Opened 6 years ago

Last modified 4 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) 6 years ago.
Portfile for NEURON
Portfile-neuron-iv (1.2 KB) - added by neurodroid (Christoph Schmidt-Hieber) 6 years ago.
Portfile for the NEURON graphics toolkit (based on InterViews)
Portfile-neuron.1 (3.4 KB) - added by neurodroid (Christoph Schmidt-Hieber) 6 years ago.
Portfile for NEURON
Portfile-neuron.2 (3.3 KB) - added by neurodroid (Christoph Schmidt-Hieber) 6 years ago.
Portfile for NEURON
Portfile-neuron-iv.2 (1.2 KB) - added by neurodroid (Christoph Schmidt-Hieber) 6 years ago.
Portfile for the NEURON graphics toolkit (based on InterViews)
Portfile-neuron-iv.3 (1.6 KB) - added by neurodroid (Christoph Schmidt-Hieber) 6 years ago.
Portfile for the NEURON graphics toolkit (based on InterViews)
Portfile-neuron.3 (3.5 KB) - added by neurodroid (Christoph Schmidt-Hieber) 6 years ago.
Portfile for NEURON
Portfile-neuron.4 (3.5 KB) - added by neurodroid (Christoph Schmidt-Hieber) 6 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) 5 years ago.
Portfile for NEURON - build fixes, py34 support
Portfile (3.9 KB) - added by neurodroid (Christoph Schmidt-Hieber) 4 years ago.
Portfile for NEURON - updated to 7.4
Portfile-neuron.6 (3.9 KB) - added by neurodroid (Christoph Schmidt-Hieber) 4 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) 4 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) 4 years ago.
Portfile for NEURON (py35 support, updated to rel 1370)

Download all attachments as: .zip

Change History (25)

Changed 6 years ago by neurodroid (Christoph Schmidt-Hieber)

Attachment: Portfile-neuron added

Portfile for NEURON

Changed 6 years ago by neurodroid (Christoph Schmidt-Hieber)

Attachment: Portfile-neuron-iv added

Portfile for the NEURON graphics toolkit (based on InterViews)

comment:1 Changed 6 years ago by ryandesign (Ryan 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 6 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 6 years ago by neurodroid (Christoph Schmidt-Hieber)

Attachment: Portfile-neuron.1 added

Portfile for NEURON

comment:3 Changed 6 years ago by ryandesign (Ryan 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 6 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 6 years ago by neurodroid (Christoph Schmidt-Hieber)

Attachment: Portfile-neuron.2 added

Portfile for NEURON

Changed 6 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 6 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 6 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 6 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 6 years ago by neurodroid (Christoph Schmidt-Hieber)

Attachment: Portfile-neuron-iv.3 added

Portfile for the NEURON graphics toolkit (based on InterViews)

Changed 6 years ago by neurodroid (Christoph Schmidt-Hieber)

Attachment: Portfile-neuron.3 added

Portfile for NEURON

Changed 6 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 5 years ago by neurodroid (Christoph Schmidt-Hieber)

Attachment: Portfile-neuron.5 added

Portfile for NEURON - build fixes, py34 support

Changed 4 years ago by neurodroid (Christoph Schmidt-Hieber)

Attachment: Portfile added

Portfile for NEURON - updated to 7.4

Changed 4 years ago by neurodroid (Christoph Schmidt-Hieber)

Attachment: Portfile-neuron.6 added

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

Changed 4 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 4 years ago by neurodroid (Christoph Schmidt-Hieber)

Cc: christsc@… added

Cc Me!

comment:9 Changed 4 years ago by lea.goetz.13@…

Cc: lea.goetz.13@… added

Cc Me!

comment:10 Changed 4 years ago by arnd.roth@…

Cc: arnd.roth@… added

Cc Me!

comment:11 Changed 4 years ago by jonathan.cornford@…

Cc: jonathan.cornford@… added

Cc Me!

comment:12 Changed 4 years ago by gizida@…

Cc: gizida@… added

Cc Me!

Changed 4 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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