Libcint interface (#132)

grimme-lab · Apr 26, 2024 · a024de0 · a024de0
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diff --git a/.github/workflows/python.yml b/.github/workflows/python.yml
@@ -0,0 +1,108 @@
+# This file is part of dxtb.
+#
+# SPDX-Identifier: Apache-2.0
+# Copyright (C) 2024 Grimme Group
+#
+# 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.
+name: Tests
+
+on:
+  push:
+    branches:
+      - main
+      - master
+    paths-ignore:
+      - "doc*/**"
+      - "./*.ya?ml"
+      - "**/*.md"
+      - "**/*.rst"
+
+  pull_request:
+    paths-ignore:
+      - "doc*/**"
+      - "./*.ya?ml"
+      - "**/*.md"
+      - "**/*.rst"
+
+  workflow_dispatch:
+
+jobs:
+  main:
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+        torch-version: ["1.11.0", "1.12.1", "1.13.1", "2.0.1", "2.1.2", "2.2.2"]
+        exclude:
+          # PyTorch now fully supports Python=<3.11
+          # see: https://github.com/pytorch/pytorch/issues/86566
+          #
+          # PyTorch does not support Python 3.12 (all platforms)
+          # see: https://github.com/pytorch/pytorch/issues/110436
+          - os: ubuntu-latest
+            python-version: "3.12"
+          - os: macos-latest
+            python-version: "3.12"
+          - os: windows-latest
+            python-version: "3.12"
+          # PyTorch<1.13.0 does only support Python=<3.10
+          - python-version: "3.11"
+            torch-version: "1.11.0"
+          - python-version: "3.11"
+            torch-version: "1.12.1"
+          # On macOS and Windows, 1.13.x is also not supported for Python>=3.10
+          - os: macos-latest
+            python-version: "3.11"
+            torch-version: "1.13.1"
+          - os: windows-latest
+            python-version: "3.11"
+            torch-version: "1.13.1"
+
+    runs-on: ${{ matrix.os }}
+
+    defaults:
+      run:
+        shell: bash {0}
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v3
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: |
+          python3 -m pip install --upgrade pip
+          python3 -m pip install tox
+
+      - name: Determine TOXENV
+        run: echo "TOXENV=py$(echo ${{ matrix.python-version }} | tr -d '.')-torch$(echo ${{ matrix.torch-version }} | tr -d '.')" >> $GITHUB_ENV
+
+      - name: Print TOXENV
+        run: echo "TOXENV is set to '${{ env.TOXENV }}'."
+
+      - name: Unittests with tox
+        run: tox -e ${{ env.TOXENV }}
+
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v3
+        if: >
+          matrix.python-version == '3.11' &&
+          matrix.torch-version == '2.2.2' &&
+          matrix.os == 'ubuntu-latest'
+        with:
+          files: ./coverage.xml # optional
diff --git a/.github/workflows/release.yaml b/.github/workflows/release.yaml
@@ -0,0 +1,93 @@
+# This file is part of dxtb.
+#
+# SPDX-Identifier: Apache-2.0
+# Copyright (C) 2024 Grimme Group
+#
+# 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.
+name: Build
+
+on:
+  push:
+    branches:
+      - main
+    tags:
+      - "v*"
+
+  pull_request:
+    branches:
+      - main
+
+  workflow_dispatch:
+
+jobs:
+  wheel:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v3
+
+      - name: Build wheel (bdist)
+        run: pipx run build --wheel
+
+      - name: Upload wheel as artifact
+        uses: actions/upload-artifact@v3
+        with:
+          path: dist/*.whl
+
+  sdist:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v3
+
+      - name: Build source distribution (sdist)
+        run: pipx run build --sdist
+
+      - name: Upload source distribution as artifact
+        uses: actions/upload-artifact@v3
+        with:
+          path: dist/*.tar.gz
+
+  upload_test_pypi:
+    needs: [sdist, wheel]
+    runs-on: ubuntu-latest
+    environment: release
+    permissions:
+      id-token: write
+    if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')
+    steps:
+      - name: Download build artifacts
+        uses: actions/download-artifact@v3
+        with:
+          path: dist
+
+      - name: Publish to Test PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          repository-url: https://test.pypi.org/legacy/
+
+  upload_pypi:
+    needs: [sdist, wheel, upload_test_pypi]
+    runs-on: ubuntu-latest
+    environment: release
+    permissions:
+      id-token: write
+    if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')
+    steps:
+      - name: Download build artifacts
+        uses: actions/download-artifact@v3
+        with:
+          path: dist
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
diff --git a/.gitignore b/.gitignore
@@ -1,3 +1,20 @@
+# This file is part of dxtb.
+#
+# SPDX-Identifier: Apache-2.0
+# Copyright (C) 2024 Grimme Group
+#
+# 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
 
@@ -189,7 +206,6 @@ data/*/processed*
 data/misc
 
 # exclude some sample and reaction files for tests
-!data/PTB/samples_HE.json
 !data/GMTKN55/samples_ACONF.json
 !data/GMTKN55/reactions_ACONF.json
 
@@ -202,16 +218,16 @@ data/misc
 # models
 models/
 
-# ML model bookkeeping
-src/lightning_logs/
-src/wandb/
-
 # other
 devel*
 
 # plots
 plots/
 figs/
+examples/*.pdf
+examples/*.svg
+
+dxtb.profile
 
 # pytorch lightning
 src/lightning_logs/*

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,36 +1,53 @@
+# This file is part of dxtb.
+#
+# SPDX-Identifier: Apache-2.0
+# Copyright (C) 2024 Grimme Group
+#
+# 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.
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.5.0
     hooks:
       - id: trailing-whitespace
       - id: end-of-file-fixer
       - id: check-shebang-scripts-are-executable
       - id: check-toml
       - id: check-yaml
       - id: check-added-large-files
+        args: ["--maxkb=20000"]
       - id: debug-statements
         language_version: python3
 
   - repo: https://github.com/asottile/setup-cfg-fmt
-    rev: v2.2.0
+    rev: v2.5.0
     hooks:
       - id: setup-cfg-fmt
         args: [--include-version-classifiers, --max-py-version, "3.11"]
 
   - repo: https://github.com/asottile/pyupgrade
-    rev: v3.3.1
+    rev: v3.15.2
     hooks:
       - id: pyupgrade
         args: [--py37-plus, --keep-runtime-typing]
 
   - repo: https://github.com/pycqa/isort
-    rev: 5.12.0
+    rev: 5.13.2
     hooks:
       - id: isort
         name: isort (python)
         args: ["--profile", "black", "--filter-files"]
 
   - repo: https://github.com/psf/black
-    rev: 23.1.0
+    rev: 24.3.0
     hooks:
       - id: black
diff --git a/.vscode/settings.json b/.vscode/settings.json
@@ -1,19 +1,17 @@
 {
   "[python]": {
+    "editor.defaultFormatter": "ms-python.black-formatter",
     "editor.detectIndentation": false,
     "editor.formatOnSave": true,
     "editor.formatOnPaste": false, // not supported by black
     "editor.insertSpaces": true,
     "editor.tabSize": 4
   },
+  "pylint.args": ["--indent-string='    '"],
   "python.analysis.diagnosticSeverityOverrides": {
     "reportPrivateImportUsage": "information"
   },
   "python.defaultInterpreterPath": "${env:CONDA_PREFIX}/envs/dxtb/bin/python",
-  "python.formatting.provider": "black",
-  "python.linting.enabled": true,
-  "python.linting.pylintEnabled": true,
-  "python.linting.pylintArgs": ["--indent-string='    '"],
   "python.testing.pytestArgs": [],
   "python.testing.unittestEnabled": false,
   "python.testing.pytestEnabled": true