Update ci

.github/workflows/pytest.yaml

@@ -3,11 +3,9 @@ name: Pytest
 on:
   push:
     branches:
-      - "master"
       - "main"
   pull_request:
     branches:
-      - "master"
       - "main"
 
 jobs:
@@ -17,12 +15,12 @@ jobs:
     strategy:
       matrix:
         os: ["ubuntu-latest"]
-        python-version: ["3.7", "3.8"]
+        python-version: ["3.8", "3.10"]
     defaults:
       run:
         shell: bash -l {0}
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Additional info about the build
       run: |
@@ -34,7 +32,7 @@ jobs:
       uses: josStorer/get-current-time@v2.0.2
       id: current-time
     - name: Cache conda env
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       id: cache
       env:
         # Increase this value to reset cache if mols.yml has not changed
@@ -49,7 +47,7 @@ jobs:
 
     # More info on the whole conda setup: https://github.com/conda-incubator/setup-miniconda
     - name: Setup Conda
-      uses: conda-incubator/setup-miniconda@v2
+      uses: conda-incubator/setup-miniconda@v3
       id: conda-setup
       with:
         # mamba-version: "*" # uncomment to activate mamba
@@ -77,7 +75,7 @@ jobs:
         pytest --doctest-modules --ignore=molSimplify/Informatics/MOF --ignore=molSimplify/Informatics/protein --ignore=molSimplify/Scripts/in_b3lyp_usetc.py --ignore=molSimplify/Informatics/jupyter_vis.py --ignore=molSimplify/Informatics/macrocycle_synthesis.py --ignore=molSimplify/Informatics/organic_fingerprints.py molSimplify
 
     - name: Upload coverage report to codecov
-      uses: codecov/codecov-action@v3
+      uses: codecov/codecov-action@v4
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         directory: ./coverage/reports/
@@ -111,7 +109,7 @@ jobs:
     - uses: actions/checkout@v4
 
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 

.github/workflows/python-linter.yaml

@@ -11,11 +11,11 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v3
-    - name: Set up Python 3.7
-      uses: actions/setup-python@v2
+    - uses: actions/checkout@v4
+    - name: Set up Python 3.8
+      uses: actions/setup-python@v5
       with:
-        python-version: 3.7
+        python-version: 3.8
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
@@ -51,11 +51,11 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v3
-    - name: Set up Python 3.7
-      uses: actions/setup-python@v2
+    - uses: actions/checkout@v4
+    - name: Set up Python 3.8
+      uses: actions/setup-python@v5
       with:
-        python-version: 3.7
+        python-version: 3.8
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip

molSimplify/python_nn/clf_analysis_tool.py

@@ -1,4 +1,4 @@
-# import matplotlib.pyplot as plt
+from typing import Callable
 import numpy as np
 from sklearn.metrics.pairwise import pairwise_distances
 from packaging import version
@@ -105,7 +105,7 @@ def get_layer_outputs(model, layer_index, input,
                                  [model.layers[layer_index].output])
         nn_outputs = get_outputs([input, training_flag])[0]
     else:
-        partial_model = Model(model.inputs, model.layers[layer_index].output)
+        partial_model = Model(model.inputs, model.layers[layer_index].output)  # type: Callable
         nn_outputs = partial_model([input], training=training_flag).numpy()  # runs the model in training mode
     return nn_outputs