Package: pymol / 2.1.0+dfsg-3

Metadata

Package Version Patches format
pymol 2.1.0+dfsg-3 3.0 (quilt)

Patch series

view the series file
Patch File delta Description
02_test suite.patch | (download)

test/pymol-test | 43 43 + 0 - 0 !
test/run | 2 1 + 1 - 0 !
2 files changed, 44 insertions(+), 1 deletion(-)

 patch to make the test-suite work during debian build-time.
03_povray.patch | (download)

modules/pymol/povray.py | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 adjust povray options
22_fix_pymol_import.patch | (download)

modules/pymol/__init__.py | 3 3 + 0 - 0 !
1 file changed, 3 insertions(+)

 fix importing of pymol by setting pymol_path explicitly
Bug-Debian: http://bugs.debian.org/556878
27_fix_pymol_path_in_setup.patch | (download)

setup.py | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

---
28_no_data_install_in_python_path.patch | (download)

setup.py | 2 0 + 2 - 0 !
1 file changed, 2 deletions(-)

---
31_fix_format security.patch | (download)

contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.cpp | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 fix "error: format not a string literal and no format arguments [-werror=format-security]" (#759860)
32_fix_spelling_lintian_warnings.patch | (download)

layer0/ShaderMgr.cpp | 3 1 + 2 - 0 !
layer1/Setting.cpp | 2 1 + 1 - 0 !
layer2/ObjectMolecule2.cpp | 2 1 + 1 - 0 !
3 files changed, 3 insertions(+), 4 deletions(-)

 fix spelling lintian warnings
33_fix_relative_paths_in_example_scripts.patch | (download)

examples/chempy/generate_amber.py | 7 4 + 3 - 0 !
examples/chempy/generate_mmff.py | 8 4 + 4 - 0 !
examples/cookbook/multiclip_ray.pml | 3 1 + 2 - 0 !
examples/devel/chempy_model02.py | 13 7 + 6 - 0 !
examples/devel/chempy_model03.py | 8 6 + 2 - 0 !
examples/devel/count_molecules.py | 7 6 + 1 - 0 !
examples/devel/mutate01.pml | 2 1 + 1 - 0 !
examples/devel/povray01.py | 10 7 + 3 - 0 !
examples/devel/sd_annotate.pml | 3 0 + 3 - 0 !
examples/devel/webgui02.py | 4 4 + 0 - 0 !
examples/launching/launch_demo.py | 12 9 + 3 - 0 !
11 files changed, 49 insertions(+), 28 deletions(-)

 fix relative paths in example scripts
 Some example scripts are intended to be used from directory they are located 
34_fix_examples_add_fetch_instead_of_load.patch | (download)

examples/cookbook/contact.pml | 3 2 + 1 - 0 !
examples/cookbook/packing.pml | 3 2 + 1 - 0 !
examples/cookbook/packsurf.pml | 3 2 + 1 - 0 !
examples/cookbook/ref_frame.pml | 9 4 + 5 - 0 !
examples/cookbook/ribosome.pml | 5 3 + 2 - 0 !
examples/cookbook/ss_xfer.pml | 14 6 + 8 - 0 !
6 files changed, 19 insertions(+), 18 deletions(-)

 use fetch instead of load in pymol scripts when necessary
 In example scripts, which require .pdb files not shipped with upstream source,
 use fetch instead of load, to download required Protein Data Bank structures.
 .
 See more on pymol's `fetch` command here: 
 http://www.pymolwiki.org/index.php/Fetch
40_mstop_movies.patch | (download)

data/demo/cgo03.py | 5 4 + 1 - 0 !
examples/cookbook/area_diff.pml | 1 1 + 0 - 0 !
examples/cookbook/scenes2movie.pml | 1 1 + 0 - 0 !
examples/devel/cgo02.py | 5 4 + 1 - 0 !
examples/devel/cgo03.py | 5 4 + 1 - 0 !
examples/devel/cgo_label_hack.py | 4 4 + 0 - 0 !
examples/devel/chempy_model03.py | 11 5 + 6 - 0 !
examples/devel/gl03.py | 4 4 + 0 - 0 !
examples/devel/mutate02.py | 2 2 + 0 - 0 !
examples/devel/scenes_to_movie01.pml | 2 1 + 1 - 0 !
examples/devel/webgui02.py | 1 1 + 0 - 0 !
11 files changed, 31 insertions(+), 10 deletions(-)

 modify examples so that they do not run forever
 When invoked in script mode (-c) pymol up until v2 used to exit; newer
 versions will loop the aninamtion forever. This patch puts an explicit
 stop at the end of each script where there is an animation being generated
 to make it stop playing.
 .
 While this potentially makes the examples less useful to run from the
 command line themselves without editing, it at least fixes the tests.

Bug: #897191

50_force_tk.patch | (download)

modules/pymol/__init__.py | 11 1 + 10 - 0 !
1 file changed, 1 insertion(+), 10 deletions(-)

 disable the qt interface to ensure the tk interface is used.
  Patch must be dropped when converting to the Qt interface.