Merge pull request #125 from nlesc-nano/md_asa_test

TST: Add more tests for the MD-ASA workflow

.github/workflows/pythonpackage.yml

@@ -10,9 +10,17 @@ on:
     pull_request:
     workflow_dispatch:
 
+concurrency:
+    group: ${{ github.workflow }}-${{ github.head_ref || github.run_id }}
+    cancel-in-progress: true
+
+defaults:
+    run:
+        shell: bash
+
 jobs:
     build:
-        name: ${{ matrix.os }} (py ${{ matrix.version }}${{ matrix.special }})
+        name: ${{ matrix.os }}; py ${{ matrix.version }}${{ matrix.special }}
         runs-on: ${{ matrix.os }}
         strategy:
             fail-fast: false
@@ -28,21 +36,31 @@ jobs:
                     special: '; slow'
                     version: '3.10'
         env:
-            CP2K_DATA_DIR: "/usr/share/cp2k"
+            CP2K_DATA_DIR: "/home/runner/work/nano-CAT/nano-CAT/cp2k/data"
+            MATCH: "/home/runner/work/nano-CAT/nano-CAT/MATCH/MATCH"
+            PerlChemistry: "/home/runner/work/nano-CAT/nano-CAT/MATCH/PerlChemistry"
 
         steps:
-            -   name: Cancel Previous Runs
-                uses: styfle/[email protected]
-                with:
-                    access_token: ${{ github.token }}
+            -   uses: actions/checkout@v3
 
-            -   uses: actions/checkout@v2
-
-            -   name: Install CP2K
+            -   name: Install cp2k
+                if: matrix.os == 'ubuntu-latest'
+                run: |
+                    git clone https://github.com/cp2k/cp2k -q
+                    cd cp2k
+                    git -c advice.detachedHead=false checkout tags/v9.1.0
+                    wget -nv https://github.com/cp2k/cp2k/releases/download/v9.1.0/cp2k-9.1-Linux-x86_64.ssmp -O cp2k.ssmp
+                    chmod a+rx cp2k.ssmp
+                    mv cp2k.ssmp /usr/local/bin/cp2k.popt
+
+            -   name: Install MATCH
                 if: matrix.special == '; slow'
                 run: |
-                    sudo apt-get update
-                    sudo apt install cp2k
+                    git clone https://github.com/nlesc-nano/MATCH -q
+                    cd MATCH
+                    git -c advice.detachedHead=false checkout main
+                    chmod -R a+rx MATCH/scripts
+                    ln -s MATCH/scripts/*.pl /usr/local/bin/
 
             -   name: Set up Python
                 uses: actions/setup-python@v2
@@ -74,7 +92,7 @@ jobs:
                 run: pip list
 
             -   name: Info CP2K
-                if: matrix.special == '; slow'
+                if: matrix.os == 'ubuntu-latest'
                 run: cp2k.popt --version
 
             -   name: Run tests

tests/test_bde_workflow.py

@@ -1,5 +1,6 @@
 from __future__ import annotations
 
+import os
 import shutil
 import textwrap
 from collections.abc import Generator
@@ -80,7 +81,7 @@ def construct_df() -> SettingsDataFrame:
     settings.optional.qd.dissociate.xyn_opt = False
 
     # Set all quantum dot properties
-    qd = readpdb(PATH / "qd" / "[HCl]2.pdb")
+    qd = readpdb(PATH / "[HCl]2.pdb")
     qd.properties.name = "[HCl]2"
     qd.properties.job_path = []
     qd[4].properties.anchor = True
@@ -109,14 +110,16 @@ class TestBDEWorkflow:
     )
 
     @pytest.fixture(scope="function", autouse=True)
-    def clear_db(self) -> Generator[None, None, None]:
+    def clear_dirs(self) -> Generator[None, None, None]:
         """Teardown script for deleting directies."""
+        os.mkdir(PATH / "qd")
         yield None
         shutil.rmtree(PATH / "database", ignore_errors=True)
-        shutil.rmtree(PATH / "qd" / "bde", ignore_errors=True)
+        shutil.rmtree(PATH / "ligand", ignore_errors=True)
+        shutil.rmtree(PATH / "qd", ignore_errors=True)
 
     @pytest.mark.parametrize("kwargs", PARAMS.values(), ids=PARAMS)
-    def test_pass(self, kwargs: dict[str, Any], clear_db: None) -> None:
+    def test_pass(self, kwargs: dict[str, Any]) -> None:
         qd_df = construct_df()
         qd_df.settings.optional.qd.dissociate.update(kwargs)
         init_bde(qd_df)

tests/test_md_asa.py

@@ -0,0 +1,97 @@
+from __future__ import annotations
+
+import shutil
+from pathlib import Path
+from collections.abc import Generator
+from distutils.spawn import find_executable
+
+import numpy as np
+import yaml
+import pytest
+from scm.plams import Settings
+from assertionlib import assertion
+from CAT.base import prep
+
+PATH = Path("tests") / "test_files"
+
+
+@pytest.mark.skipif(find_executable("cp2k.popt") is None, reason="requires CP2K")
+@pytest.mark.slow
+class TestMDASA:
+    SETTINGS = Settings(yaml.load("""\
+        path: tests/test_files
+
+        input_cores:
+            - Cd68Se55.xyz
+
+        input_ligands:
+            - 'CCCCCCCCC(=O)O'
+
+        optional:
+            core:
+                dummy: Cl
+
+            ligand:
+                optimize: True
+                split: True
+                functional_groups: 'O(C=O)[H]'
+
+            qd:
+                dirname: QD
+                optimize: False
+                activation_strain:
+                    use_ff: True
+                    md: True
+                    dump_csv: True
+                    job1: Cp2kJob
+                    s1:
+                        input:
+                            motion:
+                                md:
+                                    steps:
+                                        100
+                    shift_cutoff: True
+                    el_scale14: 1.0
+                    lj_scale14: 1.0
+                    distance_upper_bound: 10.0
+
+            forcefield:
+                charge:
+                    keys: [input, force_eval, mm, forcefield, charge]
+                    Cd: 0.9768
+                    Se: -0.9768
+                    O2D2: -0.4704
+                    C2O3: 0.4524
+                epsilon:
+                    unit: kjmol
+                    keys: [input, force_eval, mm, forcefield, nonbonded, lennard-jones]
+                    Cd Cd: 0.3101
+                    Se Se: 0.4266
+                    Cd Se: 1.5225
+                    Cd O2D2: 1.8340
+                    Se O2D2: 1.6135
+                sigma:
+                    unit: nm
+                    keys: [input, force_eval, mm, forcefield, nonbonded, lennard-jones]
+                    Cd Cd: 0.1234
+                    Se Se: 0.4852
+                    Cd Se: 0.2940
+                    Cd O2D2: 0.2471
+                    Se O2D2: 0.3526
+    """, Loader=yaml.SafeLoader))
+
+    @pytest.fixture(scope="function", autouse=True)
+    def clear_dirs(self) -> Generator[None, None, None]:
+        """Teardown script for deleting directies."""
+        yield None
+        shutil.rmtree(PATH / "database", ignore_errors=True)
+        shutil.rmtree(PATH / "ligand", ignore_errors=True)
+        shutil.rmtree(PATH / "qd", ignore_errors=True)
+
+    def test_pass(self) -> None:
+        df, *_ = prep(self.SETTINGS.copy())
+
+        values = df["ASA"].values
+        assertion.eq(values.dtype, np.float64)
+        assertion.eq(values.shape, (1, 3))
+        assertion.assert_(np.isreal, values, post_process=np.all)