Changeset d2be22 for tests/regression/Options

Timestamp:

Dec 19, 2025, 11:29:38 PM (6 weeks ago)

Author:

Frederik Heber <frederik.heber@…>

Branches:

Candidate_v1.7.1, stable

Children:

25aa214

Parents:

29ba9a

git-author:

Frederik Heber <frederik.heber@…> (11/16/25 11:12:52)

git-committer:

Frederik Heber <frederik.heber@…> (12/19/25 23:29:38)

Message:

Actions relying on BondGraph fail if not bond table is loaded.

• this is to ensure to not stumble over missing optimal bond lengths from the table, like with StretchBondAction.
• TESTFIX: All regression tests that use these actions need to load the bond-table now.

Location:

tests/regression/Options/Session

Files:

• post/complextest.py (modified) (1 diff)
• post/complextest.sh (modified) (1 diff)
• pre/complextest.py (modified) (1 diff)
• pre/complexwait.py (modified) (1 diff)
• testsuite-options-load-session-python.at (modified) (3 diffs)
• testsuite-options-store-session-cli.at (modified) (1 diff)
• testsuite-options-store-session-python.at (modified) (1 diff)

tests/regression/Options/Session/post/complextest.py

@@ -7 +7 @@
 pyMoleCuilder.AtomAdd(add_atom="1", domain_position="1,1,1")
 pyMoleCuilder.SelectionAtomById(select_atom_by_id="0 0")
+pyMoleCuilder.CommandBondLengthTable(bond_table="BONDTABLE")
 pyMoleCuilder.GraphSubgraphDissection()
 pyMoleCuilder.SelectionMoleculeOfAtom()

tests/regression/Options/Session/post/complextest.sh

@@ -1 +1 @@
 ../../molecuilder \
---verbose 2 --set-output "mpqc" "tremolo" --set-random-number-distribution "uniform_int" --random-number-distribution-parameters "p=1;" --change-box "20,0,20,0,0,20" --add-atom 1 --domain-position "1,1,1" --select-atom-by-id 0 0 --subgraph-dissection --select-atoms-molecules --fill-regular-grid --mesh-size 3 3 3 --mesh-offset "0.5,0.5,0.5" --min-distance 1 --tesselation-radius 0 --random-atom-displacement 0 --random-molecule-displacement 0 --DoRotate 0 --version
+--verbose 2 --set-output "mpqc" "tremolo" --set-random-number-distribution "uniform_int" --random-number-distribution-parameters "p=1;" --change-box "20,0,20,0,0,20" --add-atom 1 --domain-position "1,1,1" --select-atom-by-id 0 0 --bond-table BONDTABLE --subgraph-dissection --select-atoms-molecules --fill-regular-grid --mesh-size 3 3 3 --mesh-offset "0.5,0.5,0.5" --min-distance 1 --tesselation-radius 0 --random-atom-displacement 0 --random-molecule-displacement 0 --DoRotate 0 --version

tests/regression/Options/Session/pre/complextest.py

@@ -7 +7 @@
 pyMoleCuilder.AtomAdd("1", "1,1,1")
 pyMoleCuilder.SelectionAtomById("0 0")
+pyMoleCuilder.CommandBondLengthTable(bond_table="BONDTABLE")
 pyMoleCuilder.GraphSubgraphDissection()
 pyMoleCuilder.SelectionMoleculeOfAtom()

tests/regression/Options/Session/pre/complexwait.py

@@ -23 +23 @@
 i=i+1
 print("wait3 end")
+mol.CommandBondLengthTable(bond_table="BONDTABLE")
 mol.GraphSubgraphDissection()
 mol.SelectionMoleculeOfAtom()

tests/regression/Options/Session/testsuite-options-load-session-python.at

@@ -20 +20 @@
 AT_SETUP([Standard Options - load session])
 AT_KEYWORDS([options python load-session])
-AT_TESTED([python3 diff grep])
+AT_TESTED([python3 diff grep sed])
 AT_SKIP_IF([../../molecuilder --help load-session; if test $? -eq 5; then /bin/true; else /bin/false; fi])
 
@@ -38 +38 @@
 # check that session is stored and can be executed when correctly prefixed
 file=complextest.py
-AT_CHECK([../../molecuilder --load-session ${abs_top_srcdir}/tests/regression/Options/Session/pre/$file --store-session $file --session-type "python"], 0, [ignore], [ignore])
-AT_CHECK([diff $file ${abs_top_srcdir}/tests/regression/Options/Session/post/$file], 0, [ignore], [ignore]) 
+AT_CHECK([sed -e "s#BONDTABLE#${abs_top_srcdir}/data/bondtables/bondtable.dat#" ${abs_top_srcdir}/tests/regression/Options/Session/pre/$file >${file/.py}2.py], 0, [ignore], [ignore])
+AT_CHECK([../../molecuilder --load-session ${file/.py}2.py --store-session $file --session-type "python"], 0, [ignore], [ignore])
+AT_CHECK([sed -e "s#BONDTABLE#${abs_top_srcdir}/data/bondtables/bondtable.dat#" ${abs_top_srcdir}/tests/regression/Options/Session/post/$file >${file/.py}3.py], 0, [ignore], [ignore])
+AT_CHECK([diff $file ${file/.py}3.py], 0, [ignore], [ignore]) 
 AT_CHECK([../../runpython ./$file], 0, [ignore], [ignore])
 
@@ -50 +52 @@
 
 file=complexwait.py
-AT_CHECK([../../molecuilder --load-session ${abs_top_srcdir}/tests/regression/Options/Session/pre/$file], 0, [stdout], [ignore])
+AT_CHECK([sed -e "s#BONDTABLE#${abs_top_srcdir}/data/bondtables/bondtable.dat#" ${abs_top_srcdir}/tests/regression/Options/Session/pre/$file >$file], 0, [ignore], [ignore])
+AT_CHECK([../../molecuilder --load-session $file], 0, [stdout], [ignore])
 # NOTE: The output from the python script itself may or may not appear. The embedding has weird
 # effects, especially with the additional thread for the ActionQueue. Loading a python

tests/regression/Options/Session/testsuite-options-store-session-cli.at

@@ -40 +40 @@
 AT_DATA([$file], [../../molecuilder \ 
 ])
-AT_CHECK([../../molecuilder --verbose 2 --set-output "mpqc" "tremolo" --set-random-number-distribution "uniform_int" --random-number-distribution-parameters "p=1;" --change-box "20,0,20,0,0,20" --add-atom 1 --domain-position "1,1,1" --select-atom-by-id 0 0 -I --select-atoms-molecules --fill-regular-grid --DoRotate 0 --mesh-offset ".5,.5,.5" --mesh-size 3 3 3 --version --store-session $file], 0, [ignore], [ignore])
-AT_CHECK([diff $file ${abs_top_srcdir}/tests/regression/Options/Session/post/$file], 0, [ignore], [ignore]) 
+AT_CHECK([../../molecuilder --verbose 2 --set-output "mpqc" "tremolo" --set-random-number-distribution "uniform_int" --random-number-distribution-parameters "p=1;" --change-box "20,0,20,0,0,20" --add-atom 1 --domain-position "1,1,1" --select-atom-by-id 0 0 --bond-table ${abs_top_srcdir}/data/bondtables/bondtable.dat --subgraph-dissection --select-atoms-molecules --fill-regular-grid --DoRotate 0 --mesh-offset ".5,.5,.5" --mesh-size 3 3 3 --version --store-session $file], 0, [ignore], [ignore])
+AT_CHECK([sed -e "s#BONDTABLE#${abs_top_srcdir}/data/bondtables/bondtable.dat#" ${abs_top_srcdir}/tests/regression/Options/Session/post/$file >${file}2], 0, [ignore], [ignore])
+AT_CHECK([diff $file ${file}2], 0, [ignore], [ignore]) 
 AT_CHECK([bash ./$file], 0, [ignore], [ignore])
 

tests/regression/Options/Session/testsuite-options-store-session-python.at

@@ -38 +38 @@
 # check that session is stored and can be executed when correctly prefixed
 file=complextest.py
-AT_CHECK([../../molecuilder --verbose 2 --set-output "mpqc" "tremolo" --set-random-number-distribution "uniform_int" --random-number-distribution-parameters "p=1;" --change-box "20,0,20,0,0,20" --add-atom 1 --domain-position "1,1,1" --select-atom-by-id 0 0 -I --select-atoms-molecules --fill-regular-grid --DoRotate 0 --mesh-offset ".5,.5,.5" --mesh-size 3 3 3 --version --store-session $file --session-type "python"], 0, [ignore], [ignore])
-AT_CHECK([diff $file ${abs_top_srcdir}/tests/regression/Options/Session/post/$file], 0, [ignore], [ignore]) 
+AT_CHECK([../../molecuilder --verbose 2 --set-output "mpqc" "tremolo" --set-random-number-distribution "uniform_int" --random-number-distribution-parameters "p=1;" --change-box "20,0,20,0,0,20" --add-atom 1 --domain-position "1,1,1" --select-atom-by-id 0 0 --bond-table ${abs_top_srcdir}/data/bondtables/bondtable.dat --subgraph-dissection --select-atoms-molecules --fill-regular-grid --DoRotate 0 --mesh-offset ".5,.5,.5" --mesh-size 3 3 3 --version --store-session $file --session-type "python"], 0, [ignore], [ignore])
+AT_CHECK([sed -e "s#BONDTABLE#${abs_top_srcdir}/data/bondtables/bondtable.dat#" ${abs_top_srcdir}/tests/regression/Options/Session/post/$file >${file/.py}2.py], 0, [ignore], [ignore])
+AT_CHECK([diff $file ${file/.py}2.py], 0, [ignore], [ignore]) 
 AT_CHECK([../../runpython ./$file], 0, [ignore], [ignore])