v0.2.19 (#668)

Author: njzjz

.git_archival.txt

@@ -0,0 +1,4 @@
+node: $Format:%H$
+node-date: $Format:%cI$
+describe-name: $Format:%(describe:tags=true,match=*[0-9]*)$
+ref-names: $Format:%D$

.gitattributes

@@ -0,0 +1 @@
+.git_archival.txt  export-subst

.github/workflows/benchmark.yml

@@ -0,0 +1,23 @@
+name: Python package
+
+on:
+  - push
+  - pull_request
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: 3.12
+    - run: curl -LsSf https://astral.sh/uv/install.sh | sh
+    - name: Install dependencies
+      run: uv pip install --system .[amber,ase,pymatgen,benchmark] rdkit openbabel-wheel
+    - name: Run benchmarks
+      uses: CodSpeedHQ/action@v2
+      with:
+        token: ${{ secrets.CODSPEED_TOKEN }}
+        run: pytest benchmark/ --codspeed

.github/workflows/pyright.yml

@@ -0,0 +1,19 @@
+on:
+  - push
+  - pull_request
+
+name: Type checker
+jobs:
+  pyright:
+    name: pyright
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@master
+    - uses: actions/setup-python@v5
+      with:
+        python-version: '3.12'
+    - run: pip install uv
+    - run: uv pip install --system -e .[amber,ase,pymatgen] rdkit openbabel-wheel
+    - uses: jakebailey/pyright-action@v2
+      with:
+        version: 1.1.363

.github/workflows/test.yml

@@ -12,17 +12,15 @@ jobs:
         python-version: ["3.7", "3.8", "3.12"]
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     # set up conda
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
-    # install rdkit and openbabel
-    - name: Install rdkit
-      run: python -m pip install rdkit openbabel-wheel
+    - run: curl -LsSf https://astral.sh/uv/install.sh | sh
     - name: Install dependencies
-      run: python -m pip install .[amber,ase,pymatgen] coverage ./tests/plugin
+      run: uv pip install --system .[amber,ase,pymatgen] coverage ./tests/plugin rdkit openbabel-wheel
     - name: Test
       run: cd tests && coverage run --source=../dpdata -m unittest && cd .. && coverage combine tests/.coverage && coverage report
     - name: Run codecov

.github/workflows/test_import.yml

@@ -1,17 +1,18 @@
-name: test Python import
-
-on:
-  - push
-  - pull_request
-
-jobs:
-  build:
-    runs-on: ubuntu-latest
-    steps:
-    - uses: actions/checkout@v2
-    - uses: actions/setup-python@v2
-      with:
-        python-version: '3.9'
-        architecture: 'x64'
-    - run: python -m pip install .
-    - run: python -c 'import dpdata'
+name: test Python import
+
+on:
+  - push
+  - pull_request
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v5
+      with:
+        python-version: '3.9'
+        architecture: 'x64'
+    - run: python -m pip install uv
+    - run: python -m uv pip install --system .
+    - run: python -c 'import dpdata'

.pre-commit-config.yaml

@@ -2,7 +2,7 @@
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v4.6.0
     hooks:
     # there are many log files in tests
     # TODO: seperate py files and log files
@@ -16,10 +16,12 @@ repos:
     -   id: check-merge-conflict
     -   id: check-symlinks
     -   id: check-toml
+    -   id: mixed-line-ending
+        args: ["--fix=lf"]
 # Python
 -   repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.3.5
+    rev: v0.4.7
     hooks:
     - id: ruff
       args: ["--fix"]

benchmark/__init__.py

@@ -0,0 +1,20 @@
+from __future__ import annotations
+
+import subprocess
+import sys
+
+import pytest
+
+
+@pytest.mark.benchmark
+def test_import():
+    """Test import dpdata."""
+    subprocess.check_output(
+        [sys.executable, "-c", "'from dpdata import LabeledSystem'"]
+    ).decode("ascii")
+
+
+@pytest.mark.benchmark
+def test_cli():
+    """Test dpdata command."""
+    subprocess.check_output([sys.executable, "-m", "dpdata", "-h"]).decode("ascii")

benchmark/test_import.py

@@ -11,6 +11,8 @@
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 #
+from __future__ import annotations
+
 import os
 import subprocess as sp
 import sys
@@ -207,3 +209,4 @@ def setup(app):
 # jupyterlite
 jupyterlite_contents = "./nb"
 jupyterlite_bind_ipynb_suffix = False
+jupyterlite_silence = False