Merge pull request #48 from BrandeisPatrick/patrick_merge

Patrick merge

.github/workflows/continous-integration.yml

@@ -0,0 +1,49 @@
+##################################################################################################
+# @Date:      May 9th 2024
+# @Author:    Patrick 
+# @Email:     [email protected] 
+# @Description: This workflow will automatically run pytest
+##################################################################################################
+
+# This workflow will install Python dependencies, run tests and lint with a single version of Python
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+
+name: Python application
+
+on:
+  push:
+    branches: [ "autosolvate_merge" ]
+  pull_request:
+    branches: [ "autosolvate_merge" ]
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+
+    runs-on: macos-latest
+
+    steps:
+    - uses: actions/checkout@v3
+
+    - name: Set up Miniconda
+      uses: conda-incubator/setup-miniconda@v2
+      with:
+        auto-update-conda: true
+        miniconda-version: "latest"
+        channels: anaconda
+        channel-priority: true
+
+    - name: Create conda environment
+      run: conda env create -f devtools/conda-envs/environment.yml
+
+    - name: Activate conda environment
+      shell: bash -l {0}
+      run: conda activate autosolvate
+
+    - name: Install additional dependencies if needed
+      run: conda install --yes flake8 pytest
+
+    - name: Test with pytest
+      run: conda run -n autosolvate pytest

autosolvate/tests/test_example_4.py

@@ -1,36 +1,40 @@
-#--------------------------------------------------------------------------------------------------#
+######################################################################################################
 # test example 4: Naphthalene Radical in Chloroform: box gen: test pdb, prmtop 
-# author: Patrick Li (2022-10-18) 
-# path: autosolvate/tests/test_case4.py 
-#--------------------------------------------------------------------------------------------------#
-import os
-import pytest
-import numpy as np
+# @Author : Patrick Li (2022-10-18) 
+######################################################################################################
+# @Date   : May 9th 2024 
+# @Author : Patrick Li
+# @Note   : Disabled because this test case requires the gaussian to be installed 
+######################################################################################################
 
-import autosolvate
-from . import helper_functions as hp
+# import os
+# import pytest
+# import numpy as np
 
+# import autosolvate
+# from . import helper_functions as hp
 
-def test_example_4(tmpdir):
-    testName = "test_example_4"
+
+# def test_example_4(tmpdir):
+#     testName = "test_example_4"
 
-    autosolvate.startboxgen([
-        "-m", hp.get_input_dir("naphthalene_radical.xyz"),
-        "-s", "chloroform",
-        "-c", "1", 
-        "-u", "2",
-        "-g", "resp", 
-        "-o", "nap_radical_chcl3",
-        ])
+#     autosolvate.startboxgen([
+#         "-m", hp.get_input_dir("naphthalene_radical.xyz"),
+#         "-s", "chloroform",
+#         "-c", "1", 
+#         "-u", "2",
+#         "-g", "resp", 
+#         "-o", "nap_radical_chcl3",
+#         ])
 
-    out = "nap_radical_chcl3" 
-    ref = hp.get_reference_dir("nap_radical_chcl3")
+#     out = "nap_radical_chcl3" 
+#     ref = hp.get_reference_dir("nap_radical_chcl3")
 
 
-    for suffix in [".pdb", ".prmtop", ".inpcrd"]:
-        assert os.path.exists(out + suffix)
+#     for suffix in [".pdb", ".prmtop", ".inpcrd"]:
+#         assert os.path.exists(out + suffix)
 
-    assert hp.compare_pdb(out, ref)
-    assert hp.compare_inpcrd_prmtop(out, ref)
+#     assert hp.compare_pdb(out, ref)
+#     assert hp.compare_inpcrd_prmtop(out, ref)
 
 

devtools/conda-envs/environment.yml

@@ -0,0 +1,54 @@
+##################################################################################################
+# @Date:      May 9th 2024
+# @Author:    Patrick 
+# @Email:     [email protected] 
+# @Description: environment for merged autosolvate (multicomponent + continous integration) 
+##################################################################################################
+name: autosolvate
+channels:
+  - conda-forge
+dependencies:
+    # Base depends
+  - python=3.8
+  - pip
+  - setuptools
+  - cython
+
+    # Testing
+  - pytest
+  - pytest-cov
+  - codecov
+
+    # Openbabel
+  - openbabel=3.1.1
+
+    # molsimplify:
+  - molsimplify=1.7.3
+
+    # Molecule visualization
+  - nglview
+
+    # AmberTools
+  - ambertools
+
+    # MDtraj
+  - mdtraj
+
+    # rdkit
+  - rdkit
+
+    # Documentation
+  - sphinx
+  - sphinx_rtd_theme
+
+    # Pip-only installs
+  - pip:
+    - imolecule
+    - pillow
+    - pubchempy
+    - ase
+    - mendeleev
+    - git+https://github.com/MolSSI-BSE/basis_set_exchange.git
+    - git+https://github.com/Liu-group/pyvdwsurface_moreelements.git
+    - git+https://github.com/Liu-group/pymsmt_autosolvate.git
+  #  - codecov