pin jedi to 0.17.2

.github/config/linux_win_env.yml

@@ -9,11 +9,10 @@ dependencies:
   - numpy
   - scipy
   - requests
-  - rdkit>=2020.03.1.0
-  - 'libblas=*=*mkl'
+  - rdkit=2020.03.3.0
   - scikit-learn
   - scipy
-  - pytorch >=1.6.0,<2.0.0
+  - pytorch >=1.7.0,<2.0.0
   - cpuonly
   - pytest
   - pytest-cov

.github/config/macos_env.yml

@@ -1,6 +1,6 @@
 name: test
 channels:
-  - defaults
+  # - defaults
   - pytorch
   - conda-forge
 dependencies:
@@ -9,11 +9,10 @@ dependencies:
   - numpy
   - scipy
   - requests
-  - rdkit>=2020.03.1.0
-  - 'libblas=*=*mkl'
+  - rdkit=2020.03.3.0
   - scikit-learn
   - scipy
-  - pytorch >=1.6.0,<2.0.0
+  - pytorch >=1.7.0,<2.0.0
   - pytest
   - pytest-cov
   - pymatgen>=2020.10.9

README.md

@@ -2,6 +2,8 @@
   <img height="200" src="https://github.com/yoshida-lab/XenonPy/blob/master/logo.png" alt="xenonpy">
 </p>
 
+**Our XenonPy.MDL is under technical maintenance and is not available during this period, sorry for all the inconvenience. We will make an announcement as soon as the expected date of recovery is determined.**
+
 # XenonPy project
 
 [![MacOS](https://github.com/yoshida-lab/XenonPy/workflows/MacOS/badge.svg)](https://github.com/yoshida-lab/XenonPy/actions?query=workflow%3AMacOS)
@@ -43,11 +45,11 @@ The following table list some core packages in XenonPy images.
 | -------------- | --------- |
 | `PyTorch`      | 1.7.0     |
 | `tensorly`     | 0.5.0     |
-| `pymatgen`     | 2020.10.9 |
+| `pymatgen`     | 2020.03.3 |
 | `matminer`     | 0.6.2     |
 | `mordred`      | 1.2.0     |
 | `scipy`        | 1.5.2     |
-| `scikit-learn` | 0.23.0    |
+| `scikit-learn` | 0.23.2    |
 | `xgboost`      | 1.3.0     |
 | `ngboost`      | master    |
 | `fastcluster`  | 1.1.26    |
@@ -97,11 +99,11 @@ Docker image tags .
 
 | Image tag | CUDA | PyTorch |
 | --------- | ---- | ------- |
-| `latest`  | 11.0 | 1.7.0   |
-| `cpu`     | None | 1.7.0   |
-| `cuda11`  | 11.0 | 1.7.0   |
-| `cuda10`  | 10.1 | 1.7.0   |
-| `cuda9`   | 9.2  | 1.7.0   |
+| `latest`  | 11.0 | 1.7.1   |
+| `cpu`     | None | 1.7.1   |
+| `cuda11`  | 11.0 | 1.7.1   |
+| `cuda10`  | 10.2 | 1.7.1   |
+| `cuda9`   | 9.2  | 1.7.1   |
 
 ### Running XenonPy
 

conda_env/cpu.yml

@@ -7,10 +7,11 @@ dependencies:
   - scikit-learn>=0.23.0
   - scipy>=1.5.2
   - pymatgen>=2020.10.9
-  - rdkit>=2020.03.1.0
+  - rdkit=2020.03.3.0
   - 'libblas=*=*mkl'
   - jupyter>=1.0.0
-  - pytorch >=1.6.0,<2.0.0
+  - pytorch >=1.7.0,<2.0.0
+  - jedi=0.17.2
   - cpuonly
   - fastcluster
   - torchvision

conda_env/cuda101.yml

@@ -7,12 +7,13 @@ dependencies:
   - scikit-learn>=0.23.0
   - scipy>=1.5.2
   - pymatgen>=2020.10.9
-  - rdkit>=2020.03.1.0
+  - rdkit=2020.03.3.0
   - 'libblas=*=*mkl'
   - jupyter>=1.0.0
-  - pytorch >=1.6.0,<2.0.0
+  - pytorch >=1.7.0,<2.0.0
   - cudatoolkit=10.1
   - magma-cuda101=2.5.2
+  - jedi=0.17.2
   - torchvision
   - torchtext
   - fastcluster

conda_env/cuda102.yml

@@ -7,12 +7,13 @@ dependencies:
   - scikit-learn>=0.23.0
   - scipy>=1.5.2
   - pymatgen>=2020.10.9
-  - rdkit>=2020.03.1.0
+  - rdkit=2020.03.3.0
   - 'libblas=*=*mkl'
   - jupyter>=1.0.0
-  - pytorch >=1.6.0,<2.0.0
+  - pytorch >=1.7.0,<2.0.0
   - cudatoolkit=10.2
   - magma-cuda102=2.5.2
+  - jedi=0.17.2
   - torchvision
   - torchtext
   - fastcluster

conda_env/cuda110.yml

@@ -7,12 +7,13 @@ dependencies:
   - scikit-learn>=0.23.0
   - scipy>=1.5.2
   - pymatgen>=2020.10.9
-  - rdkit>=2020.03.1.0
+  - rdkit=2020.03.3.0
   - 'libblas=*=*mkl'
   - jupyter>=1.0.0
-  - pytorch >=1.6.0,<2.0.0
+  - pytorch >=1.7.0,<2.0.0
   - cudatoolkit=11.0
   - magma-cuda110=2.5.2
+  - jedi=0.17.2
   - torchvision
   - torchtext
   - fastcluster

conda_env/cuda92.yml

@@ -7,12 +7,13 @@ dependencies:
   - scikit-learn>=0.23.0
   - scipy>=1.5.2
   - pymatgen>=2020.10.9
-  - rdkit>=2020.03.1.0
+  - rdkit=2020.03.3.0
   - 'libblas=*=*mkl'
   - jupyter>=1.0.0
-  - pytorch >=1.6.0,<2.0.0
+  - pytorch >=1.7.0,<2.0.0
   - cudatoolkit=9.2
   - magma-cuda92=2.5.2
+  - jedi=0.17.2
   - torchvision
   - torchtext
   - fastcluster

conda_env/osx.yml

@@ -7,10 +7,11 @@ dependencies:
   - scikit-learn>=0.23.0
   - scipy>=1.5.2
   - pymatgen>=2020.10.9
-  - rdkit>=2020.09.1.0
+  - rdkit=2020.03.3.0
   - 'libblas=*=*mkl'
   - jupyter>=1.0.0
-  - pytorch >=1.6.0,<2.0.0
+  - pytorch >=1.7.0,<2.0.0
+  - jedi=0.17.2
   - fastcluster
   - torchvision
   - torchtext

xenonpy/model/training/checker.py

@@ -64,7 +64,8 @@ def __init__(
         self._make_file_index()
 
     @classmethod
-    @deprecated('This method is rotten and will be removed in v1.0.0, use `Checker(<model path>)` instead')
+    @deprecated(
+        'This method is rotten and will be removed in v1.0.0, use `Checker(<model path>)` instead')
     def load(cls, model_path):
         return cls(model_path)
 
@@ -127,13 +128,12 @@ def model(self):
                     model.load_state_dict(state)
                 except torch.nn.modules.module.ModuleAttributeError:
                     # pytorch 1.6.0 compatability
-                    for k, m in model.named_modules():
+                    for _, m in model.named_modules():
                         m._non_persistent_buffers_set = set()
                     model.load_state_dict(state)
                 return model
             else:
                 return model
-        print("here: return None")
         return None
 
     @model.setter
@@ -154,7 +154,8 @@ def model(self, model: Module):
             raise TypeError(f'except `torch.nn.Module` object but got {type(model)}')
 
     @property
-    @deprecated('This property is rotten and will be removed in v1.0.0, use `checker.model` instead')
+    @deprecated('This property is rotten and will be removed in v1.0.0, use `checker.model` instead'
+               )
     def trained_model(self):
         if (self._path / 'trained_model.@1.pkl.z').exists():
             return torch.load(str(self._path / 'trained_model.@1.pkl.z'), map_location=self._device)
@@ -210,7 +211,10 @@ def final_state(self, state: OrderedDict):
 
     def _make_file_index(self):
 
-        for f in [f for f in self._path.iterdir() if f.match('*.pkl.*') or f.match('*.pd.*') or f.match('*.pth.*')]:
+        for f in [
+                f for f in self._path.iterdir()
+                if f.match('*.pkl.*') or f.match('*.pd.*') or f.match('*.pth.*')
+        ]:
             # select data
             fn = '.'.join(f.name.split('.')[:-2])
             self._files[fn] = str(f)