PR: Finish xtb-YARP for pytest/Github workflow + add back organometal…

…lics pytest

Finish xtb-YARP for pytest/Github workflow + add back organometallics pytest

.github/workflows/python-test.yml

@@ -16,34 +16,26 @@ jobs:
 
     - name: Install dependencies
       run: |
-        #python -m pip install --upgrade pip
-        #conda create --name ENV python=3.9
-        #conda init
-        #conda activate ENV
-        #cd /opt/hostedtoolcache/Python/3.9.20/x64/bin/; ls
         if [ -f pytest_requirements.txt ]; then 
           pip install -r pytest_requirements.txt; 
         fi
-        #pip install pytest-executable
-        #pip install pipdeptree
-        #pip install dask
         export CONDA_ALWAYS_YES="true"
-        pip install 'numpy==1.24.0'
-        pip install rdkit
-        pip install scipy
+        pip install 'rdkit==2024.3.5'
+        pip install 'scipy==1.11.1'
         pip install xtb
-        pip install joblib
-        pip install PyYAML
+        pip install 'joblib==1.3.1'
+        pip install 'PyYAML==6.0.1'
         pip install openbabel-wheel
-        pip install pandas
-        pip install ase
-        #pip install xtb
+        pip install 'pandas==2.0.3'
+        pip install 'ase==3.22.1'
         conda install -y conda-forge::xtb
-        pip install xgboost
-        pip install h5py
+        pip install 'xgboost==1.7.6'
+        pip install 'h5py==3.9.0'
         pip install pysisyphus
         conda install -y conda-forge::crest
         unset CONDA_ALWAYS_YES
+        pip install --force-reinstall 'scikit-learn==1.3.0'
+        pip install --force-reinstall 'numpy==1.24.4'
         pip install .
 
         # CHECK
@@ -53,32 +45,28 @@ jobs:
         cp .pysisyphusrc /home/runner/.pysisyphusrc
         cond=asd
         sed -i "s|CONDA_ENV|${CONDA}|g" /home/runner/.pysisyphusrc
-        #which crest
-
-        #if [ -f env.yaml ]; then 
-        #  #conda install --file env.yaml
-        #  conda env create -f env.yaml
-        #fi
 
     - name: Run pytest
       run: |
-              #conda activate yarp
-              #cd examples/; pytest -s # Assuming your tests are in the 'tests' directory
                home=$(pwd)
                cd /opt/hostedtoolcache/Python/3.9.20/x64/bin/
                ls
                echo $CONDA
                cd $CONDA/bin
-               ls
-               which pip;    echo "GOOD1"
-               echo $(pwd)
-               $CONDA/bin/xtb --version
-               $CONDA/bin/crest --version
-               pysis --version
+               
+               #ls
+               #echo $(pwd)
+               #$CONDA/bin/xtb --version
+               #$CONDA/bin/crest --version
+               #pysis --version
+               # test Organometallics
                #obabel --version
-               cd $home/pyTEST_Example/;
+               #
+               # run Organometallic YARP Example #
+               cd $home/examples/
+               pytest -s
+               cd $home/pyTEST_Example/
                # xtb and crest are in conda bin, others in pip bin
                sed -i "s|CONDA_PATH|${CONDA}|g" test_rxn.py
                pytest -s
-
       shell: bash

pyTEST_Example/test_rxn.py

@@ -1,32 +1,10 @@
 import pytest, os, re, yaml
 import shutil
 import subprocess
+import pandas as pd
+import numpy as np
 #import yarp as yp
 #from calculator import add
-'''
-import yarp as yp
-import numpy as np
-import threading
-import pickle
-import multiprocessing as mp
-from multiprocessing import Queue
-from logging.handlers import QueueHandler
-from joblib import Parallel, delayed
-from yarp.find_lewis import all_zeros
-from yarp.find_lewis import bmat_unique
-import os, sys, yaml, fnmatch
-import logging
-from openbabel import pybel
-from utils import *
-from wrappers.reaction import *
-from job_mapping import *
-from wrappers.crest import CREST
-from qc_jobs import *
-from conf import *
-from analyze_functions import *
-from wrappers.pysis import PYSIS
-from wrappers.gsm import GSM
-'''
 def truthy(value):
     return bool(value)
 def falsy(value):
@@ -73,26 +51,41 @@ def rxn_setYAML(current_path, model_path, gsm_path, conda_path):
     with open('parameters.yaml', 'w') as file: file.write(filedata)
 
 def rxn_xtb():
-    #subprocess.call("crest ", shell=True)
-    #subprocess.call("pysis ", shell=True)
-    #subprocess.call("xtb "  , shell=True)
-
     subprocess.call("python main_xtb.py parameters.yaml", shell=True)
-    #exec(open("main_xtb.py").read()) 
+    subprocess.call("cat RESULT/IRC-record.txt", shell=True)
 
+    df = pd.read_csv('RESULT/IRC-record.txt', delim_whitespace=True)
+    # Check for 'intended' entry in 'type' column and if the barrier equals 6.747
+    intended_row = df[df['type'] == 'intended']
+    # Print result if intended row exists and barrier check
+    barrier = 1000
+    if not intended_row.empty:
+        barrier = float(intended_row['barrier'].values[0])
+    return barrier
 
 def test_file():
     current_directory = os.getcwd() + '/'
-    CONDA="CONDA_PATH"
+    #subprocess.call(f"cd {current_directory}/pyTEST_Example/", shell=True)
+
+    CONDA="CONDA_PATH" # will be replaced by a real path when running the github workflow #
+    if CONDA=="CONDA_" + "PATH":
+        # use "which crest" to find the path #
+        STR = os.popen('which crest').read().rstrip()
+        CONDA = STR.split("/bin/crest")[0]
+
     rxn_setYAML(current_path = current_directory, 
             model_path = f"{current_directory}/bin",
             gsm_path   = f"{current_directory}/bin/inpfileq",
             conda_path = f"{CONDA}/bin")
 
-    rxn_xtb()
-    with open('parameters.yaml', 'rb') as f: conf = yaml.safe_load(f.read())
-    #RUN(conf)
+    # run YARP-xtb for DA example #
+    barrier = rxn_xtb()
+    assert(np.abs(barrier - 6.747132) < 0.01)
+    print(f"YARP-xtb CHECK FINISHED\n")
+
     '''
+    # run Organometallics YARP for Fe(CO)5 #
+    subprocess.call(f"cd {current_directory}/examples/", shell=True)
     assert  os.path.exists('FeCO5.xyz')
     assert  check_metal("FeCO5.xyz")
     print("Organometallics CHECK FINISHED\n")