From 6c4eed79ad0bd4d9eda1b2c30ecc28256ff255a6 Mon Sep 17 00:00:00 2001
From: Lily Wang <lily@mdanalysis.org>
Date: Fri, 9 May 2025 15:11:34 -0400
Subject: [PATCH 1/3] update lammps class

---
 doc/source/scripts/gen_topologyparser_attrs.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/doc/source/scripts/gen_topologyparser_attrs.py b/doc/source/scripts/gen_topologyparser_attrs.py
index ebeefbe76..f458fa8a3 100755
--- a/doc/source/scripts/gen_topologyparser_attrs.py
+++ b/doc/source/scripts/gen_topologyparser_attrs.py
@@ -26,7 +26,7 @@
 from MDAnalysisTests.topology.test_gro import TestGROParser
 from MDAnalysisTests.topology.test_gsd import TestGSDParser
 from MDAnalysisTests.topology.test_hoomdxml import TestHoomdXMLParser
-from MDAnalysisTests.topology.test_lammpsdata import LammpsBase, TestDumpParser
+from MDAnalysisTests.topology.test_lammpsdata import LammpsBase, TestDumpParserFull
 from MDAnalysisTests.topology.test_mmtf import TestMMTFParser
 from MDAnalysisTests.topology.test_mol2 import TestMOL2Base
 from MDAnalysisTests.topology.test_pdb import TestPDBParser
@@ -61,7 +61,7 @@
     TestTXYZParser,
     TestXPDBParser,
     XYZBase,
-    TestDumpParser,
+    TestDumpParserFull,
 )
 
 

From e25453bcc49712c3f6892096104044711352728d Mon Sep 17 00:00:00 2001
From: Oliver Beckstein <orbeckst@gmail.com>
Date: Mon, 14 Jul 2025 16:37:44 -0700
Subject: [PATCH 2/3] updated syrupy snapshots

---
 .../__snapshots__/test_gen_topologyparser_attrs.ambr      | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/doc/source/scripts/tests/snapshot/__snapshots__/test_gen_topologyparser_attrs.ambr b/doc/source/scripts/tests/snapshot/__snapshots__/test_gen_topologyparser_attrs.ambr
index 8b46763af..55f18b3a4 100644
--- a/doc/source/scripts/tests/snapshot/__snapshots__/test_gen_topologyparser_attrs.ambr
+++ b/doc/source/scripts/tests/snapshot/__snapshots__/test_gen_topologyparser_attrs.ambr
@@ -71,7 +71,7 @@
       'charge',
       'charges',
       'partial atomic charge',
-      ':ref:`DATA <DATA-format>`, :ref:`DMS <DMS-format>`, :ref:`GSD <GSD-format>`, :ref:`MMTF <MMTF-format>`, :ref:`MOL2 <MOL2-format>`, :ref:`PDBQT <PDBQT-format>`, :ref:`PQR <PQR-format>`, :ref:`PSF <PSF-format>`, :ref:`TOP, PRMTOP, PARM7 <TOP-format>`, :ref:`TPR <TPR-format>`, :ref:`XML <XML-format>`',
+      ':ref:`DATA <DATA-format>`, :ref:`DMS <DMS-format>`, :ref:`GSD <GSD-format>`, :ref:`LAMMPSDUMP <LAMMPSDUMP-format>`, :ref:`MMTF <MMTF-format>`, :ref:`MOL2 <MOL2-format>`, :ref:`PDBQT <PDBQT-format>`, :ref:`PQR <PQR-format>`, :ref:`PSF <PSF-format>`, :ref:`TOP, PRMTOP, PARM7 <TOP-format>`, :ref:`TPR <TPR-format>`, :ref:`XML <XML-format>`',
     ]),
     list([
       'chargegroup',
@@ -101,7 +101,7 @@
       'element',
       'elements',
       'atom element',
-      ':ref:`IN, FHIAIMS <IN-format>`, :ref:`MOL2 <MOL2-format>`, :ref:`PDB, ENT <PDB-format>`, :ref:`TPR <TPR-format>`, :ref:`TXYZ, ARC <TXYZ-format>`, :ref:`XYZ <XYZ-format>`',
+      ':ref:`IN, FHIAIMS <IN-format>`, :ref:`LAMMPSDUMP <LAMMPSDUMP-format>`, :ref:`MOL2 <MOL2-format>`, :ref:`PDB, ENT <PDB-format>`, :ref:`TPR <TPR-format>`, :ref:`TXYZ, ARC <TXYZ-format>`, :ref:`XYZ <XYZ-format>`',
     ]),
     list([
       'epsilon',
@@ -288,6 +288,7 @@
       ':ref:`DATA <DATA-format>`',
       ':ref:`DMS <DMS-format>`',
       ':ref:`GSD <GSD-format>`',
+      ':ref:`LAMMPSDUMP <LAMMPSDUMP-format>`',
       ':ref:`MMTF <MMTF-format>`',
       ':ref:`MOL2 <MOL2-format>`',
       ':ref:`PDBQT <PDBQT-format>`',
@@ -307,6 +308,7 @@
     }),
     'elements': set({
       ':ref:`IN, FHIAIMS <IN-format>`',
+      ':ref:`LAMMPSDUMP <LAMMPSDUMP-format>`',
       ':ref:`MOL2 <MOL2-format>`',
       ':ref:`PDB, ENT <PDB-format>`',
       ':ref:`TPR <TPR-format>`',
@@ -509,7 +511,7 @@
     list([
       ':ref:`LAMMPSDUMP <LAMMPSDUMP-format>`',
       'LAMMPS ascii dump file',
-      'masses, types',
+      'charges, elements, masses, types',
       '',
     ]),
     list([

From 6f86217da1cafa1c770a3c5135b6ee9e84db1adf Mon Sep 17 00:00:00 2001
From: Oliver Beckstein <orbeckst@gmail.com>
Date: Mon, 14 Jul 2025 16:42:46 -0700
Subject: [PATCH 3/3] reformat to make pre-commit happy

---
 doc/source/scripts/gen_topologyparser_attrs.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/doc/source/scripts/gen_topologyparser_attrs.py b/doc/source/scripts/gen_topologyparser_attrs.py
index f458fa8a3..323101776 100755
--- a/doc/source/scripts/gen_topologyparser_attrs.py
+++ b/doc/source/scripts/gen_topologyparser_attrs.py
@@ -26,7 +26,10 @@
 from MDAnalysisTests.topology.test_gro import TestGROParser
 from MDAnalysisTests.topology.test_gsd import TestGSDParser
 from MDAnalysisTests.topology.test_hoomdxml import TestHoomdXMLParser
-from MDAnalysisTests.topology.test_lammpsdata import LammpsBase, TestDumpParserFull
+from MDAnalysisTests.topology.test_lammpsdata import (
+    LammpsBase,
+    TestDumpParserFull,
+)
 from MDAnalysisTests.topology.test_mmtf import TestMMTFParser
 from MDAnalysisTests.topology.test_mol2 import TestMOL2Base
 from MDAnalysisTests.topology.test_pdb import TestPDBParser