Merge pull request #142 from hspark1212/develop

Develop

Author: Yeonghun1675

README.md

@@ -2,10 +2,10 @@
 
 <p align="center">
  <a href="https://hspark1212.github.io/MOFTransformer/">
-     <img alt="Docs" src="https://img.shields.io/badge/Docs-v2.1.1-brightgreen.svg?style=plastic">
+     <img alt="Docs" src="https://img.shields.io/badge/Docs-v2.1.2-brightgreen.svg?style=plastic">
  </a>
   <a href="https://pypi.org/project/moftransformer/">
-     <img alt="PypI" src="https://img.shields.io/badge/PyPI-v2.1.1-blue.svg?style=plastic&logo=PyPI">
+     <img alt="PypI" src="https://img.shields.io/badge/PyPI-v2.1.2-blue.svg?style=plastic&logo=PyPI">
  </a>
   <a href="https://doi.org/10.6084/m9.figshare.21155506.v2">
      <img alt="Figshare" src="https://img.shields.io/badge/Figshare-v2-blue.svg?style=plastic&logo=figshare">

docs/source/conf.py

@@ -9,7 +9,7 @@
 project = "MOFTransformer"
 copyright = "2022, Yeonghun Kang, Hyunsoo Park"
 author = "Yeonghun Kang, Hyunsoo Park"
-release = "2.1.1"
+release = "2.1.2"
 
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration

moftransformer/__init__.py

@@ -1,7 +1,7 @@
-# MOFTransformer version 2.1.1
+# MOFTransformer version 2.1.2
 import os
 
-__version__ = "2.1.1"
+__version__ = "2.1.2"
 __root_dir__ = os.path.dirname(__file__)
 
 from moftransformer import visualize, utils, modules, libs, gadgets, datamodules, assets

moftransformer/modules/module.py

@@ -330,10 +330,13 @@ def on_predict_start(self):
     def predict_step(self, batch, batch_idx, dataloader_idx=0):
         output = self(batch)
 
-        softmax = torch.nn.Softmax(dim=1)
         if 'classification_logits' in output:
-            output['classification_logits'] = softmax(output['classification_logits'])
-            output['classification_logits_index'] = torch.argmax(output['classification_logits'], dim=1)
+            if self.hparams.config['n_classes'] == 2:
+                output['classification_logits_index'] = torch.round(output['classification_logits']).to(torch.int)
+            else:
+                softmax = torch.nn.Softmax(dim=1)
+                output['classification_logits'] = softmax(output['classification_logits'])
+                output['classification_logits_index'] = torch.argmax(output['classification_logits'], dim=1)
 
         output = {
             k: (v.cpu().tolist() if torch.is_tensor(v) else v)

moftransformer/utils/install_griday.py

@@ -65,10 +65,18 @@ def _make_griday():
     print(
         "=== Successfully download ======================================================="
     )
-    if Path(GRIDAY_PATH).exists():
+    if not Path(GRIDAY_PATH).exists():
+        raise InstallationError(f"GRIDAY is not installed. Please try again.")
+    
+    print(
+        "=== Check GIRDAY ================================================================"
+    )    
+    ps = subprocess.run([str(GRIDAY_PATH)], cwd=dir_griday, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+    if ps.stderr == b'./make_egrid spacing atom_type force_field input_cssr egrid_stem\n':
         print(f"GRIDAY is installed to {dir_griday}")
     else:
-        raise InstallationError(f"GRIDAY is not installed. Please try again.")
+        print (ps.stdout, ps.stderr)
+        print(f'GRIDAY does not installed correctly. Please uninstall griday and re-install.')    
 
 
 def install_griday(install_make=False):

requirements.txt

@@ -1,8 +1,8 @@
-# MOFTransformer version 2.0.1
+# MOFTransformer version 2.1.2
 wget
 torch<2.0.0
 pytorch-lightning==1.7.0 # pytorch-lightning>=1.7.0
-torchmetrics>=0.6.0
+torchmetrics<1.0.0, >=0.6.0
 transformers>=4.12.5
 timm>=0.4.12
 sacred>=0.8.2

updates.md

@@ -1,5 +1,10 @@
 # Update
 
+## Version 2.1.2
+- Check GRIDAY is vailed or not when you run `install_griday`
+- `torchmetrics < 1.0.0` in requirements
+- Fix bugs in predict when loss is `classification` and n_classes are 2.
+
 ## Version 2.1.1
 - Fixed a bug when the structure name of raw_[downstream].json contains a cif during prepare_data.
 - Changed an error that occurred when there were multiple devices in an interactive environment to a warning, automatically converting the configuration to a single device.