Merge branch 'devel' of https://github.com/deepmodeling/dpgen into stru

Author: root

.git_archival.txt

@@ -1,4 +1,3 @@
 node: $Format:%H$
 node-date: $Format:%cI$
 describe-name: $Format:%(describe:tags=true,match=*[0-9]*)$
-ref-names: $Format:%D$

.github/workflows/test.yml

@@ -22,7 +22,7 @@ jobs:
       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: v0.4.1
+    rev: v0.9.2
     hooks:
     - id: ruff
       args: ["--fix"]

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

doc/conf.py

@@ -19,7 +19,7 @@
 # -- Project information -----------------------------------------------------
 
 project = "DP-GEN"
-copyright = "2020-%d, DeepModeling" % date.today().year
+copyright = "2020-%d, DeepModeling" % date.today().year  # noqa: UP031
 author = "DeepModeling"
 
 
@@ -30,7 +30,7 @@
 # ones.
 # extensions = [
 #     'recommonmark',
-#     "sphinx_rtd_theme",
+#     "sphinx_book_theme",
 #     'myst_parser',
 #     'sphinx_markdown_tables',
 #     'sphinx.ext.autosummary'
@@ -39,7 +39,7 @@
 extensions = [
     "deepmodeling_sphinx",
     "dargs.sphinx",
-    "sphinx_rtd_theme",
+    "sphinx_book_theme",
     "myst_parser",
     "sphinx.ext.autosummary",
     "sphinx.ext.viewcode",
@@ -71,14 +71,20 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = "sphinx_rtd_theme"
+html_theme = "sphinx_book_theme"
 html_logo = "_static/logo.svg"
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
 html_static_path = ["_static"]
 html_css_files = ["css/custom.css"]
+html_theme_options = {
+    "logo": {
+        "image_light": "_static/logo.svg",
+        "image_dark": "_static/logo-dark.svg",
+    }
+}
 
 autodoc_default_flags = ["members"]
 autosummary_generate = True

doc/index.rst

@@ -31,7 +31,7 @@ DPGEN's documentation
    :glob:
 
    Tutorials <https://tutorials.deepmodeling.com/en/latest/Tutorials/DP-GEN/>
-   Publications <https://deepmodeling.com/blog/papers/dpgen/>
+   Publications <https://blogs.deepmodeling.com/papers/dpgen/>
 
 .. _user-guide:
 

doc/init/init-bulk-jdata.rst

@@ -2,7 +2,7 @@ dpgen init_bulk parameters
 ======================================
 
 .. note::
-   One can load, modify, and export the input file by using our effective web-based tool `DP-GUI <https://deepmodeling.com/dpgui/input/dpgen-init-bulk>`_ online or hosted using the :ref:`command line interface <cli>` :code:`dpgen gui`. All parameters below can be set in DP-GUI. By clicking "SAVE JSON", one can download the input file.
+   One can load, modify, and export the input file by using our effective web-based tool `DP-GUI <https://dpgui.deepmodeling.com/input/dpgen-init-bulk>`_ online or hosted using the :ref:`command line interface <cli>` :code:`dpgen gui`. All parameters below can be set in DP-GUI. By clicking "SAVE JSON", one can download the input file.
 
 .. dargs::
    :module: dpgen.data.arginfo

doc/init/init-bulk-mdata.rst

@@ -2,7 +2,7 @@ dpgen init_bulk machine parameters
 ==================================
 
 .. note::
-   One can load, modify, and export the input file by using our effective web-based tool `DP-GUI <https://deepmodeling.com/dpgui/input/dpgen-init-bulk-machine>`_ online or hosted using the :ref:`command line interface <cli>` :code:`dpgen gui`. All parameters below can be set in DP-GUI. By clicking "SAVE JSON", one can download the input file.
+   One can load, modify, and export the input file by using our effective web-based tool `DP-GUI <https://dpgui.deepmodeling.com/input/dpgen-init-bulk-machine>`_ online or hosted using the :ref:`command line interface <cli>` :code:`dpgen gui`. All parameters below can be set in DP-GUI. By clicking "SAVE JSON", one can download the input file.
 
 .. dargs::
    :module: dpgen.data.arginfo

doc/init/init-reaction-jdata.rst

@@ -2,7 +2,7 @@ dpgen init_reaction parameters
 ======================================
 
 .. note::
-   One can load, modify, and export the input file by using our effective web-based tool `DP-GUI <https://deepmodeling.com/dpgui/input/dpgen-init-reaction>`_ online or hosted using the :ref:`command line interface <cli>` :code:`dpgen gui`. All parameters below can be set in DP-GUI. By clicking "SAVE JSON", one can download the input file.
+   One can load, modify, and export the input file by using our effective web-based tool `DP-GUI <https://dpgui.deepmodeling.com/input/dpgen-init-reaction>`_ online or hosted using the :ref:`command line interface <cli>` :code:`dpgen gui`. All parameters below can be set in DP-GUI. By clicking "SAVE JSON", one can download the input file.
 
 .. dargs::
    :module: dpgen.data.arginfo

doc/init/init-reaction-mdata.rst

@@ -2,7 +2,7 @@ dpgen init_reaction machine parameters
 ======================================
 
 .. note::
-   One can load, modify, and export the input file by using our effective web-based tool `DP-GUI <https://deepmodeling.com/dpgui/input/dpgen-init-reaction-machine>`_ online or hosted using the :ref:`command line interface <cli>` :code:`dpgen gui`. All parameters below can be set in DP-GUI. By clicking "SAVE JSON", one can download the input file.
+   One can load, modify, and export the input file by using our effective web-based tool `DP-GUI <https://dpgui.deepmodeling.com/input/dpgen-init-reaction-machine>`_ online or hosted using the :ref:`command line interface <cli>` :code:`dpgen gui`. All parameters below can be set in DP-GUI. By clicking "SAVE JSON", one can download the input file.
 
 .. dargs::
    :module: dpgen.data.arginfo