Update dependencies to allow for numpy 2.0 (#195)

* Update dependencies to allow for numpy 2.0
* Make eigenvectors robust against sign changes

core/pyproject.toml

@@ -28,7 +28,7 @@ repository = "https://github.com/vasp-dev/py4vasp"
 
 [tool.poetry.dependencies]
 python = ">=3.9"
-numpy = "^1.23"
+numpy = ">=1.23"
 h5py = ">=3.7.0"
 
 [tool.poetry.group.dev.dependencies]

pyproject.toml

@@ -27,7 +27,7 @@ repository = "https://github.com/vasp-dev/py4vasp"
 
 [tool.poetry.dependencies]
 python = ">=3.9"
-numpy = "^1.23"
+numpy = ">=1.23"
 h5py = ">=3.7.0"
 pandas = ">=1.4.3"
 nglview = ">=3.0.5"

src/py4vasp/_calculation/force_constant.py

@@ -121,13 +121,15 @@ def _format_eigenvectors(self, eigenvectors):
         )
 
     def _format_eigenvector(self, index, eigenvector):
+        sign = np.sign(eigenvector.flatten()[np.argmax(np.abs(eigenvector))])
         eigenvector_string = "\n".join(
-            self._format_vector(vector) for vector in eigenvector
+            self._format_vector(sign * vector) for vector in eigenvector
         )
         return f"vibration {index + 1}\n{eigenvector_string}"
 
     def _format_vector(self, vector):
-        return " ".join(f"{x:12.6f}" for x in vector)
+        replace_nearly_zeros = lambda x: 0 if np.isclose(x, 0, atol=1e-9) else x
+        return " ".join(f"{replace_nearly_zeros(x):12.6f}" for x in vector)
 
 
 @dataclasses.dataclass

src/py4vasp/_calculation/selection.py

@@ -8,6 +8,7 @@
 @dataclass
 class Selection:
     "Helper class specifying which indices to extract their label."
+
     indices: Iterable[int]
     "Indices from which the specified quantity is read."
     label: str = ""

src/py4vasp/_raw/data.py

@@ -15,6 +15,7 @@ def NONE():
 @dataclasses.dataclass(order=True, frozen=True)
 class Version:
     "The version number of VASP."
+
     major: int
     "The major version number."
     minor: int = 0
@@ -126,6 +127,7 @@ class CurrentDensity(mapping.Mapping):
 @dataclasses.dataclass
 class Density:
     "The electronic charge and magnetization density on the Fourier grid."
+
     structure: Structure
     "The atomic structure to represent the densities."
     charge: VaspData
@@ -247,6 +249,7 @@ class Energy:
 @dataclasses.dataclass
 class ExcitonDensity:
     "The exciton charge density on the real space grid."
+
     structure: Structure
     "The atomic structure to represent the densities."
     exciton_charge: VaspData
@@ -500,6 +503,7 @@ class Projector:
 @dataclasses.dataclass
 class Stoichiometry:
     "Contains the type of ions in the system and how many of each type exist."
+
     number_ion_types: VaspData
     "Amount of ions of a particular type."
     ion_types: VaspData
@@ -509,6 +513,7 @@ class Stoichiometry:
 @dataclasses.dataclass
 class Stress:
     "The stress acting on the unit cell at all steps."
+
     structure: Structure
     "Structural information about the system to inform about the unit cell."
     stress: VaspData
@@ -533,12 +538,14 @@ class Structure:
 @dataclasses.dataclass
 class System:
     "The name of the system set in the input."
+
     system: str
 
 
 @dataclasses.dataclass
 class Velocity:
     "Contains the ion velocities along the trajectory."
+
     structure: Structure
     "Structural information to relate the velocities to."
     velocities: VaspData
@@ -548,6 +555,7 @@ class Velocity:
 @dataclasses.dataclass
 class Workfunction:
     "Describes the minimal energy needed to remove an electron from the crystal to the vacuum."
+
     idipol: int
     "INCAR tag of VASP describing the direction along which the potential is assessed."
     distance: VaspData

src/py4vasp/_util/index.py

@@ -1,6 +1,6 @@
 # Copyright © VASP Software GmbH,
 # Licensed under the Apache License 2.0 (http://www.apache.org/licenses/LICENSE-2.0)
-""" Select indices from an array based on a map.
+"""Select indices from an array based on a map.
 
 In multiple cases, VASP produces multiple outputs and the user wants to select one of
 its components e.g. plotting the p DOS. This module provides the Selector class that

src/py4vasp/_util/select.py

@@ -1,6 +1,6 @@
 # Copyright © VASP Software GmbH,
 # Licensed under the Apache License 2.0 (http://www.apache.org/licenses/LICENSE-2.0)
-""" Parse a string to a Tree of selections.
+"""Parse a string to a Tree of selections.
 
 In many cases, a user may want to select a certain subset of quantities to be refined.
 Examples include selecting the projected DOS or a particular component of the energy.
@@ -318,6 +318,7 @@ def _raise_error_if_content_and_operator_are_incompatible(self, operand):
 @dataclasses.dataclass
 class Group:
     "A user selection where multiple elements should be treated together."
+
     group: list
     "The individual members of the group."
     separator: str
@@ -341,6 +342,7 @@ class _Operator:
 @dataclasses.dataclass
 class Operation:
     "A mathematical operation like addition and subtraction."
+
     left_operand: tuple
     "The selection on the left-hand side of the operation."
     operator: str

src/py4vasp/exception.py

@@ -2,7 +2,8 @@
 # Licensed under the Apache License 2.0 (http://www.apache.org/licenses/LICENSE-2.0)
 """Deals with the possible exceptions in py4vasp.
 
-The design goal is that all foreseeable exceptions in py4vasp issue an exception of the Py4VaspException class. Any other kind of exception would indicate a bug in the code. If possible the part standard users interact with should not raise any exception, but should give advice on how to overcome the issue."""
+The design goal is that all foreseeable exceptions in py4vasp issue an exception of the Py4VaspException class. Any other kind of exception would indicate a bug in the code. If possible the part standard users interact with should not raise any exception, but should give advice on how to overcome the issue.
+"""
 
 
 class Py4VaspError(Exception):

src/py4vasp/raw.py

@@ -1,6 +1,6 @@
 # Copyright © VASP Software GmbH,
 # Licensed under the Apache License 2.0 (http://www.apache.org/licenses/LICENSE-2.0)
-""" Extract the raw data from the HDF5 file and transform it into dataclasses.
+"""Extract the raw data from the HDF5 file and transform it into dataclasses.
 
 In the HDF5 file, the raw data is stored with specific keys. To avoid
 propagating the name of these keys to the higher tier modules, we transform