[Debichem-devel] Pymol patches and suggestions

Daniel Leidert daniel.leidert.spam at gmx.net
Sun Feb 1 00:19:13 UTC 2009


Michael, I've checked the list of Pymol patches and found some, which I
would like to comment/discuss. Can you please clarify the situation a
bit? I would like to forward all non-Debian specific patches to upstream
to reduce our workload with this package. Some of the patches follow:

- 04_Rules.make.dpatch

For what is it used? Is it still used or is Rules.make obsolete by
setup.py? The python versions in this file look very old and a build
without this patch succeeds.

- 05_examples_data_path.dpatch

Uses "$PYMOL_DATA_PATH" which should be "$PYMOL_DATA/demo", right? Is
the `import os' necessary here for the absolute path? Sorry if this is a
dumb question. I don't know much about Python.

- 11_fix__cmd_import.dpatch

Which problem did this one solve? It looks like a patch, which could be
suggested to upstream.

- 13_activate_vmd_plugin.dpatch

Can we maybe provide a switch-based solution to upstream to get rid of
this patch? I'm not familiar with setup.py writing, but maybe someone
else is(?).

- 09_chempy_data_path.dpatch, 17_cmyk_png_data_path.dpatch

I wonder, if we should change the installation strategy for
data/{chempy,pymol} and do not install these directories
as /usr/share/{chempy,pymol}. Instead we could install these directories
as /usr/share/pymol/data/{chempy,pymol}. The rationale behind is,
that /usr/share/pymol/date IMO is similar to $PYMOL_DATA even in
upstreams code. We could then suggest to upstream to use consequently
$PYMOL_DATA instead of $PYMOL_PATH/data in its source. So we can get rid
of the above patches and IMHO this will make the upstream code a bit
cleaner for distribution packagers and upstream, because then one can
consequently rely on $PYMOL_PATH and $PYMOL_DATA (if both are different
like in our case) without needing to patch files.


Forwarded to upstream (bug tracker):
- 06_remove_shebang.dpatch
- 14_script_not_executable.dpatch
- 16_pymem_del.dpatch

I further created an item in the upstream bug-tracker to remove
executable permissions from data files. So we can remove the chmod calls
in debian/rules.

Please comment.

Regards, Daniel

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