Merge pull request #36 from bpuchala/2.X_atom_info

2.X atom info

.cirrus.yml

@@ -1,6 +1,6 @@
 build_and_store_wheels: &BUILD_AND_STORE_WHEELS
   install_cibuildwheel_script:
-    - python -m pip install cibuildwheel==2.14.1
+    - python -m pip install cibuildwheel==2.17.0
   run_cibuildwheel_script:
     - cibuildwheel
   wheels_artifacts:
@@ -24,11 +24,9 @@ linux_aarch64_task:
 macos_arm64_task:
   name: Build macOS arm64 wheels.
   macos_instance:
-    image: ghcr.io/cirruslabs/macos-monterey-xcode:latest
+    image: ghcr.io/cirruslabs/macos-sonoma-xcode
   env:
-    PATH: /opt/homebrew/opt/[email protected]/bin:$PATH
-    CIBW_ARCHS_MACOS: arm64
+    PATH: /opt/homebrew/opt/[email protected]/libexec/bin:$PATH
   install_pre_requirements_script:
     - brew install [email protected]
-    - ln -s python3 /opt/homebrew/opt/[email protected]/bin/python
   <<: *BUILD_AND_STORE_WHEELS

.github/workflows/test-linux-build.yml

@@ -32,7 +32,7 @@ jobs:
         uses: actions/cache/restore@v4
         with:
           path: CASMcode_global/dist
-          key: ${{ runner.os }}-libcasm-global-v2-0-3
+          key: ${{ runner.os }}-libcasm-global-v2-0-4
 
       - name: Install CASM dependencies
         run: |

.github/workflows/test-linux-cxx-only.yml

@@ -32,7 +32,7 @@ jobs:
         uses: actions/cache/restore@v4
         with:
           path: CASMcode_global/dist
-          key: ${{ runner.os }}-libcasm-global-v2-0-3
+          key: ${{ runner.os }}-libcasm-global-v2-0-4
 
       - name: Install CASM dependencies
         run: |

.github/workflows/test-linux-dependencies.yml

@@ -24,15 +24,15 @@ jobs:
         uses: actions/cache/restore@v4
         with:
           path: CASMcode_global/dist
-          key: ${{ runner.os }}-libcasm-global-v2-0-3
+          key: ${{ runner.os }}-libcasm-global-v2-0-4
 
       - name: checkout libcasm-global
         if: steps.cache-libcasm-global-restore.outputs.cache-hit != 'true'
         uses: actions/checkout@v4
         with:
           repository: prisms-center/CASMcode_global
           path: CASMcode_global
-          ref: v2.0.3
+          ref: v2.0.4
 
       - name: make global
         if: steps.cache-libcasm-global-restore.outputs.cache-hit != 'true'

.github/workflows/test-linux.yml

@@ -32,7 +32,7 @@ jobs:
         uses: actions/cache/restore@v4
         with:
           path: CASMcode_global/dist
-          key: ${{ runner.os }}-libcasm-global-v2-0-3
+          key: ${{ runner.os }}-libcasm-global-v2-0-4
 
       - name: Install CASM dependencies
         run: |

CHANGELOG.md

@@ -12,6 +12,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - Fix CASM::xtal::make_primitive, which was not copying unique_names. This also fixes the output of libcasm.xtal.make_primitive which was losing the occ_dof list as a result.
 - Fix JSON output of xtal::BasicStructure site label
+- Changed pseudoinverse calculation for basis changes to `completeOrthogonalDecomposition().pseudoInverse()`
 
 ### Changed
 
@@ -28,6 +29,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Add to libcasm.xtal.Prim: method labels, constructor parameter `labels`
 - Add to libcasm.xtal.Lattice: methods reciprocal, volume, lengths_and_angles, from_lengths_and_angles
 - Added `unit_cell`, `diagonal_only`, and `fixed_shape` parameters to libcasm.xtal.enumerate_superlattices.
+- Add to libcasm.xtal: combine_structures, filter_structure_by_atom_info, make_structure_atom_info, and make_structure_from_atom_info
 
 
 ## [2.0a8] - 2023-11-15

build_requirements.txt

@@ -4,4 +4,4 @@ scikit-build
 cmake>=3.20
 ninja
 pybind11>=2.6
-libcasm-global>=2.0.2
+libcasm-global>=2.0.4

include/casm/crystallography/DoFSet.hh

@@ -41,11 +41,7 @@ class DoFSet {
     assert(m_basis.rows() ==
            this->traits().dim());  // TODO: This makes sense I think?
     if (basis().cols() > 0 && basis().rows() > 0) {
-      m_inv_basis = basis()
-                        .transpose()
-                        .colPivHouseholderQr()
-                        .solve(Eigen::MatrixXd::Identity(dim(), dim()))
-                        .transpose();
+      m_inv_basis = basis().completeOrthogonalDecomposition().pseudoInverse();
     }
   }
 
@@ -224,11 +220,6 @@ struct SiteDoFSetIsEquivalent_f : private DoFSetIsEquivalent_f {
   }
 };
 
-/// Create the symmtery representation for going from one basis to another
-Eigen::MatrixXd dofset_transformation_matrix(const Eigen::MatrixXd &from_basis,
-                                             const Eigen::MatrixXd &to_basis,
-                                             double tol);
-
 }  // namespace xtal
 }  // namespace CASM
 

pyproject.toml

@@ -6,13 +6,13 @@ requires = [
     "cmake>=3.20",
     "ninja",
     "pybind11>=2.6",
-    "libcasm-global>=2.0.2",
+    "libcasm-global>=2.0.4",
 ]
 build-backend = "setuptools.build_meta"
 
 [project]
 name = "libcasm-xtal"
-version = "2.0a8"
+version = "2.0a9"
 authors = [
   { name="CASM developers", email="[email protected]" },
 ]
@@ -28,7 +28,7 @@ classifiers = [
     "Topic :: Scientific/Engineering",
 ]
 dependencies = [
-  "libcasm-global>=2.0.2",
+  "libcasm-global>=2.0.4",
   "numpy",
 ]
 
@@ -51,13 +51,13 @@ select = ["E", "F", "I"]
 known-first-party = ["libcasm", "casm"]
 
 [tool.cibuildwheel]
-# Build for python3.9, 3.10, 3.11
-build = "cp39-* cp310-* cp311-*"
+# Build for python3.9, 3.10, 3.11, 3.12
+build = "cp39-* cp310-* cp311-* cp312-*"
 # Build for cpython only
 skip =  "pp*"
 
 # Need libcasm-global at wheel repair stage
-before-build = "pip install libcasm-global>=2.0.2"
+before-build = "pip install libcasm-global>=2.0.4"
 
 # Testing
 test-requires = "pytest pytest-datadir"

python/doc/conf.py

@@ -3,7 +3,7 @@
 # -- package specific configuration --
 project = "libcasm-xtal"
 version = "2.0"  # The short X.Y version.
-release = "2.0a8"  # The full version, including alpha/beta/rc tags.
+release = "2.0a9"  # The full version, including alpha/beta/rc tags.
 project_desc = "CASM Crystallography"
 logo_text = "libcasm-xtal"
 github_url = "https://github.com/prisms-center/CASMcode_crystallography/"

python/libcasm/xtal/__init__.py

@@ -1,10 +1,14 @@
 """CASM Crystallography"""
 from ._methods import (
     StructureAtomInfo,
+    combine_structures,
+    filter_structure_by_atom_info,
     make_canonical,
     make_crystal_point_group,
     make_factor_group,
     make_primitive,
+    make_structure_atom_info,
+    make_structure_from_atom_info,
     make_within,
     sort_structure_by_atom_coordinate_cart,
     sort_structure_by_atom_coordinate_frac,