merge devel to master (v0.13.0) (#1676)

Author: njzjz

.git_archival.txt

@@ -0,0 +1,3 @@
+node: $Format:%H$
+node-date: $Format:%cI$
+describe-name: $Format:%(describe:tags=true,match=*[0-9]*)$

.gitattributes

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

.github/workflows/release.yml

@@ -6,42 +6,16 @@ on:
       - 'v*'
 
 jobs:
-  conda-publish:
-    runs-on: ubuntu-latest
-    steps:
-    - uses: actions/checkout@v2
-    - name: publish-to-conda
-      uses: felix5572/conda-publish-action@v1.9
-      with:
-        subdir: 'conda'
-        anacondatoken: ${{ secrets.ANACONDA_TOKEN }}
-        platforms: 'noarch'
-  construct-and-publish:
-    runs-on: ubuntu-latest
-    needs: conda-publish
-    steps:
-    - uses: actions/checkout@master
-    - uses: s-weigand/setup-conda@v1
-    - run: conda install constructor jinja2 -y
-    - run: constructor ./conda
-    - name: Upload to release
-      uses: softprops/action-gh-release@master
-      if: startsWith(github.ref, 'refs/tags/')
-      with:
-        files: dpgen-*.sh
-        repository: ${{ env.GITHUB_REPOSITORY }}
-      env:
-        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
   release-to-pypi:
     name: Release to pypi
     runs-on: ubuntu-latest
     permissions:
         # IMPORTANT: this permission is mandatory for trusted publishing
         id-token: write
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Setup python
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: 3.x
         architecture: x64

.github/workflows/test.yml

@@ -12,16 +12,17 @@ jobs:
         python-version: ["3.9", "3.12"]
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
+    - run: pip install uv
     - name: Install dependencies
-      run: pip install -e .[test]
+      run: uv pip install --system -e .[test]
     - name: Test
       run: coverage run --source=./dpgen -m unittest -v && coverage report
-    - uses: codecov/codecov-action@v4
+    - uses: codecov/codecov-action@v5
       env:
         CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
   pass:

.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: v4.6.0
+    rev: v5.0.0
     hooks:
     # there are many log files in tests
     # TODO: seperate py files and log files
@@ -28,7 +28,7 @@ repos:
 
 # Python
 -   repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.3.5
+    rev: v0.7.4
     hooks:
     - id: ruff
       args: ["--fix"]

.readthedocs.yaml

@@ -10,15 +10,14 @@ build:
   os: ubuntu-22.04
   tools:
     python: "3.10"
-
+  jobs:
+    post_create_environment:
+      - pip install uv
+    post_install:
+      - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH uv pip install -r doc/requirements.txt
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
    configuration: doc/conf.py
 
 # If using Sphinx, optionally build your docs in additional formats such as PDF
 formats: all
-
-# Optionally declare the Python requirements required to build your docs
-python:
-   install:
-   - requirements: doc/requirements.txt

README.md

@@ -53,7 +53,7 @@ For detailed usage and parameters, read [DP-GEN documentation](https://docs.deep
 
 * [Tutorials](https://tutorials.deepmodeling.com/en/latest/Tutorials/DP-GEN/): basic tutorials for DP-GEN.
 * [Examples](examples): input files in [JSON](https://docs.python.org/3/library/json.html) format.
-* [Publications](https://deepmodeling.com/blog/papers/dpgen/): Published research articles using DP-GEN.
+* [Publications](https://blogs.deepmodeling.com/papers/dpgen/): Published research articles using DP-GEN.
 * [User guide](https://docs.deepmodeling.com/projects/dpgen/en/latest/user-guide/): frequently asked questions listed in troubleshooting.
 
 ## License