Ci fix (#75)

* ci fix

* ci fix

* ci fix

* ci fix

* ci fix

* ci fix

* ci fix

* ci fix

* ci fix

* ci fix

* ci fix

* ci fix

* ci fix

.github/test_env.yaml

@@ -8,7 +8,6 @@ dependencies:
 
   - setuptools
   - xtb
-  - parmed
   - scipy
   - numpy
   - ase

.github/workflows/CI.yaml

@@ -1,7 +1,6 @@
 name: CI
 
 on:
-  # run once a day at noon UTC
   schedule:
     - cron: "0 12 * * *"
   push:
@@ -19,8 +18,6 @@ jobs:
 
     steps:
     - uses: actions/checkout@v2
-
-    # More info on options: https://github.com/conda-incubator/setup-miniconda
     - uses: mamba-org/setup-micromamba@main
       with:
         environment-file: .github/test_env.yaml
@@ -30,22 +27,19 @@ jobs:
             pytest=${{ matrix.pytest }}
 
     - name: Install package
-
-      # conda setup requires this special shell
       shell: bash -l {0}
       run: |
         python -m pip install . --no-deps
-        conda list
-    - name: Run tests
 
-      # conda setup requires this special shell
+    - name: Run tests
       shell: bash -l {0}
-
       run: |
-        pytest -v -m "not slow" --cov=qforce --cov-report=xml --color=yes qforce/tests/
+        pytest -v --cov=qforce --cov-report=xml --color=yes qforce/tests/
+
     - name: CodeCov
-      uses: codecov/codecov-action@v1
+      uses: codecov/codecov-action@v3
       with:
+        token: ${{ secrets.CODECOV_TOKEN }}
         file: ./coverage.xml
         flags: unittests
         name: codecov-${{ matrix.os }}-py${{ matrix.python-version }}

qforce/main.py

@@ -60,6 +60,8 @@ def run_qforce(input_arg, ext_q=None, ext_lj=None, config=None, presets=None):
 
     print_outcome(job.dir)
 
+    return mol
+
 
 def run_hessian_fitting_for_external(job_dir, qm_data, ext_q=None, ext_lj=None,
                                      config=None, presets=None):

qforce/qm/qm_base.py

@@ -54,8 +54,8 @@ def _read_fchk_file(fchk_file):
                         line = file.readline()
                         hessian.extend(line.split())
 
-        coords = np.asfarray(coords, float)
-        hessian = np.asfarray(hessian, float)
+        coords = np.asarray(coords, dtype=float)
+        hessian = np.asarray(hessian, dtype=float)
         coords = np.reshape(coords, (-1, 3))
         elements = np.array(elements)
         coords = coords * Bohr

qforce/tests/test_fragments.py

@@ -1,5 +1,6 @@
 import pytest
-
+import os
+#
 from qforce_examples import Gaussian_default
 from qforce.main import run_qforce
 
@@ -26,8 +27,10 @@ def test_BatchRun(batch_run, exist, tmpdir):
     except SystemExit:
         pass
     # Fragment file generated
-    assert tmpdir.join('propane_qforce').join('fragments').join(
-        'CC_H8C3_d91b46644317dee9c2b868166c66a18c~1.inp').isfile()
+
+    inp = [file for file in os.listdir(tmpdir.join('propane_qforce').join('fragments')) if file.endswith('.inp')][0]
+
+    assert tmpdir.join('propane_qforce').join('fragments').join(inp).isfile()
     tmpdir.join('propane_qforce').join('fragments').remove()
 
     # Second run
@@ -38,5 +41,4 @@ def test_BatchRun(batch_run, exist, tmpdir):
         pass
     # Fragment file generated again if batch_run is False
     # Fragment file not generated again if batch_run is True
-    assert tmpdir.join('propane_qforce').join('fragments').join(
-        'CC_H8C3_d91b46644317dee9c2b868166c66a18c~1.inp').isfile() is exist
+    assert tmpdir.join('propane_qforce').join('fragments').join(inp).isfile() is exist

qforce/tests/test_run_xtb.py

@@ -2,7 +2,6 @@
 
 import numpy as np
 import pytest
-import parmed as pmd
 from subprocess import call
 from qforce.main import run_qforce
 from qforce_examples import xTB_default
@@ -46,29 +45,29 @@ def propane(tmp_path_factory):
         except SystemExit:
             pass
 
+        frag_dir = outdir / 'propane_qforce' / 'fragments'
+        inp = [file for file in os.listdir(frag_dir) if file.endswith('.inp')][0]
         os.chdir('fragments')
-        run_fragment = outdir / 'propane_qforce' / 'fragments' / 'CC_H8C3_d91b46644317dee9c2b868166c66a18c~1.inp'
+        run_fragment = frag_dir / inp
+
         call(run_fragment.read_text(), shell=True)
 
         # Generate the topology
         try:
-            run_qforce(input_arg=str(xyz),
+            mol = run_qforce(input_arg=str(xyz),
                        config=str(setting))
         except SystemExit:
             pass
 
-        top = pmd.load_file(str(outdir / 'propane_qforce' / 'gas.top'),
-                            xyz = str(outdir / 'propane_qforce' / 'gas.gro'))
         os.chdir(cwd)
-        return top
+        return mol
 
-    def test_top(self, propane):
-        '''Test if the whole process runs.'''
-        assert isinstance(propane, pmd.gromacs.GromacsTopologyFile)
+    # def test_top(self, propane):
+    #     '''Test if the whole process runs.'''
+    #     assert isinstance(propane, pmd.gromacs.GromacsTopologyFile)
 
     def test_charge(self, propane):
         '''Test if the charges are generated in the same fashion.'''
-        charges = [atom.charge for atom in propane.atoms]
         ref_charge = [-0.10206769,
    -0.04738168,
     0.03075230,
@@ -81,40 +80,33 @@ def test_charge(self, propane):
     0.03359926,
     0.03359765,
 ]
-        assert np.allclose(ref_charge, charges, atol=0.01)
+        assert np.allclose(ref_charge, propane.non_bonded.q, atol=0.01)
 
     def test_elements(self, propane):
-        atom_ids = [atom.atomic_number for atom in propane.atoms]
-        assert [6, 6, 1, 1, 1, 6, 1, 1, 1, 1, 1] == atom_ids
+        assert [6, 6, 1, 1, 1, 6, 1, 1, 1, 1, 1] == list(propane.elements)
 
     def test_angles(self, propane):
-        assert len(propane.angles) == 18
-        assert propane.angles[0].funct == 5
-        assert propane.angles[0].atom1.idx == 0
-        assert propane.angles[0].atom2.idx == 1
-        assert propane.angles[0].atom3.idx == 5
-        assert np.isclose(propane.angles[0].type.k, 54.72, atol=0.01)
-        assert np.isclose(propane.angles[0].type.theteq, 111.62, atol=0.01)
+        angles = list(propane.terms['angle'])
+        assert len(angles) == 18
+        assert list(angles[0].atomids) == [0, 1, 5]
+        assert np.isclose(angles[0].fconst, 457.945, atol=0.01)
+        assert np.isclose(np.degrees(angles[0].equ), 111.62, atol=0.01)
 
     def test_bonds(self, propane):
-        assert len(propane.bonds) == 10
-        assert propane.bonds[0].funct == 1
-        assert propane.bonds[0].atom1.idx == 0
-        assert propane.bonds[0].atom2.idx == 1
-        assert np.isclose(propane.bonds[0].type.k, 211.478, atol=0.01)
-        assert np.isclose(propane.bonds[0].type.req, 1.5242, atol=0.01)
+        bonds = list(propane.terms['bond'])
+        assert len(bonds) == 10
+        assert list(bonds[0].atomids) == [0, 1]
+        assert np.isclose(bonds[0].fconst, 1769.660, atol=0.01)
+        assert np.isclose(bonds[0].equ, 1.5242, atol=0.01)
 
     def test_dihedrals(self, propane):
-        assert len(propane.rb_torsions) == 2
-        assert propane.rb_torsions[0].atom1.idx == 2
-        assert propane.rb_torsions[0].atom2.idx == 0
-        assert propane.rb_torsions[0].atom3.idx == 1
-        assert propane.rb_torsions[0].atom4.idx == 5
-        assert propane.rb_torsions[0].funct == 3
-        assert np.isclose(propane.rb_torsions[0].type.c0, 0.9964, atol=0.01)
+        diheds = list(propane.terms['dihedral/flexible'])
+        assert len(diheds) == 2
+        assert list(diheds[0].atomids) == [2, 0, 1, 5]
+        assert np.isclose(diheds[0].equ[0], 4.169, atol=0.01)
 
     def test_defaults(self, propane):
-        assert propane.defaults.comb_rule == 3
-        assert propane.defaults.fudgeLJ == 0.5
-        assert propane.defaults.fudgeQQ == 0.5
-        assert propane.defaults.nbfunc == 1
+        assert propane.non_bonded.comb_rule == 3
+        assert propane.non_bonded.fudge_lj == 0.5
+        assert propane.non_bonded.fudge_q == 0.5
+