allow strong preferences from pick_device using a string; release fid…

…dles (#85)

* pick_device allows strong preferences now
* Fixing deprecation
* using python 3.9 and above

---------

Co-authored-by: Will Dumm <wrhdumm@gmail.com>

.github/workflows/build-and-test.yml

@@ -11,7 +11,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest]
-        python-version: [3.8, "3.11"]
+        python-version: [3.9, "3.11"]
 
     runs-on: ${{ matrix.os }}
 

README.md

@@ -4,7 +4,7 @@ Neural NETworks for antibody Affinity Maturation.
 
 ## pip installation
 
-Netam is available on PyPI, and works with Python 3.8 through 3.11.
+Netam is available on PyPI, and works with Python 3.9 through 3.11.
 
 ```
 pip install netam
@@ -60,3 +60,12 @@ If you are running one of the experiment repos, such as:
 * [dnsm-experiments-1](https://github.com/matsengrp/dnsm-experiments-1/)
 
 you will want to visit those repos and follow the installation instructions there.
+
+
+## Troubleshooting
+* On some machines, pip may install a version of numpy that is too new for the
+    available version of pytorch, returning an error such as `A module that was compiled using NumPy 1.x cannot be run in
+NumPy 2.0.2 as it may crash.` The solution is to downgrade to `numpy<2`:
+    ```console
+    pip install --force-reinstall "numpy<2"
+    ```

netam/common.py

@@ -198,13 +198,23 @@ def find_least_used_cuda_gpu():
     return utilization.index(min(utilization))
 
 
-def pick_device(gpu_index=None):
+def pick_device(gpu_preference=None):
     """Pick a device for PyTorch to use.
 
-    If CUDA is available, use the least used GPU, and if all are idle use the gpu_index
+    If gpu_preference is a string, use the device with that name. This is considered a
+    strong preference from a user who knows what they are doing.
+
+    If gpu_preference is an integer, this is a weak preference for a numbered GPU.  If
+    CUDA is available, use the least used GPU, and if all are idle use the gpu_index
     modulo the number of GPUs. If gpu_index is None, then use a random GPU.
     """
 
+    # Strong preference for a specific device.
+    if gpu_preference is not None and isinstance(gpu_preference, str):
+        return torch.device(gpu_preference)
+
+    # else weak preference for a numbered GPU.
+
     # check that CUDA is usable
     def check_CUDA():
         try:
@@ -216,10 +226,10 @@ def check_CUDA():
     if torch.backends.cudnn.is_available() and check_CUDA():
         which_gpu = find_least_used_cuda_gpu()
         if which_gpu is None:
-            if gpu_index is None:
+            if gpu_preference is None:
                 which_gpu = np.random.randint(torch.cuda.device_count())
             else:
-                which_gpu = gpu_index % torch.cuda.device_count()
+                which_gpu = gpu_preference % torch.cuda.device_count()
         print(f"Using CUDA GPU {which_gpu}")
         return torch.device(f"cuda:{which_gpu}")
     elif torch.backends.mps.is_available():

netam/pretrained.py

@@ -5,15 +5,14 @@
 
 import os
 import zipfile
-import pkg_resources
+from importlib.resources import files
 
 import requests
 
 from netam.framework import load_crepe
 
-# This throws a deprecation warning. It could also be done by looking at
-# __file__, or by using importlib.resources.
-PRETRAINED_DIR = pkg_resources.resource_filename(__name__, "_pretrained")
+with files(__package__).joinpath("_pretrained") as pretrained_path:
+    PRETRAINED_DIR = str(pretrained_path)
 
 PACKAGE_LOCATIONS_AND_CONTENTS = (
     # Order of entries:

notebooks/thrifty_demo.ipynb

@@ -24,7 +24,7 @@
     "\n",
     "To get a pretrained crepe, just ask for it by name. 🍰!\n",
     "\n",
-    "Here we get the `ThriftyHumV1.0-45` model:"
+    "Here we get the `ThriftyHumV0.2-45` model:"
    ]
   },
   {

setup.py

@@ -11,7 +11,7 @@
     long_description=open("README.md").read(),
     long_description_content_type="text/markdown",
     packages=find_packages(),
-    python_requires=">=3.8,<3.12",
+    python_requires=">=3.9,<3.12",
     install_requires=[
         "biopython",
         "natsort",
@@ -22,6 +22,7 @@
         "tensorboardX",
         "torch",
         "tqdm",
+        "fire",
     ],
     classifiers=[
         "Development Status :: 3 - Alpha",

tests/conftest.py

@@ -13,6 +13,6 @@ def pcp_df():
     )
     df = add_shm_model_outputs_to_pcp_df(
         df,
-        pretrained.load("ThriftyHumV1.0-45"),
+        pretrained.load("ThriftyHumV0.2-45"),
     )
     return df

tests/test_multihit.py

@@ -64,7 +64,7 @@
 @pytest.fixture
 def mini_multihit_train_val_datasets():
     df = pd.read_csv("data/wyatt-10x-1p5m_pcp_2023-11-30_NI.first100.csv.gz")
-    crepe = pretrained.load("ThriftyHumV1.0-45")
+    crepe = pretrained.load("ThriftyHumV0.2-45")
     df = multihit.prepare_pcp_df(df, crepe, 500)
     return multihit.train_test_datasets_of_pcp_df(df)
 

tests/test_pretrained.py

@@ -0,0 +1,22 @@
+import netam.pretrained as pretrained
+from pathlib import Path
+import shutil
+
+
+def test_names_unique():
+    # Check all defined models can be loaded and they have unique names
+    assert len(set(pretrained.MODEL_TO_LOCAL.keys())) == sum(
+        len(models) for _, _, _, models in pretrained.PACKAGE_LOCATIONS_AND_CONTENTS
+    )
+
+
+def test_load_all_models():
+    # Remove cached models:
+    shutil.rmtree(Path(pretrained.PRETRAINED_DIR))
+    # Check each can be loaded without caching
+    for model_name in pretrained.MODEL_TO_LOCAL:
+        pretrained.load(model_name)
+
+    # Check each can be loaded with caching
+    for model_name in pretrained.MODEL_TO_LOCAL:
+        pretrained.load(model_name)