Merge remote-tracking branch 'upstream/devel' into PR

.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

@@ -18,11 +18,9 @@ jobs:
       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@v4
-    - uses: actions/setup-python@v5
-      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: v0.4.4
     hooks:
     - id: ruff
       args: ["--fix"]

benchmark/test_import.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")

docs/conf.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

docs/credits.rst

@@ -1,4 +1,4 @@
-Authors
-=======
-
+Authors
+=======
+
 .. git-shortlog-authors::

docs/environment.yml

@@ -1,8 +1,9 @@
 name: dpdata
 channels:
   - https://repo.mamba.pm/emscripten-forge
-  - https://repo.mamba.pm/conda-forge
+  - conda-forge
 dependencies:
+  - xeus-python
   - numpy
   - scipy
   - monty

docs/make_format.py

@@ -1,8 +1,15 @@
+from __future__ import annotations
+
 import csv
 import os
+import sys
 from collections import defaultdict
 from inspect import Parameter, Signature, cleandoc, signature
-from typing import Literal
+
+if sys.version_info >= (3, 8):
+    from typing import Literal
+else:
+    from typing_extensions import Literal
 
 from numpydoc.docscrape import Parameter as numpydoc_Parameter
 from numpydoc.docscrape_sphinx import SphinxDocString
@@ -134,13 +141,13 @@ def generate_sub_format_pages(formats: dict):
     for format, alias in formats.items():
         # format: Format, alias: list[str]
         buff = []
-        buff.append(".. _%s:" % format.__name__)
+        buff.append(f".. _{format.__name__}:")
         buff.append("")
         for aa in alias:
-            buff.append("%s format" % aa)
+            buff.append(f"{aa} format")
             buff.append("=" * len(buff[-1]))
             buff.append("")
-        buff.append("Class: %s" % get_cls_link(format))
+        buff.append(f"Class: {get_cls_link(format)}")
         buff.append("")
 
         docstring = format.__doc__
@@ -158,10 +165,10 @@ def generate_sub_format_pages(formats: dict):
             buff.append(f".. _{format.__name__}_{method}:")
             buff.append("")
             if method.startswith("from_"):
-                buff.append("Convert from this format to %s" % method_classes[method])
+                buff.append(f"Convert from this format to {method_classes[method]}")
                 buff.append("`" * len(buff[-1]))
             elif method.startswith("to_"):
-                buff.append("Convert from %s to this format" % method_classes[method])
+                buff.append(f"Convert from {method_classes[method]} to this format")
                 buff.append("`" * len(buff[-1]))
             buff.append("")
             method_obj = getattr(format, method)
@@ -224,10 +231,7 @@ def generate_sub_format_pages(formats: dict):
                     buff.append("""   :noindex:""")
                 buff.append("")
                 if docstring is None or method not in format.__dict__:
-                    docstring = (
-                        """   Convert this format to :class:`%s`."""
-                        % (method_classes[method])
-                    )
+                    docstring = f"""   Convert this format to :class:`{method_classes[method]}`."""
                 doc_obj = SphinxDocString(docstring)
                 if len(doc_obj["Parameters"]) > 0:
                     doc_obj["Parameters"] = [
@@ -295,7 +299,7 @@ def generate_sub_format_pages(formats: dict):
                     )
                 ):
                     docstring = (
-                        "Convert :class:`%s` to this format." % (method_classes[method])
+                        f"Convert :class:`{method_classes[method]}` to this format."
                     )
                 doc_obj = SphinxDocString(docstring)
                 if len(doc_obj["Parameters"]) > 0:
@@ -324,7 +328,7 @@ def generate_sub_format_pages(formats: dict):
             buff.append("")
             buff.append("")
 
-        with open("formats/%s.rst" % format.__name__, "w") as rstfile:
+        with open(f"formats/{format.__name__}.rst", "w") as rstfile:
             rstfile.write("\n".join(buff))
 
 
@@ -342,8 +346,8 @@ def generate_sub_format_pages(formats: dict):
         for kk, vv in formats.items():
             writer.writerow(
                 {
-                    "Format": ":ref:`%s`" % kk.__name__,
-                    "Alias": "\n".join("``%s``" % vvv for vvv in vv),
+                    "Format": f":ref:`{kk.__name__}`",
+                    "Alias": "\n".join(f"``{vvv}``" for vvv in vv),
                     "Supported Conversions": "\n".join(
                         method_links[mtd].format(kk.__name__, mtd)
                         for mtd in check_supported(kk)
@@ -364,7 +368,7 @@ def generate_sub_format_pages(formats: dict):
             writer.writerow(
                 {
                     "Class": get_cls_link(kk),
-                    "Alias": "\n".join("``%s``" % vvv for vvv in vv),
+                    "Alias": "\n".join(f"``{vvv}``" for vvv in vv),
                 }
             )
 
@@ -381,7 +385,7 @@ def generate_sub_format_pages(formats: dict):
             writer.writerow(
                 {
                     "Class": get_cls_link(kk),
-                    "Alias": "\n".join("``%s``" % vvv for vvv in vv),
+                    "Alias": "\n".join(f"``{vvv}``" for vvv in vv),
                 }
             )
     generate_sub_format_pages(formats)

docs/nb/try_dpdata.ipynb

@@ -13,6 +13,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "from __future__ import annotations\n",
+    "\n",
     "import dpdata"
    ]
   },

docs/rtd_environment.yml

@@ -1,6 +1,7 @@
 name: dpdata
 channels:
-  - https://repo.mamba.pm/conda-forge
+  - conda-forge
 dependencies:
+  - mamba
   - pip:
     - ..[docs]

dpdata/__about__.py

@@ -1 +1,3 @@
+from __future__ import annotations
+
 __version__ = "unknown"

dpdata/__init__.py

@@ -1,36 +1,14 @@
-# monty needs lzma
-# See https://github.com/pandas-dev/pandas/pull/27882
-try:
-    import lzma  # noqa: F401
-except ImportError:
-
-    class fakemodule:
-        pass
-
-    import sys
-
-    sys.modules["lzma"] = fakemodule
+from __future__ import annotations
 
 from . import lammps, md, vasp
+from .bond_order_system import BondOrderSystem
 from .system import LabeledSystem, MultiSystems, System
 
 try:
     from ._version import version as __version__
 except ImportError:
     from .__about__ import __version__
 
-# BondOrder System has dependency on rdkit
-try:
-    # prevent conflict with dpdata.rdkit
-    import rdkit as _  # noqa: F401
-
-    USE_RDKIT = True
-except ModuleNotFoundError:
-    USE_RDKIT = False
-
-if USE_RDKIT:
-    from .bond_order_system import BondOrderSystem
-
 __all__ = [
     "__version__",
     "lammps",

dpdata/__main__.py

@@ -0,0 +1,6 @@
+from __future__ import annotations
+
+from dpdata.cli import dpdata_cli
+
+if __name__ == "__main__":
+    dpdata_cli()

dpdata/abacus/md.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 import os
 import warnings
 
@@ -28,7 +30,7 @@ def get_path_out(fname, inlines):
     for line in inlines:
         if len(line) > 0 and "suffix" in line and "suffix" == line.split()[0]:
             suffix = line.split()[1]
-            path_out = os.path.join(fname, "OUT.%s/" % suffix)
+            path_out = os.path.join(fname, f"OUT.{suffix}/")
             break
     return path_out
 
@@ -189,7 +191,7 @@ def get_frame(fname):
             unconv_stru += "%d " % i
     ndump = len(energy)
     if unconv_stru != "":
-        warnings.warn("Structure %s are unconverged and not collected!" % unconv_stru)
+        warnings.warn(f"Structure {unconv_stru} are unconverged and not collected!")
 
     for iframe in range(ndump):
         stress[iframe] *= np.linalg.det(cells[iframe, :, :].reshape([3, 3]))

dpdata/abacus/relax.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 import os
 
 import numpy as np
@@ -183,7 +185,7 @@ def get_frame(fname):
     )
 
     logf = get_log_file(fname, inlines)
-    assert os.path.isfile(logf), "Error: can not find %s" % logf
+    assert os.path.isfile(logf), f"Error: can not find {logf}"
     with open(logf) as f1:
         lines = f1.readlines()