add worflow to main

.github/workflows/run_pytests.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: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
+
+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/test_env.yaml
+
+    - 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_boxgen_naphthalene_water.py

@@ -1,15 +1,17 @@
 import autosolvate
 import pytest
+from . import helper_functions as hp
+import os
 
 def test_example_1(tmp_path):
     autosolvate.startboxgen(["-m", "inputs/naphthalene_neutral.xyz", "-o", "neutral"])
-    compare_pdb, compare_inpcrd, compare_prmtop = compare_boxgen("neutral", "refs/naphthalene_water/neutral")
+    compare_pdb, compare_inpcrd, compare_prmtop = compare_boxgen("neutral", os.path.join(hp.get_reference_dir(), "naphthalene_water/neutral"))
     assert compare_pdb
     assert compare_inpcrd
     assert compare_prmtop
 
     autosolvate.startboxgen(["-m", "inputs/naphthalene_radical.xyz", "-o", "radical"])
-    compare_pdb, compare_inpcrd, compare_prmtop = compare_boxgen("radical", "refs/naphthalene_water/radical")
+    compare_pdb, compare_inpcrd, compare_prmtop = compare_boxgen("radical", os.path.join(hp.get_reference_dir(), "naphthalene_water/radical"))
     assert compare_pdb
     assert compare_inpcrd
     assert compare_prmtop

autosolvate/tests/test_example_4.py

@@ -1,36 +1,41 @@
-#--------------------------------------------------------------------------------------------------#
+######################################################################################################
 # 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
+######################################################################################################
+# @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)