From 7331d0461dfd01293287c7979704edd673c13420 Mon Sep 17 00:00:00 2001
From: janbridley <bradleyjenj@gmail.com>
Date: Wed, 15 Jan 2025 21:58:00 -0500
Subject: [PATCH] Rename cell to box

---
 doc/source/quickstart.rst |  4 ++--
 parsnip/parsnip.py        | 12 ++++++------
 tests/test_patterns.py    | 11 +++++++++--
 3 files changed, 17 insertions(+), 10 deletions(-)

diff --git a/doc/source/quickstart.rst b/doc/source/quickstart.rst
index 1baae62..f79f00f 100644
--- a/doc/source/quickstart.rst
+++ b/doc/source/quickstart.rst
@@ -159,8 +159,8 @@ Once `freud`_ is installed, crystal structures can be easily replicated!
 .. doctest-requires:: freud
 
     >>> import freud
-    >>> box = freud.Box(*cif.cell)
+    >>> box = freud.Box(*cif.box)
     >>> uc = freud.data.UnitCell(box, basis_positions=pos)
     >>> box, pos = uc.generate_system(num_replicas=2)
     >>> assert len(pos) == 4 * 2**3
-    >>> np.testing.assert_allclose(box.L / 2, cif.cell[:3], atol=1e-15)
+    >>> np.testing.assert_allclose(box.L / 2, 3.6, atol=1e-15)
diff --git a/parsnip/parsnip.py b/parsnip/parsnip.py
index 12cb3b2..616a1fb 100644
--- a/parsnip/parsnip.py
+++ b/parsnip/parsnip.py
@@ -526,7 +526,7 @@ def cast_values(self, cast: bool):
         self._cast_values = cast
 
     @property
-    def cell(self):
+    def box(self):
         """Read the unit cell as a `freud`_ or HOOMD `box-like`_ object.
 
         .. _`box-like`: https://hoomd-blue.readthedocs.io/en/v5.0.0/hoomd/module-box.html#hoomd.box.box_like
@@ -534,7 +534,7 @@ def cell(self):
 
         .. important::
 
-            ``cif.cell`` returns box extents and tilt factors, while
+            ``cif.box`` returns box extents and tilt factors, while
             ``CifFile.read_cell_params`` returns unit cell vector lengths and angles.
             See the `box-like`_ documentation linked above for more details.
 
@@ -542,13 +542,13 @@ def cell(self):
         -------
         This method provides a convinient interface to create box objects.
 
-        >>> cell = cif.cell
-        >>> print(cell)
+        >>> box = cif.box
+        >>> print(box)
         (3.6, 3.6, 3.6, 0.0, 0.0, 0.0)
         >>> import freud, hoomd # doctest: +SKIP
-        >>> freud.Box(*cell) # doctest: +SKIP
+        >>> freud.Box(*box) # doctest: +SKIP
         freud.box.Box(Lx=3.6, Ly=3.6, Lz=3.6, xy=0, xz=0, yz=0, ...)
-        >>> hoomd.Box(*cell) # doctest: +SKIP
+        >>> hoomd.Box(*box) # doctest: +SKIP
         hoomd.box.Box(Lx=3.6, Ly=3.6, Lz=3.6, xy=0.0, xz=0.0, yz=0.0)
 
 
diff --git a/tests/test_patterns.py b/tests/test_patterns.py
index d656a7d..f941e70 100644
--- a/tests/test_patterns.py
+++ b/tests/test_patterns.py
@@ -211,9 +211,16 @@ def test_box(cif_data):
     )
 
     freud_box = freud.Box.from_box_lengths_and_angles(*cif_box)
+    freud_box_2 = freud.Box(*cif_data.file.box)
     parsnip_box = _box_from_lengths_and_angles(*cif_box)
 
-    np.testing.assert_allclose(parsnip_box[:3], freud_box.L, atol=1e-12)
+    np.testing.assert_allclose(parsnip_box[:3], freud_box.L, atol=1e-15)
     np.testing.assert_allclose(
-        parsnip_box[3:], [freud_box.xy, freud_box.xz, freud_box.yz], atol=1e-12
+        parsnip_box[3:], [freud_box.xy, freud_box.xz, freud_box.yz], atol=1e-15
     )
+    if "PDB" not in cif_data.filename:
+        np.testing.assert_allclose(
+            [*freud_box.L, freud_box.xy, freud_box.xz, freud_box.yz],
+            [*freud_box_2.L, freud_box_2.xy, freud_box_2.xz, freud_box_2.yz],
+            atol=1e-8,
+        )