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Updates to improve the Softwipe score#77

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trongnhanuit wants to merge 42 commits intoiqtree:masterfrom
trongnhanuit:master
Open

Updates to improve the Softwipe score#77
trongnhanuit wants to merge 42 commits intoiqtree:masterfrom
trongnhanuit:master

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@trongnhanuit trongnhanuit commented Jul 8, 2025

This pull request includes a bunch of commits to improve the Softwipe score

thomaskf and others added 30 commits June 26, 2025 12:33
@thomaskf @trongnhanuit
added 10 more ASSERTs
bfc4469
@trongnhanuit
ignore softwipe_build
f0f0c30
@thomaskf @trongnhanuit
merge with "replaced NULL with nullptr (1) - 8f0f9f8"
6aa176b
@thomaskf @trongnhanuit
merge with "replace NULL by nullptr (2) - 90f1997"
039c3e4
@thomaskf @trongnhanuit
replace NULL by nullptr (3)
bc6a6df
@thomaskf @trongnhanuit
Replace NULL by nullptr (4)
46aa4fe
@thomaskf @trongnhanuit
Merge with "Fixed the issue of readability-braces-around-statements (…
1c11057 
…1) - 0fa9ba9"
@thomaskf @trongnhanuit
Add the testing scripts
f4629f7
@thomaskf @trongnhanuit
set up the testings for github workflow
440b6b4
@thomaskf @trongnhanuit
update the setting for testing in workflow
119c59e
@thomaskf @trongnhanuit
Update the scripts for verification of the testing results
966dc0b
@thomaskf @trongnhanuit
updated the test cases for testing in workflow
52ac3d7
@thomaskf @trongnhanuit
Updated the workflow so that all MacOS and all Linux will perform tes…
226a2e1 
…tings on IQTREE
@thomaskf @trongnhanuit
Update ci.yaml
b880a39
@thomaskf @trongnhanuit
Fix Indentation
e425673
@thomaskf @trongnhanuit
Update the testing workflow for Windows
3d35300
@thomaskf @trongnhanuit
Update the workflow for testing on Windows
0fd3acf
@thomaskf @trongnhanuit
fixed the issue in testing under Github Workflow on Windows
9d610ed
@trongnhanuit
avoid using namespace directive in global context in header
f07af6c
@trongnhanuit
Merge with "add "override" to functions if needed - bc3ef0e"
9dbbe0f
@trongnhanuit
add "override" to functions if needed 2
526b220
@trongnhanuit
add override to functions when needed
9b013d4
@trongnhanuit
Merge with "add () to avoid "warning: '*' has higher precedence than …
7002065 
…'+'; add parentheses to explicitly specify the order of operations" - f3754ac"
@trongnhanuit
Add ASSERT before using pointers to avoid "warning: Possible null poi…
de915e4 
…nter dereference" (cppcheck)
@trongnhanuit
Merge with "Add ASSERT before using pointers to avoid warning: Either…
52767d8 
… the condition 'var' is redundant or there is possible null pointer dereference - a6fbe97"
@trongnhanuit
avoid warning Uninitialized variable
52c2b7b
@trongnhanuit
Merge with "disable unused functions to avoid cppcheck style warnings…
e8d235c 
… 1 - 431375f"
@trongnhanuit
Merge with "disable unused functions to avoid cppcheck style warnings…
da713b1 
… 2 - 80c35c3"
@trongnhanuit
disable unused functions to avoid cppcheck style warnings 3
85aaafb
@trongnhanuit
Merge with "disable unused variables - 63767c0"
87294b5
trongnhanuit and others added 12 commits June 27, 2025 13:07
@trongnhanuit
disable unused functions to avoid cppcheck style warnings 4
a12707e
@thomaskf @trongnhanuit
Merge with "Fixed the issue of readability-braces-around-statements r…
417af6a 
…eported by Softwipe - aff81cd"
@thomaskf @trongnhanuit
Merge with "Fixed the issue of readability-braces-around-statements r…
79a5ee8 
…eported by Softwipe 2 - 4df2bad"
@trongnhanuit
Merge with "Add const to constant variables 1 - bab71d0"
f9a4f1d
@trongnhanuit
Merge with "Add const to constant variables 2 - f22982b"
0fd52d5
@trongnhanuit
Merge with "Add const to constant variables 3 - 28c39d5"
ea8b5dc
@trongnhanuit
Merge with "Add const to constant variables 4 - 6490f96"
2285e4b
@trongnhanuit
Merge with "Add const to constant variables 5 - 397326c"
c19c7d9
@trongnhanuit
comment out "using namespace std;" to avoid warnings
449dcee
@trongnhanuit
Resolve code conflicts when merging "replace NULL by nullptr (2) - 90…
9c78b67 
…f1997", confirmed with Huaiyan
@thomaskf
Remove the code duplications
1f1c0a3
@trongnhanuit
Merge branch 'softwipe_selected_wo_more_asserts'
2fbf618 
# Conflicts:
#	alignment/alignment.cpp

=> take the updated code for detectSequenceType() by Huaiyan from the master branch
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@trongnhanuit @thomaskf

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