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|| [[https://tracker.debian.org/pkg/python2.7|python2.7]] || || Sage currently doesn't work with python 2.7.13rc1 so we uploaded python 2.7.12 here. See [[https://groups.google.com/forum/#!topic/sage-devel/IbugChsM26E|sage-devel]] and [[https://trac.sagemath.org/ticket/22037|trac ticket]]. ||
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||<-3 style="border-top:1pt solid; border-bottom:1pt solid"> '''Need to be packaged:''' ||
||<-3> None at this time, but see "Needs further work" above. ||

Some people within DebianScience would like to package again Sage for Debian. An old version of Sage got packaged long time ago by Tim Abbott, but, because of lack of maintainance, it became totally unusable and was removed from Debian. The status pages (master, develop) give an overview about package versions in Sage and Debian. If you want to help out, pick one of the open tasks or issues below and get going. Or contact us via the mailing list or in #debian-science on irc.oftc.net.

Building Sage with Debian packages

We have a git repository (sagemath) to document the steps we currently do to experiment with building Sage against Debian packages. Important elements are the build dependencies of Sage, patches for Sage and a script called "pruner" that uses automake to determine if the necessary packages are installed (see also this mail).

Start with Debian unstable (sid) with experimental sources enabled. It is nice to do this in a chroot with schroot. (If your build fails with "Permission denied", try adding the following line to /etc/schroot/default/fstab: tmpfs  /dev/shm  tmpfs  rw,nosuid,nodev  0  0 - more details here)

To set up your system for working with our repo:

sudo apt-get install git quilt devscripts python-sphinx

Install packages that are required before installing the build dependencies.

for d in deb deb-src; do \
    echo "$d https://debian-science.alioth.debian.org/apt sid-sage/"; done \
  | sudo tee /etc/apt/sources.list.d/deb-sci-sage.list

Add our unstable-sage repo for patched dependencies. This is optional; if you prefer you can build these yourself from the instructions in the table below.

gpg --recv-keys 0xD1188AF4A1398A5FCC3F576654B3F967097676A0

Get the repo key.

gpg --export 0xD1188AF4A1398A5FCC3F576654B3F967097676A0 | sudo apt-key add -

Install the repo key.

printf "Package: *\nPin: release n=sid-sage\nPin-Priority: 100\n" \
  | sudo tee /etc/apt/preferences.d/deb-sci-sage
sudo apt-get update

Pin our repo at a low priority so it doesn't mess with the rest of your system. OTOH, if you really really want this repo's packages, to make sure you get the latest and greatest efforts of the Debian Sage packaging team above all else (including maybe our patched dependency packages messing up your system) then you can set the Pin-Priority to a high number like 800.

git clone --recursive https://anonscm.debian.org/git/debian-science/packages/sagemath.git

Recursive git clone to also get sage which is included as a git submodule.

To build the package, run:

debian/rules reset

Apply patches and force-reset the upstream sage submodule. Note: also removes ~/.sage/local and ~/.local/share/sagemath

debian/rules build-dep

Install build dependencies. (Run 'apt-get -f install' afterwards.)

debian/rules prune

Run the pruner script. Check that the output matches the one below.

debian/rules build

Build sage and run the test suite.

The output of the pruner tells you in the end which dependencies were not found on the machine. These will be downloaded and built in the build step, before Sage itself is built. Currently (December 2016) the pruner should output something like the following.

160 system packages will be used

See debian/README.Debian for any workarounds you might have to apply, such as patching local system files.

Open tasks

Packages in our development APT repository:

Up-to-date information about the packages in the repo can be found on the status pages. (master branch, develop branch)

Package

Bug / Link

Reason for being in the repository

Needs further work, not uploaded yet:

sagemath

841136

Please test this. Run the test suite from the installed package (see README.Debian for instructions), test with sagenb and jupyter-notebook and so on. I will try to keep this as up-to-date as possible and tag the git commits for the sage revisions.

Patched packages:

numpy

842348

Debian maintainer needs to apply this proposed upstream patch - basically accepted but needs unit tests

gap

844789

Uncompressing gz files on the fly through pipes causes the doctests failures related to GAP (and libGAP): this package uncompresses directly with zlib to avoid the underlying EPIPE signal mess.

libgap-sage

(idem)

python2.7

Sage currently doesn't work with python 2.7.13rc1 so we uploaded python 2.7.12 here. See sage-devel and trac ticket.

sympy

840621

We applied this patch to fix a doctest.

Other packages:

Package

Bug / Link

Comments

Migrate from experimental to testing:

jmol

Omitting JSmol for now. Awaiting further comments from Debian Med and ?DebiChem teams.

sagetex

Depends on sagemath, so wait for sagemath to be in unstable before uploading.

RC bugs that need to be fixed before the freeze (possibly prevent testing migration of sagemath):

ipywidgets

Can't migrate due to piuparts issue.

pyzmq

818265

zeromq3

844479

Things that can wait until after stretch:

cvxopt

An update is ready in git, ?SageMath seems to work with the old version.

thebe

https://github.com/oreillymedia/thebe, lots of javascript dependencies

jmol

Build JSmol into a binary package and use it for 3D plots in notebooks.

Uploading patched packages

We've set up a mini-dinstall APT repo to upload our patched Debian packages to, so that we can build sage against these. This is a temporary measure to make everything work more quickly, and these patched packages are unlikely to be added to Debian officially.

To upload, you must be a member of the debian-science group on alioth. Then, you should add this to your ~/.dput.cf:

[deb-sci-sage]
method = scp
fqdn = alioth.debian.org
incoming = /home/groups/debian-science/htdocs/apt/mini-dinstall/incoming/
post_upload_command = ssh alioth.debian.org /home/groups/debian-science/mini-dinstall

mini-dinstall is pretty forgiving and you can upload either higher or lower versions of what's in there currently. However, you must set the distribution in debian/changelog to sid-sage or unstable-sage, otherwise your package will get rejected. Alternatively, do the build without changing debian/changelog, then afterwards edit the .changes file to say Distribution: sid-sage, then debsign it and upload.

Please include the .orig tarball in your upload, which helps our status pages report more accurately. To do this, you can give --changes-option=-sa to dpkg-buildpackage, or if you forget to do this then you can run changestool $XXX.changes includeallsources after the build, then debsign it and upload.

If you want to upload a different version of a package with the *same version number* as what's already in there, firstly please try to avoid this since it might confuse people. If you do it by accident, mini-dinstall won't reject your upload and you will mess up the database. In this case, run /home/groups/debian-science/mini-dinstall -b --no-db on alioth.debian.org to fix things.

To remove a package

  • ssh to alioth.debian.org

  • Delete the packages from /home/groups/debian-science/htdocs/apt/sid-sage

  • Run /home/groups/debian-science/mini-dinstall -b --no-db

To sbuild using our repo

You can sbuild to make sure you didn't miss any build-dependencies (and for its other benefits).

First, make sure you've set up your local host system as described above. Then setup an sbuild schroot by following the instructions on that page. Finally, edit /etc/schroot/sbuild/copyfiles to add the line /etc/apt/trusted.gpg.

Then, for each build you want to do, run:

$ sbuild \
    --chroot-setup-commands='apt-get install -y apt-transport-https' \
    --extra-repository='deb https://debian-science.alioth.debian.org/apt sid-sage/' \
    --build-dep-resolver=aspcud \
    -s .

Replace -s . with $pkg.dsc if you already built the latter.

Links