[med-svn] [Git][med-team/autodock-vina][master] 10 commits: New upstream version 1.2.7

Sun Mar 2 11:11:36 GMT 2025

Étienne Mollier pushed to branch master at Debian Med / autodock-vina

Commits:
4764fc14 by Étienne Mollier at 2025-03-02T11:44:47+01:00
New upstream version 1.2.7
- - - - -
5f193f78 by Étienne Mollier at 2025-03-02T11:47:35+01:00
Update upstream source from tag 'upstream/1.2.7'

Update to upstream version '1.2.7'
with Debian dir 59c8fc58423390e2acade26402fcc8bcb5f49e78
- - - - -
b3a12dad by Étienne Mollier at 2025-03-02T11:53:53+01:00
boost1.83.patch: delete patch: applied upstream.

- - - - -
28dd6307 by Étienne Mollier at 2025-03-02T11:54:24+01:00
remove_static.patch: refresh patch.

- - - - -
73d85bd6 by Étienne Mollier at 2025-03-02T11:54:44+01:00
d/control: declare compliance to standards version 4.7.2.

- - - - -
bac7f2fb by Étienne Mollier at 2025-03-02T11:55:12+01:00
d/control: add myself to uploaders.

- - - - -
533ae53e by Étienne Mollier at 2025-03-02T12:00:20+01:00
d/patches/*: normalize dep3 headers.

- - - - -
58f2d5c8 by Étienne Mollier at 2025-03-02T12:08:55+01:00
d/rules: activate all hardening options.

- - - - -
f7df4d2d by Étienne Mollier at 2025-03-02T12:09:59+01:00
fortify.patch: new: propagate fortify source macro.

- - - - -
029988d6 by Étienne Mollier at 2025-03-02T12:10:43+01:00
d/changelog: ready for upload to unstable.

- - - - -

173 changed files:

- .github/workflows/compile-binaries.yaml
- .github/workflows/pypi-build.yml
- .gitignore
- build/linux/release/Makefile
- build/mac/release/Makefile
- build/makefile_common
- build/python/README.md
- build/python/build-linux-wheels.sh
- − build/python/pyproject.toml
- build/python/setup.py
- build/python/vina/__init__.py
- build/python/vina/vina.py
- build/windows/compile.bat
- build/windows/vina.vcxproj
- build/windows/vina_split.vcxproj
- debian/changelog
- debian/control
- debian/patches/annoying_static_removed_was_in_for_a_reason_questionmark.patch
- − debian/patches/boost1.83.patch
- debian/patches/do_not_link_against_unneeded_libs.patch
- + debian/patches/fortify.patch
- debian/patches/remove_static.patch
- debian/patches/series
- debian/rules
- + docs/source/colab_examples.rst
- docs/source/docking_basic.rst
- docs/source/docking_flexible.rst
- docs/source/docking_hydrated.rst
- + docs/source/docking_in_batch.rst
- docs/source/docking_multiple_ligands.rst
- docs/source/docking_requirements.rst
- docs/source/docking_zinc.rst
- + docs/source/images/docking_workflow.png
- docs/source/index.rst
- docs/source/installation.rst
- example/autodock_scripts/dry.py
- example/autodock_scripts/mapwater.py
- example/autodock_scripts/prepare_gpf4zn.py
- example/basic_docking/solution/1iep_ligand.pdbqt
- + example/basic_docking/solution/1iep_ligand.sdf
- example/basic_docking/solution/1iep_ligand_ad4_out.pdbqt
- example/basic_docking/solution/1iep_ligand_vina_out.pdbqt
- example/basic_docking/solution/1iep_receptor.A.map
- + example/basic_docking/solution/1iep_receptor.B.map
- + example/basic_docking/solution/1iep_receptor.Br.map
- example/basic_docking/solution/1iep_receptor.C.map
- + example/basic_docking/solution/1iep_receptor.Cl.map
- + example/basic_docking/solution/1iep_receptor.F.map
- example/basic_docking/solution/1iep_receptor.HD.map
- + example/basic_docking/solution/1iep_receptor.I.map
- example/basic_docking/solution/1iep_receptor.N.map
- example/basic_docking/solution/1iep_receptor.NA.map
- example/basic_docking/solution/1iep_receptor.OA.map
- + example/basic_docking/solution/1iep_receptor.P.map
- + example/basic_docking/solution/1iep_receptor.S.map
- + example/basic_docking/solution/1iep_receptor.SA.map
- + example/basic_docking/solution/1iep_receptor.Si.map
- + example/basic_docking/solution/1iep_receptor.box.pdb
- example/flexible_docking/solution/1fpu_receptor_rigid_vina_box.txt → example/basic_docking/solution/1iep_receptor.box.txt
- example/basic_docking/solution/1iep_receptor.d.map
- example/basic_docking/solution/1iep_receptor.e.map
- example/basic_docking/solution/1iep_receptor.glg
- example/basic_docking/solution/1iep_receptor.gpf
- example/basic_docking/solution/1iep_receptor.maps.fld
- example/basic_docking/solution/1iep_receptor.maps.xyz
- example/basic_docking/solution/1iep_receptor.pdbqt
- + example/basic_docking/solution/1iep_receptorH.pdb
- + example/basic_docking/solution/boron-silicon-atom_par.dat
- example/flexible_docking/solution/1fpu_ligand_flex_ad4_out.pdbqt
- example/flexible_docking/solution/1fpu_ligand_flex_vina_out.pdbqt
- + example/flexible_docking/solution/1fpu_receptor.box.pdb
- example/basic_docking/solution/1iep_receptor_vina_box.txt → example/flexible_docking/solution/1fpu_receptor.box.txt
- − example/flexible_docking/solution/1fpu_receptor.pdbqt
- + example/flexible_docking/solution/1fpu_receptorH.pdb
- example/flexible_docking/solution/1fpu_receptor_flex.pdbqt
- example/flexible_docking/solution/1fpu_receptor_rigid.A.map
- + example/flexible_docking/solution/1fpu_receptor_rigid.B.map
- + example/flexible_docking/solution/1fpu_receptor_rigid.Br.map
- example/flexible_docking/solution/1fpu_receptor_rigid.C.map
- + example/flexible_docking/solution/1fpu_receptor_rigid.Cl.map
- + example/flexible_docking/solution/1fpu_receptor_rigid.F.map
- example/flexible_docking/solution/1fpu_receptor_rigid.HD.map
- + example/flexible_docking/solution/1fpu_receptor_rigid.I.map
- example/flexible_docking/solution/1fpu_receptor_rigid.N.map
- example/flexible_docking/solution/1fpu_receptor_rigid.NA.map
- example/flexible_docking/solution/1fpu_receptor_rigid.OA.map
- + example/flexible_docking/solution/1fpu_receptor_rigid.P.map
- + example/flexible_docking/solution/1fpu_receptor_rigid.S.map
- + example/flexible_docking/solution/1fpu_receptor_rigid.SA.map
- + example/flexible_docking/solution/1fpu_receptor_rigid.Si.map
- example/flexible_docking/solution/1fpu_receptor_rigid.d.map
- example/flexible_docking/solution/1fpu_receptor_rigid.e.map
- example/flexible_docking/solution/1fpu_receptor_rigid.glg
- example/flexible_docking/solution/1fpu_receptor_rigid.gpf
- example/flexible_docking/solution/1fpu_receptor_rigid.maps.fld
- example/flexible_docking/solution/1fpu_receptor_rigid.maps.xyz
- example/flexible_docking/solution/1fpu_receptor_rigid.pdbqt
- + example/flexible_docking/solution/1iep_ligand.pdbqt
- + example/flexible_docking/solution/boron-silicon-atom_par.dat
- example/hydrated_docking/solution/1uw6_ligand.pdbqt
- + example/hydrated_docking/solution/1uw6_ligand.sdf
- + example/hydrated_docking/solution/1uw6_ligandH.sdf
- example/hydrated_docking/solution/1uw6_ligand_ad4_out.pdbqt
- example/hydrated_docking/solution/1uw6_ligand_ad4_out_DRY_SCORED.pdbqt
- example/hydrated_docking/solution/1uw6_receptor.A.map
- + example/hydrated_docking/solution/1uw6_receptor.B.map
- + example/hydrated_docking/solution/1uw6_receptor.Br.map
- example/hydrated_docking/solution/1uw6_receptor.C.map
- + example/hydrated_docking/solution/1uw6_receptor.Cl.map
- + example/hydrated_docking/solution/1uw6_receptor.F.map
- example/hydrated_docking/solution/1uw6_receptor.HD.map
- + example/hydrated_docking/solution/1uw6_receptor.I.map
- example/hydrated_docking/solution/1uw6_receptor.N.map
- example/hydrated_docking/solution/1uw6_receptor.NA.map
- example/hydrated_docking/solution/1uw6_receptor.OA.map
- + example/hydrated_docking/solution/1uw6_receptor.P.map
- + example/hydrated_docking/solution/1uw6_receptor.S.map
- + example/hydrated_docking/solution/1uw6_receptor.SA.map
- + example/hydrated_docking/solution/1uw6_receptor.Si.map
- example/hydrated_docking/solution/1uw6_receptor.W.map
- + example/hydrated_docking/solution/1uw6_receptor.box.pdb
- example/hydrated_docking/solution/1uw6_receptor.d.map
- example/hydrated_docking/solution/1uw6_receptor.e.map
- example/hydrated_docking/solution/1uw6_receptor.glg
- example/hydrated_docking/solution/1uw6_receptor.gpf
- example/hydrated_docking/solution/1uw6_receptor.maps.fld
- example/hydrated_docking/solution/1uw6_receptor.pdbqt
- + example/hydrated_docking/solution/1uw6_receptorH.pdb
- + example/hydrated_docking/solution/boron-silicon-atom_par.dat
- + example/mulitple_ligands_docking/solution/5x72.pdb
- example/mulitple_ligands_docking/solution/5x72_ligand_ad4_out.pdbqt
- example/mulitple_ligands_docking/solution/5x72_ligand_p59.pdbqt
- + example/mulitple_ligands_docking/solution/5x72_ligand_p59.sdf
- + example/mulitple_ligands_docking/solution/5x72_ligand_p59H.sdf
- example/mulitple_ligands_docking/solution/5x72_ligand_p69.pdbqt
- + example/mulitple_ligands_docking/solution/5x72_ligand_p69.sdf
- + example/mulitple_ligands_docking/solution/5x72_ligand_p69H.sdf
- example/mulitple_ligands_docking/solution/5x72_ligand_vina_out.pdbqt
- example/mulitple_ligands_docking/solution/5x72_receptor.A.map
- + example/mulitple_ligands_docking/solution/5x72_receptor.B.map
- + example/mulitple_ligands_docking/solution/5x72_receptor.Br.map
- example/mulitple_ligands_docking/solution/5x72_receptor.C.map
- + example/mulitple_ligands_docking/solution/5x72_receptor.Cl.map
- example/mulitple_ligands_docking/solution/5x72_receptor.F.map
- example/mulitple_ligands_docking/solution/5x72_receptor.HD.map
- + example/mulitple_ligands_docking/solution/5x72_receptor.I.map
- example/mulitple_ligands_docking/solution/5x72_receptor.N.map
- + example/mulitple_ligands_docking/solution/5x72_receptor.NA.map
- example/mulitple_ligands_docking/solution/5x72_receptor.OA.map
- + example/mulitple_ligands_docking/solution/5x72_receptor.P.map
- + example/mulitple_ligands_docking/solution/5x72_receptor.S.map
- + example/mulitple_ligands_docking/solution/5x72_receptor.SA.map
- + example/mulitple_ligands_docking/solution/5x72_receptor.Si.map
- + example/mulitple_ligands_docking/solution/5x72_receptor.box.pdb
- + example/mulitple_ligands_docking/solution/5x72_receptor.box.txt
- example/mulitple_ligands_docking/solution/5x72_receptor.d.map
- example/mulitple_ligands_docking/solution/5x72_receptor.e.map
- − example/mulitple_ligands_docking/solution/5x72_receptor.glg
- example/mulitple_ligands_docking/solution/5x72_receptor.gpf
- example/mulitple_ligands_docking/solution/5x72_receptor.maps.fld
- example/mulitple_ligands_docking/solution/5x72_receptor.pdbqt
- example/mulitple_ligands_docking/solution/5x72_receptorH.pdb
- + example/mulitple_ligands_docking/solution/5x72_receptor_rigid.glg
- − example/mulitple_ligands_docking/solution/5x72_receptor_vina_box.txt
- + example/mulitple_ligands_docking/solution/boron-silicon-atom_par.dat
- readthedocs.yml
- src/lib/monte_carlo.cpp
- src/lib/parallel_progress.h
- src/lib/scoring_function.h
- src/lib/vina.cpp
- src/lib/vina.h
- src/main/main.cpp
- src/split/split.cpp

The diff was not included because it is too large.

View it on GitLab: https://salsa.debian.org/med-team/autodock-vina/-/compare/a161b6b872c0a6049ade74b93905bee5c3912821...029988d69cdd9b381aa86696f017c25cc0a0698f

-- 
View it on GitLab: https://salsa.debian.org/med-team/autodock-vina/-/compare/a161b6b872c0a6049ade74b93905bee5c3912821...029988d69cdd9b381aa86696f017c25cc0a0698f
You're receiving this email because of your account on salsa.debian.org.

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20250302/874dbe6f/attachment-0001.htm>