diff --git a/.github/workflows/cd.yml b/.github/workflows/cd.yml index 61c6204..b29fa18 100644 --- a/.github/workflows/cd.yml +++ b/.github/workflows/cd.yml @@ -57,8 +57,13 @@ jobs: steps: - uses: actions/checkout@v6 + - uses: oven-sh/setup-bun@v2 + + - name: Install dependencies + run: bun install --frozen-lockfile + - name: Make slides - run: npx @marp-team/marp-cli@latest --input-dir slides --output _output + run: bun run build-slides - uses: actions/upload-artifact@v7 with: diff --git a/.gitignore b/.gitignore index cf07268..d1b7266 100644 --- a/.gitignore +++ b/.gitignore @@ -203,3 +203,9 @@ content/week09_compiled/ramses/ _output/Volumes *.doit.db _output/ + +# Node / bun +node_modules/ + +# Symlink to AGENTS.md +.claude/ diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index a968905..924adb0 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -40,6 +40,7 @@ repos: hooks: - id: codespell args: ["-L", "hist,whet,classe,nd", "-w"] + exclude: ^bun\.lock$ - repo: local hooks: diff --git a/AGENTS.md b/AGENTS.md index 550ee4b..a859c9e 100644 --- a/AGENTS.md +++ b/AGENTS.md @@ -4,22 +4,24 @@ MyST MD course site for _Software Engineering for Scientific Computing_. ## Build & run -| Target | Command | -| ---------------------------- | -------------------------------------------------------------------- | -| Book (with pixi) | `pixi run book` | -| Pyodide / JupyterLite | `nox -s pyodide` | -| Slides | `npx @marp-team/marp-cli@latest --input-dir slides --output _output` | -| Live dev server (JupyterLab) | `pixi run lab` | +| Target | Command | +| ---------------------- | -------------------------------------------------------------------- | +| Book (with pixi) | `pixi run book` | +| Pyodide / JupyterLite | `nox -s pyodide` | +| Slides | `npx @marp-team/marp-cli@latest --input-dir slides --output _output` | +| Live dev server (MyST) | `pixi run serve` | +| JupyterLab | `pixi run lab` | - `pixi run book` depends on the `install-kernel` task, which installs the project's Python kernel into the pixi environment (`--sys-prefix`), then builds the site using `myst build --execute --html`. It sets `PYDEVD_DISABLE_FILE_VALIDATION=1`. - `mystmd` is configured to **execute all notebooks** on every build - (`--execute` flag). + (`--execute` flag), so broken code in a notebook breaks CI. - Only files listed in the `toc` section of `myst.yml` are included in the - build. The `notes/` directory is explicitly excluded and contains instructor - notes—do not reference it as book content. + build. Adding a new chapter file means adding it to `myst.yml`. The `notes/` + directory is explicitly excluded and contains instructor notes—do not + reference it as book content. ## Environment @@ -33,7 +35,12 @@ MyST MD course site for _Software Engineering for Scientific Computing_. - `content/` — Book chapters (mix of `.md` and `.ipynb`). - `slides/` — Marp slide decks. These are rendered by CI and deployed to - `public/slides`. + `public/slides`. Files are named `week-NN-N.md` (e.g. `week-14-1.md`) and use + the Marp `gaia` theme; copy the front matter from an existing deck. Slides + parallel a content chapter: the chapter links to its deck near the top with + `` {button}`Slides ` ``, and + the deck opens with a `# SE4Sci` / `## ` lead slide, with `---` + separating slides. - `notes/` — Instructor notes; not built into the book. - `myst.yml` drives the project configuration and table of contents. @@ -41,7 +48,10 @@ MyST MD course site for _Software Engineering for Scientific Computing_. - Always use `prek -a --quiet` instead of `pre-commit run -a`. - Hooks include: ruff-format, blacken-docs, nbstripout, prettier, codespell, - blocklint, plus a **custom `disallow-caps` hook**. + blocklint, plus a **custom `disallow-caps` hook** that rejects + miscapitalizations of names like pybind11, NumPy, CMake, ccache, GitHub, and + pytest — always use the canonical spelling (the hook also applies to this + file). - Prettier config (`.prettierrc.toml`): prose wraps at 80 chars by default, **but never for `slides/*.md`**. diff --git a/CLAUDE.md b/CLAUDE.md new file mode 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It is +also still a fast-changing field; we'll try to balance general advice and +specific examples that might change. + +## LLM details + +The core of agentic programming is an LLM, large language model. These are +simply completion engines trained on lots of data with a limited enough number +of parameters so that they learn concepts from the dataset. + +Models don't take letters in, they take tokens. That's why you can't ask a model +to count the "r"'s in "strawberry" - it doesn't actually see the word that way. +Tokenization is model specific; Claude Opus 4.7 has a finer tokenization than +Opus 4.6. (Different tokenizations are usually associated with a newly trained +model, rather than just updated weights, but model numbering has social +implications.) + +## Selecting a harness + +The first thing you'll interact with is the harness. These tend to come in three +flavors: + +- **TUI**, short for Terminal User Interface. These run in your terminal. Works + anywhere, including on clusters. +- **GUI**, short for Graphical User Interface. These are stand-alone application + with custom graphics. These can often do a little more than TUI's, like render + webpage previews. +- **Editor plugins**: These run in your editor, usually looking like a chat + window alongside the normal editor. + +Most harnesses come in all three flavors, you just pick the one you like +interacting with best. Some harnesses are more feature rich in one flavor. For +example, Copilot usually adds features to the editor plugin first. Claude Code +and OpenCode favor the TUI. + +There's a second component to harnesses, and it's really important: the **system +prompt**. The reason most model providers have a harness is to provide a system +prompt that is customized to that model. Model specific customizations are +likely not really needed, especially for larger models, so feel free to explore +if you can. But note that's likely the biggest difference between the same model +using different harnesses. + +Some providers (like Anthropic) require you use their harness to use +subscription coding, so you don't get a choice. (Providers can cache the prompt +tokens, reducing the cost and latency of the 10k-30k tokens of system prompt). + +Harnesses provide **tools**, which are things the model can call to perform +operations. Models are mostly smart enough to figure out how to use tools, and +most harnesses provide a small set of useful tools, so this isn't usually an +issue except maybe for small local models. + +This is what makes Agentic AI special, and more useful than a simple chat; the +model can call tools, read output, and loop, fixing mistakes, just like a human +would. Many other things in this course - tests, formatters, linters, type +checking, and CI all feed into the agentic loop, letting the agent correct +mistakes and produce high quality output. + +Most harnesses have these features: + +- `/` commands - these control the harness. Common examples: + - `/init`: Set up or update the `AGENTS.md` file (equivalent) + - `/restore` (or `/sessions`): open up a previous session + - `/review`: Review a PR and/or other diff (depends on the harness) +- `@` to load files into context (just mentioning them works too, but it's up to + the model to load all or parts) + +## Selecting a model + +There are different levels of models, with different costs / subscription usages +associated with them. Small open source models can even run locally. Some models +are faster than others, too. In general, if you are just learning about agentic +AI, you should use a fairly powerful model, so you don't hit model limitations. +Once you've used it for a bit, then you can start matching model strength to the +problem description. You often have an "effort level" toggle as well. Using a +strong model with a high effort level on a simple task can actually overengineer +sometimes. + +Here's a current breakdown of some current models: + +- Frontier models: Claude Opus, GPT 5.5 +- Workhorse models: Claude Sonnet, GPT 5.4, Kimi K2.6, Composer 2.5 +- Simple models: Claude Haiku, GPT 5.4 mini +- Local models: Gemma 4, Qwen 3.6 + +(GLM 5.1 sits right in between Simple and Workhorse, and is a personal +favorite). + +Here are some suggested task breakdowns. You can always use a stronger model, +this is just a recommended minimum: + +- Local models + - Asking questions about a codebase + - Very, very simple edits + - Throw-away scripts (like plotting code) + - Writing config for AI + - Summaries +- Simple models + - Repetitive edits + - Categorization/triage of open issues + - Simple merge conflicts + - Simple tests + - Fixing lints + - Quick chores + - Setting up, compiling, running code + - Working on webpages / theming +- Workhorse models + - Complex merge conflicts + - Complex tests + - PR/diff review + - Assistance with docs + - Bug fixes + - Fixing CI + - Conversion (languages, CI providers, documentation generators, etc) + - Adding static types + - Recovering old PRs or changes + - Applying a design document / standard +- Frontier models + - Large refactors + - Profiling and optimizations + - Difficult bug fixes + - Prototyping new features + - New features + - Any of the smaller model items if they fail to do it first + +## Setting up the harness + +Once you've picked a harness and model provider, then you'll need to download +and install it, and get signed in or your API key set somewhere. + +Your harness has a central location for config and a user-level +`AGENTS.md`-equivalent file. You can add a little bit of text here that will +always be loaded right after the system prompt. Here's a template: + +```md +You are on macOS. The github user is `<username>`. `python3` can be used if +python without dependencies is needed. Use `uv run` if in a python package. + +Use `prek -a --quiet` instead of `pre-commit run -a` for linting. + +If you make a commit, follow conventional commits and add a trailer: +`Assisted-by: <harness>:<model>`, where `<harness>` is the current agent harness +(like ClaudeCode), and `<model>` is the AI model (Like claude-opus-4.8). + +Prefix PR descriptions and comments on PRs with the line ":robot: _AI text +below_ :robot:" to indicate you are an agent speaking on a user's behalf. +``` + +(You would insert your GitHub username above). This does several things: + +- Some basic system setup, so the agents don't have to keep asking the same + questions +- Guide for running prek, since I use that everywhere +- Enforce conventional commits and Linux kernel style trailer. If using claude, + `You don't need to add a coauthored-by claude when you have this.` can be + added. +- Not needed for a large model, but if using local models, add + `Use relative paths when possible.`, this reduces the errors in making paths. +- Makes sure AI text is clearly marked (Claude also seems to comment on PRs + sometimes without asking, so this helps there too). + +Some example locations for this file: + +- Claude Code: `~/.claude/CLAUDE.md` +- OpenCode: `~/.config/opencode/AGENTS.md` +- Pi: `~/.pi/agent/APPEND_SYSTEM.md` + +There are also useful settings in these folders, too, like auto approve for +certain tools. + +## Setting up the project + +When you start up a harness, you are starting fresh, there's no knowledge about +the high level project features or low level details, everything must be +investigated by the agent. To speed this up, reduce token usage, and give the +agent a better "big-picture" view, you should create a project-level `AGENTS.md` +file. You can type `/init` into your harness, and that should generate one. Some +tools have custom file names; if yours does, move it to `AGENTS.md` after it is +generated. The only tool that does not support the `AGENTS.md` standard is +Claude Code; if you are using that then you'll also need to run +`ln -s AGENTS.md CLAUDE.md` and add `CLAUDE.md` to your gitignore (also +`.claude` while you are at it). Feel free to review and edit if it got anything +wrong (like best way to run the tests, etc). + +If it's a new project, you can write one shortly after getting started. You can +update it with AI as well, so feel free to include specifics that might change. +You can even instruct the AI to update `AGENTS.md` when things change in the +`AGENTS.md`! + +## Things to try first + +You can do nearly anything, but some ideas to get started. + +Try investigating the codebase. Some example prompts: + +- `How do I run the tests?` +- `Write an ARCHITECTURE.md describing how this project works.` +- `Who wrote the majority of the CI?` + +Your agent can look up git history, webpages, and much more, as it needs, +without being explicitly told. + +Try reviewing code: + +- `/review` (some harnesses require a PR number or description of what to + review) +- `Review this repository and look for things that can be modernized or simplified` + +And try this on issues or PRs if you have any: + +- `Categorize the open issues and tell me which ones are easiest to close` +- `Fix #123` +- `Is #234 still broken?` +- `Fix the CI` (on a failing PR) diff --git a/myst.yml b/myst.yml index 04b74fc..8b28801 100644 --- a/myst.yml +++ b/myst.yml @@ -92,6 +92,9 @@ project: children: - file: content/week13_misc/webassembly.md - file: content/week13_misc/shell.md + - title: "WIP: Agentic AI" + children: + - file: content/week14_agents/setup.md site: title: SE4Sci nav: diff --git a/package.json b/package.json new file mode 100644 index 0000000..b55c80d --- /dev/null +++ b/package.json @@ -0,0 +1,12 @@ +{ + "name": "se-for-sci", + "private": true, + "type": "module", + "scripts": { + "build-slides": "marp --input-dir slides --output _output", + "clean": "rm -rf _output" + }, + "dependencies": { + "@marp-team/marp-cli": "^4.0" + } +} diff --git a/slides/week-14-1.md b/slides/week-14-1.md new file mode 100644 index 0000000..7860dea --- /dev/null +++ b/slides/week-14-1.md @@ -0,0 +1,177 @@ +--- +marp: true +theme: gaia +_class: lead +paginate: false +backgroundColor: #fff +backgroundImage: url('https://marp.app/assets/hero-background.svg') +--- + +# SE4Sci + +## Setting up Agentic AI + +--- + +## Agentic AI + +- The most significant change to software engineering ever +- Still a fast-changing field +- We'll balance general advice with specific (and changing) examples + +--- + +## LLM details + +- The core of agentic programming is an LLM (large language model) +- Simply completion engines trained on lots of data +- Limited number of parameters, so they learn _concepts_ from the data + +--- + +## Tokenization + +- Models don't take in letters, they take in **tokens** +- That's why a model can't count the "r"'s in "strawberry" +- Tokenization is model specific + - Claude Opus 4.7 has finer tokenization than Opus 4.6 + - Usually tied to a newly trained model, not just updated weights + +--- + +## Selecting a harness + +The first thing you interact with. Three flavors: + +- **TUI** (Terminal User Interface) — runs in your terminal, works anywhere, even on clusters +- **GUI** (Graphical User Interface) — stand-alone app, can render extras like webpage previews +- **Editor plugins** — chat window alongside your editor + +Most harnesses come in all three; pick the one you like best. + +--- + +## The system prompt + +- The biggest reason providers ship a harness +- A system prompt customized to that model (10k–30k tokens, cached) +- Model-specific tuning often isn't really needed for larger models +- Likely the **biggest difference** between the same model in different harnesses +- Some providers (e.g. Anthropic) require their harness for subscription coding + +--- + +## Tools and the agentic loop + +- Harnesses provide **tools** — things the model can call to do work +- Models are mostly smart enough to figure out how to use them +- The model can call tools, read output, and **loop**, fixing mistakes — like a human +- Tests, formatters, linters, type checking, and CI all feed the loop, producing high quality output + +--- + +## Common harness features + +- `/` commands control the harness: + - `/init`: set up or update the `AGENTS.md` file + - `/restore` (or `/sessions`): open a previous session + - `/review`: review a PR and/or other diff +- `@` to load files into context (mentioning them often works too) + +--- + +## Selecting a model + +- Different levels, with different costs / subscription usage +- Some models are faster; small open source models can run locally +- Learning agentic AI? Use a fairly powerful model so you don't hit limits +- Later, match model strength to the problem +- An "effort level" toggle exists too — strong model + high effort on a simple task can **overengineer** + +--- + +## A current breakdown + +- **Frontier**: Claude Opus, GPT 5.5 +- **Workhorse**: Claude Sonnet, GPT 5.4, Kimi K2.6, Composer 2.5 +- **Simple**: Claude Haiku, GPT 5.4 mini +- **Local**: Gemma 4, Qwen 3.6 + +(GLM 5.1 sits between Simple and Workhorse, and is a personal favorite.) + +--- + +## Suggested tasks (minimums) + +- **Local**: codebase questions, very simple edits, throw-away scripts, AI config, summaries +- **Simple**: repetitive edits, issue triage, simple merge conflicts/tests, fixing lints, building & running code, theming +- **Workhorse**: complex merge conflicts/tests, PR review, docs, bug fixes, fixing CI, conversions, static types +- **Frontier**: large refactors, profiling/optimization, hard bugs, prototyping and new features + +--- + +## Setting up the harness + +- Download, install, sign in or set your API key +- Each harness has a user-level `AGENTS.md`-equivalent, loaded right after the system prompt + +Some locations: + +- Claude Code: `~/.claude/CLAUDE.md` +- OpenCode: `~/.config/opencode/AGENTS.md` +- Pi: `~/.pi/agent/APPEND_SYSTEM.md` + +--- + +## A user config template + +```md +You are on macOS. The github user is `<username>`. `python3` can be used if python without dependencies is needed. Use `uv run` if in a python package. + +Use `prek -a --quiet` instead of `pre-commit run -a` for linting. + +If you make a commit, follow conventional commits and add a trailer: `Assisted-by: <harness>:<model>`. + +Prefix PR descriptions and comments with ":robot: _AI text below_ :robot:". +``` + +For local models, add `Use relative paths when possible.` + +--- + +## Setting up the project + +- A fresh harness knows nothing — everything must be investigated +- A project-level `AGENTS.md` speeds this up, cuts tokens, gives a big-picture view +- Type `/init` to generate one; rename to `AGENTS.md` if needed +- Claude Code is the only tool not supporting `AGENTS.md`: + - `ln -s AGENTS.md CLAUDE.md` and gitignore `CLAUDE.md` (and `.claude`) +- Review and edit anything it got wrong + +--- + +## Things to try first + +Investigate the codebase: + +- `How do I run the tests?` +- `Write an ARCHITECTURE.md describing how this project works.` +- `Who wrote the majority of the CI?` + +Review code: + +- `/review` +- `Review this repository and look for things that can be modernized or simplified` + +--- + +## Things to try first (2) + +On issues or PRs: + +- `Categorize the open issues and tell me which ones are easiest to close` +- `Fix #123` +- `Is #234 still broken?` +- `Fix the CI` (on a failing PR) + +The agent can look up git history, webpages, and more — without being told.