Merge pull request #33 from bpuchala/2.X_enumerate_superlattices_shape

Various for 2.0a9

.github/workflows/build_wheels.yml

@@ -8,42 +8,42 @@ jobs:
     runs-on: ubuntu-22.04
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Build wheels
         uses: pypa/[email protected]
         env:
           CIBW_ARCHS_LINUX: x86_64
 
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
-          name: dist
+          name: dist_linux
           path: ./wheelhouse/*.whl
 
   build_wheels_macos_x86_64:
     name: Build x86_64 wheels on macos-12
     runs-on: macos-12
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Build wheels
         uses: pypa/[email protected]
         env:
           CIBW_ARCHS_MACOS: x86_64
 
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
-          name: dist
+          name: dist_macos
           path: ./wheelhouse/*.whl
 
   build_sdist:
     name: Build sdist
     runs-on: ubuntu-latest
     timeout-minutes: 60
     steps:
-      - uses: actions/checkout@v3
-      - uses: actions/setup-python@v4
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: '3.11'
 
@@ -60,7 +60,7 @@ jobs:
 
       - name: upload sdist
         if: always()
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
-          name: dist
+          name: dist_sdist
           path: dist/*.tar.gz

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

@@ -14,8 +14,8 @@ jobs:
     runs-on: ubuntu-latest
     timeout-minutes: 60
     steps:
-      - uses: actions/checkout@v3
-      - uses: actions/setup-python@v4
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: '3.11'
 
@@ -29,7 +29,7 @@ jobs:
       ### libcasm-global ###
       - name: restore libcasm-global cache
         id: cache-libcasm-global-restore
-        uses: actions/cache/restore@v3
+        uses: actions/cache/restore@v4
         with:
           path: CASMcode_global/dist
           key: ${{ runner.os }}-libcasm-global-v2-0-3

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

@@ -14,8 +14,8 @@ jobs:
     runs-on: ubuntu-latest
     timeout-minutes: 60
     steps:
-      - uses: actions/checkout@v3
-      - uses: actions/setup-python@v4
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: '3.11'
 
@@ -29,7 +29,7 @@ jobs:
       ### libcasm-global ###
       - name: restore libcasm-global cache
         id: cache-libcasm-global-restore
-        uses: actions/cache/restore@v3
+        uses: actions/cache/restore@v4
         with:
           path: CASMcode_global/dist
           key: ${{ runner.os }}-libcasm-global-v2-0-3
@@ -79,7 +79,7 @@ jobs:
 
       - name: upload test log
         if: always()
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: libcasm-xtal-cxx-test-log
           path: build_cxx_test/Testing/Temporary/LastTest.log

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

@@ -8,7 +8,7 @@ jobs:
     runs-on: ubuntu-latest
     timeout-minutes: 60
     steps:
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: '3.11'
 
@@ -21,14 +21,14 @@ jobs:
       ### libcasm-global ###
       - name: restore libcasm-global cache
         id: cache-libcasm-global-restore
-        uses: actions/cache/restore@v3
+        uses: actions/cache/restore@v4
         with:
           path: CASMcode_global/dist
           key: ${{ runner.os }}-libcasm-global-v2-0-3
 
       - name: checkout libcasm-global
         if: steps.cache-libcasm-global-restore.outputs.cache-hit != 'true'
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           repository: prisms-center/CASMcode_global
           path: CASMcode_global
@@ -47,7 +47,7 @@ jobs:
 
       - name: save libcasm-global cache
         id: cache-libcasm-global-save
-        uses: actions/cache/save@v3
+        uses: actions/cache/save@v4
         with:
           path: CASMcode_global/dist
           key: ${{ steps.cache-libcasm-global-restore.outputs.cache-primary-key }}

.github/workflows/test-linux.yml

@@ -14,8 +14,8 @@ jobs:
     runs-on: ubuntu-latest
     timeout-minutes: 60
     steps:
-      - uses: actions/checkout@v3
-      - uses: actions/setup-python@v4
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: '3.11'
 
@@ -29,7 +29,7 @@ jobs:
       ### libcasm-global ###
       - name: restore libcasm-global cache
         id: cache-libcasm-global-restore
-        uses: actions/cache/restore@v3
+        uses: actions/cache/restore@v4
         with:
           path: CASMcode_global/dist
           key: ${{ runner.os }}-libcasm-global-v2-0-3
@@ -62,7 +62,7 @@ jobs:
 
       - name: upload docs
         if: always()
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: libcasm-xtal-docs
           path: python/doc/_build/html

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

@@ -7,8 +7,8 @@ jobs:
     runs-on: macOS-latest
     timeout-minutes: 60
     steps:
-      - uses: actions/checkout@v3
-      - uses: actions/setup-python@v4
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: '3.11'
 
@@ -36,7 +36,7 @@ jobs:
 
       - name: upload libcasm-xtal-macos-latest-x86_64-dist
         if: always()
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: libcasm-xtal-macos-latest-x86_64-dist
           path: dist

.github/workflows/test-macos.yml

@@ -7,8 +7,8 @@ jobs:
     runs-on: macOS-latest
     timeout-minutes: 60
     steps:
-      - uses: actions/checkout@v3
-      - uses: actions/setup-python@v4
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: '3.11'
 

CHANGELOG.md

@@ -6,11 +6,12 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
 
-## [2.0a9] - X
+## [2.0a9] - Unreleased
 
 ### Fixed
 
 - 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
 
@@ -20,10 +21,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Added
 
-- Add to libcasm.xtal: make_primitive_prim (equivalent to current make_primitive), make_primtive_structure, and make_canonical_structure. 
+- Add to libcasm.xtal: make_primitive_prim (equivalent to current make_primitive), make_primitive_structure, and make_canonical_structure. 
 - Add options to the BCC and FCC structure factory functions in libcasm.xtal.structures to make the conventional cubic unit cells.
 - Add to libcasm.xtal: StructureAtomInfo namedtuple, and methods sort_structure_by_atom_info, sort_structure_by_atom_type, sort_structure_by_atom_coordinate_frac, and sort_structure_by_atom_coordinate_cart
 - Add to libcasm.xtal: substitute_structure_species 
+- 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.
+
 
 ## [2.0a8] - 2023-11-15
 

include/casm/crystallography/Lattice.hh

@@ -33,15 +33,17 @@ class Lattice : public Comparisons<CRTPBase<Lattice>> {
 
   Lattice(Eigen::Ref<const Eigen::Vector3d> const &vec1,
           Eigen::Ref<const Eigen::Vector3d> const &vec2,
-          Eigen::Ref<const Eigen::Vector3d> const &vec3, double xtal_tol = TOL,
-          bool force = false);
+          Eigen::Ref<const Eigen::Vector3d> const &vec3, double xtal_tol = TOL);
 
   /// Construct Lattice from a matrix of lattice vectors, where lattice vectors
   /// are columns
   ///(e.g., lat_mat is equivalent to coord_trans[FRAC])
   Lattice(Eigen::Ref<const Eigen::Matrix3d> const &lat_mat =
               Eigen::Matrix3d::Identity(),
-          double xtal_tol = TOL, bool force = false);
+          double xtal_tol = TOL);
+
+  static Lattice from_lengths_and_angles(std::vector<double> lengths_and_angles,
+                                         double xtal_tol = TOL);
 
   /// \brief Construct FCC primitive cell of unit volume
   static Lattice fcc(double tol = TOL);

python/doc/conf.py

@@ -1,3 +1,18 @@
+import os
+
+# -- 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.
+project_desc = "CASM Crystallography"
+logo_text = "libcasm-xtal"
+github_url = "https://github.com/prisms-center/CASMcode_crystallography/"
+pypi_url = "https://pypi.org/project/libcasm-xtal/"
+intersphinx_libcasm_packages = [("global", "2.0"), ("configuration", "2.0")]
+
+
+# -- CASM common configuration ---
+
 # -*- coding: utf-8 -*-
 #
 # CASM documentation build configuration file, created by
@@ -12,7 +27,6 @@
 # All configuration values have a default; values that are commented out
 # serve to show the default.
 
-import os
 
 # -- General configuration ------------------------------------------------
 
@@ -35,8 +49,7 @@
 
 # if LIBCASM_LOCAL_PYDOCS env variable is set, create local docs
 pydocs_path = os.environ.get("LIBCASM_LOCAL_PYDOCS", None)
-packages = [("global", "2.0"), ("configuration", "2.0")]
-for package, vers in packages:
+for package, vers in intersphinx_libcasm_packages:
     if pydocs_path is None:
         url = (
             f"https://prisms-center.github.io/CASMcode_pydocs/libcasm/{package}/{vers}/"
@@ -87,18 +100,14 @@
 master_doc = "index"
 
 # General information about the project.
-project = "libcasm-xtal"
 copyright = "2023, CASM Developers"
 author = "CASM Developers"
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 #
-# The short X.Y version.
-version = "2.0"
-# The full version, including alpha/beta/rc tags.
-release = "2.0a8"
+
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -132,12 +141,29 @@
 html_logo = "_static/small_logo.svg"
 html_theme_options = {
     "logo": {
-        "text": "libcasm-xtal",
+        "text": logo_text,
         "image_light": "_static/small_logo.svg",
         "image_dark": "_static/small_logo_dark.svg",
     },
     "pygment_light_style": "xcode",
     "pygment_dark_style": "lightbulb",
+    "icon_links": [
+        {
+            # Label for this link
+            "name": "GitHub",
+            "url": github_url,  # required
+            "icon": "fa-brands fa-github",
+            "type": "fontawesome",
+        },
+        {
+            # Label for this link
+            "name": "PyPI",
+            "url": pypi_url,  # required
+            "icon": "fa-brands fa-python",
+            "type": "fontawesome",
+        },
+    ],
+    # "primary_sidebar_end": ["primary_sidebar_end"]
 }
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
@@ -192,8 +218,8 @@
 latex_documents = [
     (
         master_doc,
-        "libcasm-xtal.tex",
-        "libcasm-xtal Documentation",
+        f"{project}.tex",
+        f"{project} Documentation",
         "CASM Developers",
         "manual",
     ),
@@ -203,7 +229,7 @@
 
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
-man_pages = [(master_doc, "libcasm-xtal", "libcasm-xtal Documentation", [author], 1)]
+man_pages = [(master_doc, f"{project}", f"{project} Documentation", [author], 1)]
 
 # -- Options for Texinfo output -------------------------------------------
 
@@ -213,11 +239,11 @@
 texinfo_documents = [
     (
         master_doc,
-        "libcasm-xtal",
-        "libcasm-xtal Documentation",
+        f"{project}",
+        f"{project} Documentation",
         author,
-        "libcasm-xtal",
-        "CASM Crystallography",
+        f"{project}",
+        project_desc,
         "Miscellaneous",
     ),
 ]

python/doc/index.rst

@@ -24,7 +24,7 @@ The libcasm-xtal package is the CASM crystallography module. This includes:
 About CASM
 ==========
 
-The libcasm-global package is part of the CASM_ open source software package, which is designed to perform first-principles statistical mechanical studies of multi-component crystalline solids.
+The libcasm-xtal package is part of the CASM_ open source software package, which is designed to perform first-principles statistical mechanical studies of multi-component crystalline solids.
 
 CASM is developed by the Van der Ven group, originally at the University of Michigan and currently at the University of California Santa Barbara.
 

python/doc/reference/libcasm/index.rst

@@ -1,8 +1,8 @@
 ..
     DO NOT DELETE! This causes _autosummary to generate stub files
 
-libcasm.xtal module
-===================
+Reference (libcasm-xtal)
+========================
 
 .. autosummary::
     :toctree: _autosummary