Opened 10 years ago

Closed 10 years ago

Last modified 10 years ago

#27909 closed defect (fixed)

relax 1.3.6 packaging

Reported by: howarth@… Owned by: ryandesign (Ryan Schmidt)
Priority: Normal Milestone:
Component: ports Version:
Keywords: haspatch maintainer Cc:
Port: relax

Description

The attached Portfile.diff updates the relax package to the latest upstream 1.3.6 release. A replacement relax.patch is also attached and the previous sample.patch is dropped as it is no longer needed.

Attachments (2)

Portfile.diff (1.3 KB) - added by howarth@… 10 years ago.
Portfile changes for relax-1.3.6 update
relax.patch (1.4 KB) - added by howarth@… 10 years ago.
replacement relax.patch file

Download all attachments as: .zip

Change History (9)

Changed 10 years ago by howarth@…

Attachment: Portfile.diff added

Portfile changes for relax-1.3.6 update

Changed 10 years ago by howarth@…

Attachment: relax.patch added

replacement relax.patch file

comment:1 Changed 10 years ago by howarth@…

Note that the installed relax package is tested on the command line with the command...

relax --test-suite

comment:2 Changed 10 years ago by jmroot (Joshua Root)

Keywords: haspatch maintainer added; science removed
Version: 1.9.2

comment:3 Changed 10 years ago by ryandesign (Ryan Schmidt)

Owner: changed from macports-tickets@… to ryandesign@…
Status: newassigned

Thanks.

comment:4 Changed 10 years ago by ryandesign (Ryan Schmidt)

Resolution: fixed
Status: assignedclosed

I committed your patch in r74961.

I also disabled the universal variant, because though the port installed with the universal variant, the software it installed was not universal.

I also tweaked the reinplace statements in the post-patch block. Using the MacPorts base patch from #15514 I was getting this warning:

Warning: reinplace s|@DEST_ROOT@|/opt/local/var/macports/build/_Users_rschmidt_macports_dports_science_relax/work/destroot|g didn't change anything in /opt/local/var/macports/build/_Users_rschmidt_macports_dports_science_relax/work/relax-1.3.6/scons/install.py
Warning: reinplace s|@PREFIX@|/opt/local|g didn't change anything in /opt/local/var/macports/build/_Users_rschmidt_macports_dports_science_relax/work/relax-1.3.6/scons/install.py

Though relax.patch does patch install.py, it does not insert any placeholders into it. So I changed the reinplace to not attempt to affect that file.

comment:5 in reply to:  1 Changed 10 years ago by ryandesign (Ryan Schmidt)

Replying to howarth@…:

relax --test-suite

FYI, running this produces the error:

Traceback (most recent call last):
  File "/opt/local/bin/relax", line 58, in <module>
    from prompt import interpreter
  File "/opt/local/lib/relax/prompt/interpreter.py", line 57, in <module>
    from dx import OpenDX
  File "/opt/local/lib/relax/prompt/dx.py", line 32, in <module>
    import opendx.main
  File "/opt/local/lib/relax/opendx/main.py", line 32, in <module>
    import isosurface_3D
  File "/opt/local/lib/relax/opendx/isosurface_3D.py", line 31, in <module>
    from base_map import Base_Map
  File "/opt/local/lib/relax/opendx/base_map.py", line 36, in <module>
    from specific_fns.setup import get_specific_fn
  File "/opt/local/lib/relax/specific_fns/setup.py", line 25, in <module>
    from specific_fns.frame_order import Frame_order
  File "/opt/local/lib/relax/specific_fns/frame_order.py", line 45, in <module>
    from maths_fns import frame_order, order_parameters
  File "/opt/local/lib/relax/maths_fns/frame_order.py", line 34, in <module>
    from maths_fns.frame_order_matrix_ops import compile_2nd_matrix_free_rotor, compile_2nd_matrix_iso_cone, compile_2nd_matrix_iso_cone_free_rotor,compile_2nd_matrix_iso_cone_torsionless, compile_2nd_matrix_pseudo_ellipse, compile_2nd_matrix_pseudo_ellipse_free_rotor, compile_2nd_matrix_pseudo_ellipse_torsionless, compile_2nd_matrix_rotor, reduce_alignment_tensor
  File "/opt/local/lib/relax/maths_fns/frame_order_matrix_ops.py", line 30, in <module>
    from scipy.integrate import quad
ImportError: No module named scipy.integrate

comment:6 Changed 10 years ago by howarth@…

From the http://www.nmr-relax.com/download.html...

SciPy

Numerical integration is required for the frame order theory. This is currently not implemented within relax so the QUADPACK numerical integration provided by SciPy is used. Without this package being installed, the frame order analysis will not be accessible.

so it looks like relax now needs port:py26-scipy added to depend_lib. I happen to already have that installed from another port.

comment:7 Changed 10 years ago by ryandesign (Ryan Schmidt)

Ok, I added the py26-scipy dependency in r74964, and the test suite seems to run ok now.

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