[MacPorts] #38516: update pymol to newer svn and add fixes
#38516: update pymol to newer svn and add fixes -----------------------+-------------------------------- Reporter: howarth@… | Owner: macports-tickets@… Type: update | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.1.3 Keywords: science | Port: pymol -----------------------+-------------------------------- The attached Portfile.diff and revised setup_py.diff patch updates pymol to the current svn revision 4024.[[BR]] It also adds support for the gcc48 variant and adopts the same approach as Fedora towards eliminating the use[[BR]] of the pymol_path symlink. The patch to setup.py is also adjusted to handle the changes in current svn regarding[[BR]] the prefix_path search by placing macports' directory first. Note that the breakage in the apsb tools plugin from the[[BR]] switch to tcl/tk 8.6 still exists and I am awaiting for a fix from the developer (if one exists for the current blt code). -- Ticket URL: <https://trac.macports.org/ticket/38516> MacPorts <http://www.macports.org/> Ports system for OS X
#38516: pymol: update to svn 4024, add gcc48 variant, etc ------------------------+--------------------------------- Reporter: howarth@… | Owner: macports-tickets@… Type: update | Status: new Priority: Normal | Milestone: Component: ports | Version: Resolution: | Keywords: haspatch maintainer Port: pymol | ------------------------+--------------------------------- Changes (by larryv@…): * keywords: science => haspatch maintainer * version: 2.1.3 => Old description:
The attached Portfile.diff and revised setup_py.diff patch updates pymol to the current svn revision 4024.[[BR]] It also adds support for the gcc48 variant and adopts the same approach as Fedora towards eliminating the use[[BR]] of the pymol_path symlink. The patch to setup.py is also adjusted to handle the changes in current svn regarding[[BR]] the prefix_path search by placing macports' directory first. Note that the breakage in the apsb tools plugin from the[[BR]] switch to tcl/tk 8.6 still exists and I am awaiting for a fix from the developer (if one exists for the current blt code).
New description: The attached Portfile.diff and revised setup_py.diff patch updates pymol to the current svn revision 4024. It also adds support for the gcc48 variant and adopts the same approach as Fedora towards eliminating the use of the pymol_path symlink. The patch to setup.py is also adjusted to handle the changes in current svn regarding the prefix_path search by placing macports' directory first. Note that the breakage in the apsb tools plugin from the switch to tcl/tk 8.6 still exists and I am awaiting for a fix from the developer (if one exists for the current blt code). -- -- Ticket URL: <https://trac.macports.org/ticket/38516#comment:1> MacPorts <http://www.macports.org/> Ports system for OS X
#38516: pymol: update to svn 4024, add gcc48 variant, etc ------------------------+--------------------------------- Reporter: howarth@… | Owner: macports-tickets@… Type: update | Status: new Priority: Normal | Milestone: Component: ports | Version: Resolution: | Keywords: haspatch maintainer Port: pymol | ------------------------+--------------------------------- Comment (by howarth@…): Updated proposed changes to add missing license field as well as add new apbs_tkinter.patch to fix apbstools plugin under tcl/tk 8.6. -- Ticket URL: <https://trac.macports.org/ticket/38516#comment:2> MacPorts <http://www.macports.org/> Ports system for OS X
#38516: pymol: update to svn 4024, add gcc48 variant, etc ------------------------+--------------------------------- Reporter: howarth@… | Owner: macports-tickets@… Type: update | Status: new Priority: Normal | Milestone: Component: ports | Version: Resolution: | Keywords: haspatch maintainer Port: pymol | ------------------------+--------------------------------- Comment (by howarth@…): The attached files include the previous changes but update the pymol packaging to build the new 1.6.0 release which has huge improvements on graphics cards whose performance (like Radeon X1600) was degraded severely in the 1.5.x releases. -- Ticket URL: <https://trac.macports.org/ticket/38516#comment:3> MacPorts <http://www.macports.org/> Ports system for OS X
#38516: pymol: update to svn 4024, add gcc48 variant, etc ------------------------+--------------------------------- Reporter: howarth@… | Owner: macports-tickets@… Type: update | Status: new Priority: Normal | Milestone: Component: ports | Version: Resolution: | Keywords: haspatch maintainer Port: pymol | ------------------------+--------------------------------- Comment (by mojca@…): I fetched your patches and did some slight modifications: * used a `python` `PortGroup` instead of the outdated/deprecated `python26` * switched to `python27`, removed dependency on `python` (it should already be added by the `PortGroup`) * also added the `gcc49` variant * the latest version in SVN doesn't use dependencies on `gcc4x` ports, so I also removed that from `gcc48`, even though I didn't test those options * fixed a few offsets and "fuzzes" in the patches * replaced tabs with spaces in some patches (I'm not sure how python handles mixtures of tabs and spaces, so just in case) * adjusted some whitespace in the `Portfile` I noticed that the version in SVN is now 4039, but I didn't dare to change that. I didn't do any extensive testing of the port. If you agree with these changes, I'll commit them. If you need to upload a large number of files next time, please do a unified diff like the one I attached: {{{ svn co https://svn.macports.org/repository/macports/trunk/dports/science/pymol cd pymol # do your modifications svn diff > output-file.patch }}} -- Ticket URL: <https://trac.macports.org/ticket/38516#comment:5> MacPorts <http://www.macports.org/> Ports system for OS X
#38516: pymol: update to svn 4024, add gcc48 variant, etc ------------------------+--------------------------------- Reporter: howarth@… | Owner: macports-tickets@… Type: update | Status: new Priority: Normal | Milestone: Component: ports | Version: Resolution: | Keywords: haspatch maintainer Port: pymol | ------------------------+--------------------------------- Comment (by mojca@…): Also: #38532 (which indicated PSF). -- Ticket URL: <https://trac.macports.org/ticket/38516#comment:6> MacPorts <http://www.macports.org/> Ports system for OS X
#38516: pymol: update to svn 4024, add gcc48 variant, etc ------------------------+--------------------------------- Reporter: howarth@… | Owner: macports-tickets@… Type: update | Status: new Priority: Normal | Milestone: Component: ports | Version: Resolution: | Keywords: haspatch maintainer Port: pymol | ------------------------+--------------------------------- Comment (by howarth@…): The changes in pymol-1.6.0.diff are fine. Don't forget to also commit the update to blt at https://trac.macports.org/ticket/40203 otherwise the APBS Tools plugin in pymol will crash under tcl/tk 8.6 when the "Choose Externally Generated PQR:" button is clicked in the PyMOL APBS Tools window. -- Ticket URL: <https://trac.macports.org/ticket/38516#comment:7> MacPorts <http://www.macports.org/> Ports system for OS X
#38516: pymol: update to svn 4024, add gcc48 variant, etc ------------------------+--------------------------------- Reporter: howarth@… | Owner: macports-tickets@… Type: update | Status: new Priority: Normal | Milestone: Component: ports | Version: Resolution: | Keywords: haspatch maintainer Port: pymol | ------------------------+--------------------------------- Comment (by mojca@…): Thank you for pointing that out (next time it makes sense to provide a link to related tickets early enough). Now - ouch, I don't understand a bit about the other ticket, so I feel a bit uncomfortable committing that one, even though the time is way past the maintainer timeout. I suggest asking on the developer mailing list. Just a question: does the Tcl/Tk patch need to be committed before upgrading pymol? If the answer is no, I can commit pymol now. If not, I would really like to see someone else confirm the Tcl/Tk patch. Just a hint: it might help if you provide some links to the origin of the patch or discussion(s) about it in the other ticket. -- Ticket URL: <https://trac.macports.org/ticket/38516#comment:8> MacPorts <http://www.macports.org/> Ports system for OS X
#38516: pymol: update to svn 4024, add gcc48 variant, etc ------------------------+--------------------------------- Reporter: howarth@… | Owner: macports-tickets@… Type: update | Status: new Priority: Normal | Milestone: Component: ports | Version: Resolution: | Keywords: haspatch maintainer Port: pymol | ------------------------+--------------------------------- Comment (by howarth@…): Blt is a pretty much a nightmare. The upstream developer no longer works on it and basically wants to be left alone. One reason is that the package is incorrectly written to use many private data structures and calls in tcl/tk (which are simply hard coded into the blt sources from an ancient tcl/tk release). The proposed change in https://trac.macports.org/ticket/40203 resolves the tk side of this by replacing the out of date local declarations of private tk data structures and calls with those from the private headers of tcl/tk 8.6.0. Since MacPorts doesn't package the tcl/tk private headers, the proposed patch bundles these from the tcl/tk 8.6.0 sources for the blt build. Eventually someone needs to do the same for the tcl private header usage in blt (as it uses a number of data structure fields that are no longer used in tcl as of 8.5). -- Ticket URL: <https://trac.macports.org/ticket/38516#comment:9> MacPorts <http://www.macports.org/> Ports system for OS X
#38516: pymol: update to svn 4024, add gcc48 variant, etc ------------------------+--------------------------------- Reporter: howarth@… | Owner: macports-tickets@… Type: update | Status: new Priority: Normal | Milestone: Component: ports | Version: Resolution: | Keywords: haspatch maintainer Port: pymol | ------------------------+--------------------------------- Comment (by howarth@…): The blt fix doesn't have to be committed for pymol to build. The issue is that blt (as used in the APBS Tools plugin of pymol) is broken due to the switch to tcl/tk 8.6.0 in MacPorts. The private tk internals forked enough to break using blt in this context. You can easily see this by the following steps. 1) Install pymol using the pymol-1.6.0.diff changes. 2) execute pymol and select the APBS Tools plugin 2.1 menu item from the Plugin menu in pymol 3) when the APBS Tools window appears click on the "Choose Externally Generated PQR" button. This will crash pymol under the current blt. If you install the proposed blt packaging from https://trac.macports.org/ticket/40203 and repeat these steps, the file chooser will appear instead of pymol crashing. -- Ticket URL: <https://trac.macports.org/ticket/38516#comment:10> MacPorts <http://www.macports.org/> Ports system for OS X
#38516: pymol: update to svn 4024, add gcc48 variant, etc ------------------------+--------------------------------- Reporter: howarth@… | Owner: macports-tickets@… Type: update | Status: new Priority: Normal | Milestone: Component: ports | Version: Resolution: | Keywords: haspatch maintainer Port: pymol | ------------------------+--------------------------------- Comment (by mojca@…): The main question is: do you prefer me to commit the new version of pymol now or do you prefer to wait until the issue with Tcl/Tk is solved? -- Ticket URL: <https://trac.macports.org/ticket/38516#comment:11> MacPorts <http://www.macports.org/> Ports system for OS X
#38516: pymol: update to svn 4024, add gcc48 variant, etc ------------------------+--------------------------------- Reporter: howarth@… | Owner: macports-tickets@… Type: update | Status: new Priority: Normal | Milestone: Component: ports | Version: Resolution: | Keywords: haspatch maintainer Port: pymol | ------------------------+--------------------------------- Comment (by howarth@…): Replying to [comment:11 mojca@…]:
The main question is: do you prefer me to commit the new version of pymol now or do you prefer to wait until the issue with Tcl/Tk is solved?
I don't understand the question. There are no issues with Tcl/Tk and pymol. Blt has issues with Tcl/Tk (due to its own improper use of private header data structure and calls) but that issue is orthogonal to updating pymol. Please commit the changes in pymol-1.6.0.diff. -- Ticket URL: <https://trac.macports.org/ticket/38516#comment:12> MacPorts <http://www.macports.org/> Ports system for OS X
#38516: pymol: update to svn 4024, add gcc48 variant, etc ------------------------+--------------------------------- Reporter: howarth@… | Owner: macports-tickets@… Type: update | Status: closed Priority: Normal | Milestone: Component: ports | Version: Resolution: fixed | Keywords: haspatch maintainer Port: pymol | ------------------------+--------------------------------- Changes (by mojca@…): * status: new => closed * resolution: => fixed Comment: Committed in r110734. -- Ticket URL: <https://trac.macports.org/ticket/38516#comment:13> MacPorts <http://www.macports.org/> Ports system for OS X
#38516: pymol: update to svn 4024, add gcc48 variant, etc ------------------------+--------------------------------- Reporter: howarth@… | Owner: macports-tickets@… Type: update | Status: closed Priority: Normal | Milestone: Component: ports | Version: Resolution: fixed | Keywords: haspatch maintainer Port: pymol | ------------------------+--------------------------------- Comment (by mojca@…): Just curious: is it possible to build pymol with Tcl with `+corefoundation` at all? The nasty issue is that now pymol and its dependencies (at least stimfit, but possibly others) all fail to build on the buildbot: * https://build.macports.org/builders/buildports-lion-x86_64/builds/14039 -- Ticket URL: <https://trac.macports.org/ticket/38516#comment:14> MacPorts <http://www.macports.org/> Ports system for OS X
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