#14962 closed task (fixed)
make sure all optional packages work in the git repository
Reported by: | ohanar | Owned by: | |
---|---|---|---|
Priority: | major | Milestone: | sage-6.0 |
Component: | packages: optional | Keywords: | |
Cc: | schilly | Merged in: | |
Authors: | Volker Braun | Reviewers: | Volker Braun |
Report Upstream: | N/A | Work issues: | |
Branch: | u/vbraun/optional_databases (Commits, GitHub, GitLab) | Commit: | 5b72359a8c98b14002e8a4e35600d9252280c7c7 |
Dependencies: | #15172, #15261, #15263, #15370 #15302, #15814 | Stopgaps: |
Description (last modified by )
we support them, so we need to make sure they will continue to work
Script to systematically try out all optional spkgs: http://boxen.math.washington.edu/home/vbraun/Sage/Testing/test_optional_packages.sh
The optional databases will be dealt with here, other packages should make separate tickets. Use the following new "upstream" tarballs:
Leave for later, don't work and no SPKG.txt:
- cunningham_tables
- database_jones_numfield
- database_kohel
- database_odlyzko_zeta
- database_sloane_oeis
- database_stein_watkins_mini.p0
Move to experimental (broken with or without git, probably for a long time):
- fricas (doesn't build with our ecl)
- fricas-aldor (dito)
- libcocoa (doesn't build with our gmp/mpir)
Delete for other reasons:
- jsmath_image_fonts (we switched to mathjax)
Change History (34)
comment:1 Changed 9 years ago by
- Branch set to u/ohanar/optional
comment:2 Changed 9 years ago by
- Commit set to acbbe0dce4ad570153083146a34e660dd620ab6f
comment:3 Changed 9 years ago by
- Branch changed from u/ohanar/optional to u/ohanar/test
comment:4 Changed 9 years ago by
- Commit changed from acbbe0dce4ad570153083146a34e660dd620ab6f to cfd9dd10cf3ff3dab9d10f61f82c418723b0e395
comment:5 Changed 9 years ago by
- Commit changed from cfd9dd10cf3ff3dab9d10f61f82c418723b0e395 to cf45f4588bbc4e8ec59cc11b96dd4afc1abc7500
comment:6 Changed 9 years ago by
- Commit changed from cf45f4588bbc4e8ec59cc11b96dd4afc1abc7500 to 728e542453259b59b7e012f382e141652671d425
Branch pushed to git repo; I updated commit sha1. New commits:
comment:7 Changed 9 years ago by
- Commit changed from 728e542453259b59b7e012f382e141652671d425 to cf45f4588bbc4e8ec59cc11b96dd4afc1abc7500
comment:8 Changed 9 years ago by
- Commit cf45f4588bbc4e8ec59cc11b96dd4afc1abc7500 deleted
- Dependencies set to #15172
- Description modified (diff)
4ti2 is currently broken (not related to the git transition) but works with the update at #15172.
comment:9 Changed 9 years ago by
- Branch u/ohanar/test deleted
comment:10 Changed 9 years ago by
- Dependencies changed from #15172 to #15172, #15258
#15258 fails, because it implements a dependency check in the spkg-install
using newest-version
. How should optional spkgs handle dependencies when they transition to the new layout, by adding to deps
? Or put the dependency rule in a <packagename>/deps
file that is included from deps
? Or no dependency management?
comment:11 Changed 9 years ago by
For right now I would say no dependency management -- any other solution at this point in time would require messing with the build system, which I don't want to do at the moment (so that we can get through this git transition).
On top of our current faux package manager I would say the best solution would be to replace (at least most of) deps
with <packagename>/deps
, but I'm not particularly interested in continuing the development of the current build system.
comment:12 Changed 9 years ago by
The following spkgs failed to install:
brian cunningham_tables database_cremona_ellcurve database_jones_numfield database_kohel database_odlyzko_zeta database_sloane_oeis database_stein_watkins_mini.p0 database_symbolic_data fricas fricasaldor jsmath_image_fonts libcocoa libtheora mpi4py openssl p_group_cohomology PyQt_x11 TOPCOM valgrind
Logfiles are here: http://boxen.math.washington.edu/home/vbraun/Sage/Testing/optional/
comment:13 Changed 9 years ago by
- Branch set to u/vbraun/optional_databases
- Commit set to 5b72359a8c98b14002e8a4e35600d9252280c7c7
New commits:
[changeset:5b72359] | switched the large Cremona ellcurve database to the new git directory layout |
comment:14 Changed 9 years ago by
SAGE_DATA
is now SAGE_LOCAL/share
, for the record.
comment:15 Changed 9 years ago by
- Description modified (diff)
comment:16 Changed 9 years ago by
Also, extra_docs
barfs the extra docs into SAGE_ROOT
.
comment:17 Changed 9 years ago by
I am not online with the git layout yet (need to attend a tutorial, at the least, though Volker's video was a helpful start) so I can't help with this writing or reviewing yet BUT I have diagnosed the brian problem.
./spkg-install: line 10: cd: /mnt/storage2TB/vbraun-data/Sage/spkg/standard/: No such file or directory ./spkg-install: line 10: ./newest_version: No such file or directory Failed to find numpy. Please install the numpy spkg.
There are four tests of the following kind:
NUMPY=`cd $SAGE_ROOT/spkg/standard/; ./newest_version numpy`
So where would we check the "newest version" now? That's all one would need to do, or even check "presence" if the spkg placeholder txt files are no longer there. (That said, I'm not sure if those checks are even really necessary, which would also fix it, I'm sure. But if the fix is easy, then we should try that first.)
comment:18 follow-up: ↓ 19 Changed 9 years ago by
The brian spkg just needs to strip out all the dependency checking, then it should work. You can still make spkgs as in the old workflow. Git installation instructions are, by now, easy:
git clone git://github.com/sagemath/sage.git cd sage make
comment:19 in reply to: ↑ 18 ; follow-up: ↓ 20 Changed 9 years ago by
The brian spkg just needs to strip out all the dependency checking, then it should work.
As I said:
That said, I'm not sure if those checks are even really necessary, which would also fix it, I'm sure.
I just don't remember why that was introduced. #9675 doesn't make it clear, so when I open this ticket, I'll cc: the original author. Otherwise I agree we should get rid of this. I'll update the patch situation as well and perhaps upgrade Brian if I find time for all this- should be able to in the next couple days.
You can still make spkgs as in the old workflow. Git installation instructions are, by now, easy:
Good to know! And that includes all the spkg stuff.
comment:20 in reply to: ↑ 19 Changed 9 years ago by
I just don't remember why that was introduced. #9675 doesn't make it clear, so when I open this ticket, I'll cc: the original author. Otherwise I agree we should get rid of this. I'll update the patch situation as well and perhaps upgrade Brian if I find time for all this- should be able to in the next couple days.
This is now #15261.
comment:21 Changed 9 years ago by
- Dependencies changed from #15172, #15258 to #15172, #15261
comment:22 Changed 9 years ago by
- Description modified (diff)
- mpi4py actually works, just needs openmpi libraries/compiler wrapper installed
comment:23 Changed 9 years ago by
- Dependencies changed from #15172, #15261 to #15172, #15261, #15263, #15302
comment:24 Changed 9 years ago by
- Dependencies changed from #15172, #15261, #15263, #15302 to #15172, #15261, #15263, #15370 #15302
comment:25 Changed 8 years ago by
- Description modified (diff)
- Status changed from new to needs_review
comment:26 follow-up: ↓ 29 Changed 8 years ago by
- Cc schilly added
- Description modified (diff)
- Reviewers set to Volker Braun
- Status changed from needs_review to positive_review
I'm setting this to positive review since clearly nobody else has the guts to review this ticket.
The database_cremona_ellcurve-20121022.tar.bz2
tarball is already in the upstream dir, apparently.
Harald, can you delete/move to trash: fricas
, fricas-aldor
, libcocoa
, and jsmath_image_fonts
? They are (and have been for a while) useless with or without git.
comment:27 Changed 8 years ago by
- Status changed from positive_review to closed
comment:28 Changed 8 years ago by
- Resolution set to fixed
comment:29 in reply to: ↑ 26 Changed 8 years ago by
Replying to vbraun:
Harald, can you delete/move to trash:
fricas
,fricas-aldor
,libcocoa
, andjsmath_image_fonts
?
ok.
comment:30 Changed 8 years ago by
My copy of database_stein_watkins_mini.p0.spkg does contain SPKG.txt:
jec@atkin:~/spkg/database_stein_watkins_mini.p0$ ls -l total 12 -rwx------ 1 jec jec 49 Mar 12 2010 spkg-install -rw------- 1 jec jec 389 Mar 13 2010 SPKG.txt drwx------ 2 jec jec 4096 Nov 7 2005 stein-watkins-ecdb
so I think this one should be easy -- no compilaton, it just copies recurseively the directory to SAGE_DATA:
jec@atkin:~/spkg/database_stein_watkins_mini.p0$ cat spkg-install #!/bin/sh cp -rf stein-watkins-ecdb $SAGE_DATA/
comment:31 Changed 8 years ago by
If I was going to work on converting stein_watkins_mini, should I open a new ticket to hold the branch?
comment:32 follow-up: ↓ 33 Changed 8 years ago by
Please open a new ticket, this one is closed.
stein_watkins_mini contains a skeleton SPKG.txt, but no description (what is it anyways?) and no license (=potentially not legal to distribute). William indicated in the ensuing thread on sage-devel that it is public domain afair.
comment:33 in reply to: ↑ 32 Changed 8 years ago by
Replying to vbraun:
Please open a new ticket, this one is closed.
See #15556.
stein_watkins_mini contains a skeleton SPKG.txt, but no description (what is it anyways?) and no license (=potentially not legal to distribute). William indicated in the ensuing thread on sage-devel that it is public domain afair.
It's a large collection of elliptic curves compiled by William Stein and Mark Watkins about 10 years ago, stored in simple compressed text files. I'll put a reference to their paper in the SPKG.txt (it is already cited properly in the docstrings).
comment:34 Changed 8 years ago by
- Dependencies changed from #15172, #15261, #15263, #15370 #15302 to #15172, #15261, #15263, #15370 #15302, #15814
See also #15814
Branch pushed to git repo; I updated commit sha1. This was a forced push. Recent commits: