Refactor (#41)

- use *tad-mctc* library for common functions
- remove duplicate tests
- add mypy and fix all remaining issues
- update docs

.gitignore

@@ -1,3 +1,18 @@
+# This file is part of tad-dftd3.
+# SPDX-Identifier: Apache-2.0
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
 # Prerequisites
 *.d
 

.pre-commit-config.yaml

@@ -1,3 +1,20 @@
+# This file is part of tad-dftd3.
+# SPDX-Identifier: Apache-2.0
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+ci:
+    skip: [mypy]
+
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.5.0
@@ -28,22 +45,24 @@ repos:
     rev: v3.15.0
     hooks:
       - id: pyupgrade
-        args: [--py37-plus]
+        args: [--py37-plus, --keep-runtime-typing]
 
   - repo: https://github.com/pycqa/isort
-    rev: 5.13.0
+    rev: 5.13.2
     hooks:
       - id: isort
         name: isort (python)
         args: ["--profile", "black", "--filter-files"]
 
   - repo: https://github.com/psf/black
-    rev: 23.11.0
+    rev: 23.12.0
     hooks:
       - id: black
+        stages: [commit]
 
   - repo: https://github.com/pre-commit/mirrors-mypy
     rev: v1.7.1
     hooks:
       - id: mypy
         additional_dependencies: [types-all]
+        exclude: 'test/conftest.py'

.readthedocs.yaml

@@ -1,3 +1,18 @@
+# This file is part of tad-dftd3.
+# SPDX-Identifier: Apache-2.0
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
 # .readthedocs.yaml
 # Read the Docs configuration file
 # See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
@@ -9,7 +24,7 @@ version: 2
 build:
   os: ubuntu-22.04
   tools:
-    python: "3.8"
+    python: "3.10"
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:

.vscode/settings.json

@@ -11,7 +11,7 @@
   "python.analysis.diagnosticSeverityOverrides": {
     "reportPrivateImportUsage": "information"
   },
-  "python.defaultInterpreterPath": "${env:CONDA_PREFIX}/envs/dxtb/bin/python",
+  "python.defaultInterpreterPath": "${env:CONDA_PREFIX}/envs/torch/bin/python",
   "python.testing.pytestArgs": [],
   "python.testing.unittestEnabled": false,
   "python.testing.pytestEnabled": true