merge devel to master to release v0.2.22

.github/workflows/benchmark.yml

@@ -13,7 +13,12 @@ jobs:
       uses: actions/setup-python@v5
       with:
         python-version: 3.12
-    - run: curl -LsSf https://astral.sh/uv/install.sh | sh
+    - uses: astral-sh/setup-uv@v5
+      with:
+        enable-cache: true
+        cache-dependency-glob: |
+          **/requirements*.txt
+          **/pyproject.toml
     - name: Install dependencies
       run: uv pip install --system .[test,amber,ase,pymatgen,benchmark] rdkit openbabel-wheel
     - name: Run benchmarks

.github/workflows/test.yml

@@ -6,10 +6,10 @@ on:
 
 jobs:
   build:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     strategy:
       matrix:
-        python-version: ["3.7", "3.8", "3.12"]
+        python-version: ["3.8", "3.12"]
 
     steps:
     - uses: actions/checkout@v4
@@ -18,13 +18,19 @@ jobs:
       uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
-    - run: curl -LsSf https://astral.sh/uv/install.sh | sh
+    - uses: astral-sh/setup-uv@v5
+      with:
+        enable-cache: true
+        cache-dependency-glob: |
+          **/requirements*.txt
+          **/pyproject.toml
+        cache-suffix: "py${{ matrix.python-version }}"
     - name: Install dependencies
       run: uv pip install --system .[test,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
-      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
@@ -21,7 +21,7 @@ repos:
 # Python
 -   repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.6.5
+    rev: v0.9.2
     hooks:
     - id: ruff
       args: ["--fix"]
@@ -36,7 +36,7 @@ repos:
       args: ["--write"]
 # Python inside docs
 -   repo: https://github.com/asottile/blacken-docs
-    rev: 1.18.0
+    rev: 1.19.1
     hooks:
     -   id: blacken-docs
 ci:

.readthedocs.yaml

@@ -3,7 +3,7 @@ version: 2
 build:
   os: ubuntu-22.04
   tools:
-    python: "mambaforge-22.9"
+    python: "mambaforge-23.11"
 conda:
   environment: docs/rtd_environment.yml
 sphinx:

README.md

@@ -8,7 +8,7 @@
 
 ## Installation
 
-DP-GEN only supports Python 3.7 and above. You can [setup a conda/pip environment](https://docs.deepmodeling.com/faq/conda.html), and then use one of the following methods to install DP-GEN:
+dpdata only supports Python 3.8 and above. You can [setup a conda/pip environment](https://docs.deepmodeling.com/faq/conda.html), and then use one of the following methods to install dpdata:
 
 - Install via pip: `pip install dpdata`
 - Install via conda: `conda install -c conda-forge dpdata`

docs/conf.py

@@ -24,7 +24,7 @@
 # -- Project information -----------------------------------------------------
 
 project = "dpdata"
-copyright = "2019-%d, DeepModeling " % date.today().year
+copyright = "2019-%d, DeepModeling " % date.today().year  # noqa: UP031
 author = "Han Wang"
 
 # The short X.Y version
@@ -44,7 +44,7 @@
 # ones.
 extensions = [
     "deepmodeling_sphinx",
-    "sphinx_rtd_theme",
+    "sphinx_book_theme",
     "sphinx.ext.mathjax",
     "sphinx.ext.viewcode",
     "sphinx.ext.intersphinx",
@@ -87,7 +87,7 @@
 # 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"
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the

docs/installation.md

@@ -1,6 +1,6 @@
 # Installation
 
-DP-GEN only supports Python 3.7 and above. You can [setup a conda/pip environment](https://docs.deepmodeling.com/faq/conda.html), and then use one of the following methods to install DP-GEN:
+dpdata only supports Python 3.8 and above. You can [setup a conda/pip environment](https://docs.deepmodeling.com/faq/conda.html), and then use one of the following methods to install dpdata:
 
 - Install via pip: `pip install dpdata`
 - Install via conda: `conda install -c conda-forge dpdata`

docs/make_format.py

@@ -2,14 +2,9 @@
 
 import csv
 import os
-import sys
 from collections import defaultdict
 from inspect import Parameter, Signature, cleandoc, signature
-
-if sys.version_info >= (3, 8):
-    from typing import Literal
-else:
-    from typing_extensions import Literal
+from typing import Literal
 
 from numpydoc.docscrape import Parameter as numpydoc_Parameter
 from numpydoc.docscrape_sphinx import SphinxDocString

docs/rtd_environment.yml

@@ -2,6 +2,7 @@ name: dpdata
 channels:
   - conda-forge
 dependencies:
-  - mamba
+  - python <3.13
+  - mamba <2
   - pip:
     - ..[docs]

dpdata/abacus/md.py

@@ -56,9 +56,9 @@ def get_coords_from_dump(dumplines, natoms):
     if "VIRIAL" in dumplines[6]:
         calc_stress = True
         check_line = 10
-    assert (
-        "POSITION" in dumplines[check_line]
-    ), "keywords 'POSITION' cannot be found in the 6th line. Please check."
+    assert "POSITION" in dumplines[check_line], (
+        "keywords 'POSITION' cannot be found in the 6th line. Please check."
+    )
     if "FORCE" in dumplines[check_line]:
         calc_force = True
 
@@ -68,7 +68,7 @@ def get_coords_from_dump(dumplines, natoms):
     else:
         nframes_dump = int(nlines / (total_natoms + 9))
     assert nframes_dump > 0, (
-        "Number of lines in MD_dump file = %d. Number of atoms = %d. The MD_dump file is incomplete."
+        "Number of lines in MD_dump file = %d. Number of atoms = %d. The MD_dump file is incomplete."  # noqa: UP031
         % (nlines, total_natoms)
     )
     cells = np.zeros([nframes_dump, 3, 3])
@@ -125,7 +125,7 @@ def get_coords_from_dump(dumplines, natoms):
                     )
             iframe += 1
     assert iframe == nframes_dump, (
-        "iframe=%d, nframe_dump=%d. Number of frames does not match number of lines in MD_dump."
+        "iframe=%d, nframe_dump=%d. Number of frames does not match number of lines in MD_dump."  # noqa: UP031
         % (iframe, nframes_dump)
     )
     stresses *= kbar2evperang3
@@ -145,7 +145,7 @@ def get_energy(outlines, ndump, dump_freq):
                 energy.append(np.nan)
             nenergy += 1
     assert ndump == len(energy), (
-        "Number of total energies in running_md.log = %d. Number of frames in MD_dump = %d. Please check."
+        "Number of total energies in running_md.log = %d. Number of frames in MD_dump = %d. Please check."  # noqa: UP031
         % (len(energy), ndump)
     )
     energy = np.array(energy)
@@ -167,7 +167,7 @@ def get_frame(fname):
     with open_file(geometry_path_in) as fp:
         geometry_inlines = fp.read().split("\n")
     celldm, cell = get_cell(geometry_inlines)
-    atom_names, natoms, types, coords = get_coords(
+    atom_names, natoms, types, coords, move, magmom = get_coords(
         celldm, cell, geometry_inlines, inlines
     )
     # This coords is not to be used.
@@ -191,7 +191,7 @@ def get_frame(fname):
             force = np.delete(force, i - ndump, axis=0)
             stress = np.delete(stress, i - ndump, axis=0)
             energy = np.delete(energy, i - ndump, axis=0)
-            unconv_stru += "%d " % i
+            unconv_stru += "%d " % i  # noqa: UP031
     ndump = len(energy)
     if unconv_stru != "":
         warnings.warn(f"Structure {unconv_stru} are unconverged and not collected!")
@@ -220,6 +220,8 @@ def get_frame(fname):
     if len(magmom) > 0:
         data["spins"] = magmom
     if len(magforce) > 0:
-        data["mag_forces"] = magforce
+        data["force_mags"] = magforce
+    if len(move) > 0:
+        data["move"] = move
 
     return data

dpdata/abacus/relax.py

@@ -47,7 +47,7 @@ def get_coords_from_log(loglines, natoms):
             natoms_log += int(line.split()[-1])
 
     assert natoms_log > 0 and natoms_log == natoms, (
-        "ERROR: detected atom number in log file is %d" % natoms
+        "ERROR: detected atom number in log file is %d" % natoms  # noqa: UP031
     )
 
     energy = []
@@ -76,7 +76,7 @@ def get_coords_from_log(loglines, natoms):
                         list(map(lambda x: float(x) * a0, loglines[i + k].split()[1:4]))
                     )
             else:
-                assert False, "Unrecongnized coordinate type, %s, line:%d" % (
+                assert False, "Unrecongnized coordinate type, %s, line:%d" % (  # noqa: UP031
                     loglines[i].split()[0],
                     i,
                 )
@@ -183,7 +183,7 @@ def get_frame(fname):
     with open_file(geometry_path_in) as fp:
         geometry_inlines = fp.read().split("\n")
     celldm, cell = get_cell(geometry_inlines)
-    atom_names, natoms, types, coord_tmp = get_coords(
+    atom_names, natoms, types, coord_tmp, move, magmom = get_coords(
         celldm, cell, geometry_inlines, inlines
     )
 
@@ -217,6 +217,8 @@ def get_frame(fname):
     if len(magmom) > 0:
         data["spins"] = magmom
     if len(magforce) > 0:
-        data["mag_forces"] = magforce
+        data["force_mags"] = magforce
+    if len(move) > 0:
+        data["move"] = move
 
     return data