Opened 13 years ago

Closed 12 years ago

#30331 closed enhancement (fixed)

switch pymol from numeric to numpy/scipy as well as clang on darwin11

Reported by: howarth@… Owned by: macports-tickets@…
Priority: Normal Milestone:
Component: ports Version: 2.0.0
Keywords: haspatch Cc: mf2k (Frank Schima), ryandesign (Ryan Carsten Schmidt)
Port: pymol

Description

The attached Portfile.diff and pymol_numpy.diff patch switches pymol from using Numeric to using py26-numpy and py26-scipy instead. The Portfile.diff also switches the build compilers to clang/clang++ on darwin11.

Attachments (4)

pymol_numpy.diff (2.7 KB) - added by howarth@… 13 years ago.
pymol_numpy.diff to use oldnumeric support
setup_py.diff (1.5 KB) - added by howarth@… 13 years ago.
replacement setup_py.diff
pymol-configure.compiler.diff (1.8 KB) - added by ryandesign (Ryan Carsten Schmidt) 13 years ago.
proposed patch
Portfile.diff (2.2 KB) - added by howarth@… 13 years ago.
Portfile.diff with requested use of configure.compiler and svn bump

Download all attachments as: .zip

Change History (14)

Changed 13 years ago by howarth@…

Attachment: pymol_numpy.diff added

pymol_numpy.diff to use oldnumeric support

comment:1 Changed 13 years ago by ryandesign (Ryan Carsten Schmidt)

Keywords: haspatch added; science removed

comment:2 Changed 13 years ago by mf2k (Frank Schima)

Using this diff, I see the following error.

--->  Applying /opt/mports/trunk/dports/science/pymol/files/setup_py.diff
patching file setup.py
Hunk #2 FAILED at 115.
1 out of 3 hunks FAILED -- saving rejects to file setup.py.rej

comment:3 Changed 13 years ago by mf2k (Frank Schima)

Cc: macsforever2000@… added

Cc Me!

comment:4 Changed 13 years ago by howarth@…

I'll look into this issue later this evening.

Changed 13 years ago by howarth@…

Attachment: setup_py.diff added

replacement setup_py.diff

comment:5 Changed 13 years ago by howarth@…

Sorry about that. This ticket needs the Portfile.diff applied and the replacement setup_py.diff used. Again the current svn of pymol no longer requires the pymol_numpy.diff file (but these forms don't allow files to be deleted from a Ticket).

comment:6 Changed 13 years ago by mf2k (Frank Schima)

Resolution: fixed
Status: newclosed

comment:7 Changed 13 years ago by ryandesign (Ryan Carsten Schmidt)

Cc: ryandesign@… added
Resolution: fixed
Status: closedreopened

Why clang on Darwin 11? Is it that you don't want to use llvm-gcc-4.2? If so, then that's what you should test for. If you want to be more selective than that, test the Xcode version, not the Mac OS X version. Several recent commits show examples of this.

Why disable archflags for clang? Clang understands archflags. Only MacPorts gcc compilers don't.

I really wish this port would use configure.compiler. Consider the attached patch.

Changed 13 years ago by ryandesign (Ryan Carsten Schmidt)

proposed patch

comment:8 Changed 13 years ago by howarth@…

Have you actually tried to build the gcc4x variants with your patch. This simply won't work...

#29345

due to the use of the setup.py build method, CC and CXX must to appear before setup.py. Only the use of build.env achieves this
The use of configure.compiler will place CC/CXX after setup.py and they won't be honored in the build.

comment:9 Changed 13 years ago by ryandesign (Ryan Carsten Schmidt)

Yes, I did try it—not all the way through, but enough to see that it was building with the compiler I asked for. Did you read my patch? I'm not removing the use of build.env.

Changed 13 years ago by howarth@…

Attachment: Portfile.diff added

Portfile.diff with requested use of configure.compiler and svn bump

comment:10 Changed 12 years ago by ryandesign (Ryan Carsten Schmidt)

Resolution: fixed
Status: reopenedclosed

These changes got included in r90200.

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