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docs[installation]: Add CCD sync to test setup instructions #101

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31 changes: 16 additions & 15 deletions docs/installation.rst
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Expand Up @@ -60,21 +60,7 @@ To install in a fresh environment:

To run the AtomWorks test suite, you need to download the test data and configure environment variables.

**Step 1: Download test data**

From the repository root, run:

.. code-block:: bash

atomworks setup tests

This downloads and extracts the test pack (~500 MB) to ``tests/data/``, which includes:

* ``tests/data/pdb/`` — A mini PDB mirror with test structures
* ``tests/data/ccd/`` — A mini CCD mirror with test ligand definitions
* ``tests/data/shared/`` — MSA files, templates, and metadata for ML tests

**Step 2: Create a .env file**
**Step 1: Create a .env file**

Create a ``.env`` file in the repository root with the paths to the test data:

Expand All @@ -91,6 +77,21 @@ You can copy ``.env.sample`` as a starting point:
cp .env.sample .env
# Then edit .env to set the paths above

**Step 2: Download test data**

From the repository root, run:

.. code-block:: bash

atomworks setup tests
atomworks ccd sync tests/data/ccd # (or $CCD_MIRROR_PATH if you exported the variable to your shell)

This downloads and extracts the test pack (~500 MB) to ``tests/data/``, which includes:

* ``tests/data/pdb/`` — A mini PDB mirror with test structures
* ``tests/data/ccd/`` — A mini CCD mirror with test ligand definitions
* ``tests/data/shared/`` — MSA files, templates, and metadata for ML tests

**Step 3: Run the tests**

.. code-block:: bash
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