Merge pull request #11 from deepmodeling/devel

style: enforce LF line ending (#661)

.github/workflows/test_import.yml

@@ -1,18 +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 uv
-    - run: python -m uv pip install --system .
-    - 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

@@ -16,6 +16,8 @@ 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.

docs/credits.rst

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

dpdata/orca/output.py

@@ -1,64 +1,64 @@
-from __future__ import annotations
-
-import numpy as np
-
-
-def read_orca_sp_output(fn: str) -> tuple[np.ndarray, np.ndarray, float, np.ndarray]:
-    """Read from ORCA output.
-
-    Note that both the energy and the gradient should be printed.
-
-    Parameters
-    ----------
-    fn : str
-        file name
-
-    Returns
-    -------
-    np.ndarray
-        atomic symbols
-    np.ndarray
-        atomic coordinates
-    float
-        total potential energy
-    np.ndarray
-        atomic forces
-    """
-    coord = None
-    symbols = None
-    forces = None
-    energy = None
-    with open(fn) as f:
-        flag = 0
-        for line in f:
-            if flag in (1, 3, 4):
-                flag += 1
-            elif flag == 2:
-                s = line.split()
-                if not len(s):
-                    flag = 0
-                else:
-                    symbols.append(s[0].capitalize())
-                    coord.append([float(s[1]), float(s[2]), float(s[3])])
-            elif flag == 5:
-                s = line.split()
-                if not len(s):
-                    flag = 0
-                else:
-                    forces.append([float(s[3]), float(s[4]), float(s[5])])
-            elif line.startswith("CARTESIAN COORDINATES (ANGSTROEM)"):
-                # coord
-                flag = 1
-                coord = []
-                symbols = []
-            elif line.startswith("CARTESIAN GRADIENT"):
-                flag = 3
-                forces = []
-            elif line.startswith("FINAL SINGLE POINT ENERGY"):
-                energy = float(line.split()[-1])
-    symbols = np.array(symbols)
-    forces = -np.array(forces)
-    coord = np.array(coord)
-    assert coord.shape == forces.shape
-
-    return symbols, coord, energy, forces
+from __future__ import annotations
+
+import numpy as np
+
+
+def read_orca_sp_output(fn: str) -> tuple[np.ndarray, np.ndarray, float, np.ndarray]:
+    """Read from ORCA output.
+
+    Note that both the energy and the gradient should be printed.
+
+    Parameters
+    ----------
+    fn : str
+        file name
+
+    Returns
+    -------
+    np.ndarray
+        atomic symbols
+    np.ndarray
+        atomic coordinates
+    float
+        total potential energy
+    np.ndarray
+        atomic forces
+    """
+    coord = None
+    symbols = None
+    forces = None
+    energy = None
+    with open(fn) as f:
+        flag = 0
+        for line in f:
+            if flag in (1, 3, 4):
+                flag += 1
+            elif flag == 2:
+                s = line.split()
+                if not len(s):
+                    flag = 0
+                else:
+                    symbols.append(s[0].capitalize())
+                    coord.append([float(s[1]), float(s[2]), float(s[3])])
+            elif flag == 5:
+                s = line.split()
+                if not len(s):
+                    flag = 0
+                else:
+                    forces.append([float(s[3]), float(s[4]), float(s[5])])
+            elif line.startswith("CARTESIAN COORDINATES (ANGSTROEM)"):
+                # coord
+                flag = 1
+                coord = []
+                symbols = []
+            elif line.startswith("CARTESIAN GRADIENT"):
+                flag = 3
+                forces = []
+            elif line.startswith("FINAL SINGLE POINT ENERGY"):
+                energy = float(line.split()[-1])
+    symbols = np.array(symbols)
+    forces = -np.array(forces)
+    coord = np.array(coord)
+    assert coord.shape == forces.shape
+
+    return symbols, coord, energy, forces

dpdata/plugins/orca.py

@@ -1,53 +1,53 @@
-from __future__ import annotations
-
-import numpy as np
-
-from dpdata.format import Format
-from dpdata.orca.output import read_orca_sp_output
-from dpdata.unit import EnergyConversion, ForceConversion
-
-energy_convert = EnergyConversion("hartree", "eV").value()
-force_convert = ForceConversion("hartree/bohr", "eV/angstrom").value()
-
-
-@Format.register("orca/spout")
-class ORCASPOutFormat(Format):
-    """ORCA single point energy output.
-
-    Note that both the energy and the gradient should be
-    printed into the output file.
-    """
-
-    def from_labeled_system(self, file_name: str, **kwargs) -> dict:
-        """Read from ORCA single point energy output.
-
-        Parameters
-        ----------
-        file_name : str
-            file name
-        **kwargs
-            keyword arguments
-
-        Returns
-        -------
-        dict
-            system data
-        """
-        symbols, coord, energy, forces = read_orca_sp_output(file_name)
-
-        atom_names, atom_types, atom_numbs = np.unique(
-            symbols, return_inverse=True, return_counts=True
-        )
-        natoms = coord.shape[0]
-
-        return {
-            "atom_types": atom_types,
-            "atom_names": list(atom_names),
-            "atom_numbs": list(atom_numbs),
-            "coords": coord.reshape((1, natoms, 3)),
-            "energies": np.array([energy * energy_convert]),
-            "forces": (forces * force_convert).reshape((1, natoms, 3)),
-            "cells": np.zeros((1, 3, 3)),
-            "orig": np.zeros(3),
-            "nopbc": True,
-        }
+from __future__ import annotations
+
+import numpy as np
+
+from dpdata.format import Format
+from dpdata.orca.output import read_orca_sp_output
+from dpdata.unit import EnergyConversion, ForceConversion
+
+energy_convert = EnergyConversion("hartree", "eV").value()
+force_convert = ForceConversion("hartree/bohr", "eV/angstrom").value()
+
+
+@Format.register("orca/spout")
+class ORCASPOutFormat(Format):
+    """ORCA single point energy output.
+
+    Note that both the energy and the gradient should be
+    printed into the output file.
+    """
+
+    def from_labeled_system(self, file_name: str, **kwargs) -> dict:
+        """Read from ORCA single point energy output.
+
+        Parameters
+        ----------
+        file_name : str
+            file name
+        **kwargs
+            keyword arguments
+
+        Returns
+        -------
+        dict
+            system data
+        """
+        symbols, coord, energy, forces = read_orca_sp_output(file_name)
+
+        atom_names, atom_types, atom_numbs = np.unique(
+            symbols, return_inverse=True, return_counts=True
+        )
+        natoms = coord.shape[0]
+
+        return {
+            "atom_types": atom_types,
+            "atom_names": list(atom_names),
+            "atom_numbs": list(atom_numbs),
+            "coords": coord.reshape((1, natoms, 3)),
+            "energies": np.array([energy * energy_convert]),
+            "forces": (forces * force_convert).reshape((1, natoms, 3)),
+            "cells": np.zeros((1, 3, 3)),
+            "orig": np.zeros(3),
+            "nopbc": True,
+        }