Modernizing packaging

.github/workflows/code_quality.yml

@@ -0,0 +1,78 @@
+name: Code quality
+
+on:
+  pull_request:
+    types: [opened, synchronize, reopened]
+
+permissions:
+  contents: read
+
+jobs:
+  lockfile:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v5
+      - uses: astral-sh/setup-uv@v7
+        with:
+          enable-cache: true
+          python-version: "3.12"
+      - run: uv lock --locked
+
+  lint:
+    runs-on: ubuntu-latest
+    needs: lockfile
+    steps:
+      - uses: actions/checkout@v5
+      - uses: astral-sh/setup-uv@v7
+        with:
+          enable-cache: true
+          python-version: "3.12"
+      - run: uv sync --locked --group dev
+      - run: uv run ruff check
+
+  format:
+    runs-on: ubuntu-latest
+    needs: lockfile
+    steps:
+      - uses: actions/checkout@v5
+      - uses: astral-sh/setup-uv@v7
+        with:
+          enable-cache: true
+          python-version: "3.12"
+      - run: uv sync --locked --group dev
+      - run: uv run ruff format --check
+
+  typecheck:
+    runs-on: ubuntu-latest
+    needs: lockfile
+    steps:
+      - uses: actions/checkout@v5
+      - uses: astral-sh/setup-uv@v7
+        with:
+          enable-cache: true
+          python-version: "3.12"
+      - run: uv sync --locked --group dev
+      - run: uv run mypy
+
+  test:
+    runs-on: ubuntu-latest
+    needs: lockfile
+    steps:
+      - uses: actions/checkout@v5
+      - uses: astral-sh/setup-uv@v7
+        with:
+          enable-cache: true
+          python-version: "3.12"
+      - run: uv sync --locked --group dev
+      - run: uv run pytest test/ -v
+
+  build:
+    runs-on: ubuntu-latest
+    needs: [lint, format, typecheck, test]
+    steps:
+      - uses: actions/checkout@v5
+      - uses: astral-sh/setup-uv@v7
+        with:
+          enable-cache: true
+          python-version: "3.12"
+      - run: uv build

.github/workflows/sphinx.yml

@@ -18,20 +18,16 @@ jobs:
       with:
         persist-credentials: false
 
-    - name: Set up conda
-      uses: conda-incubator/setup-miniconda@v3
+    - name: Set up uv
+      uses: astral-sh/setup-uv@v3
       with:
-        auto-activate-base: true
-        activate-environment: labcore-docs
-        environment-file: environment-docs.yml
-
-    - name: Install labcore package
-      shell: bash -l {0}
-      run: pip install -e .
-
+        enable-cache: true
+    - name: Install system deps
+      run: sudo apt-get update && sudo apt-get install -y pandoc
+    - name: Install dependencies
+      run: uv sync --frozen --group docs
     - name: Build HTML
-      shell: bash -l {0}
-      run: cd docs && make html
+      run: uv run --directory docs -- make html
 
     - name: Upload artifacts
       uses: actions/upload-artifact@v4
@@ -44,4 +40,4 @@ jobs:
       if: github.ref == 'refs/heads/main'
       with:
         github_token: ${{ secrets.GITHUB_TOKEN }}
-        publish_dir: docs/build/html
+        publish_dir: docs/build/html

AGENTS.md

@@ -0,0 +1,64 @@
+## 1. Think Before Coding
+
+**Don't assume. Don't hide confusion. Surface tradeoffs.**
+
+Before implementing:
+
+- State your assumptions explicitly. If uncertain, ask.
+- If multiple interpretations exist, present them - don't pick silently.
+- If a simpler approach exists, say so. Push back when warranted.
+- If something is unclear, stop. Name what's confusing. Ask.
+
+## 2. Simplicity First
+
+**Minimum code that solves the problem. Nothing speculative.**
+
+- No features beyond what was asked.
+- No abstractions for single-use code.
+- No "flexibility" or "configurability" that wasn't requested.
+- No error handling for impossible scenarios.
+- If you write 200 lines and it could be 50, rewrite it.
+
+Ask yourself: "Would a senior engineer say this is overcomplicated?" If yes, simplify.
+
+## 3. Surgical Changes
+
+**Touch only what you must. Clean up only your own mess.**
+
+When editing existing code:
+
+- Don't "improve" adjacent code, comments, or formatting.
+- Don't refactor things that aren't broken.
+- Match existing style, even if you'd do it differently.
+- If you notice unrelated dead code, mention it - don't delete it.
+
+When your changes create orphans:
+
+- Remove imports/variables/functions that YOUR changes made unused.
+- Don't remove pre-existing dead code unless asked.
+
+The test: Every changed line should trace directly to the user's request.
+
+## 4. Goal-Driven Execution
+
+**Define success criteria. Loop until verified.**
+
+Transform tasks into verifiable goals:
+
+- "Add validation" → "Write tests for invalid inputs, then make them pass"
+- "Fix the bug" → "Write a test that reproduces it, then make it pass"
+- "Refactor X" → "Ensure tests pass before and after"
+
+For multi-step tasks, state a brief plan:
+
+```
+1. [Step] → verify: [check]
+2. [Step] → verify: [check]
+3. [Step] → verify: [check]
+```
+
+Strong success criteria let you loop independently. Weak criteria ("make it work") require constant clarification.
+
+---
+
+**These guidelines are working if:** fewer unnecessary changes in diffs, fewer rewrites due to overcomplication, and clarifying questions come before implementation rather than after mistakes.

CLAUDE.md

@@ -0,0 +1 @@
+Treat @AGENTS.md the same way you would CLAUDE.md

README.md

@@ -1,15 +1,92 @@
 # labcore
-Code for measuring and such.
-
-## installation
-- clone from github
-- make the right environment: use ``$ conda env create -n labcore --file environment.yml``
-- install into your measurement environment:
-  ``$ pip install -e <path_to_cloned_repository>``
-- you should then be able to import:
-  ``>>> import labcore``
-
-## requirements
-what other packages are needed will depend a lot on which tools from this package you'll be using.
-In general, this will be used in a typical qcodes measurement environment.
-The different submodules in this package should list in their documentation if additional packages are required.
+
+A Python toolkit for acquiring, processing, and analyzing data in a condensed matter / quantum information physics lab.
+
+labcore is designed to complement the [QCodes](https://qcodes.github.io/Qcodes/) ecosystem — it sits alongside QCodes instruments and parameters, adding a flexible sweep framework, structured HDF5 storage, and analysis tools.
+
+**[Get started in 15 minutes →](https://toolsforexperiments.github.io/labcore/first_steps/15_min_guide.html)**
+
+---
+
+## What's inside
+
+- **Sweep framework** — compose parameter sweeps with `+` (sequential), `*` (zip), and `@` (nested) operators; decorate functions with `@recording` to produce structured records automatically
+- **Structured data storage** — `DataDict` and `DDH5Writer` for writing and reading HDF5 data files; `find_data`, `load_as_xr`, and `load_as_df` for data discovery and loading
+- **Fitting** — lmfit-based fitting framework with built-in fit functions (cosine, exponential, linear, exponentially decaying sine, and more) and xarray integration
+- **Analysis base** — a lightweight framework for organizing, saving, and loading analysis artifacts (figures, datasets, parameters)
+
+---
+
+## Installation
+
+labcore is not yet on PyPI. Install directly from GitHub:
+
+```bash
+pip install git+https://github.com/toolsforexperiments/labcore.git
+```
+
+Or clone and install in editable mode:
+
+```bash
+git clone https://github.com/toolsforexperiments/labcore.git
+pip install -e labcore/
+```
+
+Requires Python ≥ 3.11.
+
+---
+
+## Quick example
+
+```python
+from labcore.measurement import sweep_parameter, record_as, recording, dep, independent
+
+# Define what to record
+@recording(dep('signal', ['frequency']))
+def measure(frequency):
+    return {'signal': my_instrument.read(frequency)}
+
+# Run a sweep and save to HDF5
+from labcore.measurement.storage import run_and_save_sweep
+folder, _ = run_and_save_sweep(
+    sweep_parameter('frequency', range(100, 200)) @ measure,
+    data_dir='./data',
+    name='resonator_scan',
+)
+
+# Load the result as xarray
+from labcore.data.datadict_storage import load_as_xr
+ds = load_as_xr(folder)
+```
+
+See the [15-minute guide](https://toolsforexperiments.github.io/labcore/first_steps/15_min_guide.html) for a full walkthrough.
+
+---
+
+## Command-line tools
+
+| Command | Description |
+|---|---|
+| `autoplot` | Live plotting server for monitoring running measurements |
+| `reconstruct-data` | Reconstruct HDF5 files from safe-write temporary data |
+
+---
+
+## Development
+
+```bash
+git clone https://github.com/toolsforexperiments/labcore.git
+cd labcore
+uv sync --group dev
+uv run pytest test/ -v
+```
+
+---
+
+## License
+
+MIT. See [LICENSE](LICENSE) for details.
+
+## Authors
+
+Wolfgang Pfaff and Marcos Frenkel.