Opened 11 years ago

Last modified 9 years ago

#40457 new submission

NEW: NEURON

Reported by: neurodroid (Christoph Schmidt-Hieber) Owned by: macports-tickets@…
Priority: Normal Milestone:
Component: ports Version:
Keywords: Cc: neurodroid (Christoph Schmidt-Hieber), lea.goetz.13@…, arnd.roth@…, jonathan.cornford@…, gizida@…
Port: neuron

Description

NEURON is a simulation environment for neurons and networks of neurons that is widely used in neuroscience. Some comments on the Portfiles:

  • A separate port is required for the graphics toolkit (neuron-iv) because it's optional (neuron has a +nogui variant), the source changes more rarely than neuron's, and it's under a different license.
  • The source tarballs are currently hosted on a mirror because the the version on the official server may change its url at any time.
  • The patch that comes with this Portfile has been accepted upstream and will be included in the upcoming version 7.4.

Attachments (13)

Portfile-neuron (3.4 KB) - added by neurodroid (Christoph Schmidt-Hieber) 11 years ago.
Portfile for NEURON
Portfile-neuron-iv (1.2 KB) - added by neurodroid (Christoph Schmidt-Hieber) 11 years ago.
Portfile for the NEURON graphics toolkit (based on InterViews)
Portfile-neuron.1 (3.4 KB) - added by neurodroid (Christoph Schmidt-Hieber) 11 years ago.
Portfile for NEURON
Portfile-neuron.2 (3.3 KB) - added by neurodroid (Christoph Schmidt-Hieber) 11 years ago.
Portfile for NEURON
Portfile-neuron-iv.2 (1.2 KB) - added by neurodroid (Christoph Schmidt-Hieber) 11 years ago.
Portfile for the NEURON graphics toolkit (based on InterViews)
Portfile-neuron-iv.3 (1.6 KB) - added by neurodroid (Christoph Schmidt-Hieber) 11 years ago.
Portfile for the NEURON graphics toolkit (based on InterViews)
Portfile-neuron.3 (3.5 KB) - added by neurodroid (Christoph Schmidt-Hieber) 11 years ago.
Portfile for NEURON
Portfile-neuron.4 (3.5 KB) - added by neurodroid (Christoph Schmidt-Hieber) 11 years ago.
Portfile for NEURON - updated to work with new *-default versions of mpi
Portfile-neuron.5 (3.9 KB) - added by neurodroid (Christoph Schmidt-Hieber) 10 years ago.
Portfile for NEURON - build fixes, py34 support
Portfile (3.9 KB) - added by neurodroid (Christoph Schmidt-Hieber) 9 years ago.
Portfile for NEURON - updated to 7.4
Portfile-neuron.6 (3.9 KB) - added by neurodroid (Christoph Schmidt-Hieber) 9 years ago.
Portfile for NEURON - updated to 7.4 (clarified file name)
Portfile-neuron-iv.4 (1.6 KB) - added by neurodroid (Christoph Schmidt-Hieber) 9 years ago.
Portfile for the NEURON graphics toolkit (based on InterViews) - updated to IV 19
Portfile-neuron.7 (3.9 KB) - added by neurodroid (Christoph Schmidt-Hieber) 9 years ago.
Portfile for NEURON (py35 support, updated to rel 1370)

Download all attachments as: .zip

Change History (25)

Changed 11 years ago by neurodroid (Christoph Schmidt-Hieber)

Attachment: Portfile-neuron added

Portfile for NEURON

Changed 11 years ago by neurodroid (Christoph Schmidt-Hieber)

Attachment: Portfile-neuron-iv added

Portfile for the NEURON graphics toolkit (based on InterViews)

comment:1 Changed 11 years ago by ryandesign (Ryan Carsten Schmidt)

Variants whose names begin with "no" are deprecated and should not be added to new ports. Instead, if there must be a variant, name it "gui" and enable it by default.

comment:2 in reply to:  1 Changed 11 years ago by neurodroid (Christoph Schmidt-Hieber)

Replying to ryandesign@…:

Variants whose names begin with "no" are deprecated and should not be added to new ports. Instead, if there must be a variant, name it "gui" and enable it by default.

Thanks for your review. A revised Portfile is attached.

To make the binaries directly executable without prefix, I was thinking to add the following to post-destroot:

ln -s ${applications_dir}/NEURON/nrn/${arch}/bin/* ${destroot}${prefix}/bin/

Is there a better way to achieve this?

Changed 11 years ago by neurodroid (Christoph Schmidt-Hieber)

Attachment: Portfile-neuron.1 added

Portfile for NEURON

comment:3 Changed 11 years ago by ryandesign (Ryan Carsten Schmidt)

"destroot.destdir DESTDIR=${destroot}" is the default so it should be removed.

Why does neuron-iv set prefix to ${applications_dir}? It doesn't install any OS X application bundles there. It just installs headers, binaries and libraries which would seem to be more at home in ${prefix}.

comment:4 in reply to:  3 ; Changed 11 years ago by neurodroid (Christoph Schmidt-Hieber)

Replying to ryandesign@…:

"destroot.destdir DESTDIR=${destroot}" is the default so it should be removed.

Fixed in the revised Portfiles.

Why does neuron-iv set prefix to ${applications_dir}? It doesn't install any OS X application bundles there. It just installs headers, binaries and libraries which would seem to be more at home in ${prefix}.

NEURON has somewhat unusual installation habits. The default prefix for source installations and binary installers is /Applications/NEURON/iv. Coming from a previous installation, users will expect neuron-iv to reside in NEURON's application directory rather than in ${prefix}.

Changed 11 years ago by neurodroid (Christoph Schmidt-Hieber)

Attachment: Portfile-neuron.2 added

Portfile for NEURON

Changed 11 years ago by neurodroid (Christoph Schmidt-Hieber)

Attachment: Portfile-neuron-iv.2 added

Portfile for the NEURON graphics toolkit (based on InterViews)

comment:5 in reply to:  4 ; Changed 11 years ago by larryv (Lawrence Velázquez)

Replying to christsc@…:

NEURON has somewhat [http://www.neuron.yale.edu/neuron/download/compilestd_osx#ivandnrn unusual installation habits]. The default prefix for source installations and binary installers is /Applications/NEURON/iv. Coming from a previous installation, users will expect neuron-iv to reside in NEURON's application directory rather than in ${prefix}.

Maybe you could install to ${prefix} and symlink into ${applications_dir}?

comment:6 in reply to:  5 Changed 11 years ago by neurodroid (Christoph Schmidt-Hieber)

Replying to larryv@…:

Replying to christsc@…:

NEURON has somewhat [http://www.neuron.yale.edu/neuron/download/compilestd_osx#ivandnrn unusual installation habits]. The default prefix for source installations and binary installers is /Applications/NEURON/iv. Coming from a previous installation, users will expect neuron-iv to reside in NEURON's application directory rather than in ${prefix}.

Maybe you could install to ${prefix} and symlink into ${applications_dir}?

Given that none of neuron-iv's headers, binaries and libraries will be used by any port other than NEURON, wouldn't it be cleaner not to install anything in ${prefix}? This would also avoid any potential file naming collisions. See original post why neuron-iv still needs to be a separate port.

comment:7 Changed 11 years ago by neurodroid (Christoph Schmidt-Hieber)

I've updated the Portfiles to work on OS X 10.9. The patch has made into the repository and is not required any longer. Please let me know what remains to be done to get this into MacPorts.

Changed 11 years ago by neurodroid (Christoph Schmidt-Hieber)

Attachment: Portfile-neuron-iv.3 added

Portfile for the NEURON graphics toolkit (based on InterViews)

Changed 11 years ago by neurodroid (Christoph Schmidt-Hieber)

Attachment: Portfile-neuron.3 added

Portfile for NEURON

Changed 11 years ago by neurodroid (Christoph Schmidt-Hieber)

Attachment: Portfile-neuron.4 added

Portfile for NEURON - updated to work with new *-default versions of mpi

Changed 10 years ago by neurodroid (Christoph Schmidt-Hieber)

Attachment: Portfile-neuron.5 added

Portfile for NEURON - build fixes, py34 support

Changed 9 years ago by neurodroid (Christoph Schmidt-Hieber)

Attachment: Portfile added

Portfile for NEURON - updated to 7.4

Changed 9 years ago by neurodroid (Christoph Schmidt-Hieber)

Attachment: Portfile-neuron.6 added

Portfile for NEURON - updated to 7.4 (clarified file name)

Changed 9 years ago by neurodroid (Christoph Schmidt-Hieber)

Attachment: Portfile-neuron-iv.4 added

Portfile for the NEURON graphics toolkit (based on InterViews) - updated to IV 19

comment:8 Changed 9 years ago by neurodroid (Christoph Schmidt-Hieber)

Cc: christsc@… added

Cc Me!

comment:9 Changed 9 years ago by lea.goetz.13@…

Cc: lea.goetz.13@… added

Cc Me!

comment:10 Changed 9 years ago by arnd.roth@…

Cc: arnd.roth@… added

Cc Me!

comment:11 Changed 9 years ago by jonathan.cornford@…

Cc: jonathan.cornford@… added

Cc Me!

comment:12 Changed 9 years ago by gizida@…

Cc: gizida@… added

Cc Me!

Changed 9 years ago by neurodroid (Christoph Schmidt-Hieber)

Attachment: Portfile-neuron.7 added

Portfile for NEURON (py35 support, updated to rel 1370)

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