Octave extensions by davydden · Pull Request #1113 · spack/spack

davydden · 2016-06-24T22:40:19Z

UPDATE: does install now, octave seems to pick up the installed package:

octave:1> pkg list
Package Name  | Version | Installation directory
--------------+---------+-----------------------
     specfun  |   1.1.0 | /Users/davydden/spack/opt/spack/darwin-elcapitan-x86_64/clang-7.3.0-apple/octave-specfun-1.1.0-z4jrho7a7tnkiflm4d6s373yzpavrj3h/specfun-1.1.0
     splines  |   1.2.7 | /Users/davydden/octave/splines-1.2.7

relevant documentation
https://www.gnu.org/software/octave/doc/v4.0.1/Installing-and-Removing-Packages.html
https://www.gnu.org/software/octave/doc/v4.0.1/Command-Line-Options.html#Command-Line-Options

TODO if possible:

on uninstallation i need to call octave --eval pkg uninstall <name>. Otherwise octave still consider the package to be installed.

outdated:
I can install packages from Spack's env bash:

$ spack env octave-specfun bash
bash-3.2$ octave --texi-macros-file=/dev/null --eval "pkg install /Users/davydden/Downloads/specfun-1.1.0.tar.gz"

but i can't make it work from within Spack:

$ spack install octave-specfun
==> Installing octave-specfun
==> octave is already installed in /Users/davydden/spack/opt/spack/darwin-elcapitan-x86_64/clang-7.3.0-apple/octave-4.0.2-3odgkplg75v5myrzy3bgyme425p64l4j
==> Already downloaded /Users/davydden/spack/var/spack/stage/octave-specfun-1.1.0-z4jrho7a7tnkiflm4d6s373yzpavrj3h/specfun-1.1.0.tar.gz
==> Already staged octave-specfun-1.1.0-z4jrho7a7tnkiflm4d6s373yzpavrj3h in /Users/davydden/spack/var/spack/stage/octave-specfun-1.1.0-z4jrho7a7tnkiflm4d6s373yzpavrj3h
==> No patches needed for octave-specfun
==> Building octave-specfun
==> Error: Install failed for octave-specfun.  Nothing was installed!
==> Error: Installation process had nonzero exit code : 256

whereas from log you see that it did something

==> '/Users/davydden/spack/opt/spack/darwin-elcapitan-x86_64/clang-7.3.0-apple/octave-4.0.2-3odgkplg75v5myrzy3bgyme425p64l4j/bin/octave' '--quiet' '--norc' '--built-in-docstrings-file=/dev/null' '--texi-macros-file=/dev/null' '--eval' 'pkg install /Users/davydden/spack/var/spack/stage/octave-specfun-1.1.0-z4jrho7a7tnkiflm4d6s373yzpavrj3h/specfun-1.1.0.tar.gz'
mkoctfile: stripping disabled on this platform
clang: warning: argument unused during compilation: '-pthread'
warning: function /Users/davydden/octave/specfun-1.1.0/ellipke.m shadows a core library function
warning: function /Users/davydden/octave/specfun-1.1.0/erfcinv.m shadows a built-in function
warning: function /Users/davydden/octave/specfun-1.1.0/expint.m shadows a core library function
/var/folders/5k/sqpp24tx3ylds4fgm13pfht00000gn/T/octave-help-9OPCdN:13: Unknown command `seealso'.
/var/folders/5k/sqpp24tx3ylds4fgm13pfht00000gn/T/octave-help-9OPCdN:13: Misplaced {.
/var/folders/5k/sqpp24tx3ylds4fgm13pfht00000gn/T/octave-help-9OPCdN:13: Misplaced }.
warning: doc_cache_create: unusable help text found in file 'Ci'
/var/folders/5k/sqpp24tx3ylds4fgm13pfht00000gn/T/octave-help-WRdpHY:13: Unknown command `seealso'.
/var/folders/5k/sqpp24tx3ylds4fgm13pfht00000gn/T/octave-help-WRdpHY:13: Misplaced {.
/var/folders/5k/sqpp24tx3ylds4fgm13pfht00000gn/T/octave-help-WRdpHY:13: Misplaced }.
warning: doc_cache_create: unusable help text found in file 'cosint'
/var/folders/5k/sqpp24tx3ylds4fgm13pfht00000gn/T/octave-help-HeNvrN:6: Unknown command `seealso'.
/var/folders/5k/sqpp24tx3ylds4fgm13pfht00000gn/T/octave-help-HeNvrN:6: Misplaced {.
/var/folders/5k/sqpp24tx3ylds4fgm13pfht00000gn/T/octave-help-HeNvrN:6: Misplaced }.
warning: doc_cache_create: unusable help text found in file 'dirac'
/var/folders/5k/sqpp24tx3ylds4fgm13pfht00000gn/T/octave-help-cnbSxE:14: Unknown command `seealso'.
/var/folders/5k/sqpp24tx3ylds4fgm13pfht00000gn/T/octave-help-cnbSxE:14: Misplaced {.
/var/folders/5k/sqpp24tx3ylds4fgm13pfht00000gn/T/octave-help-cnbSxE:14: Misplaced }.
warning: doc_cache_create: unusable help text found in file 'ellipke'
/var/folders/5k/sqpp24tx3ylds4fgm13pfht00000gn/T/octave-help-FGVA9x:6: Unknown command `seealso'.
/var/folders/5k/sqpp24tx3ylds4fgm13pfht00000gn/T/octave-help-FGVA9x:6: Misplaced {.
/var/folders/5k/sqpp24tx3ylds4fgm13pfht00000gn/T/octave-help-FGVA9x:6: Misplaced }.
warning: doc_cache_create: unusable help text found in file 'erfcinv'
/var/folders/5k/sqpp24tx3ylds4fgm13pfht00000gn/T/octave-help-omRfau:13: Unknown command `seealso'.
/var/folders/5k/sqpp24tx3ylds4fgm13pfht00000gn/T/octave-help-omRfau:13: Misplaced {.
/var/folders/5k/sqpp24tx3ylds4fgm13pfht00000gn/T/octave-help-omRfau:13: Misplaced }.
warning: doc_cache_create: unusable help text found in file 'expint'
/var/folders/5k/sqpp24tx3ylds4fgm13pfht00000gn/T/octave-help-XeOy1r:13: Unknown command `seealso'.
/var/folders/5k/sqpp24tx3ylds4fgm13pfht00000gn/T/octave-help-XeOy1r:13: Misplaced {.
/var/folders/5k/sqpp24tx3ylds4fgm13pfht00000gn/T/octave-help-XeOy1r:13: Misplaced }.
warning: doc_cache_create: unusable help text found in file 'expint_E1'
/var/folders/5k/sqpp24tx3ylds4fgm13pfht00000gn/T/octave-help-u0HNCs:13: Unknown command `seealso'.
/var/folders/5k/sqpp24tx3ylds4fgm13pfht00000gn/T/octave-help-u0HNCs:13: Misplaced {.
/var/folders/5k/sqpp24tx3ylds4fgm13pfht00000gn/T/octave-help-u0HNCs:13: Misplaced }.
warning: doc_cache_create: unusable help text found in file 'expint_Ei'
/var/folders/5k/sqpp24tx3ylds4fgm13pfht00000gn/T/octave-help-XHmHqv:18: Unknown command `seealso'.
/var/folders/5k/sqpp24tx3ylds4fgm13pfht00000gn/T/octave-help-XHmHqv:18: Misplaced {.
/var/folders/5k/sqpp24tx3ylds4fgm13pfht00000gn/T/octave-help-XHmHqv:18: Misplaced }.
warning: doc_cache_create: unusable help text found in file 'heaviside'
/var/folders/5k/sqpp24tx3ylds4fgm13pfht00000gn/T/octave-help-ai08hV:27: Unknown command `seealso'.
/var/folders/5k/sqpp24tx3ylds4fgm13pfht00000gn/T/octave-help-ai08hV:27: Misplaced {.
/var/folders/5k/sqpp24tx3ylds4fgm13pfht00000gn/T/octave-help-ai08hV:27: Misplaced }.
warning: doc_cache_create:

and actually installed the package

$ octave
octave:1> pkg list
Package Name  | Version | Installation directory
--------------+---------+-----------------------
     specfun  |   1.1.0 | /Users/davydden/octave/specfun-1.1.0
     splines  |   1.2.7 | /Users/davydden/octave/splines-1.2.7
octave:2>

Any advices/ideas?

p.s. ideally fixes #1111

davydden · 2016-06-25T11:13:19Z

@adamjstewart ping.

adamjstewart · 2016-06-25T14:00:00Z

Looks good to me. Is there a particular file found in the tar that is indicative of Octave extensions? If so one of us can add logic to create.py to automatically detect the build system, add extends('octave'), add the install logic, and prefix the name of the package with "octave-". I'm already working on create.py so I'm willing to do it if you want.

davydden · 2016-06-25T16:57:54Z

judging from the list of packages http://octave.sourceforge.net/packages.php , they are have the same prefix in the url http://downloads.sourceforge.net/octave/<package>-<version>.tar.gz?download. Otherwise, each package appears to unarchive into a single folder inside which there is DESCRIPTION

Name: splines
Version: 1.3.1
Date: 2016-06-02
Author: various authors
Maintainer: Nir Krakauer <[email protected]>
Title: Splines.
Description: Additional spline functions.
Categories: Splines
Depends: octave (>= 3.6.0)
Autoload: no
License: GPLv3+, public domain
Url: http://octave.sf.net

with octave in Depends.

alalazo · 2016-06-28T09:20:58Z

var/spack/repos/builtin/packages/octave/package.py

+            Octave('--eval', 'pkg install %s' % self.stage.archive_file)
+        """
+        # Octave extension builds can have a global Octave executable function
+        module.Octave = Executable(join_path(self.spec.prefix.bin, 'octave'))


Why Octave and not octave (like the binary it is tied to)?

adamjstewart · 2016-06-29T18:10:30Z

I think spack create can handle the octave build system. I don't really want to expand the file and check the contents, but I think I can search for files from that particular URL. What should the default install() look like for an octave package?

davydden · 2016-06-29T18:14:49Z

@adamjstewart as far as i can tell, this should work for majority of cases

     def install(self, spec, prefix):
         octave('--quiet',
                '--norc',
                '--built-in-docstrings-file=/dev/null',
                '--texi-macros-file=/dev/null',
                '--eval', 'pkg prefix %s; pkg install %s' %
                (prefix, self.stage.archive_file))

.

adamjstewart · 2016-06-29T18:16:16Z

Will do.

davydden changed the title ~~[WIP] Octave extensions~~ Octave extensions Jun 27, 2016

octave: make extendable and add a package

0faa6dd

davydden force-pushed the octave_extensions branch from 1332575 to 0faa6dd Compare June 27, 2016 11:45

alalazo reviewed Jun 28, 2016
View reviewed changes

octave: rename executable Octave to octave

c4c167c

tgamblin merged commit 7df8989 into spack:develop Jun 29, 2016

adamjstewart mentioned this pull request Jul 5, 2016

Allow spack create to automatically detect octave build system #1171

Merged

davydden deleted the octave_extensions branch May 28, 2017 21:01

olupton pushed a commit to olupton/spack that referenced this pull request Feb 7, 2022

Fix py-deprecation dependencies (spack#1113)

6b437b1

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Octave extensions#1113

Octave extensions#1113
tgamblin merged 2 commits intospack:developfrom
davydden:octave_extensions

davydden commented Jun 24, 2016 •

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davydden commented Jun 24, 2016 •

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