Add option to evaluate unit cells symbolically

.github/requirements-3.10.txt

@@ -1,5 +1,5 @@
 # This file was autogenerated by uv via the following command:
-#    uv pip compile --python-version=3.10 pyproject.toml tests/requirements.in
+#    uv --allow-python-downloads pip compile --python-version=3.10 pyproject.toml requirements-sympy.txt tests/requirements.in
 ase==3.24.0
     # via -r tests/requirements.in
 contourpy==1.3.1
@@ -8,19 +8,21 @@ cycler==0.12.1
     # via matplotlib
 exceptiongroup==1.2.2
     # via pytest
-fonttools==4.56.0
+fonttools==4.57.0
     # via matplotlib
-gemmi==0.7.0
+gemmi==0.7.1
     # via -r tests/requirements.in
-iniconfig==2.0.0
+iniconfig==2.1.0
     # via pytest
 kiwisolver==1.4.8
     # via matplotlib
 matplotlib==3.10.1
     # via ase
 more-itertools==10.6.0
     # via parsnip-cif (pyproject.toml)
-numpy==2.2.3
+mpmath==1.3.0
+    # via sympy
+numpy==2.2.4
     # via
     #   parsnip-cif (pyproject.toml)
     #   ase
@@ -39,9 +41,11 @@ pluggy==1.5.0
     # via pytest
 ply==3.11
     # via pycifrw
-pycifrw==4.4.6
+prettytable==3.16.0
+    # via pycifrw
+pycifrw==5.0.1
     # via -r tests/requirements.in
-pyparsing==3.2.1
+pyparsing==3.2.3
     # via matplotlib
 pytest==8.3.5
     # via
@@ -55,5 +59,11 @@ scipy==1.15.2
     # via ase
 six==1.17.0
     # via python-dateutil
+sympy==1.13.3
+    # via
+    #   -r requirements-sympy.txt
+    #   -r tests/requirements.in
 tomli==2.2.1
     # via pytest
+wcwidth==0.2.13
+    # via prettytable

.github/requirements-3.11.txt

@@ -1,24 +1,26 @@
 # This file was autogenerated by uv via the following command:
-#    uv pip compile --python-version=3.11 pyproject.toml tests/requirements.in
+#    uv --allow-python-downloads pip compile --python-version=3.11 pyproject.toml requirements-sympy.txt tests/requirements.in
 ase==3.24.0
     # via -r tests/requirements.in
 contourpy==1.3.1
     # via matplotlib
 cycler==0.12.1
     # via matplotlib
-fonttools==4.56.0
+fonttools==4.57.0
     # via matplotlib
-gemmi==0.7.0
+gemmi==0.7.1
     # via -r tests/requirements.in
-iniconfig==2.0.0
+iniconfig==2.1.0
     # via pytest
 kiwisolver==1.4.8
     # via matplotlib
 matplotlib==3.10.1
     # via ase
 more-itertools==10.6.0
     # via parsnip-cif (pyproject.toml)
-numpy==2.2.3
+mpmath==1.3.0
+    # via sympy
+numpy==2.2.4
     # via
     #   parsnip-cif (pyproject.toml)
     #   ase
@@ -37,9 +39,11 @@ pluggy==1.5.0
     # via pytest
 ply==3.11
     # via pycifrw
-pycifrw==4.4.6
+prettytable==3.16.0
+    # via pycifrw
+pycifrw==5.0.1
     # via -r tests/requirements.in
-pyparsing==3.2.1
+pyparsing==3.2.3
     # via matplotlib
 pytest==8.3.5
     # via
@@ -53,3 +57,9 @@ scipy==1.15.2
     # via ase
 six==1.17.0
     # via python-dateutil
+sympy==1.13.3
+    # via
+    #   -r requirements-sympy.txt
+    #   -r tests/requirements.in
+wcwidth==0.2.13
+    # via prettytable

.github/requirements-3.12.txt

@@ -1,24 +1,26 @@
 # This file was autogenerated by uv via the following command:
-#    uv pip compile --python-version=3.12 pyproject.toml tests/requirements.in
+#    uv --allow-python-downloads pip compile --python-version=3.12 pyproject.toml requirements-sympy.txt tests/requirements.in
 ase==3.24.0
     # via -r tests/requirements.in
 contourpy==1.3.1
     # via matplotlib
 cycler==0.12.1
     # via matplotlib
-fonttools==4.56.0
+fonttools==4.57.0
     # via matplotlib
-gemmi==0.7.0
+gemmi==0.7.1
     # via -r tests/requirements.in
-iniconfig==2.0.0
+iniconfig==2.1.0
     # via pytest
 kiwisolver==1.4.8
     # via matplotlib
 matplotlib==3.10.1
     # via ase
 more-itertools==10.6.0
     # via parsnip-cif (pyproject.toml)
-numpy==2.2.3
+mpmath==1.3.0
+    # via sympy
+numpy==2.2.4
     # via
     #   parsnip-cif (pyproject.toml)
     #   ase
@@ -37,9 +39,11 @@ pluggy==1.5.0
     # via pytest
 ply==3.11
     # via pycifrw
-pycifrw==4.4.6
+prettytable==3.16.0
+    # via pycifrw
+pycifrw==5.0.1
     # via -r tests/requirements.in
-pyparsing==3.2.1
+pyparsing==3.2.3
     # via matplotlib
 pytest==8.3.5
     # via
@@ -53,3 +57,9 @@ scipy==1.15.2
     # via ase
 six==1.17.0
     # via python-dateutil
+sympy==1.13.3
+    # via
+    #   -r requirements-sympy.txt
+    #   -r tests/requirements.in
+wcwidth==0.2.13
+    # via prettytable

.github/requirements-3.13.txt

@@ -1,24 +1,26 @@
 # This file was autogenerated by uv via the following command:
-#    uv pip compile --python-version=3.13 pyproject.toml tests/requirements.in
+#    uv --allow-python-downloads pip compile --python-version=3.13 pyproject.toml requirements-sympy.txt tests/requirements.in
 ase==3.24.0
     # via -r tests/requirements.in
 contourpy==1.3.1
     # via matplotlib
 cycler==0.12.1
     # via matplotlib
-fonttools==4.56.0
+fonttools==4.57.0
     # via matplotlib
-gemmi==0.7.0
+gemmi==0.7.1
     # via -r tests/requirements.in
-iniconfig==2.0.0
+iniconfig==2.1.0
     # via pytest
 kiwisolver==1.4.8
     # via matplotlib
 matplotlib==3.10.1
     # via ase
 more-itertools==10.6.0
     # via parsnip-cif (pyproject.toml)
-numpy==2.2.3
+mpmath==1.3.0
+    # via sympy
+numpy==2.2.4
     # via
     #   parsnip-cif (pyproject.toml)
     #   ase
@@ -37,9 +39,11 @@ pluggy==1.5.0
     # via pytest
 ply==3.11
     # via pycifrw
-pycifrw==4.4.6
+prettytable==3.16.0
+    # via pycifrw
+pycifrw==5.0.1
     # via -r tests/requirements.in
-pyparsing==3.2.1
+pyparsing==3.2.3
     # via matplotlib
 pytest==8.3.5
     # via
@@ -53,3 +57,9 @@ scipy==1.15.2
     # via ase
 six==1.17.0
     # via python-dateutil
+sympy==1.13.3
+    # via
+    #   -r requirements-sympy.txt
+    #   -r tests/requirements.in
+wcwidth==0.2.13
+    # via prettytable

.github/requirements-3.8.txt

@@ -1,5 +1,5 @@
 # This file was autogenerated by uv via the following command:
-#    uv pip compile --python-version=3.8 pyproject.toml tests/requirements.in
+#    uv --allow-python-downloads pip compile --python-version=3.8 pyproject.toml requirements-sympy.txt tests/requirements.in
 ase==3.23.0
     # via -r tests/requirements.in
 contourpy==1.1.1
@@ -8,23 +8,25 @@ cycler==0.12.1
     # via matplotlib
 exceptiongroup==1.2.2
     # via pytest
-fonttools==4.55.3
+fonttools==4.57.0
     # via matplotlib
-gemmi==0.7.0
+gemmi==0.7.1
     # via -r tests/requirements.in
 importlib-resources==6.4.5
     # via matplotlib
-iniconfig==2.0.0
+iniconfig==2.1.0
     # via pytest
 kiwisolver==1.4.7
     # via matplotlib
 matplotlib==3.7.5
     # via ase
 more-itertools==10.5.0
-    # via parsnip (pyproject.toml)
+    # via parsnip-cif (pyproject.toml)
+mpmath==1.3.0
+    # via sympy
 numpy==1.24.4
     # via
-    #   parsnip (pyproject.toml)
+    #   parsnip-cif (pyproject.toml)
     #   ase
     #   contourpy
     #   matplotlib
@@ -41,11 +43,13 @@ pluggy==1.5.0
     # via pytest
 ply==3.11
     # via pycifrw
-pycifrw==4.4.6
+prettytable==3.11.0
+    # via pycifrw
+pycifrw==5.0.1
     # via -r tests/requirements.in
 pyparsing==3.1.4
     # via matplotlib
-pytest==8.3.4
+pytest==8.3.5
     # via
     #   -r tests/requirements.in
     #   pytest-doctestplus
@@ -57,7 +61,13 @@ scipy==1.10.1
     # via ase
 six==1.17.0
     # via python-dateutil
+sympy==1.13.3
+    # via
+    #   -r requirements-sympy.txt
+    #   -r tests/requirements.in
 tomli==2.2.1
     # via pytest
+wcwidth==0.2.13
+    # via prettytable
 zipp==3.20.2
     # via importlib-resources

.github/requirements-3.9.txt

@@ -1,5 +1,5 @@
 # This file was autogenerated by uv via the following command:
-#    uv pip compile --python-version=3.9 pyproject.toml tests/requirements.in
+#    uv --allow-python-downloads pip compile --python-version=3.9 pyproject.toml requirements-sympy.txt tests/requirements.in
 ase==3.24.0
     # via -r tests/requirements.in
 contourpy==1.3.0
@@ -8,20 +8,22 @@ cycler==0.12.1
     # via matplotlib
 exceptiongroup==1.2.2
     # via pytest
-fonttools==4.56.0
+fonttools==4.57.0
     # via matplotlib
-gemmi==0.7.0
+gemmi==0.7.1
     # via -r tests/requirements.in
 importlib-resources==6.5.2
     # via matplotlib
-iniconfig==2.0.0
+iniconfig==2.1.0
     # via pytest
 kiwisolver==1.4.7
     # via matplotlib
 matplotlib==3.9.4
     # via ase
 more-itertools==10.6.0
     # via parsnip-cif (pyproject.toml)
+mpmath==1.3.0
+    # via sympy
 numpy==2.0.2
     # via
     #   parsnip-cif (pyproject.toml)
@@ -41,9 +43,11 @@ pluggy==1.5.0
     # via pytest
 ply==3.11
     # via pycifrw
-pycifrw==4.4.6
+prettytable==3.16.0
+    # via pycifrw
+pycifrw==5.0.1
     # via -r tests/requirements.in
-pyparsing==3.2.1
+pyparsing==3.2.3
     # via matplotlib
 pytest==8.3.5
     # via
@@ -57,7 +61,13 @@ scipy==1.13.1
     # via ase
 six==1.17.0
     # via python-dateutil
+sympy==1.13.3
+    # via
+    #   -r requirements-sympy.txt
+    #   -r tests/requirements.in
 tomli==2.2.1
     # via pytest
+wcwidth==0.2.13
+    # via prettytable
 zipp==3.21.0
     # via importlib-resources

.github/workflows/update-uv-lockfiles.sh

@@ -1,5 +1,5 @@
 #!/bin/bash
 
-for version in 3.{9..13}; do
-    uv pip compile --python-version="$version" pyproject.toml tests/requirements.in > ".github/requirements-$version.txt"
+for version in 3.{8..13}; do
+    uv pip compile --python-version="$version" pyproject.toml requirements-sympy.txt tests/requirements.in > ".github/requirements-$version.txt"
 done

README.rst

@@ -75,7 +75,8 @@ additional dependencies are required to run the tests and build the docs.
 .. code:: bash
 
     pip install .            # Install with no additional dependencies
-    pip install .[tests]     # Install with dependencies required to run tests
+    pip install .[sympy]     # Install with sympy for symbolic unit cell math
+    pip install .[tests]     # Install with dependencies required to run tests (including sympy)
     pip install .[tests,doc] # Install with dependencies required to run tests and make docs
 
 Dependencies

changelog.rst

@@ -10,11 +10,19 @@ v0.X.X - 20XX-XX-XX
 Added
 ~~~~~
 - Additional testpath flag to conftest
+- Symbolic parsing mode for ``build_unit_cell``
+
+Changed
+~~~~~~~
+- ``build_unit_cell`` now uses sympy by default if it is intalled - otherwise, it falls
+  back to the previous variant
 
 Fixed
 ~~~~~
 - Accessing data pairs with ``get_from_pairs`` or ``__getitem__`` now allows for case-insensitive searches
 - Quote-delimited strings containing the delimiting character are now parsed properly
+- ``build_unit_cell`` now rounds coordinates before wrapping into the box, fixing edge cases
+  where boundary atoms were not properly deduplicated
 
 v0.2.1 - 2025-03-12
 -------------------