets-868303598437) project, [*yeLLowhaMMer: A Multi-modal Tool-calling Agent for Accelerated Research Data Management*](https://github.com/bocarsly-group/llm-hackathon-2024). + +This repository will explore using the Jupyter AI plugin to provide an agentic interface to [*datalab*](https://github.com/datalab-org/datalab), with the idea of having this as an additional UI that *datalab* users can use to interact with their data, either deployed for their instance, or run locally. + +## Initial development tasks + +- [ ] Reproduce the hackathon project with the Jupyter AI plugin, probably by extending the `%%ai` cell magic to something like `%%yellowhammer` that includes the yellowhammer system prompt, and guides through the registration of a *datalab* API key and any provided LLM API keys. +- [ ] Use yellowhammer to generate API examples for the underlying [*datalab-python-api*](https://github.com/datalab-org/datalab-python-api) package. +- [ ] Consider deploying this as a JupyterHub that *datalab* instances can link to directly. +- [ ] Integrate the results much more closely into *datalab* itself, i.e., attaching notebooks to the relevant samples, and recording the provenance of AI generated data recording. + +## Installation + +This repository uses [`uv`](https://docs.astral.sh/uv/) for the entire packaging workflow. +Once you have installed `uv` following their documentation, you can install this repository by cloning and running `uv sync` in the root directory. + +```shell +git clone git@github.com:datalab-org/yellowhammer +cd yellowhammer +uv sync +``` + +### Launching example notebooks + +You can launch the example notebook locally with `uv` too: + +```shell +uv run jupyter lab examples/ +``` + +The examples will require you to bring your own *datalab* API key (for your instance of choice) and API keys for any underlying LLM providers (OpenAI, Anthropic, etc.). +`yellowhammer` by default will come preloaded with the relevant OpenAI and Anthropic packages. +You can see how to configure other providers in the [Jupyter AI plugin documentation](https://jupyter-ai.readthedocs.io/en/latest/users/index.html#model-providers). diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 0000000..86e0e9b --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,36 @@ +[project] +name = "yellowhammer" +readme = "README.md" +license = { text = "MIT" } +requires-python = ">=3.10" +dynamic = ["version"] +dependencies = [ + "datalab-api>=0.2.4", + "jupyter-ai>=2.24.1", + "jupyterlab>=4.2.5", + "langchain-anthropic>=0.1.23", + "langchain-openai>=0.1.25", +] + +[project.urls] +homepage = "https://github.com/datalab-org/yellowhammer" +repository = "https://github.com/datalab-org/yellowhammer" +documentation = "https://github.com/datalab-org/yellowhammer" + +[build-system] +requires = ["setuptools >= 70", "setuptools_scm ~= 8.1", "wheel"] +build-backend = "setuptools.build_meta" + +[tool.setuptools_scm] +fallback_version = "0.1.0" + +[tool.ruff] +line-length = 100 +target-version = "py310" + +[tool.mypy] 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hash = "sha256:bc9eb26f4506fda01b81bcde0ca78103b6e62f991b381fec825435c836edbc29", size = 24199 } +wheels = [ + { url = "https://files.pythonhosted.org/packages/62/8b/5ba542fa83c90e09eac972fc9baca7a88e7e7ca4b221a89251954019308b/zipp-3.20.2-py3-none-any.whl", hash = "sha256:a817ac80d6cf4b23bf7f2828b7cabf326f15a001bea8b1f9b49631780ba28350", size = 9200 }, +] From 217ecd52b5efe6855c94c9a0a12577d9f75ca1e5 Mon Sep 17 00:00:00 2001 From: Matthew Evans Date: Mon, 7 Oct 2024 17:51:07 +0100 Subject: [PATCH 2/7] Add initial example notebook --- examples/001-getting-started.ipynb | 131 +++++++++++++++++++++++++++++ 1 file changed, 131 insertions(+) create mode 100644 examples/001-getting-started.ipynb diff --git a/examples/001-getting-started.ipynb b/examples/001-getting-started.ipynb new file mode 100644 index 0000000..5bf27ef --- /dev/null +++ b/examples/001-getting-started.ipynb @@ -0,0 +1,131 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": null, + "id": "929301f6-5982-4662-b68f-9e72269cace7", + "metadata": {}, + "outputs": [], + "source": [ + "%reload_ext jupyter_ai " + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "id": "f7f8325c-18b8-4943-b7e8-14a839060958", + "metadata": {}, + "outputs": [ + { + "data": { + "text/markdown": [ + "Here's the information about Datalab in markdown format:\n", + "\n", + "# Datalab\n", + "\n", + "Datalab is a tool developed by Google Cloud Platform that provides an interactive environment for data exploration, analysis, and machine learning. Key features include:\n", + "\n", + "## Features\n", + "\n", + "- **Jupyter Notebooks**: Uses Jupyter notebooks for interactive coding and visualization\n", + "- **Cloud Integration**: Seamlessly integrates with Google Cloud services\n", + "- **Big Data Support**: Designed to work with large datasets using BigQuery and other Google Cloud data services\n", + "- **Pre-installed Libraries**: Comes with popular data science libraries like pandas, numpy, and scikit-learn\n", + "- **Collaborative**: Allows for easy sharing and collaboration on data projects\n", + "\n", + "## Use Cases\n", + "\n", + "- Data exploration and visualization\n", + "- Machine learning model development\n", + "- Big data analysis\n", + "- Prototyping data pipelines\n", + "\n", + "## Advantages\n", + "\n", + "- Easy setup and configuration\n", + "- Cost-effective (pay only for resources used)\n", + "- Scalable to handle large datasets\n", + "- Integrates well with other Google Cloud services\n", + "\n", + "Datalab is particularly useful for data scientists and analysts who work with Google Cloud Platform and need a powerful, cloud-based environment for their data projects." + ], + "text/plain": [ + "" + ] + }, + "execution_count": 5, + "metadata": { + "text/markdown": { + "jupyter_ai": { + "model_id": "claude-3-5-sonnet-20240620", + "provider_id": "anthropic-chat" + } + } + }, + "output_type": "execute_result" + } + ], + "source": [ + "%%ai anthropic-chat:claude-3-5-sonnet-20240620\n", + "Do you know what datalab is?" + ] + }, + { + "cell_type": "code", + "execution_count": 15, + "id": "12aaa0b1-6ccd-4645-b578-d1fde5cd2614", + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "UsageError: Line magic function `%%yellowhammer` not found.\n" + ] + } + ], + "source": [ + "\"\"\" (mock up ) \"\"\"\n", + "%%yellowhammer\n", + "Do you know what datalab is?" + ] + }, + { + "cell_type": "markdown", + "id": "b943d5eb-a83a-4ed5-b531-e69a44d6d701", + "metadata": {}, + "source": [ + "Yes, *datalab* is ACTUALLY an open source research data management tool for chemistry and materials science, and here is the functionality I know about..." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "8d93f30b-3dde-457a-8aa9-9d08cc19f3ad", + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3 (ipykernel)", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.10.13" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} From d14184987dd38105c48b396a6aa8b3b6fb9ab3d2 Mon Sep 17 00:00:00 2001 From: Matthew Evans Date: Mon, 7 Oct 2024 17:53:55 +0100 Subject: [PATCH 3/7] Add pre-commit config --- .pre-commit-config.yaml | 36 +++++++++++++++++++++++++++++++++++ README.md | 4 ++-- src/yellowhammmer/__init__.py | 5 +++++ uv.lock | 2 +- 4 files changed, 44 insertions(+), 3 deletions(-) create mode 100644 .pre-commit-config.yaml create mode 100644 src/yellowhammmer/__init__.py diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml new file mode 100644 index 0000000..e2c207b --- /dev/null +++ b/.pre-commit-config.yaml @@ -0,0 +1,36 @@ +default_language_version: + python: python3.10 + +repos: + - repo: https://github.com/pre-commit/pre-commit-hooks + rev: v4.6.0 + hooks: + - id: trailing-whitespace + exclude: (pydatalab/example_data/)|(.*.snap) + args: [--markdown-linebreak-ext=md] + - id: check-yaml + args: [--unsafe] + - id: check-json + - id: end-of-file-fixer + exclude: ^(pydatalab/example_data/|pydatalab/schemas) + - id: check-added-large-files + args: [--maxkb=1024] + - id: check-symlinks + - id: mixed-line-ending + + - repo: https://github.com/astral-sh/ruff-pre-commit + rev: "v0.5.0" + hooks: + - id: ruff + args: [--fix] + - id: ruff-format + + - repo: https://github.com/asottile/pyupgrade + rev: v3.16.0 + hooks: + - id: pyupgrade + + - repo: https://github.com/pre-commit/mirrors-mypy + rev: v1.10.1 + hooks: + - id: mypy diff --git a/README.md b/README.md index 297e66b..013bfde 100644 --- a/README.md +++ b/README.md @@ -18,11 +18,11 @@ This repository will explore using the Jupyter AI plugin to provide an agentic i ## Installation -This repository uses [`uv`](https://docs.astral.sh/uv/) for the entire packaging workflow. +This repository uses [`uv`](https://docs.astral.sh/uv/) for the entire packaging workflow. Once you have installed `uv` following their documentation, you can install this repository by cloning and running `uv sync` in the root directory. ```shell -git clone git@github.com:datalab-org/yellowhammer +git clone git@github.com:datalab-org/yellowhammer cd yellowhammer uv sync ``` diff --git a/src/yellowhammmer/__init__.py b/src/yellowhammmer/__init__.py new file mode 100644 index 0000000..9485887 --- /dev/null +++ b/src/yellowhammmer/__init__.py @@ -0,0 +1,5 @@ +from importlib import metadata + +__version__ = metadata.version("yellowhammer") + +__all__ = ("__version__",) diff --git a/uv.lock b/uv.lock index ae0532b..7efbb59 100644 --- a/uv.lock +++ b/uv.lock @@ -3037,7 +3037,7 @@ wheels = [ [[package]] name = "yellowhammer" -version = "0.1.dev4+gc3af54d.d20241007" +version = "0.1.dev5+g217ecd5.d20241007" source = { editable = "." } dependencies = [ { name = "datalab-api" }, From fa8f9d98b2a24658b4f7ddacb9c3d5691cc68914 Mon Sep 17 00:00:00 2001 From: Matthew Evans Date: Mon, 7 Oct 2024 18:00:18 +0100 Subject: [PATCH 4/7] Add test stubs and CI --- .github/workflows/ci.yml | 70 ++++++++++++++++++++++++++++++++++++++++ README.md | 4 +-- pyproject.toml | 1 + tests/test_import.py | 4 +++ uv.lock | 3 +- 5 files changed, 79 insertions(+), 3 deletions(-) create mode 100644 .github/workflows/ci.yml create mode 100644 tests/test_import.py diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml new file mode 100644 index 0000000..06fc48b --- /dev/null +++ b/.github/workflows/ci.yml @@ -0,0 +1,70 @@ +name: CI tests +on: + pull_request: + + push: + branches: + - main + +env: + FORCE_COLOR: true + +concurrency: + group: ${{ github.head_ref || github.run_id }} + cancel-in-progress: true + +jobs: + pre-commit: + name: Run linters and other pre-commit hooks + runs-on: ubuntu-latest + + steps: + - uses: actions/checkout@v4 + + - name: Set up Python 3.10 + uses: actions/setup-python@v5 + with: + python-version: "3.10" + + - name: Set up uv + uses: astral-sh/setup-uv@v3 + with: + version: "0.4.x" + enable-cache: true + + - name: Install dependencies + run: | + uv sync --all-extras + + - name: Run pre-commit + run: | + uv run pre-commit run --all-files --show-diff-on-failure + + pytest: + name: Run Python unit tests + runs-on: ubuntu-latest + + steps: + - uses: actions/checkout@v4 + with: + # tests need an unshallowed version of the repository to check the version + fetch-depth: 0 + + - name: Set up Python 3.10 + uses: actions/setup-python@v5 + with: + python-version: '3.10' + + - name: Set up uv + uses: astral-sh/setup-uv@v3 + with: + version: "0.4.x" + enable-cache: true + + - name: Install locked versions of dependencies + run: | + uv sync --all-extras + + - name: Run all tests + run: | + uv run pytest -rs -vvv diff --git a/README.md b/README.md index 013bfde..a7f63af 100644 --- a/README.md +++ b/README.md @@ -19,12 +19,12 @@ This repository will explore using the Jupyter AI plugin to provide an agentic i ## Installation This repository uses [`uv`](https://docs.astral.sh/uv/) for the entire packaging workflow. -Once you have installed `uv` following their documentation, you can install this repository by cloning and running `uv sync` in the root directory. +Once you have installed `uv` following their documentation, you can install this repository by cloning and running `uv sync` in the root directory (optionally with `--dev` if you plan to develop it further). ```shell git clone git@github.com:datalab-org/yellowhammer cd yellowhammer -uv sync +uv sync --dev ``` ### Launching example notebooks diff --git a/pyproject.toml b/pyproject.toml index 86e0e9b..6c01a08 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -10,6 +10,7 @@ dependencies = [ "jupyterlab>=4.2.5", "langchain-anthropic>=0.1.23", "langchain-openai>=0.1.25", + "yellowhammer", ] [project.urls] diff --git a/tests/test_import.py b/tests/test_import.py new file mode 100644 index 0000000..766bca1 --- /dev/null +++ b/tests/test_import.py @@ -0,0 +1,4 @@ +def test_version(): + from yellowhammer import __version__ + + assert __version__ diff --git a/uv.lock b/uv.lock index 7efbb59..a33da1f 100644 --- a/uv.lock +++ b/uv.lock @@ -3037,7 +3037,7 @@ wheels = [ [[package]] name = "yellowhammer" -version = "0.1.dev5+g217ecd5.d20241007" +version = "0.1.dev6+gd141849.d20241007" source = { editable = "." } dependencies = [ { name = "datalab-api" }, @@ -3061,6 +3061,7 @@ requires-dist = [ { name = "jupyterlab", specifier = ">=4.2.5" }, { name = "langchain-anthropic", specifier = ">=0.1.23" }, { name = "langchain-openai", specifier = ">=0.1.25" }, + { name = "yellowhammer" }, ] [package.metadata.requires-dev] From 117550e9450948684e271db1305238d3e35c8382 Mon Sep 17 00:00:00 2001 From: Matthew Evans Date: Mon, 7 Oct 2024 18:36:01 +0100 Subject: [PATCH 5/7] pre-commit autoupdate --- .pre-commit-config.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index e2c207b..b6914c5 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -3,7 +3,7 @@ default_language_version: repos: - repo: https://github.com/pre-commit/pre-commit-hooks - rev: v4.6.0 + rev: v5.0.0 hooks: - id: trailing-whitespace exclude: (pydatalab/example_data/)|(.*.snap) @@ -19,18 +19,18 @@ repos: - id: mixed-line-ending - repo: https://github.com/astral-sh/ruff-pre-commit - rev: "v0.5.0" + rev: "v0.6.9" hooks: - id: ruff args: [--fix] - id: ruff-format - repo: https://github.com/asottile/pyupgrade - rev: v3.16.0 + rev: v3.17.0 hooks: - id: pyupgrade - repo: https://github.com/pre-commit/mirrors-mypy - rev: v1.10.1 + rev: v1.11.2 hooks: - id: mypy From cbf8e784d11bc757661102c361a10305fdab3614 Mon Sep 17 00:00:00 2001 From: Matthew Evans Date: Tue, 8 Oct 2024 02:34:11 +0100 Subject: [PATCH 6/7] Add explicit Jupyter notebook dep --- pyproject.toml | 1 + uv.lock | 20 +++++++++++++++++++- 2 files changed, 20 insertions(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 6c01a08..ed363dc 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -10,6 +10,7 @@ dependencies = [ "jupyterlab>=4.2.5", "langchain-anthropic>=0.1.23", "langchain-openai>=0.1.25", + "notebook>=7.2.2", "yellowhammer", ] diff --git a/uv.lock b/uv.lock index a33da1f..5939b9a 100644 --- a/uv.lock +++ b/uv.lock @@ -1741,6 +1741,22 @@ wheels = [ { url = "https://files.pythonhosted.org/packages/d2/1d/1b658dbd2b9fa9c4c9f32accbfc0205d532c8c6194dc0f2a4c0428e7128a/nodeenv-1.9.1-py2.py3-none-any.whl", hash = "sha256:ba11c9782d29c27c70ffbdda2d7415098754709be8a7056d79a737cd901155c9", size = 22314 }, ] +[[package]] +name = "notebook" +version = "7.2.2" +source = { registry = "https://pypi.org/simple" } +dependencies = [ + { name = "jupyter-server" }, + { name = "jupyterlab" }, + { name = "jupyterlab-server" }, + { name = "notebook-shim" }, + { name = "tornado" }, +] +sdist = { url = "https://files.pythonhosted.org/packages/0f/33/30b83c1c84e368087059bde1269549612584924db156bff53654e165a498/notebook-7.2.2.tar.gz", hash = "sha256:2ef07d4220421623ad3fe88118d687bc0450055570cdd160814a59cf3a1c516e", size = 4948876 } +wheels = [ + { url = "https://files.pythonhosted.org/packages/46/77/53732fbf48196af9e51c2a61833471021c1d77d335d57b96ee3588c0c53d/notebook-7.2.2-py3-none-any.whl", hash = "sha256:c89264081f671bc02eec0ed470a627ed791b9156cad9285226b31611d3e9fe1c", size = 5037123 }, +] + [[package]] name = "notebook-shim" version = "0.2.4" @@ -3037,7 +3053,7 @@ wheels = [ [[package]] name = "yellowhammer" -version = "0.1.dev6+gd141849.d20241007" +version = "0.1.dev8+g117550e.d20241008" source = { editable = "." } dependencies = [ { name = "datalab-api" }, @@ -3045,6 +3061,7 @@ dependencies = [ { name = "jupyterlab" }, { name = "langchain-anthropic" }, { name = "langchain-openai" }, + { name = "notebook" }, ] [package.dev-dependencies] @@ -3061,6 +3078,7 @@ requires-dist = [ { name = "jupyterlab", specifier = ">=4.2.5" }, { name = "langchain-anthropic", specifier = ">=0.1.23" }, { name = "langchain-openai", specifier = ">=0.1.25" }, + { name = "notebook", specifier = ">=7.2.2" }, { name = "yellowhammer" }, ] From f2945305c76df95c19d88656d868524d1d70817e Mon Sep 17 00:00:00 2001 From: Matthew Evans <7916000+ml-evs@users.noreply.github.com> Date: Tue, 8 Oct 2024 02:35:11 +0100 Subject: [PATCH 7/7] Add LLM API key examples to README Co-authored-by: Josh Bocarsly <32345545+jdbocarsly@users.noreply.github.com> --- README.md | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/README.md b/README.md index a7f63af..a4704ba 100644 --- a/README.md +++ b/README.md @@ -36,5 +36,12 @@ uv run jupyter lab examples/ ``` The examples will require you to bring your own *datalab* API key (for your instance of choice) and API keys for any underlying LLM providers (OpenAI, Anthropic, etc.). + +These can be set in your shell profile, or simply in your shell before launching Jupyter, using: +```bash +export OPENAI_API_KEY=sk-proj... +export ANTHROPIC_API_KEY=sk-ant... +``` + `yellowhammer` by default will come preloaded with the relevant OpenAI and Anthropic packages. You can see how to configure other providers in the [Jupyter AI plugin documentation](https://jupyter-ai.readthedocs.io/en/latest/users/index.html#model-providers).