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Author SHA1 Message Date
Geoff Hutchison
889c350feb
Merge pull request #2747 from romanbsd/inchi-crash-fix 
Fix crash when converting some bad CML to inchi
 2024-12-20 19:24:53 -05:00
Geoff Hutchison
134f91711e
Merge pull request #2751 from e-kwsm/2715 
build(intel): use CMake IPO and strip at linkage for Release build
 2024-12-20 19:24:09 -05:00
Eisuke Kawashima
5d453a0c9a
build(intel): use CMake IPO and strip at linkage for Release build 
IntelLLVM, icpx, does not support `-ipo` with argument
fix #2715
 2024-12-12 01:33:38 +09:00
Roman Shterenzon
289a9ab9a4 Fix crash when converting some bad CML to inchi 2024-12-08 11:24:22 +02:00
Geoff Hutchison
10da8d7b89
Merge pull request #2574 from correaa/patch-1 
OpenBabel3Config.cmake to keep include information
 2024-12-07 13:26:09 -05:00
Geoff Hutchison
44eab115b1
Merge pull request #2684 from fredrikw/gh_1996 
Change check for rpc/xdr.h
 2024-12-07 13:15:20 -05:00
Geoff Hutchison
c6a4cfd7ef
Merge pull request #2744 from openbabel/dependabot/github_actions/actions/setup-python-5 
Bump actions/setup-python from 4 to 5
 2024-12-07 11:22:43 -05:00
Geoff Hutchison
1c0a2bb22a
Merge branch 'master' into dependabot/github_actions/actions/setup-python-5 2024-12-07 11:22:33 -05:00
Geoff Hutchison
a852c5b85c
Merge pull request #2743 from openbabel/dependabot/github_actions/peter-evans/create-pull-request-7.0.5 
Bump peter-evans/create-pull-request from 3.8.0 to 7.0.5
 2024-12-07 11:21:42 -05:00
Geoff Hutchison
e83eb008ec
Merge pull request #2742 from openbabel/dependabot/github_actions/github/codeql-action-3 
Bump github/codeql-action from 2 to 3
 2024-12-07 11:21:26 -05:00
Geoff Hutchison
d4468054f4
Merge pull request #2741 from openbabel/dependabot/github_actions/actions/checkout-4 
Bump actions/checkout from 2 to 4
 2024-12-07 11:20:55 -05:00
Geoff Hutchison
f81ffb6610
Merge pull request #2740 from openbabel/dependabot/github_actions/actions/upload-artifact-4 
Bump actions/upload-artifact from 1 to 4
 2024-12-07 11:20:40 -05:00
dependabot[bot]
86a53e5878
Bump actions/setup-python from 4 to 5 
Bumps [actions/setup-python](https://github.com/actions/setup-python) from 4 to 5.
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](https://github.com/actions/setup-python/compare/v4...v5)

---
updated-dependencies:
- dependency-name: actions/setup-python
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
 2024-12-07 16:19:12 +00:00
dependabot[bot]
3fab3acfe0
Bump peter-evans/create-pull-request from 3.8.0 to 7.0.5 
Bumps [peter-evans/create-pull-request](https://github.com/peter-evans/create-pull-request) from 3.8.0 to 7.0.5.
- [Release notes](https://github.com/peter-evans/create-pull-request/releases)
- [Commits](https://github.com/peter-evans/create-pull-request/compare/v3.8.0...v7.0.5)

---
updated-dependencies:
- dependency-name: peter-evans/create-pull-request
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
 2024-12-07 16:19:09 +00:00
dependabot[bot]
f7c15dc6bc
Bump github/codeql-action from 2 to 3 
Bumps [github/codeql-action](https://github.com/github/codeql-action) from 2 to 3.
- [Release notes](https://github.com/github/codeql-action/releases)
- [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md)
- [Commits](https://github.com/github/codeql-action/compare/v2...v3)

---
updated-dependencies:
- dependency-name: github/codeql-action
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
 2024-12-07 16:19:07 +00:00
dependabot[bot]
3464963e84
Bump actions/checkout from 2 to 4 
Bumps [actions/checkout](https://github.com/actions/checkout) from 2 to 4.
- [Release notes](https://github.com/actions/checkout/releases)
- [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md)
- [Commits](https://github.com/actions/checkout/compare/v2...v4)

---
updated-dependencies:
- dependency-name: actions/checkout
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
 2024-12-07 16:19:06 +00:00
dependabot[bot]
b3edf3ad6e
Bump actions/upload-artifact from 1 to 4 
Bumps [actions/upload-artifact](https://github.com/actions/upload-artifact) from 1 to 4.
- [Release notes](https://github.com/actions/upload-artifact/releases)
- [Commits](https://github.com/actions/upload-artifact/compare/v1...v4)

---
updated-dependencies:
- dependency-name: actions/upload-artifact
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
 2024-12-07 16:19:01 +00:00
Geoff Hutchison
ed52008b48
Merge pull request #2739 from ghutchis/add-dependabot 
Add GitHub dependabot scanning for GitHub actions
 2024-12-07 11:18:11 -05:00
Geoff Hutchison
25fb5bb3ef Add GitHub dependabot scanning for GitHub actions 
Signed-off-by: Geoff Hutchison <geoff.hutchison@gmail.com>
 2024-12-07 11:16:49 -05:00
Geoff Hutchison
e2135c8c8f
Merge pull request #2551 from DavidKorczynski/cifuzz 
ci: add CIFuzz Github Action
 2024-12-07 11:14:37 -05:00
Geoff Hutchison
60c2ca1f77
Merge pull request #2546 from lgtm-migrator/codeql 
Add CodeQL workflow for GitHub code scanning
 2024-12-07 11:12:29 -05:00
Geoff Hutchison
03dfbd1ffa
Merge pull request #2698 from romanbsd/uninitialized 
ReadyToInput member wasn't initialized
 2024-12-07 11:06:54 -05:00
Geoff Hutchison
060334f5ba
Merge pull request #2695 from romanbsd/int-overflow 
Fix ASAN reported integer overflow
 2024-12-07 11:06:28 -05:00
Geoff Hutchison
3c3702e0c1
Merge pull request #2705 from romanbsd/cml-parsing-crash 
Fix crash on specific CML format
 2024-12-07 11:05:56 -05:00
Geoff Hutchison
abbbcb4dcb
Merge pull request #2717 from romanbsd/inchi-crash 
Don't crash on an invalid InChI
 2024-12-07 11:05:25 -05:00
Geoff Hutchison
81b2e6c4d1
Merge pull request #2737 from tyler92/fuzz_convert 
Implement fuzz_convert fuzzer
 2024-12-07 10:52:00 -05:00
Geoff Hutchison
378e91983e
Merge pull request #2721 from matterhorn103/master 
Fetch more recent rapidjson codebase rather than last release
 2024-12-07 10:48:48 -05:00
Geoff Hutchison
c82abd1796
Merge pull request #2678 from fredrikw/gh_2677 
Make CorrectForPH respect perceived chains.
 2024-12-07 10:48:01 -05:00
Geoff Hutchison
7e6dedd942
Merge pull request #2734 from ghutchis/set-residues-fasta 
Ensure chains and residues are retained in FASTA generation
 2024-12-07 10:46:15 -05:00
Mikhail Khachayants
291f165b51 Implement fuzz_convert fuzzer 2024-12-07 15:04:38 +02:00
Geoff Hutchison
3a60721a49 Ensure chains and residues are retained in FASTA generation 
(Useful for Avogadro "insert DNA" command)

Signed-off-by: Geoff Hutchison <geoff.hutchison@gmail.com>
 2024-12-01 10:20:29 -05:00
Geoff Hutchison
00d3595fd3
Merge pull request #2706 from romanbsd/inchi-memory-leak 
Fix memory leak in InChi handling
 2024-12-01 10:19:42 -05:00
Matt Milner
693d3db568
Use current rapidjson commit hash rather than master 2024-09-16 23:52:54 +02:00
Matthew J. Milner
cc447423b0 Use 'master' as version number 2024-09-16 09:35:45 +02:00
Matthew J. Milner
4beabdafd0 Fetch current rapidjson codebase rather than last release 2024-09-16 09:11:57 +02:00
Roman Shterenzon
9c1cea7c27 Don't crash on an invalid InChI 2024-08-16 10:41:28 +03:00
Roman Shterenzon
450ebfc21f Fix memory leak in InChi handling 2024-07-10 13:08:59 +03:00
Roman Shterenzon
1d6b6fe820 Fix crash on specific CML format 2024-07-07 17:21:24 +03:00
Geoff Hutchison
7acf50c9d7
Merge pull request #2702 from merkys/libxml2-2.12.7 
Restore compatibility with libxml 2.12.7
 2024-06-21 08:37:08 -04:00
Andrius Merkys
3601e081f9 Restore compatibility with libxml2 2.12.7. 2024-06-21 14:23:31 +03:00
Roman Shterenzon
e13da94e54 ReadyToInput member wasn't initialized 2024-05-23 12:28:55 +03:00
Geoff Hutchison
756ebaaa2f
Merge pull request #2697 from fredrikw/gh2696 
Clear ImplicitHydrogens on multi-fragment cdxml documents.
 2024-05-22 10:27:43 -04:00
Fredrik Wallner
2724e31813 Clear ImplicitHydrogens on multi-fragment cdxml documents. 
Fixes segfault when converting particular CDXML file #2696
 2024-05-22 15:48:28 +02:00
Roman Shterenzon
6841d54e65 Fix ASAN reported integer overflow 2024-05-07 15:49:20 +03:00
fredrikw
765078d657
Change check for rpc/xdr.h 
Change from checking if the file exists to if the symbol xdrstdio_create exists. Should fix https://github.com/openbabel/openbabel/issues/1996
 2024-03-22 09:45:51 +01:00
Geoff Hutchison
fffa4afe95
Merge pull request #2682 from fredrikw/fix_test_obconvwriter_pcjson 
Fix failing test in testobconv_writers
 2024-03-11 12:23:18 -04:00
fredrikw
5a0d001685
Fix failing test in testobconv_writers 
To match the bug fix in https://github.com/openbabel/openbabel/pull/2596
 2024-03-11 16:33:07 +01:00
Fredrik Wallner
1e20208972 Make CorrectForPH respect perceived chains. 2024-03-05 09:37:48 +01:00
Geoff Hutchison
32cf131444
Merge pull request #2654 from ghutchis/more-cjson 
Add more cjson features, including conformer energies
 2023-12-06 09:59:04 -05:00
Geoff Hutchison
f67d6bc3e4
Merge pull request #2653 from ghutchis/fix-xtb-gaussian-vibrations 
Fix parsing "Gaussian" vibration output from xtb program
 2023-12-06 00:08:04 -05:00