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

deepmodeling · Nov 23, 2024 · e02e6a2 · e02e6a2
2 parents 6943db5 + c4f05db
commit e02e6a2
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diff --git a/.git_archival.txt b/.git_archival.txt
@@ -0,0 +1,3 @@
+node: $Format:%H$
+node-date: $Format:%cI$
+describe-name: $Format:%(describe:tags=true,match=*[0-9]*)$
diff --git a/.gitattributes b/.gitattributes
@@ -0,0 +1 @@
+.git_archival.txt  export-subst
diff --git a/.github/workflows/release.yml b/.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

diff --git a/.github/workflows/test.yml b/.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:

diff --git a/.pre-commit-config.yaml b/.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"]

diff --git a/.readthedocs.yaml b/.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
diff --git a/README.md b/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

diff --git a/conda/conda_build_config.yaml b/conda/conda_build_config.yaml
diff --git a/conda/construct.yaml b/conda/construct.yaml
diff --git a/conda/meta.yaml b/conda/meta.yaml
diff --git a/doc/conf.py b/doc/conf.py
@@ -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

diff --git a/doc/index.rst b/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:
 

diff --git a/doc/init/init-bulk-jdata.rst b/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

diff --git a/doc/init/init-bulk-mdata.rst b/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

diff --git a/doc/init/init-reaction-jdata.rst b/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

diff --git a/doc/init/init-reaction-mdata.rst b/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

diff --git a/doc/init/init-surf-jdata.rst b/doc/init/init-surf-jdata.rst
@@ -2,7 +2,7 @@ dpgen init_surf 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-surf>`_ 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-surf>`_ 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

diff --git a/doc/init/init-surf-mdata.rst b/doc/init/init-surf-mdata.rst
@@ -2,7 +2,7 @@ dpgen init_surf 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-surf-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-surf-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

diff --git a/doc/overview/code-structure.md b/doc/overview/code-structure.md
@@ -19,7 +19,7 @@ Let's look at the home page of DP-GEN. https://github.com/deepmodeling/dpgen
 - `tests` : unittest tools for developers.
 - `examples`: templates for PARAM and MACHINE files for different software, versions and tasks.
 For details of the parameters in PARAM, you can refer to `TASK parameters` chapters in this document.
-If you are confused about how to set up a JSON file, you can also use [dpgui](https://mobile.deepmodeling.com/dpgui/)
+If you are confused about how to set up a JSON file, you can also use [dpgui](https://mobile.dpgui.deepmodeling.com/)
 
 Most of the code related to DP-GEN functions is in the `dpgen` directory. Open the `dpgen` directory, and we can see
 ````

diff --git a/doc/requirements.txt b/doc/requirements.txt
@@ -1,11 +1,11 @@
 # https://github.com/sphinx-doc/sphinx/issues/11662
 sphinx>=4.0.2,!=7.2.5
 recommonmark
-sphinx_rtd_theme
+sphinx-book-theme
 sphinx_markdown_tables
-sphinx-argparse
+sphinx-argparse<0.5.0
 myst-parser
-deepmodeling_sphinx>=0.1.1
+deepmodeling-sphinx>=0.3.0
 dargs>=0.3.1
 numpydoc
 .
diff --git a/doc/run/mdata.rst b/doc/run/mdata.rst
@@ -1,7 +1,7 @@
 dpgen run 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-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-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.generator.arginfo

diff --git a/doc/run/param.rst b/doc/run/param.rst
@@ -3,7 +3,7 @@ dpgen run param 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-run>`_ 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-run>`_ 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.generator.arginfo

diff --git a/doc/simplify/simplify-jdata.rst b/doc/simplify/simplify-jdata.rst
@@ -2,7 +2,7 @@ dpgen simplify 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-simplify>`_ 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-simplify>`_ 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.simplify.arginfo

diff --git a/doc/simplify/simplify-mdata.rst b/doc/simplify/simplify-mdata.rst
@@ -2,7 +2,7 @@ dpgen simplify 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-simplify-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-simplify-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.simplify.arginfo

diff --git a/doc/simplify/simplify.md b/doc/simplify/simplify.md
@@ -84,7 +84,6 @@ Here is an example of `param.json` for QM7 dataset:
             "limit_pref_pf": 0
         },
         "training": {
-            "set_prefix": "set",
             "numb_steps": 10000,
             "disp_file": "lcurve.out",
             "disp_freq": 1000,

diff --git a/dpgen/__init__.py b/dpgen/__init__.py
@@ -11,6 +11,7 @@
 # dlogf_formatter=logging.Formatter('%(asctime)s - %(name)s - [%(filename)s:%(funcName)s - %(lineno)d ] - %(levelname)s \n %(message)s')
 dlogf.setFormatter(dlogf_formatter)
 dlog.addHandler(dlogf)
+logging.basicConfig(level=logging.WARNING)
 
 __author__ = "Han Wang"
 __copyright__ = "Copyright 2019"