More Tests (#155)

docs/source/01_quickstart/getting_started.rst

@@ -73,40 +73,6 @@ use corresponding getters :meth:`~dxtb.Calculator.get_energy`:
 
 We recommend using the getters, as they provide the familiar ASE-like interface.
 
-.. warning::
-
-    If you supply the **same inputs** to the calculator multiple times with
-    gradient tracking enabled, you have to reset the calculator in between with
-    :meth:`~dxtb.Calculator.reset_all`. Otherwise, the gradients will be wrong.
-
-    .. admonition:: Example
-       :class: toggle
-
-       .. code-block:: python
-
-           import torch
-           import dxtb
-
-           dd = {"dtype": torch.double, "device": torch.device("cpu")}
-
-           numbers = torch.tensor([3, 1], device=dd["device"])
-           positions = torch.tensor([[0.0, 0.0, 0.0], [0.0, 0.0, 1.0]], **dd)
-
-           calc = dxtb.calculators.GFN1Calculator(numbers, **dd)
-
-           pos = positions.clone().requires_grad_(True)
-           energy = calc.energy(pos)
-           (g1,) = torch.autograd.grad(energy, pos)
-
-           # wrong gradients without reset here
-           calc.reset_all()
-
-           pos = positions.clone().requires_grad_(True)
-           energy = calc.energy(pos)
-           (g2,) = torch.autograd.grad(energy, pos)
-
-           assert torch.allclose(g1, g2)
-
 
 Gradients
 ---------
@@ -146,6 +112,41 @@ The equivalency of the two methods (except for the sign) can be verified by
 the example `here <https://github.com/grimme-lab/dxtb/blob/main/examples/forces.py>`_.
 
 
+.. warning::
+
+    If you supply the **same inputs** to the calculator multiple times with
+    gradient tracking enabled, you have to reset the calculator in between with
+    :meth:`~dxtb.Calculator.reset_all`. Otherwise, the gradients will be wrong.
+
+    .. admonition:: Example
+       :class: toggle
+
+       .. code-block:: python
+
+           import torch
+           import dxtb
+
+           dd = {"dtype": torch.double, "device": torch.device("cpu")}
+
+           numbers = torch.tensor([3, 1], device=dd["device"])
+           positions = torch.tensor([[0.0, 0.0, 0.0], [0.0, 0.0, 1.0]], **dd)
+
+           calc = dxtb.calculators.GFN1Calculator(numbers, **dd)
+
+           pos = positions.clone().requires_grad_(True)
+           energy = calc.energy(pos)
+           (g1,) = torch.autograd.grad(energy, pos)
+
+           # wrong gradients without reset here
+           calc.reset_all()
+
+           pos = positions.clone().requires_grad_(True)
+           energy = calc.energy(pos)
+           (g2,) = torch.autograd.grad(energy, pos)
+
+           assert torch.allclose(g1, g2)
+
+
 More Properties
 ---------------
 

docs/source/conf.py

@@ -47,8 +47,8 @@
 
 html_theme = "sphinx_book_theme"
 html_title = project
-html_logo = "_static/dxtb.svg"
-html_favicon = "_static/dxtb-favicon.svg"
+html_logo = "_static/dxtb.png"
+html_favicon = "_static/dxtb-favicon.png"
 
 html_theme_options = {
     "navigation_with_keys": False,
@@ -81,6 +81,7 @@
     "python": ("https://docs.python.org/3", None),
     "tad_dftd3": ("https://tad-dftd3.readthedocs.io/en/latest/", None),
     "tad_dftd4": ("https://tad-dftd4.readthedocs.io/en/latest/", None),
+    "tad_libcint": ("https://tad-libcint.readthedocs.io/en/latest/", None),
     "tad_mctc": ("https://tad-mctc.readthedocs.io/en/latest/", None),
     "tad_multicharge": ("https://tad-multicharge.readthedocs.io/en/latest/", None),
     "torch": ("https://pytorch.org/docs/stable/", None),
@@ -113,7 +114,9 @@
 exclude_patterns = [
     # Sometimes sphinx reads its own outputs as inputs!
     "build/html",
+    "_build/html",
     "build/jupyter_execute",
+    "_build/jupyter_execute",
     "notebooks/README.md",
     "README.md",
     "notebooks/*.md",

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
 

pyproject.toml

@@ -45,7 +45,7 @@ source = ["./src"]
 omit = [
   "./src/dxtb/_src/exlibs/xitorch/*",
   "./src/dxtb/_src/exlibs/scipy/*",
-  "./src/dxtb/_src/typing.py",
+  "./src/dxtb/_src/typing/*",
   "./src/dxtb/components/*",
 ]
 

src/dxtb/__version__.py

@@ -22,5 +22,5 @@
 
 __all__ = ["__version__", "__tversion__"]
 
-__version__ = "0.0.0"
+__version__ = "0.0.1"
 """Version of ``dxtb`` in semantic versioning."""

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

@@ -26,6 +26,7 @@
 import torch
 
 from dxtb.__version__ import __tversion__
+from dxtb._src.typing import Any
 
 __all__ = [
     "get_mkl_num_threads",
@@ -70,7 +71,7 @@ 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 +130,7 @@ 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