Merge branch 'release/0.0.8'

.github/workflows/constraints.txt

@@ -1,4 +1,4 @@
-pip==23.3.1
+pip==23.3.2
 nox==2023.4.22
 nox-poetry==1.0.3
 poetry==1.7.1

.github/workflows/tests.yml

@@ -43,24 +43,6 @@ jobs:
           pipx install --pip-args=--constraint=.github/workflows/constraints.txt poetry
           poetry --version
 
-      - name: Install System Dependencies (Ubuntu)
-        if: startsWith(matrix.os, 'ubuntu') && (matrix.session == 'no')
-        run: |
-          sudo apt-get update
-          sudo apt-get install -y python3-dev python3-setuptools python3-scipy python3-matplotlib python3-pytest python3-sympy g++ build-essential gfortran libopenblas-dev liblapack-dev libmumps-scotch-dev
-
-      - name: Install Python dependencies (Ubuntu)
-        if: startsWith(matrix.os, 'ubuntu') && (matrix.session == 'no')
-        run: |
-          python -m pip install cython tinyarray
-
-      - name: Clone and Install kwant (Ubuntu)
-        if: startsWith(matrix.os, 'ubuntu') && (matrix.session == 'no')
-        run: |
-          git clone https://github.com/kwant-project/kwant.git
-          cd kwant
-          git checkout master
-
       - name: Install Nox
         run: |
           pipx install --pip-args=--constraint=.github/workflows/constraints.txt nox

README.md

@@ -32,15 +32,44 @@ KPM Tools is an open-source Python package that extends the Kernel Polynomial Me
 ## Requirements
 
 - Python >=3.9
+- Kwant >= 1.4.4
 
 ## Installation
 
+### Installing KPM Tools
+
 You can install _KPM Tools_ via [pip] from [PyPI]:
 
 ```console
 $ pip install kpm-tools
 ```
 
+### Important Note on Kwant Dependency
+
+While _KPM Tools_ requires Kwant to function, direct installation of Kwant via pip can sometimes be problematic due to its specific build requirements. To ensure a smooth setup, we recommend the following installation approach:
+
+1. **Try installing with pip (optional):**
+
+   You can attempt to install Kwant along with KPM Tools via pip:
+
+   ```console
+   $ pip install kpm-tools[kwant]
+   ```
+
+   If this installation fails, proceed to the next step.
+
+2. **Install Kwant using Conda or follow Kwant's installation guide:**
+
+   We recommend using Conda to install Kwant, which typically handles its build requirements more reliably:
+
+   ```console
+   $ conda install -c conda-forge kwant
+   ```
+
+   Alternatively, refer to the [Kwant installation page](https://kwant-project.org/install) for detailed instructions on installing Kwant in different environments.
+
+After installing Kwant, you can then install KPM Tools using pip as shown above.
+
 ## Python API
 
 Please see the [python api reference] for details.

noxfile.py

@@ -112,8 +112,8 @@ def activate_virtualenv_in_precommit_hooks(session: Session) -> None:
 
 @nox.session(python=python_versions)
 def install_kwant(session: Session):
-    """Install kwant from source."""
-    session.install("cython", "numpy", "scipy", "sympy", "tinyarray", "kwant")
+    """Install kwant from PyPi."""
+    session.install("kwant")
 
 
 @nox.session(python=python_versions)
@@ -146,8 +146,8 @@ def build_kwant(session: Session):
     # Navigate to the cloned directory
     session.cd(str(kwant_dir))
 
-    # Checkout the master branch
-    session.run("git", "checkout", "master", external=True)
+    # Checkout the stable branch
+    session.run("git", "checkout", "stable", external=True)
 
     # Install kwant from source
     if need_to_build:

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "kpm-tools"
-version = "0.0.7"
+version = "0.0.8"
 description = "KPM Tools"
 authors = ["Pablo Piskunow <[email protected]>"]
 license = "BSD 2-Clause"
@@ -51,6 +51,10 @@ sphinx-click = ">=3.0.2"
 typeguard = ">=2.13.3"
 xdoctest = {extras = ["colors"], version = ">=0.15.10"}
 myst-parser = {version = ">=0.16.1"}
+kwant = { version = "^1.4.4", optional = true }
+
+[tool.poetry.extras]
+kwant = ["kwant"]
 
 [tool.poetry.scripts]
 kpm-tools = "kpm_tools.__main__:main"

src/kpm_tools/__init__.py

@@ -1,5 +1,12 @@
 """KPM Tools."""
 # flake8: noqa
+try:
+    import kwant
+except ImportError:
+    raise ImportError(
+        "Missing dependency 'kwant'. Please install it manually. "
+        "Visit https://kwant-project.org/ for installation instructions."
+    )
 from .bloch import _hopping_distance
 from .bloch import separate_bloch_components
 from .bloch import wrap_distance

src/kpm_tools/bloch.py

@@ -6,20 +6,24 @@
 import collections
 import inspect
 import warnings
+from functools import cache
 
+import kwant.system
 import numpy as np
 import tinyarray as ta
-from kwant._common import get_parameters
-from kwant._common import memoize
 from kwant.builder import Builder
+from kwant.builder import HermConjOfFunc
 from kwant.builder import herm_conj
 from kwant.lattice import TranslationalSymmetry
-from kwant.system import SiteArray
 from kwant.wraparound import WrappedBuilder
-from kwant.wraparound import _callable_herm_conj
 from kwant.wraparound import _set_signature
 from kwant.wraparound import wraparound
 
+from .utils import get_parameters
+
+
+support_site_array = hasattr(kwant.system, "SiteArray")
+
 
 def wraparound_by_parts(
     builder, keep=None, *, coordinate_names="xyz", separate_sites=False
@@ -55,7 +59,12 @@ def wraparound_by_parts(
 
     """
 
-    @memoize
+    @cache
+    def _callable_herm_conj(val):
+        """Keep the same id for every 'val'."""
+        return HermConjOfFunc(val)
+
+    @cache
     def bind_site(val):
         def f(*args):
             a, *args = args
@@ -66,7 +75,7 @@ def f(*args):
         _set_signature(f, get_parameters(val) + momenta)
         return f
 
-    @memoize
+    @cache
     def bind_hopping_as_site(elem, val):
         def f(*args):
             a, *args = args
@@ -81,7 +90,7 @@ def f(*args):
         _set_signature(f, params + momenta)
         return f
 
-    @memoize
+    @cache
     def bind_hopping(elem, val):
         def f(*args):
             a, b, *args = args
@@ -95,7 +104,7 @@ def f(*args):
         _set_signature(f, params + momenta)
         return f
 
-    @memoize
+    @cache
     def bind_sum(num_sites, *vals):
         """Construct joint signature for all 'vals'."""
 
@@ -203,7 +212,8 @@ def f(*in_args):
     ret.particle_hole = None
     ret.time_reversal = None
 
-    ret.vectorize = builder.vectorize
+    if hasattr(builder, "vectorize"):
+        ret.vectorize = builder.vectorize
 
     sites = {}
     hops = collections.defaultdict(list)
@@ -340,21 +350,36 @@ def separate_bloch_components(builder):
     return fsyst_bloch_superonsite, fsyst_bloch_superhopping
 
 
+def _get_positions(site):
+    """Extract positions from a site. Handles both Site and SiteArray.
+
+    Args:
+    - site (Any): A Site or SiteArray object.
+
+    Returns:
+    - np.ndarray: Position array.
+    """
+    if hasattr(site, "positions"):  # Handle SiteArray
+        return site.positions().transpose()
+    if hasattr(site, "pos"):  # Handle Site
+        return site.pos
+    else:
+        raise TypeError("The site object does not have a valid position attribute.")
+
+
 def _hopping_distance(site1, site2, direction):
     norbs = site1.family.norbs
     if norbs != site2.family.norbs:
         raise NotImplementedError(
             "Only hopppings between sites of equal number of orbitals is implemented."
         )
 
-    if isinstance(site1, SiteArray):
-        pos1 = site1.positions().transpose()
-        pos2 = site2.positions().transpose()
-        d = np.dot(direction, (pos1 - pos2))[:, np.newaxis, np.newaxis]
-    else:
-        pos1 = site1.pos
-        pos2 = site2.pos
-        d = np.dot(direction, (pos1 - pos2))
+    pos1 = _get_positions(site1)
+    pos2 = _get_positions(site2)
+    d = np.dot(direction, (pos1 - pos2))
+
+    if support_site_array and hasattr(site1, "positions"):
+        d = d[:, np.newaxis, np.newaxis]
 
     # return an imaginary number so that the matrix is antisymmetric
     # but hermitian
@@ -376,7 +401,7 @@ def wrap_velocity(builder):
     direction = ("direction",)
     dnp = -len(direction)
 
-    @memoize
+    @cache
     def bind_velocity_hopping(val):
         def f(*args):
             a, b, *args = args  # first two args are sites
@@ -392,7 +417,10 @@ def f(*args):
         _set_signature(f, params + direction)
         return f
 
-    velocity_builder = Builder(builder.symmetry, vectorize=builder.vectorize)
+    if hasattr(builder, "vectorize"):
+        velocity_builder = Builder(builder.symmetry, vectorize=builder.vectorize)
+    else:
+        velocity_builder = Builder(builder.symmetry)
 
     for s in builder.sites():
         norbs = s.family.norbs
@@ -419,7 +447,10 @@ def wrap_distance(builder):
     Hamiltonian of the original system, and does not depends on the
     paramters of the original system, the 'builder'.
     """
-    distance_builder = Builder(builder.symmetry, vectorize=builder.vectorize)
+    if hasattr(builder, "vectorize"):
+        distance_builder = Builder(builder.symmetry, vectorize=builder.vectorize)
+    else:
+        distance_builder = Builder(builder.symmetry)
 
     for s in builder.sites():
         norbs = s.family.norbs

src/kpm_tools/hamiltonians.py

@@ -6,7 +6,7 @@
 
 import kwant
 import numpy as np
-from kwant import HoppingKind
+from kwant.builder import HoppingKind
 
 
 # neighbors for honeycomb lattice

src/kpm_tools/kpm_generator.py

@@ -14,6 +14,7 @@
 from scipy.sparse.linalg import eigsh
 
 from .common import identity_operator
+from .utils import ensure_rng
 
 
 DEFAULT_MOMENTS = 100
@@ -245,7 +246,7 @@ def __init__(
         self.operator = _normalize_operator(operator, params)
 
         self.mean = mean
-        rng0 = kwant._common.ensure_rng(rng)
+        rng0 = ensure_rng(rng)
 
         _v0 = None
         if bounds is None:

src/kpm_tools/tiles.py

@@ -4,7 +4,8 @@
 
 import kwant
 import numpy as np
-from kwant._common import ensure_rng
+
+from .utils import ensure_rng
 
 
 def momentum_to_ts(k, ts):