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Merged
JanCBrammer merged 24 commits into from
Feb 13, 2024
Merged

CI: Add musl+gcc to regression test workflow #6

JanCBrammer merged 24 commits into from
Feb 13, 2024

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@flange-ipb
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@flange-ipb flange-ipb commented Feb 12, 2024

Add CI workflow for compilation and regression testing of libinchi using gcc and musl (a popular C standard library). Flawless compilation with musl has become possible with 1.07-beta.3's definition of is_ascii in INCHI-1-SRC/INCHI_BASE/src/util.c (see commit c778dfa).

Changes to the CI workflow:

  • rename existing gcc+glibc job
  • move most steps of the workflow to a reusable Action
  • uploaded artifacts (test logs/reports) from different jobs receive distinct names
  • show information on gcc and ldd
  • use alpine as docker image for the gcc+musl job

Lessons learned:

  • actions/setup-python cannot be used in Alpine containers, so Python installation is done via Alpine's package manager.
  • Virtual environments in Python do not work across different workflow steps, thus special care needs to be taken for Python's package manager pip due to PEP 668.
  • musl's ldd --version does not return with exitcode 0.

@flange-ipb
CI: move regression test to a reuseable workflow
0bb8ab6
@flange-ipb
checkout is required to access reuseable workflow
d40a427
@flange-ipb
change position of "uses"
68f28d1
@flange-ipb
regression test as reuseable action
df979f5
@flange-ipb
specify shell in composite action
a679082
@flange-ipb
show gcc and ldd versions in action
c47d7b1
@flange-ipb
add CI workflow for musl+gcc
d747dc4
@flange-ipb
add bash
da73892
@flange-ipb
install python in alpine
aaba0fd
@flange-ipb
move setup-python out of the reuseable action
7dc14d2
@flange-ipb
use Python venv
7e9efb0
@flange-ipb
try to set up Python environment in bash
033aac1
@flange-ipb
run pip with venv
15cd8d7
@flange-ipb
What happens when pip runs in a different step?
93c08bc
@flange-ipb
use pipx
abc50d3
@flange-ipb
remove upgrade of pip
f750730
@flange-ipb
let pip break the system packages
ec7ae30
@flange-ipb
install git
ba53b78
@flange-ipb
make sure ldd --version call always exists with exitcode 0
2622175
@flange-ipb
parameterize artifact name
7b40d97
@flange-ipb
parameterize artifact name without input
6bfa090
@flange-ipb
revert back to using input
526a807
@flange-ipb
fix string concatenation
bd0495d
@flange-ipb
revert back to explicit artifact names
04346b8
JanCBrammer
JanCBrammer approved these changes Feb 13, 2024
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Looks good! The workflow fails as intended with a manipulated reference (https://github.com/flange-ipb/InChI/actions/runs/7846614779).

@JanCBrammer JanCBrammer merged commit 1ba86af into IUPAC-InChI:main Feb 13, 2024
@flange-ipb flange-ipb mentioned this pull request Aug 16, 2024
Open
ricrogz added a commit to ricrogz/InChI that referenced this pull request Feb 22, 2025
@ricrogz
Fix heap-buffer-overflow: we try to move more bytes than we have.
485d9bd 
    (if we start moving from the 7th byte, we have to reduce the number
    of bytes by the same amount, or we'll overflow the buffer!)

==7771==ERROR: AddressSanitizer: heap-buffer-overflow on address 0x503000000084 at pc 0x7b8e82ee93c0 bp 0x7ffe4113cbb0 sp 0x7ffe4113c370
READ of size 18 at 0x503000000084 thread T0
    #0 0x7b8e82ee93bf in memmove (/usr/local/lib64/libasan.so.8+0xf73bf)
    IUPAC-InChI#1 0x5f5cdd in get_V3000_input_line_to_strbuf ../../../INCHI_BASE/src/mol_fmt3.c:1875
    IUPAC-InChI#2 0x5f5e95 in MolfileV3000ReadCTABBeginAndCountsLine ../../../INCHI_BASE/src/mol_fmt3.c:475
    IUPAC-InChI#3 0x5ec962 in MolfileReadDataLines ../../../INCHI_BASE/src/mol_fmt1.c:252
    IUPAC-InChI#4 0x5f216f in ReadMolfile ../../../INCHI_BASE/src/mol_fmt1.c:130
    IUPAC-InChI#5 0x60559b in ReadMolfileToInpAtoms ../../../INCHI_BASE/src/mol2atom.c:373
    IUPAC-InChI#6 0x605b7e in CreateOrigInpDataFromMolfile ../../../INCHI_BASE/src/mol2atom.c:160
    IUPAC-InChI#7 0x61bcc5 in ReadTheStructure ../../../INCHI_BASE/src/runichi2.c:470
    IUPAC-InChI#8 0x61cc8c in GetOneStructure ../../../INCHI_BASE/src/runichi2.c:229
    IUPAC-InChI#9 0x659b16 in GetTheNextRecordOfInputFile ../src/ichimain.c:1092
    IUPAC-InChI#10 0x65e7f1 in ProcessSingleInputFile ../src/ichimain.c:816
    IUPAC-InChI#11 0x65f9ae in main ../src/ichimain.c:250
    IUPAC-InChI#12 0x7b8e828be249  (/lib/x86_64-linux-gnu/libc.so.6+0x27249) (BuildId: c047672cae7964324658491e7dee26748ae5d2f8)
    IUPAC-InChI#13 0x7b8e828be304 in __libc_start_main (/lib/x86_64-linux-gnu/libc.so.6+0x27304) (BuildId: c047672cae7964324658491e7dee26748ae5d2f8)
    IUPAC-InChI#14 0x4025a0 in _start (/inchi/INCHI-1-TEST/exes/inchi-1+0x4025a0)
djb-rwth pushed a commit that referenced this pull request Feb 23, 2025
@ricrogz @djb-rwth
Fix heap-buffer-overflow: we try to move more bytes than we have.
a73d353 
    (if we start moving from the 7th byte, we have to reduce the number
    of bytes by the same amount, or we'll overflow the buffer!)

==7771==ERROR: AddressSanitizer: heap-buffer-overflow on address 0x503000000084 at pc 0x7b8e82ee93c0 bp 0x7ffe4113cbb0 sp 0x7ffe4113c370
READ of size 18 at 0x503000000084 thread T0
    #0 0x7b8e82ee93bf in memmove (/usr/local/lib64/libasan.so.8+0xf73bf)
    #1 0x5f5cdd in get_V3000_input_line_to_strbuf ../../../INCHI_BASE/src/mol_fmt3.c:1875
    #2 0x5f5e95 in MolfileV3000ReadCTABBeginAndCountsLine ../../../INCHI_BASE/src/mol_fmt3.c:475
    #3 0x5ec962 in MolfileReadDataLines ../../../INCHI_BASE/src/mol_fmt1.c:252
    #4 0x5f216f in ReadMolfile ../../../INCHI_BASE/src/mol_fmt1.c:130
    #5 0x60559b in ReadMolfileToInpAtoms ../../../INCHI_BASE/src/mol2atom.c:373
    #6 0x605b7e in CreateOrigInpDataFromMolfile ../../../INCHI_BASE/src/mol2atom.c:160
    #7 0x61bcc5 in ReadTheStructure ../../../INCHI_BASE/src/runichi2.c:470
    #8 0x61cc8c in GetOneStructure ../../../INCHI_BASE/src/runichi2.c:229
    #9 0x659b16 in GetTheNextRecordOfInputFile ../src/ichimain.c:1092
    #10 0x65e7f1 in ProcessSingleInputFile ../src/ichimain.c:816
    #11 0x65f9ae in main ../src/ichimain.c:250
    #12 0x7b8e828be249  (/lib/x86_64-linux-gnu/libc.so.6+0x27249) (BuildId: c047672cae7964324658491e7dee26748ae5d2f8)
    #13 0x7b8e828be304 in __libc_start_main (/lib/x86_64-linux-gnu/libc.so.6+0x27304) (BuildId: c047672cae7964324658491e7dee26748ae5d2f8)
    #14 0x4025a0 in _start (/inchi/INCHI-1-TEST/exes/inchi-1+0x4025a0)
@dan2097 dan2097 mentioned this pull request Apr 18, 2025
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@schatzsc schatzsc mentioned this pull request Jan 8, 2026
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@gblanke02 gblanke02 mentioned this pull request Jan 9, 2026
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