More tests

examples/integrals.py

@@ -15,7 +15,7 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 """
-Simple integral interface.
+Simple integral interface. Can be helpful for testing.
 """
 from pathlib import Path
 

examples/limitation_xitorch.py

@@ -15,7 +15,7 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 """
-Calculating forces for vancomycin via AD.
+Example for xitorch's inability to be used together with functorch.
 """
 from pathlib import Path
 

src/dxtb/_src/cli/driver.py

@@ -108,7 +108,7 @@ def _set_attr(self, attr: str) -> int | list[int]:
         for path in self.base:
             # use charge (or spin) from file or set to zero
             if Path(path, FILES[attr]).is_file():
-                vals.append(io.read_chrg(Path(path, FILES[attr])))
+                vals.append(read.read_chrg_from_path(Path(path, FILES[attr])))
             else:
                 vals.append(0)
 
@@ -176,7 +176,7 @@ def singlepoint(self) -> Result | None:
             numbers = pack(_n)
             positions = pack(_p)
         else:
-            _n, _p = io.read_structure_from_file(args.file[0], args.filetype)
+            _n, _p = read.read_from_path(args.file[0], args.filetype)
             numbers = torch.tensor(_n, dtype=torch.long, device=dd["device"])
             positions = torch.tensor(_p, **dd)
 

src/dxtb/_src/io/__init__.py

@@ -18,15 +18,5 @@
 Functions for reading and writing files.
 """
 
-from . import read
 from .handler import *
-from .logutils import DEFAULT_LOG_CONFIG
 from .output import *
-from .read import (
-    read_chrg,
-    read_coord,
-    read_orca_engrad,
-    read_qcschema,
-    read_structure_from_file,
-    read_xyz,
-)

src/dxtb/_src/io/logutils.py

@@ -15,7 +15,7 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 """
-Logging
+Logging.
 """
 
 from __future__ import annotations

src/dxtb/_src/io/output/header.py

@@ -26,7 +26,7 @@
 WIDTH = 70
 
 
-def get_header() -> str:
+def get_header() -> str:  # pragma: no cover
     logo = [
         r"      _      _   _      ",
         r"     | |    | | | |     ",

src/dxtb/_src/io/output/info.py

@@ -24,7 +24,7 @@
 import platform
 
 import torch
-
+from dxtb._src.typing import Any
 from dxtb.__version__ import __tversion__
 
 __all__ = [
@@ -70,7 +70,7 @@ def get_system_info():
     }
 
 
-def get_pytorch_info():
+def get_pytorch_info() -> dict[str, Any]:  # pragma: no cover
     is_cuda = torch.cuda.is_available()
 
     backends = []
@@ -129,7 +129,7 @@ def get_pytorch_info():
     }
 
 
-def print_system_info(punit=print):
+def print_system_info(punit=print) -> None:  # pragma: no cover
     system_info = get_system_info()["System Information"]
     pytorch_info = get_pytorch_info()["PyTorch Information"]
     sep = 17