From fd0b2986f6110823f5f29cfd4ca706c4527c5794 Mon Sep 17 00:00:00 2001
From: Jamie Rowe <jpkrowe@hotmail.co.uk>
Date: Fri, 23 Oct 2026 11:06:09 +0100
Subject: [PATCH] Add CIF format

PR MDAnalysis/mdanalysis#4712 added an mmCIF reader and parser
registered as CIF, CIF.GZ, MMCIF and MMCIF.GZ, which caused the
userguide to fail with KeyError: 'CIF'.

- add a CIF entry to DESCRIPTIONS
- add `.upper` to format dictionary key selection to avoid having to
define entries for cif.gz, mmcif and mmcif.gz
---
 doc/source/scripts/core.py                    |  1 +
 .../scripts/gen_format_overview_classes.py    |  2 +-
 .../test_gen_format_overview_classes.ambr     | 56 +++++++++++++++++++
 3 files changed, 58 insertions(+), 1 deletion(-)

diff --git a/doc/source/scripts/core.py b/doc/source/scripts/core.py
index 9b1455a50..37f2356f8 100644
--- a/doc/source/scripts/core.py
+++ b/doc/source/scripts/core.py
@@ -4,6 +4,7 @@
 
 DESCRIPTIONS = {
     "CHEMFILES": "use readers from `chemfiles <https://chemfiles.org/>`_ library",
+    "CIF": "PDBx/mmCIF file",
     "CRD": "CHARMM CARD file",
     "CONFIG": "DL_Poly CONFIG file",
     "COOR": "NAMD binary restart file",
diff --git a/doc/source/scripts/gen_format_overview_classes.py b/doc/source/scripts/gen_format_overview_classes.py
index e733f0a9b..25b173223 100644
--- a/doc/source/scripts/gen_format_overview_classes.py
+++ b/doc/source/scripts/gen_format_overview_classes.py
@@ -46,7 +46,7 @@ def _create_key(fmt: str, handlers: dict[HANDLER_T, Type[Any]]) -> str:
     if fmt in DESCRIPTIONS:
         key = fmt
     else:
-        key = list(handlers.values())[0].format[0]
+        key = list(handlers.values())[0].format[0].upper()
 
         # raise an informative error
         if key not in DESCRIPTIONS:
diff --git a/doc/source/scripts/tests/snapshot/__snapshots__/test_gen_format_overview_classes.ambr b/doc/source/scripts/tests/snapshot/__snapshots__/test_gen_format_overview_classes.ambr
index e9bd3e623..e49e1c26b 100644
--- a/doc/source/scripts/tests/snapshot/__snapshots__/test_gen_format_overview_classes.ambr
+++ b/doc/source/scripts/tests/snapshot/__snapshots__/test_gen_format_overview_classes.ambr
@@ -13,6 +13,18 @@
       '',
       '',
     ]),
+    list([
+      ':ref:`CIF <CIF-format>`',
+      'PDBx/mmCIF file',
+      '',
+      '',
+    ]),
+    list([
+      ':ref:`CIF.GZ <CIF-format>`',
+      'PDBx/mmCIF file',
+      '',
+      '',
+    ]),
     list([
       ':ref:`CONFIG <CONFIG-format>`',
       'DL_Poly CONFIG file',
@@ -133,6 +145,18 @@
       '',
       '',
     ]),
+    list([
+      ':ref:`MMCIF <CIF-format>`',
+      'PDBx/mmCIF file',
+      '',
+      '',
+    ]),
+    list([
+      ':ref:`MMCIF.GZ <CIF-format>`',
+      'PDBx/mmCIF file',
+      '',
+      '',
+    ]),
     list([
       ':ref:`MMTF <MMTF-format>`',
       'MMTF file',
@@ -291,6 +315,22 @@
       '✓',
       '✓',
     ]),
+    list([
+      ':ref:`CIF <CIF-format>`',
+      'PDBx/mmCIF file',
+      '✓',
+      '✓',
+      '✓',
+      '',
+    ]),
+    list([
+      ':ref:`CIF.GZ <CIF-format>`',
+      'PDBx/mmCIF file',
+      '✓',
+      '✓',
+      '✓',
+      '',
+    ]),
     list([
       ':ref:`CONFIG <CONFIG-format>`',
       'DL_Poly CONFIG file',
@@ -459,6 +499,22 @@
       '✓',
       '',
     ]),
+    list([
+      ':ref:`MMCIF <CIF-format>`',
+      'PDBx/mmCIF file',
+      '✓',
+      '✓',
+      '✓',
+      '',
+    ]),
+    list([
+      ':ref:`MMCIF.GZ <CIF-format>`',
+      'PDBx/mmCIF file',
+      '✓',
+      '✓',
+      '✓',
+      '',
+    ]),
     list([
       ':ref:`MMTF <MMTF-format>`',
       'MMTF file',