refact: refactor format backends into dpdata.formats (#970)

This PR fixes the CI failures from #946 after moving implementation
modules.

Changes:
- Keep real format backends under `dpdata.formats`.
- Move the non-format MD analysis/tool modules back to `dpdata.md`
instead of `dpdata.formats.md`.
- Do not preserve `dpdata.lammps` / `dpdata.vasp` as top-level exports.
- Add explicit package exports for the newly moved format subpackages
under `dpdata.formats`.
- Update direct helper imports in tests/internal code to their new
locations:
  - `dpdata.formats.cp2k.cell.cell_to_low_triangle`
  - `dpdata.formats.gaussian.gjf.detect_multiplicity`
  - `dpdata.formats.qe.traj.convert_celldm`
  - `dpdata.formats.amber.md.cell_lengths_angles_to_cell`
  - `dpdata.md.msd.msd`
  - `dpdata.md.water.*`

Follow-up:
- Removed the legacy `dpdata.<format>` wrapper modules that were added
earlier; this branch no longer keeps those old import paths alive.

Local checks:
- `cd tests && uv run pytest test_amber_md.py
test_cell_to_low_triangle.py
test_gaussian_driver.py::TestMakeGaussian::test_detect_multiplicity
test_qe_cp_traj.py::TestConverCellDim test_msd.py test_water_ions.py -q`
→ 45 passed
- `uv run pyright` → currently reports 2 pre-existing missing `_version`
/ `__version__` diagnostics in `dpdata/__init__.py` and `dpdata/cli.py`
- `git grep -n "from dpdata\.formats\..* import \*\|legacy" -- dpdata
tests` → no matches

Authored by OpenClaw (model: custom-chat-jinzhezeng-group/gpt-5.5)


<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->

## Summary by CodeRabbit

## Release Notes

* **Refactor**
* Reorganized internal format handler modules into a dedicated `formats`
subdirectory for improved code structure and maintainability.
* Updated internal import paths throughout the codebase to reflect the
new module organization structure.

<!-- end of auto-generated comment: release notes by coderabbit.ai -->

---------

Co-authored-by: OpenClaw Bot <bot@openclaw.dev>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Author: 3 people

dpdata/__init__.py

@@ -1,6 +1,6 @@
 from __future__ import annotations
 
-from . import lammps, md, vasp
+from . import md
 from .bond_order_system import BondOrderSystem
 from .system import LabeledSystem, MultiSystems, System
 
@@ -9,11 +9,10 @@
 except ImportError:
     from .__about__ import __version__
 
+
 __all__ = [
     "__version__",
-    "lammps",
     "md",
-    "vasp",
     "System",
     "LabeledSystem",
     "MultiSystems",

dpdata/bond_order_system.py

@@ -6,11 +6,11 @@
 
 import numpy as np
 
-import dpdata.rdkit.utils
-from dpdata.rdkit.sanitize import Sanitizer
+import dpdata.formats.rdkit.utils
+from dpdata.formats.rdkit.sanitize import Sanitizer
 from dpdata.system import Axis, DataType, System
 
-# import dpdata.rdkit.mol2
+# import dpdata.formats.rdkit.mol2
 
 
 class BondOrderSystem(System):
@@ -79,7 +79,7 @@ def __init__(
         self.sanitizer = Sanitizer(sanitize_level, raise_errors, verbose)
 
         if data:
-            mol = dpdata.rdkit.utils.system_data_to_mol(data)
+            mol = dpdata.formats.rdkit.utils.system_data_to_mol(data)
             self.from_rdkit_mol(mol)
         if file_name:
             self.from_fmt(
@@ -161,7 +161,7 @@ def __add__(self, other):
     #         magic method "+" operation
     #     '''
     #     if isinstance(other, BondOrderSystem):
-    #         if dpdata.rdkit.utils.check_same_molecule(self.rdkit_mol, other.rdkit_mol):
+    #         if dpdata.formats.rdkit.utils.check_same_molecule(self.rdkit_mol, other.rdkit_mol):
     #             self.__class__(self, data=other.data)
     #         else:
     #             raise RuntimeError("The two systems are not of the same topology.")
@@ -171,7 +171,7 @@ def __add__(self, other):
     def from_rdkit_mol(self, rdkit_mol):
         """Initialize from a rdkit.Chem.rdchem.Mol object."""
         rdkit_mol = self.sanitizer.sanitize(rdkit_mol)
-        self.data = dpdata.rdkit.utils.mol_to_system_data(rdkit_mol)
+        self.data = dpdata.formats.rdkit.utils.mol_to_system_data(rdkit_mol)
         self.data["bond_dict"] = dict(
             [(f"{int(bond[0])}-{int(bond[1])}", bond[2]) for bond in self.data["bonds"]]
         )

dpdata/formats/__init__.py

@@ -0,0 +1 @@
+# Format modules for dpdata

dpdata/abacus/__init__.py dpdata/formats/abacus/__init__.pydpdata/abacus/__init__.py renamed to dpdata/formats/abacus/__init__.py

@@ -8,7 +8,7 @@
 
 from dpdata.utils import open_file
 
-from ..unit import LengthConversion, PressureConversion
+from ...unit import LengthConversion, PressureConversion
 from .stru import get_frame_from_stru
 
 bohr2ang = LengthConversion("bohr", "angstrom").value()

dpdata/abacus/md.py dpdata/formats/abacus/md.pydpdata/abacus/md.py renamed to dpdata/formats/abacus/md.py

@@ -6,7 +6,7 @@
 
 import numpy as np
 
-from ..unit import LengthConversion
+from ...unit import LengthConversion
 
 bohr2ang = LengthConversion("bohr", "angstrom").value()