Merge pull request #5 from molssi-seamm/bugfixes

Fixed small typos and bugs.
molssi-seamm · Oct 13, 2021 · ad02b34 · ad02b34
2 parents de52dcf + 9a96838
commit ad02b34
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Showing 8 changed files with 27 additions and 22 deletions.
diff --git a/.github/workflows/BranchCI.yaml b/.github/workflows/BranchCI.yaml
@@ -7,7 +7,7 @@ on:
 
 jobs:
   light-ci:
-    name: Lint ubuntu-latest Py3.8
+    name: Lint ubuntu-latest Py3.9
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v1
@@ -20,7 +20,7 @@ jobs:
     # More info on options: https://github.com/conda-incubator/setup-miniconda
     - uses: conda-incubator/setup-miniconda@v2
       with:
-        python-version: 3.8
+        python-version: 3.9
         environment-file: devtools/conda-envs/test_env.yaml
         activate-environment: test
         auto-update-conda: false
@@ -46,5 +46,5 @@ jobs:
       with:
         file: ./coverage.xml
         flags: unittests
-        name: codecov-ubuntu-latest-py3.8
+        name: codecov-ubuntu-latest-py3.9
 
diff --git a/.github/workflows/CI.yaml b/.github/workflows/CI.yaml
@@ -15,7 +15,7 @@ on:
 
 jobs:
   lint:
-    name: Lint ubuntu-latest Py3.8
+    name: Lint ubuntu-latest Py3.9
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v1
@@ -31,7 +31,7 @@ jobs:
     # More info on options: https://github.com/conda-incubator/setup-miniconda
     - uses: conda-incubator/setup-miniconda@v2
       with:
-        python-version: 3.8
+        python-version: 3.9
         environment-file: devtools/conda-envs/test_env.yaml
         activate-environment: test
         auto-update-conda: false
@@ -56,7 +56,7 @@ jobs:
     strategy:
       matrix:
         os: [macOS-latest, ubuntu-latest, windows-latest]
-        python-version: [3.7, 3.8]
+        python-version: [3.8, 3.9]
     steps:
     - uses: actions/checkout@v1
     - name: Additional info about the build

diff --git a/.github/workflows/Docs.yaml b/.github/workflows/Docs.yaml
@@ -4,7 +4,7 @@ on: push
 
 jobs:
   docs:
-    name: Docs ubuntu-latest Py3.8
+    name: Docs ubuntu-latest Py3.9
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v1
@@ -20,7 +20,7 @@ jobs:
     # More info on options: https://github.com/conda-incubator/setup-miniconda
     - uses: conda-incubator/setup-miniconda@v2
       with:
-        python-version: 3.8
+        python-version: 3.9
         environment-file: devtools/conda-envs/test_env.yaml
         activate-environment: test
         auto-update-conda: false

diff --git a/.github/workflows/Release.yaml b/.github/workflows/Release.yaml
@@ -8,7 +8,7 @@ on:
 
 jobs:
   lint:
-    name: Lint ubuntu-latest Py3.8
+    name: Lint ubuntu-latest Py3.9
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v1
@@ -21,7 +21,7 @@ jobs:
     # More info on options: https://github.com/conda-incubator/setup-miniconda
     - uses: conda-incubator/setup-miniconda@v2
       with:
-        python-version: 3.8
+        python-version: 3.9
         environment-file: devtools/conda-envs/test_env.yaml
         activate-environment: test
         auto-update-conda: false
@@ -46,7 +46,7 @@ jobs:
     strategy:
       matrix:
         os: [macOS-latest, ubuntu-latest, windows-latest]
-        python-version: [3.7, 3.8]
+        python-version: [3.8, 3.9]
     steps:
     - uses: actions/checkout@v1
     - name: Additional info about the build
@@ -80,18 +80,18 @@ jobs:
         name: codecov-${{ matrix.os }}-py${{ matrix.python-version }}
 
   deploy:
-    name: PyPi ubuntu-latest Py3.8
+    name: PyPi ubuntu-latest Py3.9
     # Run only for tagged releases publishing development or release candidates
     # only to test.pypi, otherwise to both it and the main pypi.
     if: github.event_name == 'release' && startsWith(github.ref, 'refs/tags')
     runs-on: ubuntu-latest
     needs: [lint, test]
     steps:
     - uses: actions/checkout@v1
-    - name: Set up Python 3.8
+    - name: Set up Python 3.9
       uses: actions/setup-python@v1
       with:
-        python-version: 3.8
+        python-version: 3.9
     - name: Install package
       shell: bash -l {0}
       run: |

diff --git a/devtools/conda-envs/test_env.yaml b/devtools/conda-envs/test_env.yaml
@@ -8,6 +8,7 @@ dependencies:
 
   # molsystem requires, and only available via Conda.
   - openbabel
+  - seamm
 
   # Testing
   - black
@@ -18,8 +19,6 @@ dependencies:
 
     # Pip-only installs
   - pip:
-    - seamm
-
     # Documentation
     - rinohtype
     - pygments

diff --git a/dftbplus_step/choose_parameters.py b/dftbplus_step/choose_parameters.py
@@ -100,24 +100,30 @@ def get_input(self):
         if P["subset"] == "none":
             subset = None
         else:
-            subset = dataset[P["subset"]]
+            subset = datasets[P["subset"]]
             subpairs = subset["potential pairs"]
 
-        # Broadcast to the parent so that other substesp can use
+        # Broadcast to the parent so that other substeps can use
         self.parent._dataset = dataset
         self.parent._subset = subset
 
         for el1 in elements:
             for el2 in elements:
                 key = f"{el1}-{el2}"
+                # Not sure if flipping the key is valid....
+                key2 = f"{el2}-{el1}"
                 if subset is not None and key in subpairs:
                     md5sum = subpairs[key]["md5sum"]
                 elif key in pairs:
                     md5sum = pairs[key]["md5sum"]
+                elif subset is not None and key2 in subpairs:
+                    md5sum = subpairs[key2]["md5sum"]
+                elif key2 in pairs:
+                    md5sum = pairs[key2]["md5sum"]
                 else:
                     raise RuntimeError(
                         f"Could not find the Slater-Koster file for {key} "
-                        "for dataset {P['dataset']}, subset {P['subset']}."
+                        f"for dataset {P['dataset']}, subset {P['subset']}."
                     )
                 parameters[key] = str(slako_dir / potentials[md5sum]["filename"])
 

diff --git a/dftbplus_step/energy.py b/dftbplus_step/energy.py
@@ -180,8 +180,8 @@ def get_input(self):
                             damping = P["Damping Exponent"]
                         block["Exponent"] = damping
                 else:
-                    dftb["HCorrection"] = "No"
-                    PP["HCorrection"] = "No"
+                    dftb["HCorrection"] = "None {}"
+                    PP["HCorrection"] = "None {}"
             else:
                 dftb["HCorrection"] = hcorrection
                 if hcorrection == "Damping":

diff --git a/setup.py b/setup.py
@@ -74,8 +74,8 @@
         'License :: OSI Approved :: BSD License',
         'Natural Language :: English',
         'Programming Language :: Python :: 3 :: Only',
-        'Programming Language :: Python :: 3.7',
         'Programming Language :: Python :: 3.8',
+        'Programming Language :: Python :: 3.9',
     ],
     entry_points={
         'console_scripts': [