update giac spkg #19873

frederichan-IMJPRG · 2016-01-12T15:17:12Z

update the giac spkg to the current upstream stable version: 1.2.2-37

The tarball built from spkg-src to put in upstream/ can be downloaded at

http://webusers.imj-prg.fr/~frederic.han/xcas/sage/giac-1.2.2.37.tar.gz

Update the giacpy spkg to 0.5.5. The tarball to put in upstream can be downloaded at

http://webusers.imj-prg.fr/~frederic.han/xcas/giacpy/sage/giacpy-0.5.5.tar.gz

This new release of giacpy is just an update of giac keywords + an update of setup.py for #20258. cf https://gitlab.math.univ-paris-diderot.fr/han/giacpy-sage

From 1.2.0.x to 1.2.2.x some multithreading was introduced in groebner basis computation over prime fields.

on a Xeon E5520@2.27Ghz (2 cpu with 4 cores) I got a groebner basis (from the sage with conversion to sage and 8threads allowed) for cyclic9 over GF(101)
giac 1.2.0: Time: CPU 1328.82 s, Wall: 1328.61 s
giac 1.2.2: Time: CPU 824.29 s, Wall: 326.89 s

Component: packages: optional

Author: Frederic Han

Branch/Commit: a959e08

Reviewer: Vincent Delecroix

Issue created by migration from https://trac.sagemath.org/ticket/19873

The text was updated successfully, but these errors were encountered:

sagetrac-git · 2016-01-27T10:36:44Z

Branch pushed to git repo; I updated commit sha1. New commits:

`04b4906`	`Merge branch 'develop' of git://trac.sagemath.org/sage into giac122`
`1ba0c18`	`update to 1.2.2.21`
`215ae00`	`update to giac source 1.2.2.23`
`275aa45`	`update doctest to the timing strings added in gbasis in giac122.`

sagetrac-git · 2016-01-27T10:36:44Z

Changed commit from a13d26c to 275aa45

sagetrac-git · 2016-02-01T13:27:22Z

Branch pushed to git repo; I updated commit sha1. New commits:

`276017e`	`Merge tag '7.1.beta0' of git://trac.sagemath.org/sage into giac122`
`ad95056`	`update to giac upstream source 1.2.2.27`

sagetrac-git · 2016-02-01T13:27:22Z

Changed commit from 275aa45 to ad95056

frederichan-IMJPRG · 2016-02-04T11:53:23Z

comment:9

I have found that eliminate is slower with this version of giac
http://xcas.e.ujf-grenoble.fr/XCAS/viewtopic.php?f=3&t=1694
so I put this in needwork state to wait if this can be easily fixed.

sagetrac-git · 2016-02-07T13:28:54Z

Changed commit from ad95056 to df2422e

sagetrac-git · 2016-02-07T13:28:54Z

Branch pushed to git repo; I updated commit sha1. New commits:

`df2422e`	`updage giacpy to 0.5.2 (update giac keywords)`

sagetrac-git · 2016-02-15T09:32:27Z

Changed commit from df2422e to bb55869

sagetrac-git · 2016-02-15T09:32:27Z

Branch pushed to git repo; I updated commit sha1. New commits:

`bb55869`	`update to giac 1.2.2-29`

sagetrac-git · 2016-03-25T09:36:24Z

Branch pushed to git repo; I updated commit sha1. New commits:

`9325136`	`update to giac 1.2.2.35`

sagetrac-git · 2016-03-25T09:36:24Z

Changed commit from bb55869 to 9325136

sagetrac-git · 2016-03-25T13:12:52Z

Changed commit from 9325136 to 004ca90

sagetrac-git · 2016-03-25T13:12:52Z

Branch pushed to git repo; I updated commit sha1. New commits:

`004ca90`	`giacpy 0.5.3 (use cythonize in setup.py)`

sagetrac-git · 2016-03-25T13:18:33Z

Changed commit from 004ca90 to 0b61e86

sagetrac-git · 2016-03-25T13:18:33Z

Branch pushed to git repo; I updated commit sha1. New commits:

`0b61e86`	`run doctests from the pkgs directory`

sagetrac-git · 2016-03-25T13:28:32Z

Branch pushed to git repo; I updated commit sha1. New commits:

`9e017b7`	`clean up for spkg-check`

sagetrac-git · 2016-03-25T13:28:32Z

Changed commit from 0b61e86 to 9e017b7

videlec · 2016-03-29T20:37:25Z

comment:22

I just tried to install the package and ran into

$ sage -p giacpy
Found local metadata for giacpy-0.5.3
Using cached file /opt/sage/upstream/giacpy-0.5.3.tar.gz
giacpy-0.5.3
====================================================
Setting up build directory for giacpy-0.5.3
mv: cannot stat 'giacpy-0.5.3*': No such file or directory
Finished set up
****************************************************

frederichan-IMJPRG · 2016-03-29T21:57:02Z

comment:23

and the built doesn't start after this message?
with 7.1.beta6 I have also this message but the built start. Is it a problem that the tarball giacpy-0.5.3.tar.gz looks like this:

tar -tzf giacpy-0.5.3.tar.gz 
src/
src/exemple.sage
src/giacpy.pyx
src/misc.h
src/sage-release.txt
src/README.txt
src/INSTALL.txt
src/setup.py
src/giacpy.pxd
src/keywords.pxi

frederichan-IMJPRG · 2016-03-30T05:25:05Z

comment:24

with 7.2.beta1 I have doctest failure due to

    doctest:858: DeprecationWarning: when constructing a matrix, the ring must be the first argument
    See http://trac.sagemath.org/20015 for details.

sagetrac-git · 2016-03-31T17:37:47Z

Changed commit from 31f2368 to 3df5520

sagetrac-git · 2016-03-31T17:37:47Z

Branch pushed to git repo; I updated commit sha1. New commits:

`3187337`	`Merge branch 'develop' of git://trac.sagemath.org/sage into giac122`
`e6ece40`	`giacpy 0.5.4 (doctest fixes for deprecated syntax: matrix(M,ring)`
`3df5520`	`Fix doctests for deprecated matrix(M,ring)`

videlec · 2016-03-31T18:30:51Z

comment:27

Replying to @frederichan-IMJPRG:

and the built doesn't start after this message?
with 7.1.beta6 I have also this message but the built start. Is it a problem that the tarball giacpy-0.5.3.tar.gz looks like this:
tar -tzf giacpy-0.5.3.tar.gz 
src/
src/exemple.sage
src/giacpy.pyx
src/misc.h
src/sage-release.txt
src/README.txt
src/INSTALL.txt
src/setup.py
src/giacpy.pxd
src/keywords.pxi

It does. The thing is that the sage install script is starting with the command tar xf PKG and then mv PKG_DIR/ src/. It would be better if the archive name would take the same name as the directory. It would be less error-prone.

videlec · 2016-03-31T19:36:08Z

comment:28

Following the "Short usage" example on your webpage I got two warnings (sage-7.2.beta1):

sage: import giacpy
...: DeprecationWarning: import "cysignals/signals.pxi" instead
of "sage/ext/interrupt.pxi"
See http://trac.sagemath.org/20002 for details.

and

sage: f.diff()
...: DeprecationWarning: DisplayFormatter._ipython_display_formatter_default
is deprecated: use @default decorator instead.
15*(x+y+z+1)^14

frederichan-IMJPRG · 2016-04-01T06:14:48Z

comment:29

Replying to @videlec:

Following the "Short usage" example on your webpage I got two warnings (sage-7.2.beta1):

...

sage: f.diff()
...: DeprecationWarning: DisplayFormatter._ipython_display_formatter_default
is deprecated: use @default decorator instead.
15*(x+y+z+1)^14

I have no idea to fix this warning. It looks similar to #20206. NB it looks to appear only once. (ie doing another f.diff() is OK)

sagetrac-git · 2016-04-01T08:18:40Z

Changed commit from 3df5520 to a959e08

sagetrac-git · 2016-04-01T08:18:40Z

Branch pushed to git repo; I updated commit sha1. New commits:

`a959e08`	`use cysignals instead of deprecated interrupt.pxi`

frederichan-IMJPRG · 2016-04-01T08:19:57Z

New commits:

`a959e08`	`use cysignals instead of deprecated interrupt.pxi`

frederichan-IMJPRG · 2016-04-01T12:56:15Z

comment:32

NB: the current 1.2.2.37 giac tar ball that I have made with spkg-src also expand as src. So I am waiting for 1.2.2.39 release (parisse said next week) to fix this.

videlec · 2016-04-01T13:46:31Z

comment:34

The examples from your webpage in the section " Syntaxes with reserved or unknown Python symbols" do not work. There is no assume, cos, sin, solve or fMax imported from giacpy

sage: from giacpy import *
// Giac share root-directory:/opt/sage/local/share/giac/
// Giac share root-directory:/opt/sage/local/share/giac/
Help file /opt/sage/local/share/giac/doc/fr/aide_cas not found
Added 0 synonyms
sage: solve.__module__
'sage.symbolic.relation'
sage: sin.__module__
'sage.functions.trig'
sage: cos.__module__
'sage.functions.trig'
sage: assume.__module__
'sage.symbolic.assumptions'

frederichan-IMJPRG · 2016-04-01T16:42:50Z

comment:35

I think that you are looking at the doc of the Python version of giacpy. It differs from the sage version (gmp, avoid conflics with SR...)
Similar doc is available with

libgiac?

videlec · 2016-04-01T17:33:29Z

comment:36

All right. I was able to run the doctests after decompressing the archive

$ sage -t --long --force-lib exemple.sage giacpy.pyx
Doctesting 2 files.
sage -t --long exemple.sage
    [0 tests, 0.00 s]
sage -t --long giacpy.pyx
    [221 tests, 23.89 s]
----------------------------------------------------------------------
All tests passed!
----------------------------------------------------------------------
Total time for all tests: 24.0 seconds
    cpu time: 24.0 seconds
    cumulative wall time: 23.9 seconds

This is good enough for this version...

Though

you should think about fitting Sage conventions for doctests:
- a = b instead of a=b for affectation
- no semicolon at the end of the statement
The way the two packages are organized do not follow the Sage conventions, see Packaging from the developer manual. In particular, it would be good to have a test suite for giac. And to explicit the dependencies of the packages.

videlec · 2016-04-01T17:33:29Z

Reviewer: Vincent Delecroix

frederichan-IMJPRG · 2016-04-02T07:33:47Z

comment:37

Replying to @videlec:

All right. I was able to run the doctests after decompressing the archive

$ sage -t --long --force-lib exemple.sage giacpy.pyx
Doctesting 2 files.
sage -t --long exemple.sage
    [0 tests, 0.00 s]
sage -t --long giacpy.pyx
    [221 tests, 23.89 s]
----------------------------------------------------------------------
All tests passed!
----------------------------------------------------------------------
Total time for all tests: 24.0 seconds
    cpu time: 24.0 seconds
    cumulative wall time: 23.9 seconds

This is good enough for this version...

Thank you

Though

...

The way the two packages are organized do not follow the Sage conventions, see Packaging from the developer manual. In particular, it would be good to have a test suite for giac. And to explicit the dependencies of the packages.

I don't understand,

env SAGE_CHECK=yes make giac

has a long test suite, and build/pkgs/giac and giacpy have both a dependencies file.

https://github.com/sagemath/sagetrac-mirror/blob/develop/build/pkgs/giac?id=98506d3754ddb14ca4548d644b2ed6b7a2d2a5d7

https://github.com/sagemath/sagetrac-mirror/blob/develop/build/pkgs/giacpy?id=98506d3754ddb14ca4548d644b2ed6b7a2d2a5d7

NB: running the giacpy testsuite is not enough for a review because some sage doctests have the # optional - giac or giacpy flag.

src/sage/interfaces/giac.py
src/sage/matrix/matrix1.pyx 
src/sage/modules/free_module_element.pyx 
src/sage/symbolic/expression.pyx 
src/sage/calculus/calculus.py
src/sage/libs/giac.py
src/sage/rings/polynomial/multi_polynomial_ideal.py

vbraun · 2016-04-02T09:59:41Z

Changed branch from u/frederichan/giac122 to a959e08

frederichan-IMJPRG added this to the sage-7.0 milestone Jan 12, 2016

frederichan-IMJPRG added p: minor / 4 labels Jan 12, 2016

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vbraun closed this as completed in 8819744 Apr 2, 2016

sagetrac-tmonteil mannequin mentioned this issue Aug 27, 2019

giacpy does not build on 7.1 #20258

Closed

update giac spkg #19873

update giac spkg #19873

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