Merge pull request #40 from dhruvdcoder/dhruvdcoder/issue10-v2

Full test suite and CI

Author: dhruvdcoder

.github/workflows/tests.yml

@@ -0,0 +1,35 @@
+name: Tests
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+jobs:
+  pytest:
+    runs-on: ubuntu-latest
+    timeout-minutes: 60
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -e .
+          pip install -e xlm-models/
+          pip install -r requirements/test_requirements.txt
+
+      - name: Run non-GPU tests
+        run: pytest -m "not gpu and not cli and not integration" --cov-report=xml
+
+      - name: Upload coverage reports to Codecov
+        uses: codecov/codecov-action@v5
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          files: ./coverage.xml
+          fail_ci_if_error: false

.gitignore

@@ -46,10 +46,12 @@ site
 # editor files
 .cursorindexingignore
 oracle/fpscores.pkl
-.cursor/plans/dreamon_in_xlm-core_e37b5d3d.plan.md
+.cursor/plans
 
 # protein eval — generated artifacts and eval venvs
 vendor/dplm/.venv-esmfold/
 evals/protein_eval/*/esmfold_pdb/
 evals/protein_eval/*/metrics.jsonl
 evals/protein_eval/logs/
+.pytest_cache/
+docs/**/linkedin

README.md

@@ -10,6 +10,7 @@
 
 <p align="center">
   <a href="https://pypi.org/project/xlm-core/"><img src="https://img.shields.io/pypi/v/xlm-core?color=blue&label=PyPI" alt="PyPI version"></a>
+  <a href="https://codecov.io/gh/dhruvdcoder/xlm-core"><img src="https://img.shields.io/codecov/c/github/dhruvdcoder/xlm-core" alt="Code coverage"></a>
   <a href="https://dhruveshp.com/xlm-core/latest/guide/external-models/"><img src="https://img.shields.io/badge/Documentation-blue.svg" alt="Documentation"></a>
   <a href="https://github.com/dhruvdcoder/xlm-core"><img src="https://img.shields.io/badge/Python-3.11+-green.svg" alt="Python 3.11+"></a>
   <a href="https://github.com/dhruvdcoder/xlm-core/blob/main/LICENSE"><img src="https://img.shields.io/badge/License-MIT-yellow.svg" alt="License"></a>

docs/developers/dependencies.md

@@ -0,0 +1,131 @@
+# Dependencies
+
+This page describes how dependencies are laid out for **xlm-core** and how to install subsets for runtime, testing, docs, linting, and extras.
+
+## How packages are wired
+
+[`setup.py`](https://github.com/dhruvdcoder/xlm-core/blob/main/setup.py) loads **`requirements.txt`** at the repo root via `install_requires`:
+
+- `pip install xlm-core` installs those runtime dependencies.
+- **`requirements/core_requirements.txt`** is a complementary file with stricter pins, extra comments (e.g. Lightning / Torch / datasets), and tooling lines used for local/full dev installs—not every line is mirrored in `requirements.txt`.
+
+Run commands below from the **repository root** (where `setup.py` and `requirements/` live).
+
+## Requirement files overview
+
+| File | Purpose |
+|------|---------|
+| [`requirements.txt`](https://github.com/dhruvdcoder/xlm-core/blob/main/requirements.txt) (root) | Runtime dependencies used when publishing / `pip install xlm-core` |
+| [`requirements/core_requirements.txt`](https://github.com/dhruvdcoder/xlm-core/blob/main/requirements/core_requirements.txt) | Full core stack with version pins and inline notes |
+| [`requirements/test_requirements.txt`](https://github.com/dhruvdcoder/xlm-core/blob/main/requirements/test_requirements.txt) | pytest, hypothesis, coverage |
+| [`requirements/dev_requirements.txt`](https://github.com/dhruvdcoder/xlm-core/blob/main/requirements/dev_requirements.txt) | Notebooks / experiment tracking helpers |
+| [`requirements/docs_requirements.txt`](https://github.com/dhruvdcoder/xlm-core/blob/main/requirements/docs_requirements.txt) | MkDocs site build |
+| [`requirements/lint_requirements.txt`](https://github.com/dhruvdcoder/xlm-core/blob/main/requirements/lint_requirements.txt) | Typecheck, formatting, flake8 ecosystem |
+| [`requirements/extra_requirements.txt`](https://github.com/dhruvdcoder/xlm-core/blob/main/requirements/extra_requirements.txt) | Optional analysis / plotting (lighter set) |
+| [`requirements/plotting_requirements.txt`](https://github.com/dhruvdcoder/xlm-core/blob/main/requirements/plotting_requirements.txt) | Heavier plotting / stats stack |
+
+---
+
+## Root `requirements.txt`
+
+**Install:**
+
+```bash
+pip install -r requirements.txt
+```
+
+**Role:** Canonical list consumed by setuptools for `pip install xlm-core`. Matches the pinned core stack where it matters but may omit duplicated or heavily commented lines present in `core_requirements.txt`.
+
+---
+
+## Core requirements (`requirements/core_requirements.txt`)
+
+**Install:**
+
+```bash
+pip install -r requirements/core_requirements.txt
+```
+
+**Role:** Day-to-day / CI-style full environment for training and pipelines: PyTorch, Lightning, Hydra extras, HF `datasets`, `transformers`, `torchdata`, `jaxtyping`, `tensorboard`, `simple_slurm`, etc.
+
+Inline comments document choices (Torch range, Lightning version, datasets upper bound).
+
+---
+
+## Test dependencies
+
+**Install:**
+
+```bash
+pip install -r requirements/test_requirements.txt
+```
+
+**Included packages:**
+
+- `pytest`
+- `hypothesis`
+- `coverage[toml]`
+
+For workflows and invocation, see also [Running tests](testing/running-tests.md).
+
+Coverage configuration and pytest markers live in `pyproject.toml`.
+
+---
+
+## Development (`requirements/dev_requirements.txt`)
+
+**Install:**
+
+```bash
+pip install -r requirements/dev_requirements.txt
+```
+
+Includes `jupytext` and `wandb`.
+
+---
+
+## Documentation build (`requirements/docs_requirements.txt`)
+
+**Install:**
+
+```bash
+pip install -r requirements/docs_requirements.txt
+```
+
+Includes `mkdocs`, `mkdocs-material`, `mkdocstrings` (Python handler), `mike`, and `mkdocs-api-autonav`. Used when building this site locally or in CI.
+
+---
+
+## Lint / quality (`requirements/lint_requirements.txt`)
+
+**Install:**
+
+```bash
+pip install -r requirements/lint_requirements.txt
+```
+
+Includes `mypy`, `pre-commit`, `black`, `flake8` and related plugins (`flake8-docstrings`, `flake8-annotations`, `flake8-black`), `pytest-flake8`, `autoflake`, `darglint`, and `pre-commit-hooks`.
+
+---
+
+## Extra (`requirements/extra_requirements.txt`)
+
+**Install:**
+
+```bash
+pip install -r requirements/extra_requirements.txt
+```
+
+Includes `matplotlib`, `seaborn`, `networkx`, and `wandb` (overlapping with dev for experiment tracking).
+
+---
+
+## Plotting (`requirements/plotting_requirements.txt`)
+
+**Install:**
+
+```bash
+pip install -r requirements/plotting_requirements.txt
+```
+
+Includes `matplotlib`, `seaborn`, `statsmodels`, and `tueplots` for richer plotting notebooks or papers-style figures.