Merge pull request #9 from aqlaboratory/feature/update-setup

Feature/update setup

Author: jnwei

docs/environment.yml

@@ -0,0 +1,7 @@
+name: openfold3-docs
+channels:
+  - conda-forge
+dependencies:
+  - sphinx
+  - myst-parser
+  - furo

docs/source/Installation.md

@@ -80,7 +80,8 @@ This script will:
 - Setup a directory for OpenFold3 model parameters [default: `~/.openfold3`]
     - Writes the path to `$OPENFOLD_CACHE/ckpt_path` 
 - Download the model parameters, if the parameter file does not already exist 
-- Runs an inference integration test on two samples, without MSA alignments (~5 min on A100)
+- Optionally runs an inference integration test on two samples, without MSA alignments (~5 min on A100)
+    - N.B. To run the integration tests, `pytest` must be installed. 
 
 
 ### Downloading the model parameters manually

docs/source/conf.py

@@ -13,7 +13,7 @@
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
 
-extensions = ["myst_parser", "sphinx.ext.autodoc", "sphinxcontrib.autodoc_pydantic"]
+extensions = ["myst_parser"]
 
 templates_path = ["_templates"]
 exclude_patterns = []

openfold3/setup_openfold.py

@@ -18,14 +18,13 @@
 Downloads model parameters and runs verification tests.
 """
 
+import importlib.util
 import logging
 import os
 import subprocess
 import sys
 from pathlib import Path
 
-import pytest
-
 logging.basicConfig(level=logging.INFO, format="%(message)s")
 logger = logging.getLogger(__name__)
 
@@ -175,10 +174,23 @@ def download_parameters(param_dir) -> None:
 
 def run_integration_tests() -> None:
     """Run integration tests."""
+    confirm = input("Run integration tests? (yes/no)")
+    if confirm.lower() not in ["yes", "y"]:
+        logger.info("Skipping integration tests, exiting setup.")
+        return
+
     logger.info("Running integration tests...")
+    pytest_is_installed = importlib.util.find_spec("pytest")
+    if not pytest_is_installed:
+        logger.error("Pytest is required to run integration tests.")
+        logger.error(
+            "Please install pytest e.g. `pip install pytest` and rerun the script."
+        )
+        return
 
     # Set environment variables for tests
     os.environ["OPENFOLD_SETUP_SCRIPT"] = "1"
+    import pytest
 
     exit_code = pytest.main(
         [

pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "openfold3"
-version = "0.3.0"
+version = "0.3.1"
 dependencies = [
   "awscli",
   "torch",# ==2.5.1",
@@ -69,6 +69,7 @@ dev = [
   # used for documentation
   "sphinx",
   "myst-parser",
+  "furo"
 ]
 cuequivariance = [
   "cuequivariance>=0.6.1",