Restrict pymatgen version to under 2022 (#235)

* Restrict pymatgen version to under 2022 * improve github actions
yoshida-lab · Mar 12, 2021 · bfeb571 · bfeb571
1 parent 7b48997
commit bfeb571
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Showing 15 changed files with 144 additions and 109 deletions.
diff --git a/.github/config/linux_win_env.yml b/.github/config/linux_win_env.yml
@@ -16,7 +16,7 @@ dependencies:
   - cpuonly
   - pytest
   - pytest-cov
-  - pymatgen>=2020.10.9
+  - pymatgen>=2020.10.9,<2022.0
   - ruamel.yaml
   - tqdm
   - mordred

diff --git a/.github/config/macos_env.yml b/.github/config/macos_env.yml
@@ -15,7 +15,7 @@ dependencies:
   - pytorch >=1.7.0,<2.0.0
   - pytest
   - pytest-cov
-  - pymatgen>=2020.10.9
+  - pymatgen>=2020.10.9,<2022.0
   - ruamel.yaml
   - tqdm
   - mordred

diff --git a/.github/workflows/mac.yml b/.github/workflows/mac.yml
@@ -5,27 +5,37 @@ on:
     branches:
       - master
     paths-ignore:
-      - 'docs/**'
-      - '.**'
-      - '**.md'
-      - '**.yml'
-      - '**.txt'
-      - '**.in'
-      - '**.cfg'
+      - "conda_env/**"
+      - "devtools/**"
+      - "docs/**"
+      - "samples/**"
+      - "licenses/**"
+      - "hooks/**"
+      - ".**"
+      - "**.md"
+      - "**.yml"
+      - "**.txt"
+      - "**.in"
+      - "**.cfg"
   pull_request:
     branches:
       - master
     paths-ignore:
-      - 'docs/**'
-      - '.**'
-      - '**.md'
-      - '**.yml'
-      - '**.txt'
-      - '**.in'
-      - '**.cfg'
+      - "conda_env/**"
+      - "devtools/**"
+      - "docs/**"
+      - "samples/**"
+      - "licenses/**"
+      - "hooks/**"
+      - ".**"
+      - "**.md"
+      - "**.yml"
+      - "**.txt"
+      - "**.in"
+      - "**.cfg"
 
 env:
-  MPLBACKEN: 'Agg'
+  MPLBACKEN: "Agg"
 
 jobs:
   test_macos:
@@ -35,7 +45,7 @@ jobs:
       max-parallel: 4
       matrix:
         python-version: [3.6, 3.7]
-        os: ['macos-11.0', 'macos-10.15']
+        os: ["macos-11.0", "macos-10.15"]
 
     steps:
       - uses: actions/checkout@v2

diff --git a/.github/workflows/ubuntu.yml b/.github/workflows/ubuntu.yml
@@ -5,27 +5,37 @@ on:
     branches:
       - master
     paths-ignore:
-      - 'docs/**'
-      - '.**'
-      - '**.md'
-      - '**.yml'
-      - '**.txt'
-      - '**.in'
-      - '**.cfg'
+      - "conda_env/**"
+      - "devtools/**"
+      - "docs/**"
+      - "samples/**"
+      - "licenses/**"
+      - "hooks/**"
+      - ".**"
+      - "**.md"
+      - "**.yml"
+      - "**.txt"
+      - "**.in"
+      - "**.cfg"
   pull_request:
     branches:
       - master
     paths-ignore:
-      - 'docs/**'
-      - '.**'
-      - '**.md'
-      - '**.yml'
-      - '**.txt'
-      - '**.in'
-      - '**.cfg'
+      - "conda_env/**"
+      - "devtools/**"
+      - "docs/**"
+      - "samples/**"
+      - "licenses/**"
+      - "hooks/**"
+      - ".**"
+      - "**.md"
+      - "**.yml"
+      - "**.txt"
+      - "**.in"
+      - "**.cfg"
 
 env:
-  MPLBACKEN: 'Agg'
+  MPLBACKEN: "Agg"
 
 jobs:
   test_ubuntu:
@@ -35,7 +45,7 @@ jobs:
       max-parallel: 4
       matrix:
         python-version: [3.6, 3.7]
-        os: ['ubuntu-18.04', 'ubuntu-latest']
+        os: ["ubuntu-18.04", "ubuntu-latest"]
 
     steps:
       - uses: actions/checkout@v2

diff --git a/.github/workflows/win.yml b/.github/workflows/win.yml
@@ -5,27 +5,37 @@ on:
     branches:
       - master
     paths-ignore:
-      - 'docs/**'
-      - '.**'
-      - '**.md'
-      - '**.yml'
-      - '**.txt'
-      - '**.in'
-      - '**.cfg'
+      - "conda_env/**"
+      - "devtools/**"
+      - "docs/**"
+      - "samples/**"
+      - "licenses/**"
+      - "hooks/**"
+      - ".**"
+      - "**.md"
+      - "**.yml"
+      - "**.txt"
+      - "**.in"
+      - "**.cfg"
   pull_request:
     branches:
       - master
     paths-ignore:
-      - 'docs/**'
-      - '.**'
-      - '**.md'
-      - '**.yml'
-      - '**.txt'
-      - '**.in'
-      - '**.cfg'
+      - "conda_env/**"
+      - "devtools/**"
+      - "docs/**"
+      - "samples/**"
+      - "licenses/**"
+      - "hooks/**"
+      - ".**"
+      - "**.md"
+      - "**.yml"
+      - "**.txt"
+      - "**.in"
+      - "**.cfg"
 
 env:
-  MPLBACKEN: 'Agg'
+  MPLBACKEN: "Agg"
 
 jobs:
   test_win:
@@ -35,7 +45,7 @@ jobs:
       max-parallel: 2
       matrix:
         python-version: [3.6, 3.7]
-        os: ['windows-latest']
+        os: ["windows-latest"]
 
     steps:
       - uses: actions/checkout@v2

diff --git a/conda_env/cpu.yml b/conda_env/cpu.yml
@@ -6,12 +6,12 @@ dependencies:
   - pandas>=1.1.3
   - scikit-learn>=0.23.0
   - scipy>=1.5.2
-  - pymatgen>=2020.10.9
+  - pymatgen>=2020.10.9,<2022.0
   - rdkit=2020.09
-  - 'libblas=*=*mkl'
+  - "libblas=*=*mkl"
   - jupyter>=1.0.0
   - pytorch >=1.7.0,<2.0.0
-  - jedi=0.17.2
+  - jedi>=0.16
   - cpuonly
   - fastcluster
   - torchvision

diff --git a/conda_env/cuda101.yml b/conda_env/cuda101.yml
@@ -6,14 +6,14 @@ dependencies:
   - pandas>=1.1.3
   - scikit-learn>=0.23.0
   - scipy>=1.5.2
-  - pymatgen>=2020.10.9
+  - pymatgen>=2020.10.9,<2022.0
   - rdkit=2020.09
-  - 'libblas=*=*mkl'
+  - "libblas=*=*mkl"
   - jupyter>=1.0.0
   - pytorch >=1.7.0,<2.0.0
   - cudatoolkit=10.1
   - magma-cuda101=2.5.2
-  - jedi=0.17.2
+  - jedi>=0.16
   - torchvision
   - torchtext
   - fastcluster

diff --git a/conda_env/cuda102.yml b/conda_env/cuda102.yml
@@ -6,14 +6,14 @@ dependencies:
   - pandas>=1.1.3
   - scikit-learn>=0.23.0
   - scipy>=1.5.2
-  - pymatgen>=2020.10.9
+  - pymatgen>=2020.10.9,<2022.0
   - rdkit=2020.09
-  - 'libblas=*=*mkl'
+  - "libblas=*=*mkl"
   - jupyter>=1.0.0
   - pytorch >=1.7.0,<2.0.0
   - cudatoolkit=10.2
   - magma-cuda102=2.5.2
-  - jedi=0.17.2
+  - jedi>=0.16
   - torchvision
   - torchtext
   - fastcluster

diff --git a/conda_env/cuda110.yml b/conda_env/cuda110.yml
@@ -6,14 +6,14 @@ dependencies:
   - pandas>=1.1.3
   - scikit-learn>=0.23.0
   - scipy>=1.5.2
-  - pymatgen>=2020.10.9
+  - pymatgen>=2020.10.9,<2022.0
   - rdkit=2020.09
-  - 'libblas=*=*mkl'
+  - "libblas=*=*mkl"
   - jupyter>=1.0.0
   - pytorch >=1.7.0,<2.0.0
   - cudatoolkit=11.0
   - magma-cuda110=2.5.2
-  - jedi=0.17.2
+  - jedi>=0.16
   - torchvision
   - torchtext
   - fastcluster

diff --git a/conda_env/cuda92.yml b/conda_env/cuda92.yml
@@ -6,14 +6,14 @@ dependencies:
   - pandas>=1.1.3
   - scikit-learn>=0.23.0
   - scipy>=1.5.2
-  - pymatgen>=2020.10.9
+  - pymatgen>=2020.10.9,<2022.0
   - rdkit=2020.09
-  - 'libblas=*=*mkl'
+  - "libblas=*=*mkl"
   - jupyter>=1.0.0
   - pytorch >=1.7.0,<2.0.0
   - cudatoolkit=9.2
   - magma-cuda92=2.5.2
-  - jedi=0.17.2
+  - jedi>=0.16
   - torchvision
   - torchtext
   - fastcluster

diff --git a/conda_env/osx.yml b/conda_env/osx.yml
@@ -6,12 +6,12 @@ dependencies:
   - pandas>=1.1.3
   - scikit-learn>=0.23.0
   - scipy>=1.5.2
-  - pymatgen>=2020.10.9
+  - pymatgen>=2020.10.9,<2022.0
   - rdkit=2020.09
-  - 'libblas=*=*mkl'
+  - "libblas=*=*mkl"
   - jupyter>=1.0.0
   - pytorch >=1.7.0,<2.0.0
-  - jedi=0.17.2
+  - jedi>=0.16
   - fastcluster
   - torchvision
   - torchtext

diff --git a/devtools/readthedocs.yml b/devtools/readthedocs.yml
@@ -1,26 +1,29 @@
 channels:
-  - defaults
   - pytorch
-  - rdkit
+  - conda-forge
 dependencies:
-  - pandas
+  - pandas>=1.1.3
+  - scikit-learn>=0.23.0
+  - scipy>=1.5.2
+  - pymatgen>=2020.10.9,<2022.0
+  - rdkit=2020.03.3.0
+  - "libblas=*=*mkl"
+  - jupyter>=1.0.0
+  - pytorch >=1.7.0,<2.0.0
+  - jedi>=0.16
+  - cpuonly
+  - fastcluster
+  - torchtext
   - seaborn
   - requests
-  - rdkit
-  - scikit-learn
-  - scipy
-  - pytorch>=1.7.0,<2.0
-  - cpuonly
-  - sphinx
-  - sphinx_rtd_theme
+  - plotly
+  - ruamel.yaml
+  - jupyterlab
+  - pybtex
+  - mordred
+  - tqdm
   - pip
   - pip:
-      - pymatgen
-      - matminer
-      - nbsphinx
       - Python-Deprecated
-      - OpenNMT-py==1.2
-      - sphinx-autodoc-typehints
-      - ruamel.yaml
-      - mordred
-      - tqdm
+      - matminer
+      - xenonpy
diff --git a/xenonpy/contrib/extend_descriptors/descriptor/organic_comp_descriptor.py b/xenonpy/contrib/extend_descriptors/descriptor/organic_comp_descriptor.py
@@ -16,7 +16,7 @@ def __init__(self, n_jobs=-1, *, featurizers='all', on_errors='raise', return_ty
         """
         A featurizer for extracting XenonPy compositional descriptors from SMILES or MOL
         """
-            
+
         # fix n_jobs to be 0 to skip automatic wrapper in XenonPy BaseFeaturizer class
         super().__init__(n_jobs=0, on_errors=on_errors, return_type=return_type)
         self._cal = Compositions(n_jobs=n_jobs, featurizers=featurizers, on_errors=on_errors)
@@ -36,15 +36,15 @@ def featurize(self, x):
                     raise ValueError('can not convert Mol from SMILES %s' % z)
         else:
             x_mol = x
-        
+
         # convert to counting dictionary
         mol = [Chem.AddHs(z) for z in x_mol]
         d_list = [dict(Counter([atom.GetSymbol() for atom in z.GetAtoms()])) for z in mol]
 
         self.output = self._cal.transform(d_list)
-        
+
         return self.output
-    
+
     @property
     def feature_labels(self):
         return self.output.columns