update repo

.github/workflows/ci.yml

@@ -0,0 +1,78 @@
+name: CI
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  build:
+    name: ${{ matrix.os }} / Python ${{ matrix.python-version }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+        python-version: ["3.10", "3.12"]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install build dependencies (Linux)
+        if: runner.os == 'Linux'
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y gfortran liblapack-dev libblas-dev pkg-config
+
+      - name: Install build dependencies (macOS)
+        if: runner.os == 'macOS'
+        run: |
+          brew install gcc pkg-config
+          # gfortran ships inside the gcc formula
+          echo "FC=$(brew --prefix gcc)/bin/gfortran" >> "$GITHUB_ENV"
+
+      - name: Build and install
+        run: python -m pip install --upgrade pip && python -m pip install '.[test]'
+
+      - name: Check the console scripts are installed
+        run: |
+          csld_main --help
+          cs-fit --help
+          polaron_main --help
+
+      - name: Run tests
+        run: python -m pytest tests -v
+
+  wheel:
+    name: Build wheel
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Install build dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y gfortran liblapack-dev libblas-dev pkg-config
+
+      - name: Build wheel
+        run: |
+          python -m pip install --upgrade pip build
+          python -m build --wheel
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: csld-wheel
+          path: dist/*.whl

.gitignore

@@ -0,0 +1,24 @@
+# build artefacts
+build/
+builddir/
+dist/
+*.egg-info/
+.mesonpy-*/
+
+# compiled objects
+*.so
+*.o
+*.a
+*.mod
+*.pyc
+__pycache__/
+
+# cython/f2py generated sources
+compile/c_util/_c_util.cpp
+*module.c
+*-f2pywrappers2.f90
+.f2py_f2cmap
+
+# tooling
+.pytest_cache/
+.venv/

README.md

@@ -4,12 +4,41 @@ A comprehensive package to study lattice dynamics from first-principles. The int
 Getting Started
 -------------------
 
-To install CSLD, make sure you have Python, C++ and Fortran 90 compilers.
-Then:
+CSLD builds C++ and Fortran extensions, so you need a C++ compiler, a Fortran 90
+compiler and BLAS/LAPACK. Everything else is handled by `pip`.
 
     $ git clone https://github.com/LLNL/csld.git
     $ cd csld
-    $ ./setup.py install --user
+    $ pip install .
+
+### With conda
+
+If you do not have compilers or BLAS/LAPACK available, the bundled environment
+provides them:
+
+    $ conda env create -f environment.yml
+    $ conda activate csld
+    $ pip install .
+
+### With a system toolchain
+
+On Debian/Ubuntu, `sudo apt install gfortran liblapack-dev libblas-dev`; on
+macOS, `brew install gcc lapack`. Then `pip install .` as above. Use
+`pip install --user .` to install without admin rights.
+
+### For development
+
+    $ pip install -e . --no-build-isolation
+
+An editable install serves the Python modules straight from the checkout and
+rebuilds the compiled extensions on import, replacing the old
+`setup.py develop`.
+
+After installing, the `csld_main`, `cs-fit`, `polaron_main` and `phonopy-qha`
+commands are on your `PATH`. To check the install:
+
+    $ pip install '.[test]'
+    $ pytest
 
 Documentation
 ----------------

compile/c_util/_c_util.pyx

@@ -1,3 +1,4 @@
+# cython: language_level=3
 """
 C code for csld, including
 fct_trans

compile/c_util/meson.build

@@ -0,0 +1,20 @@
+# Cython/C++ extension, installed as csld._c_util
+py.extension_module(
+  '_c_util',
+  [
+    '_c_util.pyx',
+    'fct_trans.cpp',
+    'iid-mc.cpp',
+    'intDigits.cpp',
+    'LDCorr.cpp',
+    'LDFFCorr.cpp',
+    'nullspace.cpp',
+    'structure_ordering.cpp',
+  ],
+  override_options: ['cython_language=cpp'],
+  cpp_args: ['-DNDEBUG'],
+  include_directories: [inc_np, include_directories('.')],
+  dependencies: [py_dep],
+  install: true,
+  subdir: 'csld',
+)

compile/f_util/meson.build

@@ -0,0 +1,17 @@
+# f2py extension, installed as csld.f_util
+f_util_gen = custom_target(
+  'f_utilmodule.c',
+  input: ['f_util.f90'],
+  output: ['f_utilmodule.c', 'f_util-f2pywrappers2.f90'],
+  command: [f2py, '@INPUT@', '-m', 'f_util', '--lower', '--build-dir', '@OUTDIR@'],
+)
+
+py.extension_module(
+  'f_util',
+  ['f_util.f90', f_util_gen, fortranobject_c],
+  include_directories: [inc_np, inc_f2py],
+  dependencies: [py_dep],
+  fortran_args: fortran_args,
+  install: true,
+  subdir: 'csld',
+)

csld/analyzer.py

@@ -77,7 +77,7 @@ def get_space_group_symbol(self):
         Returns:
             (str): Spacegroup symbol for structure.
         """
-        return self._space_group_data["international"]
+        return self._space_group_data.international
 
     def get_space_group_number(self):
         """
@@ -86,7 +86,7 @@ def get_space_group_number(self):
         Returns:
             (int): International spacegroup number for structure.
         """
-        return int(self._space_group_data["number"])
+        return int(self._space_group_data.number)
 
     def get_hall(self):
         """
@@ -95,7 +95,7 @@ def get_hall(self):
         Returns:
             (str): Hall symbol
         """
-        return self._space_group_data["hall"]
+        return self._space_group_data.hall
 
     def get_crystal_system(self):
         """
@@ -105,7 +105,7 @@ def get_crystal_system(self):
         Returns:
             (str): Crystal system for structure.
         """
-        n = self._space_group_data["number"]
+        n = self._space_group_data.number
 
         f = lambda i, j: i <= n <= j
         cs = {"triclinic": (1, 2), "monoclinic": (3, 15),
@@ -131,7 +131,7 @@ def get_lattice_type(self):
         Returns:
             (str): Lattice type for structure.
         """
-        n = self._space_group_data["number"]
+        n = self._space_group_data.number
         system = self.get_crystal_system()
         if n in [146, 148, 155, 160, 161, 166, 167]:
             return "rhombohedral"
@@ -142,10 +142,10 @@ def get_lattice_type(self):
 
     def get_symmetry_dataset(self):
         """
-        Returns the symmetry dataset as a dict.
+        Returns the symmetry dataset as returned by spglib.
 
         Returns:
-            (dict): With the following properties:
+            (spglib.SpglibDataset): With the following attributes:
             number: International space group number
             international: International symbol
             hall: Hall symbol
@@ -219,7 +219,7 @@ def get_point_group_symbol(rotations):
         return s[0].strip(), s[1]
 
     def point_group_symbol(self):
-        return SpacegroupAnalyzer.get_point_group_symbol(self._space_group_data["rotations"])
+        return SpacegroupAnalyzer.get_point_group_symbol(self._space_group_data.rotations)
 
     def get_point_group_operations(self):
         """
@@ -254,7 +254,7 @@ def get_symmetrized_structure(self, check_prim=2):
             :class:`SymmetrizedStructure` object.
         """
         return SymmetrizedStructure(self._structure, self.get_spacegroup(),
-                                    self.get_symmetry_dataset()["equivalent_atoms"], self, warn_prim=check_prim)
+                                    self.get_symmetry_dataset().equivalent_atoms, self, warn_prim=check_prim)
 
     def get_refined_structure(self):
         """

csld/basic_lattice_model.py

@@ -14,7 +14,7 @@
 from .atomic_model import AtomicModel
 from .util.mathtool import relativePosition
 from .util.tool import pad_right, matrix2text
-from _c_util import get_structure_ordering
+from csld._c_util import get_structure_ordering
 logger = logging.getLogger(__name__)
 
 
@@ -274,7 +274,7 @@ def translate_cluster_to_supercell(sc, clus):
         coords= clus.frac_coords
         use_compiled_code = True
         if use_compiled_code:
-            from f_util import f_util
+            from csld.f_util import f_util
             allclus= f_util.tr_cl_sc(sc._ijkl.T, sc.sc_mat.T, sc.inv_sc_mat.T, sc.sc_ref.T, sc.prim.frac_coords.T, clus._ijkls_np.T).T-1
         else:
             allclus = [get_structure_ordering((coords+ijk[None,:]).dot(sc.inv_sc_mat), sc.frac_coords,0) for ijk in sc.ijk_ref]