pymol should be updated to 2.1.0 to use PyQt interface

[Jack Howarth]

It is trivial to update the current pymol packaging in 18.04 to the newest pymol 2.1.0 tarball at available on https://sourceforge.net/projects/pymol/files/pymol/2/. The 2.1.0 release now runs under a PyQt when present so the control file for the deb build only needs...

         python-pyqt5,
         python-pyqt5.qtopengl,

added for the Depends of the pymol Package section to insure that the PyQt support is available for use.

[Jack Howarth (jwhowarth)]

The 02_test-suite.patch has to be regenerated to cope with context changes in the pymol 2.1.0 sources.

[Jack Howarth (jwhowarth)]

The 22_fix_pymol_import.patch has to be regenerated to cope with context changes in the pymol 2.1.0 sources.

[Jack Howarth (jwhowarth)]

The 33_fix_relative_paths_in_example_scripts.patch has to be regenerated to cope with context changes in the pymol 2.1.0 sources.

[Jack Howarth (jwhowarth)]

Add additional 40_fix_apbstools_search_path.patch should be added to solve the long standing issue of the apbstools plugin not being able to find the required psize.py and pdb2pqr.py files from the pdb2pqr package in ubuntu. Trivial to fix.

[Jack Howarth (jwhowarth)]

The PyQt GUI for pymol appears as shown in the attached screen shot under 18.04.

[Ubuntu Foundations Team Bug Bot (crichton)]

The attachment "02_test-suite.patch" seems to be a patch. If it isn't, please remove the "patch" flag from the attachment, remove the "patch" tag, and if you are a member of the ~ubuntu-reviewers, unsubscribe the team.

[This is an automated message performed by a Launchpad user owned by ~brian-murray, for any issues please contact him.]

[Jack Howarth (jwhowarth)]

Just to be clear, the changes required to the existing packaging are...

--- pymol-1.8.4.0+dfsg/debian/control 2016-10-20 11:33:21.000000000 -0400
+++ pymol-2.1.0+dfsg/debian/control 2018-04-14 13:57:37.000000000 -0400
@@ -24,6 +24,8 @@
 Package: pymol
 Architecture: any
 Depends: python-numpy,
+ python-pyqt5,
+ python-pyqt5.qtopengl,
          python-pmw,
          python-tk,
          ${misc:Depends},

--- pymol-1.8.4.0+dfsg/debian/patches/series 2016-10-20 11:33:21.000000000 -0400
+++ pymol-2.1.0+dfsg/debian/patches/series 2018-04-14 14:04:52.000000000 -0400
@@ -4,8 +4,8 @@
 #24_autodock_plugin.patch
 27_fix_pymol_path_in_setup.patch
 28_no_data_install_in_python_path.patch
-29_fix_path_to_splash.patch
 31_fix_format-security.patch
 32_fix_spelling_lintian_warnings.patch
 33_fix_relative_paths_in_example_scripts.patch
 34_fix_examples_add_fetch_instead_of_load.patch
+40_fix_apbstools_search_path.patch

[Jeremy Bícha (jbicha)]

Ubuntu's pymol has no changes compared to Debian. Therefore, it would be useful if you could report this bug to the Debian maintainers of pymol.

https://wiki.ubuntu.com/Debian/Bugs

[Graham Inggs (ginggs)]

It seems this was fixed in disco.

pymol (2.2.0+dfsg-3) unstable; urgency=medium

  * Team Upload.
  * Upload Qt5 GUI to unstable for wider testing.
  * Merge changes from previous NMU 2.2.0+dfsg-1.1.
  * Update Standards-Version to 4.3.0 (no changes required).
  * Remove unneeded Suggests: python3-tk from pymol-data.
  * Fix up autopkgtest tests for Qt5 GUI.

 -- Stuart Prescott <email address hidden> Mon, 31 Dec 2018 17:22:59 +1100