Settings update

.github/workflows/cont_int.yml

@@ -124,7 +124,7 @@ jobs:
     - name: Cache Packages
       uses: actions/cache@v2
       env:
-        CACHE_NUMBER: 0
+        CACHE_NUMBER: 1
       with:
         path: ~/conda_pkgs_dir
         key:
@@ -144,7 +144,7 @@ jobs:
         key: conda-${{ runner.os }}--${{ runner.arch }}-arcenv-${{ env.CACHE_NUMBER}}
       env:
         # Increase this value to reset cache if etc/example-environment.yml has not changed
-        CACHE_NUMBER: 0
+        CACHE_NUMBER: 1
       id: cache-arc-env
     - name: Update environment
       run: mamba env update -n arc_env -f environment.yml

arc/settings/settings.py

@@ -285,74 +285,36 @@
 # An imaginary frequency is valid if it is between the following range (in cm-1):
 LOWEST_MAJOR_TS_FREQ, HIGHEST_MAJOR_TS_FREQ = 75.0, 10000.0
 
-# default environment names for sister repos
-TS_GCN_PYTHON, TANI_PYTHON, AUTOTST_PYTHON, ARC_PYTHON, XTB, OB_PYTHON = None, None, None, None, None, None
-home = os.getenv("HOME") or os.path.expanduser("~")
-
-tani_pypath_1 = os.path.join(os.path.dirname(os.path.dirname(os.path.dirname(sys.executable))),
-                            'tani_env', 'bin', 'python')
-tani_pypath_2 = os.path.join(home, 'mambaforge', 'envs', 'tani_env', 'bin', 'python')
-tani_pypath_3 = os.path.join(home, 'anaconda3', 'envs', 'tani_env', 'bin', 'python')
-tani_pypath_4 = os.path.join(home, 'miniconda3', 'envs', 'tani_env', 'bin', 'python')
-tani_pypath_5 = os.path.join(home, '.conda', 'envs', 'tani_env', 'bin', 'python')
-tani_pypath_6 = os.path.join('/Local/ce_dana', 'anaconda3', 'envs', 'tani_env', 'bin', 'python')
-for tani_pypath in [tani_pypath_1, tani_pypath_2, tani_pypath_3, tani_pypath_4, tani_pypath_5, tani_pypath_6]:
-    if os.path.isfile(tani_pypath):
-        TANI_PYTHON = tani_pypath
-
-ob_pypath_1 = os.path.join(os.path.dirname(os.path.dirname(os.path.dirname(sys.executable))),
-                            'ob_env', 'bin', 'python')
-ob_pypath_2 = os.path.join(home, 'mambaforge', 'envs', 'ob_env', 'bin', 'python')
-ob_pypath_3 = os.path.join(home, 'anaconda3', 'envs', 'ob_env', 'bin', 'python')
-ob_pypath_4 = os.path.join(home, 'miniconda3', 'envs', 'ob_env', 'bin', 'python')
-ob_pypath_5 = os.path.join(home, '.conda', 'envs', 'ob_env', 'bin', 'python')
-ob_pypath_6 = os.path.join('/Local/ce_dana', 'anaconda3', 'envs', 'ob_env', 'bin', 'python')
-for ob_pypath in [ob_pypath_1, ob_pypath_2, ob_pypath_3, ob_pypath_4, ob_pypath_5, ob_pypath_6]:
-    if os.path.isfile(ob_pypath):
-        OB_PYTHON = ob_pypath
-        break
-
-gcn_pypath_1 = os.path.join(os.path.dirname(os.path.dirname(os.path.dirname(sys.executable))),
-                            'ts_gcn', 'bin', 'python')
-gcn_pypath_2 = os.path.join(home, 'anaconda3', 'envs', 'ts_gcn', 'bin', 'python')
-gcn_pypath_3 = os.path.join(home, 'miniconda3', 'envs', 'ts_gcn', 'bin', 'python')
-gcn_pypath_4 = os.path.join(home, '.conda', 'envs', 'ts_gcn', 'bin', 'python')
-gcn_pypath_5 = os.path.join('/Local/ce_dana', 'anaconda3', 'envs', 'ts_gcn', 'bin', 'python')
-for gcn_pypath in [gcn_pypath_1, gcn_pypath_2, gcn_pypath_3, gcn_pypath_4, gcn_pypath_5]:
-    if os.path.isfile(gcn_pypath):
-        TS_GCN_PYTHON = gcn_pypath
-        break
-
-autotst_pypath_1 = os.path.join(os.path.dirname(os.path.dirname(os.path.dirname(sys.executable))),
-                                'tst_env', 'bin', 'python')
-autotst_pypath_2 = os.path.join(home, 'anaconda3', 'envs', 'tst_env', 'bin', 'python')
-autotst_pypath_3 = os.path.join(home, 'miniconda3', 'envs', 'tst_env', 'bin', 'python')
-autotst_pypath_4 = os.path.join(home, '.conda', 'envs', 'tst_env', 'bin', 'python')
-autotst_pypath_5 = os.path.join('/Local/ce_dana', 'anaconda3', 'envs', 'tst_env', 'bin', 'python')
-for autotst_pypath in [autotst_pypath_1, autotst_pypath_2, autotst_pypath_3, autotst_pypath_4, autotst_pypath_5]:
-    if os.path.isfile(autotst_pypath):
-        AUTOTST_PYTHON = autotst_pypath
-        break
-
-paths = list()
-paths.append(os.path.join(os.path.dirname(os.path.dirname(os.path.dirname(sys.executable))),
-                            'xtb_env', 'bin', 'xtb'))
-paths.append(os.path.join(home, 'anaconda3', 'envs', 'xtb_env', 'bin', 'xtb'))
-paths.append(os.path.join(home, 'miniconda3', 'envs', 'xtb_env', 'bin', 'xtb'))
-paths.append(os.path.join(home, '.conda', 'envs', 'xtb_env', 'bin', 'xtb'))
-paths.append(os.path.join('/Local/ce_dana', 'anaconda3', 'envs', 'xtb_env', 'bin', 'xtb'))
-for xtb_path in paths:
-    if os.path.isfile(xtb_path):
-        XTB = xtb_path
-        break
-
-arc_pypath_1 = os.path.join(os.path.dirname(os.path.dirname(os.path.dirname(sys.executable))),
-                            'arc_env', 'bin', 'python')
-arc_pypath_2 = os.path.join(home, 'anaconda3', 'envs', 'arc_env', 'bin', 'python')
-arc_pypath_3 = os.path.join(home, 'miniconda3', 'envs', 'arc_env', 'bin', 'python')
-arc_pypath_4 = os.path.join(home, '.conda', 'envs', 'arc_env', 'bin', 'python')
-arc_pypath_5 = os.path.join('/Local/ce_dana', 'anaconda3', 'envs', 'arc_env', 'bin', 'python')
-for arc_pypath in [arc_pypath_1, arc_pypath_2, arc_pypath_3, arc_pypath_4, arc_pypath_5]:
-    if os.path.isfile(arc_pypath):
-        ARC_PYTHON = arc_pypath
-        break
+def find_executable_path(env_name, executable):
+    """Determine the path to an executable in a conda environment.
+
+    Args:
+        env_name (string): The name of the conda environment.
+        executable (string): The name of the executable.
+
+    Returns:
+        string: The path to the executable.
+    """
+    home = os.getenv("HOME") or os.path.expanduser("~")
+    default_path = os.path.join(os.path.dirname(os.path.dirname(os.path.dirname(sys.executable))), env_name, 'bin', executable)
+
+    alternative_paths = [
+        os.path.join(home, 'mambaforge', 'envs', env_name, 'bin', executable),
+        os.path.join(home, 'anaconda3', 'envs', env_name, 'bin', executable),
+        os.path.join(home, 'miniconda3', 'envs', env_name, 'bin', executable),
+        os.path.join(home, '.conda', 'envs', env_name, 'bin', executable),
+        os.path.join('/Local/ce_dana', 'anaconda3', 'envs', env_name, 'bin', executable)
+    ]
+
+    for path in [default_path] + alternative_paths:
+        if os.path.isfile(path):
+            return path
+    return None
+
+TANI_PYTHON = find_executable_path('tani_env', 'python')
+OB_PYTHON = find_executable_path('ob_env', 'python')
+TS_GCN_PYTHON = find_executable_path('ts_gcn', 'python')
+AUTOTST_PYTHON = find_executable_path('tst_env', 'python')
+XTB = find_executable_path('xtb_env', 'xtb')
+ARC_PYTHON = find_executable_path('arc_env', 'python')
+PYSCF_PYTHON = find_executable_path('pyscf_env', 'python')

environment.yml

@@ -1,61 +1,62 @@
 name: arc_env
 channels:
+  - anaconda
+  - cantera
+  - conda-forge
   - defaults
   - rmg
-  - conda-forge
-  - cantera
-  - anaconda
 dependencies:
+  - anaconda::sphinx
+  - anaconda::sphinx_rtd_theme
+  - anaconda::sphinxcontrib-jsmath
   - cairo
   - cairocffi
   - cantera::cantera=2.6
+  - conda-forge::ase >=3.15.0
   - conda-forge::cclib >=1.7.0
-  - rmg::chemprop
+  - conda-forge::descriptastorus
+  - conda-forge::ipython
+  - conda-forge::mopac
+  - conda-forge::openbabel >= 3
+  - conda-forge::paramiko >=2.6.0
+  - conda-forge::py3dmol >= 0.8.0
+  - conda-forge::qcelemental
+  - conda-forge::pytest
+  - conda-forge::pytest-cov
   - coolprop
   - coverage
   - cython >=0.25.2
   - ffmpeg
-  - rmg::gprof2dot
   - graphviz
   - h5py
   - jinja2
   - jupyter
-  - rmg::lpsolve55
+  - mako
   - markupsafe
   - matplotlib >=1.5
-  - conda-forge::mopac
   - mpmath
-  - rmg::muq2
   - networkx
-  - rmg::numdifftools
   - numpy==1.20.1
-  - conda-forge::openbabel >= 3
   - pandas
   - psutil
-  - rmg::pydas >=1.0.2
   - pydot
-  - rmg::pydqed >=1.0.1
-  - pymongo
   - pyparsing
-  - rmg::pyrdl
+  - pymongo
+  - pytables
   - python >=3.7
   - pyyaml
+  - rmg::chemprop
+  - rmg::gprof2dot
+  - rmg::lpsolve55
+  - rmg::muq2
+  - rmg::numdifftools
+  - rmg::pydas >=1.0.2
+  - rmg::pydqed >=1.0.1
+  - rmg::pyrdl
   - rmg::quantities
   - rmg::rdkit >=2020.03.3.0
+  - rmg::symmetry
   - scikit-learn
   - scipy
-  - rmg::symmetry
   - xlrd
   - xlwt
-  - anaconda::sphinx_rtd_theme
-  - anaconda::paramiko >=2.6.0
-  - conda-forge::py3dmol >= 0.8.0
-  - conda-forge::ase >=3.15.0
-  - anaconda::ipython
-  - anaconda::sphinx
-  - anaconda::sphinxcontrib-jsmath
-  - conda-forge::qcelemental
-  - mako
-  - pytables
-  - anaconda::pytest
-  - conda-forge::pytest-cov