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160 Commits

Author SHA1 Message Date
wszqkzqk
8947d3bc06 fix: update launch script handling for mingw-w64/msys2 on Windows (#487) 
Signed-off-by: Zhou Qiankang <wszqkzqk@qq.com>
 2026-02-12 21:12:49 -05:00
wszqkzqk
58cfe7b422 build: support to build pymol with mingw-w64 on Windows (#486) 
Signed-off-by: Zhou Qiankang <wszqkzqk@qq.com>
 2025-12-08 09:35:24 -05:00
Jarrett Johnson
6977216eb1 PYMOL-5169: Move VertexBufferGL to generalized VertexBuffer (etc) 2025-09-26 12:07:31 -04:00
Jarrett Johnson
33c5c7c36a Support CIF structure factors to Density Map (#455) 2025-05-13 01:10:54 -04:00
Jarrett Johnson
9698d6ccd2 Upgrade vtk-m dep to [2.0, 2.3] (#453) 
`GetCoordinateSystem` no longer returns reference, so some of our API usage had to be changed a bit. Ref: 2d30e6d45a
 2025-05-05 01:54:00 -04:00
Bernhard M. Wiedemann
18175bcbc0 Allow to override build date with SOURCE_DATE_EPOCH (#404) 
to make builds reproducible.
See https://reproducible-builds.org/ for why this is good
and https://reproducible-builds.org/specs/source-date-epoch/
for the definition of this variable.
 2025-01-24 23:42:44 -05:00
jrom99
1f6e7b30ad Fix INSTALL instructions for newer versions of pip (#418) 2025-01-24 23:41:16 -05:00
Jarrett Johnson
a0d739f8e0 use site_packages_dir as base for script installation 2024-08-07 22:31:51 -04:00
ye11owSub
757270eb1d format of setup.py 2024-08-07 21:13:14 -04:00
ye11owSub
516c015e31 small refactoring of the setup.py 2024-08-07 21:13:14 -04:00
ye11owSub
78b591d9f1 moving the content of create_shadertext.py to the setup.py 2024-08-07 21:13:14 -04:00
ye11owSub
6f7b752bdc adding building with pyproject 2024-08-07 21:13:14 -04:00
Jarrett Johnson
74ffc07ea7 Replace monkeypatch distutils with CMake setuptools Extensions 2024-05-20 08:37:33 -04:00
Jarrett Johnson
a4cc70c2ff Add CI for Windows and Mac 2024-05-12 12:20:12 -04:00
Jarrett Johnson
3faec30816 temp C++17 flag on windows 2024-01-31 11:01:58 -05:00
Jarrett Johnson
82fc418035 autopep8 format setup.py 2024-01-30 16:11:12 -05:00
Jarrett Johnson
6bfc590446 PYMOL-4025 ObjectCurve 2024-01-30 15:30:40 -05:00
reneeotten
f7048b4275 Allow building with latst vtk-m release (v1.7) 2021-12-22 10:45:41 -05:00
Thomas Holder
5a6d65e8a5 Fix build with VTK-m 1.6 
New `--use-vtkm` choices: ('1.5', '1.6', 'no')
 2021-07-07 11:52:16 -04:00
Jarrett Johnson
ec85885784 Don't use Vtkm by default 2021-04-28 06:04:18 -04:00
Thomas Holder
b85270bc30 PYMOL-3528 isosurface with VTKm 
New setting: isosurface_algorithm
 2021-04-28 05:17:34 -04:00
Thomas Holder
f3c0419654 rebond pbc=1 
- Add `pbc` argument to cmd.rebond()
- Refactor ObjectMoleculeConnect
- Add support for OpenMP
 2021-02-11 19:05:08 +01:00
Thomas Holder
5ea147db01 Move tnt -> include/, cealign -> layer0/ 2020-12-03 18:10:46 +01:00
Thomas Holder
8298707a6b Remove libexecinfo dependency 
Remove the unix-only `backtrace` code from `print_trace()`. Kept the
function so that it can be used to set a breakpoint with a debugger.

Closes https://github.com/schrodinger/pymol-open-source/issues/135
 2020-10-05 14:06:38 +02:00
Thomas Holder
fe5de619bf Debug build (Unix): Use _GLIBCXX_ASSERTIONS 
This would have revealed this bug early:
https://github.com/schrodinger/pymol-open-source/issues/119
 2020-07-29 11:54:57 +02:00
Thomas Holder
bcd4ef2001 setup.py: Improve get_prefix_path() with venv 
When detecting Homebrew/MacPorts/etc. on macOS, use `sys.base_prefix`
which works for virtual environments.

Closes #46
 2020-07-04 12:41:00 +02:00
Thomas Holder
4492413cdb Launch script: No PYMOL_PATH for default 2020-06-26 19:17:23 +02:00
Thomas Holder
cf0a014d2b remove -ffast-math -funroll-loops -fcommon 
- We have no proof that `-ffast-math` or `-funroll-loops` really
  improve performance
- `-ffast-math` is problematic for testing because results sometimes
  differ between compilers
- Recent clang fails to compile with `-ffast-math`
 2020-04-09 16:04:56 +02:00
Thomas Holder
1d98290033 refactor symmetry function 
get_symmetry
set_symmetry
symmetry_copy
 2020-02-20 12:31:22 +01:00
Thomas Holder
7975686e46 add netcdf molfile plugin 2019-12-02 14:06:13 +01:00
Thomas Holder
baee4694d0 detect netcdf trajectories 2019-12-02 14:04:13 +01:00
Thomas Holder
b57f131940 -Wunused-variable 2019-11-27 13:18:08 +01:00
Pedro Lacerda
b82f8b30ac Add exec call to launcher 2019-11-12 00:48:57 -08:00
Thomas Holder
276640cd29 Port EPAM's VR fork to PyMOL 2.4 
Porting the essential parts of EPAM System's "openvr" branch to the
master branch.

Original authors:
Natalia Smirnova, EPAM Systems, Inc.
Pavel Smirnov, EPAM Systems, Inc.

Original fork:
https://github.com/epam/pymol-open-source/tree/openvr

Adjustments:
- Make feature optional with "--openvr" compile option
- Python 3 support
- Remove C++11 workarounds
- Exclude build system changes

Co-authored-by: Natalia Smirnova <Natalia_Smirnova@epam.com>
Co-authored-by: Pavel Smirnov <pavel_smirnov1@epam.com>
 2019-11-11 00:50:01 -08:00
Thomas Holder
5a4ab0eaa9 PYMOL-3272 remove obsolete metaphorics code 
cex files and m4x annotated PDB files don't exist anymore.
cex loading was broken for a long time, proof that nobody was using it.
 2019-08-19 22:07:24 +02:00
Thomas Holder
55135c8d04 pymol::zstring_view 2019-06-07 16:22:08 +02:00
Thomas Holder
1fe652c0bf setup.py: handle DEBUG in build_ext 2019-05-16 08:56:06 +02:00
Thomas Holder
723166140a PYMOL-3219 eliminate _PYMOL_INLINE 2019-03-29 13:37:41 +01:00
Thomas Holder
d53d23d2cc DEBUG=1 -> -Og instead of -O0 2019-03-29 12:40:32 +01:00
Thomas Holder
b59ce09d8a refactor: pymol::malloc<T> 
- use typed/namespaced malloc wrapper
- remove Alloc et al.
- remove mmalloc et al.
- remove CINTERFACE define
 2019-02-21 17:41:58 +01:00
Thomas Holder
09ad21e3ed cleanup: remove SVN stuff 2019-02-12 16:58:50 +01:00
Thomas Holder
abb3b2f265 remove --bundled-pmw 2019-01-24 20:32:01 +01:00
Thomas Holder
2162bb8d2e setup.py: cleanup 2018-12-04 20:31:35 +01:00
Jarrett Johnson
d859e67b5b Added catch2 unit testing framework 2018-11-15 17:53:25 +01:00
Thomas Holder
1b1910cfbb setup.py: --glut --no-osx-frameworks 
Change the defaults of these flags
 2018-11-15 16:04:43 +01:00
Thomas Holder
b04f3a1eac DEBUG=1 -> -O0 instead of -O3 2018-09-25 12:03:10 +02:00
Thomas Holder
33937d8543 setup.py: drop --no-cxx11 option 2018-09-03 15:27:33 +02:00
Thomas Holder
4f3c781a74 cleanup: compiler warnings 
-Wdangling-else
-Wmisleading-indentation
-Wmismatched-tags
-Wparentheses
-Wsometimes-uninitialized
-Wunused-but-set-variable
-Wunused-function
-Wunused-label
-Wunused-variable
 2018-08-16 19:00:17 +02:00
Thomas Holder
f21c61958e Graphics refactoring, ported from Incentive PyMOL 2018-07-03 20:19:12 +02:00
Thomas Holder
1742d75d13 anaglyph batch mode, all_states measurements, ... 
* fix anaglyph stereo in batch (headless) mode
* fix possible memory corruption with boolean settings
* measurement wizard: distances between states (all_states=on)
* get_fastastr: nucleic acid, by chain
* menu: A (Action) > group
* sequence viewer menu: ss (Secondary Structure)
* MAE export of groups (s_m_subgroupid)
* macOS: -O3 -fno-strict-aliasing (bugs/205)
 2018-05-03 14:46:44 +00:00