[sagemath] annotated tag deb-sci-sage/7.4-0sage1 created (now 2a9dece)
Tobias Hansen
thansen at moszumanska.debian.org
Sun Dec 4 14:05:59 UTC 2016
This is an automated email from the git hooks/post-receive script.
thansen pushed a change to annotated tag deb-sci-sage/7.4-0sage1
in repository sagemath.
at 2a9dece (tag)
tagging 2208123502f1b8f1f96b32bd240664ec919a2fb1 (commit)
tagged by Tobias Hansen
on Sun Dec 4 14:05:34 2016 +0000
- Log -----------------------------------------------------------------
sagemath deb-sci-sage release 7.4-0sage1
Felix Salfelder (15):
debian/control stub
add gap-dev version
extra section for runtime deps
more deps
palp version bump
fix cddlib dep
version bump and gap dependency
remove rpy
python-pexpect: require >=2.4
still need pexpect=2.0
move palp to runtime-deps. add rubiks
add README, bump singular version
move version to changelog.
polybori stuff has moved to testing
libppl1.2 in testing
Jerome BENOIT (1):
Polish Debian patches for libgap-sage support
Jerome Benoit (26):
quilt refresh[ment]
Bump d/compat from 8 to 9
Add Ximin and Jerome to Uploaders list
Bump Standards-Version to 3.9.8
Update dpkg-parsechangelog usage in d/rules
Set up dh parallel machinery
Introduce d/clean (and revisit d/rules accordingly)
Revisit the arallel machinery in d/rules
Build-Depends on gdb
Depend on python-polybori
Build-Depends on libgap-sage
Provide libgap-sage check in d/pr/configure.ac
Remove Build-Depends on gap-dev
Import Debian patches for libgap-sage support
Build-Depends on pkg-config
Correct libgap-sage[-dev] dependancy
Hardden gap check in d/pr/configure.ac
Add sagetex to Build-Depends + pruner support
Add m4 directory to pruner autoconf in d/rules
Depend on python-nbconvert
Remove patch d/debian-cysignals.patch
Discard cysignals relatif stuff from patch d/p/debian-temp-userdir.patch
Depend on python-cysignals-pari
Refresh section 1 in d/README.Debian: libpari-dev has been fixed
Update GAP/libGAP situation
Depend on GAP and libGAP 4.8.6
Julien Puydt (19):
Completed the colors.py patch within unbreak.patch
Updated the pruner's configure.ac
Added a chunk to find pari's datadir and help in unbreak.patch
Added a patch to avoid exceptions if/when documentation isn't found
Added a patch to silence an ECL doctest failure
Added a patch to silence a memory error related to debian bug #780186
Added a patch to silence a matplotlib doctest failure
Added a patch to silence tests related to python's issue 16202
Added all previous patches to the series
Break the renaming of the rubiks package executable into a separate patch
Split the patches to install python in userdir in a new patch
Added a patch to make a tachyon failure disappear
Added proper detection of cddlib to the pruner configure script
Added correct pruner test for mistune
Remove now-misleading FIXME comment
Silenced one more ECL configuration doctest
Put things in alphabetical order in the pruner's configure.ac
Add planarity support to the pruner script
add rw support to the pruner script
Tobias Hansen (250):
Make a buildable metapackage.
Merge branch 'master' of git+ssh://git.debian.org/git/debian-science/packages/sagelib
Start sorting packages into 3 metapackages.
Make the testing metapackage installable on testing.
Depend on libgivaro dev package and a higher flint version.
Add meta-package for dependencies in experimental.
Make the dependencies of sagelib-builddeps-git satisfyable.
Add dependency python-ply (for hacking gap).
Depend on libatlas-base-dev instead of libatlas-dev.
lrcalc is in unstable.
python-pexpect 2.0 is not in Debian.
lrcalc is now in testing.
Adjust version number for native package.
linbox is now up-to-date in unstable.
Merge deps that are required by the test suite into the other builddeps.
The required palp version is in unstable.
Some packages migrated to testing and gap 4r6p5-3 is required.
gap and gfan are now in testing.
Polybori is now in unstable.
Some packages moved to testing/unstable.
Some new packages, libppl0.12-dev is now libppl-dev, and bump to 6.3.
sagemath-database-combinatorial-designs moved to testing.
Change libgnutls-dev to libgnutls28-dev.
Rename source package to sagemath.
Add sage as submodule.
Add get-orig-source rules target.
Put build dependencies into Build-Depends field.
Add Juliens unbreak patch.
Create README.Debian with build instructions.
Delete old README.
Don't build all these builddeps packages.
Some minor cleanups.
Set builddirectory.
Add Snarks pruner scripts.
pruner: include m4's in configure.ac, don't check for sglalchemy, run pruner from debian/rules.
Fix debian/rules clean after configure.
Add build and test commands to debian/rules.
Add missing build-deps.
Add more build-depends.
Update sage to 6.5.
Update unbreak.patch.
Bump version in changelog to 6.5
Add new rules target prune for the pruner.
Create .gitignore for .pc folder.
debian/rules: Build with -j4 and add test target for make ptestlong.
Import new version of unbreak.patch.
Add libboost1.55-dev to build-depends.
debian/rules: make test target depend on configure.
Add patch to work around singular doc problem.
Add maxima.patch to look for maxima.fas in the right place.
Improve debian/rules, avoid double building/pruning.
Fix prune-stamp in debian/rules.
Look for maxima.fas in /usr/lib/ecl.
Create ptestlong target for rules to allow for separate testing.
Remove comment about polybori bug from pruner (fixed).
Add patch for trac 17796.
Add patch to remove singular warning (Singular will be updated to 4.0 anyway).
Set dh compat lvl to 8 to disable custom build flags (fixes combinat.py doctest) and build with 5 threads.
Update debian/README.Debian (point to Wiki).
Fetch latest sage (develop): 6.6.beta3.
Remove trac_17796.patch (applied upstream).
Update unbreak.patch.
Update version in changelog.
Add patch from Snark to deal with Singular doctests.
Add new dependencies to pruner and debian/control:
Boost is now needed for sage (update pruner).
Remove polybori comment from pruner (#751098 is fixed).
Update sage to 6.7.
Update version in changelog to 6.7.
Refresh patches for sage 6.7.
Remove gdmodule from pruner.
Add markupsafe and mistune entries to pruner.
Add pari.patch to let sage find pari.desc.
Move parts of unbreak.patch to maxima.patch and pari.patch.
Fix python_installs_in_userdir.patch after recent move of the python setup.py install command.
Allow ipython spkg install in user path.
Build-Depend on python-pil.
Update sage submodule to 7.1.
Update unbreak.patch.
Remove trac_17872.patch
Update maxima.patch.
Refresh two singular related patches.
Refresh some patches.
Remove silence_matplotlib_1_3_changes.patch (was applied upstream).
Refresh more patches.
Remove rw-spkg.patch (was applied upstream).
Update version in changelog.
Create SAGE_SHARE before creating symlinks there.
Update sage to 7.2.
Update version in changelog.
Disable update-sphinx.patch and update-libgap.patch, refresh some other patches.
Refresh remaining patches.
Check for Python modules directly from prunter.py (for new dependencies).
Add new dependencies for Sage 7.2.
Install speaklater spkg to userdir.
pruner: Do all checks for Python modules directly from pruner.py.
Depend on cython >= 0.24.
Update debian-singular.patch for singular 3.1.7 package.
Depend on singular 3.1.7p1.
Fix gap version to the one in our repo.
Sort output of pruner.py.
Depend on python-tk to fix some tests.
Fix pexpect to our version.
Do not build the documentation.
Change SINGULARPATH in sage-env.
Fix broken timeit with Python 2.7.11.
Depend on libcdd-tools.
Apply ecm 7 patch from Arch Linux.
Use planarity from sage.
Include the Cython headers from the source directory.
Add nbformat to pruner and d/control.
Apply patch to work with linbox 1.4.
Organize patches.
Depend on linbox 1.4.
Refresh linbox patch.
Add patch to work with ipython 5.
Depend on ipython 5.
Depend on python-backports-shutil-get-terminal-size.
Remove comment about matplotlib from d/control.
Remove comment about missing standard.lib from README.Debian.
Link with -lflint-arb instead of -larb.
Remove 'patch lrcalc' from README.Debian (fixed in unstable).
Remove flint-arb workaround from README.Debian (fixed in unstable).
Add versioned dependencies for lrcalc and flint-arb.
Add sys.path to Cython includes
Depend on cython 0.24.1.
Fix parallel doctesting by appending -jX to MAKE.
Patch sage-env only in two patches instead of four.
Update sage to version 7.3.
Start refreshing patches.
Import new version of linbox 1.4 patch from Arch Linux.
Refresh remaining patches.
Import new version of ipython 5 patch from Arch Linux.
Add future and backports_shutil_get_terminal_size to pruner (and python-future to build-deps).
Install sagenb_export and widgetsnbextension with --user.
Use print() function in debian-singular.patch.
Mark speaklater as unneeded in pruner.
Update pari related dependencies.
Update build-deps for renamed packages polybori -> brial.
Depend on pexpect >= 4.1.
Add failed-tests target to d/rules to count failed tests.
Build with 4 threads by default.
Add todo-stretch.md with todos regarding stretch freezes.
todo-stretch: upload sagetex together with sagemath
Depend on brial >= 0.8.5-0+sage4 to get a fix for brial segfaulting.
Port to Singular 4.
pruner: Use pkg-config to check for singular 4.
Depend on singular >= 4.0.3-p3.
Add a patch description and update todo-stretch.md.
todo-stretch.md: Remove linbox and add fpylll.
Depend on ecl from Debian unstable.
todo-stretch: Remove comment for ipython (we already have a patch) and mention cysignals-pari.
Mention packages with testing migration issues.
Fix typo in package description.
Update todo-stetch.md.
Update sage to 7.4.
Update changelog.
Delete patches for wrong versions of givaro, ipython and linbox.
Remove fixsage-mpfi.patch (seems to be applied) and refresh some patches.
Refresh fixsage-allow-override-sage-local.patch.
Use new singular-4 patch from Arch Linux.
Refresh more patches.
Refresh debian-fix-trivial-test-cases.patch.
Refresh debian-install-paths.patch - two chunks removed, might need fixing.
Delete 2 obsolete patches, finish refreshing.
Add new python deps to pruner and d/control.
Add appnope to pruner.
Add openblas to pruner and d/control.
Depend on fplll 5.0.3.
Patch spkg's to install to user dir again and disable widgetsnbextension in pruner.
Fix installation of sagelib to debian/build.
Update todo-stretch.md.
Update versioned build depends.
Update todo-stretch.md (jmol needs a transition, brial not).
Do not set MAXIMA_PREFIX in sage-env.
Update todo-stretch: The jupyter packages are now in unstable.
Apply patch from sage trac #21765 to improve the situation with pari 2.9.
Lower build-depends on cysignals to allow version from unstable.
Update todo-stretch: pari transition is done and brial is in unstable.
Apply pari 2.9 patch from sage trac #21756.
Apply changes from sage trac #21749 to fix ~2700 doctest failures related to linbox.
Increase pari build dependency.
Depend on gap and libgap 4.8.5.
todo-stretch: move maxima-sage to new package, issues regarding testing migration need to be fixed before soft freeze as well.
Use maxima-sage Debian package.
Remove Felix Salfelder from Uploaders.
Add jupyter-notebook to pruner.
Do not install Sage's jmol.
Apply patch to fix 3 doctests with wrong brial hashes.
Add comment regarding jmol to todo.stretch.
Document fixed tests in pbori.pyx.
Depend on python-notebook.
Add thebe to pruner and disable it.
todo-stretch: how to get along without thebe.
todo-stretch: mention other testing migration issues.
todo-stretch: remove finished tasks.
Change debian/compat to 10.
Disable check for root in configure.ac.
Use dh_auto_clean to clean up after autoreconf.
Do not abort package build when tests fail.
Disable jmol as the default viewer.
Depend on cython >= 0.25.
Apply cython 0.25 patch from Arch Linux.
Do not abort package build due to tests for now. Change this back before uploading.
Set the default PARI stack size to 16*10^6 bytes.
Prevent doctests to fail when looking for optional packages.
Change pari dependency to work with version in Debian.
Some packaging cleanups.
Write some patch descriptions.
Add sagenb_export to d/control and pruner.
Remove unneeded parts from debian-temp-userdir.patch.
Update cython-0.25 patch.
Cleanups inspired by lintian.
Do not install everything from /usr/bin.
Do not install sage_setup Python module.
Add lintian-override for sagemath-doc-en: extra-license-file/
Create doc-base files for doc packages.
Improve debian/copyright.
Export SAGE_LOCAL in sage-env.
Set correct language specific index files in doc-base files and fix a typo in d/copyright.
Update todo-stretch.md.
Remove build-dep on libtachyon-dev.
Move depends that are both Build-Depends and Depends for sagemath into a separate file debian/runtime-depends.
Create extend-diff-ignore rule with files that are generated by distclean target.
Add non-working update to debian-pari-stackwarn.patch.
Update todo-stretch.md.
Rename d/runtime-depends to d/control.runtime-depends.
Remove sage revisions from dependencies.
Install jmol from sage for now to avoid failing tests.
Don't set a different SAGE_ROOT when in sage source directory.
Don't check if in sage source directory.
Allow overriding SAGE_SRC.
Install SAGE_SPKG_INST folder and set this variable accordingly.
Disable disable-jmol.patch.
Running tests from installed package works, write instructions in README.Debian.
Revert "Do not install sage_setup Python module."
Create a temporary sagemath-deps-common package to install jmol.
Install scripts to /usr/share/sage/bin.
Don't install .bat files.
Add sage/ext to cython include path also when sage is installed.
Create man page for sage.
Add missing empty line to doc-base files.
Add libsingular4-dev to depends of sagemath.
Revert "Create a temporary sagemath-deps-common package to install jmol."
Use jmol package.
Update todo-stretch.md.
Don't patch JmolData.jar path.
Ignore pari stack warnings in tests.
Prepare changelog for upload to unstable-sage.
Clean up some files that conflict with the orig tarball otherwise.
Ximin Luo (171):
Update some Build-Depends for current sid. Build still fails though
Update Debian build, still breaking though
Lock Build-Depends to our debian-science repo
Use Debian system singular; build still failing with polybori-related errors
Update some Build-Depends for current sid, haven't tried building yet
Update dependent packages as per upstream
Tentatively use system libplanarity, haven't yet tested
Lock polybori/brial to our debian-science repo
Update ecl version
Update polybori/brial detection for 0.8.4.3
Force all files to have the same timestamp, otherwise sage's Makefiles destroy all our hard work
Add more dependencies for Sage 7.1
Report missing standard packages
Remove empty patches
Update patches for Sage 7.1
Bump libpari-dev version
Lock cython to our debian-science repo
Update pari version to the one actually used by Sage 7.1
Update python userdirs patch
Remove patches for spkgs we're no longer using (because we're using the Debian packages instead)
Update Sage's planarity module to use API v3
Bump version for libfplll-dev to what Sage 7.1 is using
Bump version for libntl-dev to (approx) what Sage 7.1 is using
Update python-userdir patch for install_data and list remaining tasks
Update python-userdir patch for install_kernel_spec
Make Sage able to detect Debian's GSL CBLAS, and add some notes about the latest errors
Fix Sage not to use private MPFI functions, update python-userdir patch
Make cysignals use multiarch paths
Minor tweaks and fixes
Document our patch for arb, and supply an easy-to-apply local workaround
Update build-deps for post NTL transition
Patch Sage's use of Sphinx, add maxima-ecl as a build-dep
Temporarily disable parallel sphinx build to make the GAP failure more obvious
Update Sage's libgap to (roughly) match version of GAP in Debian
Make the "sage-starts" test work so we can run the other tests and watch how they fail
Organise patches
Disable a convoluted "build log buffering" mechanism which was causing problems
Temporary disable parallel build for docbuild until we figure out the segfault
Update docs on latest situation, and other clean ups
Update fflas-ffpack/givaro build-dep versions
Build the pruner in debian/pruner and add .gitignore rules
Add a "reset" convenience target
Add a "build-dep" convenience target
It should be sufficient to rm ~/.sage/local only
debian/rules: build-dep should fail correctly on e.g. permissions errors
Fix reference to variable in Makefile
Use aptitude to resolve dependencies if it's available
Update clean paths for pruner
- fix debian/.gitignore
Fix libGAP patch
More robust/standard debian rules
Rename update-planarity.patch to match the other patches, even though it's not used
Add a local workaround to get the docbuild working
Fix build-deps
Fix octave path for Debian
Run submodule update in debian/rules reset
Add octave to build-depends, it's run by the tests
Add a comment explaining why we don't use `make ptestlong`
Add some test debugging tips
Bump dependency on python-numpy
Add another tip about running all tests with -i
Fix python-numpy version
Also remove built documentation in clean, 9GB on my system
- whitespace fix
Add python-entrypoints to Build-Depends because sagenb needs it to build
Add cysignals-tools to B-D; needed for docbuild
Unfortunately the pari linking issue is not exactly resolved
Add a reminder to myself to rebuild linbox
Clarify linbox note, it's "Illegal instruction"
More docbuild fixes
Add support for ccache. To use, add pkg.sagemath.ccache to DEB_BUILD_PROFILES
Fix the cython include path for cysignals
Our symlink hacks are needed for the doctests, even when not building docs
Actually, this is more to do with sage's patched Cython rather than cysignals
When cleaning, remove userdir stuff that sage installs
Refresh patch
Fix 57 failing GAP-related tests
Fix 15/16 of test failures in sage/symbolic/expression.pyx
Add a direct build-dependency on pari-gp and bump versions for all pari packages
Bump version for sagenb to what Sage 7.3 is using
Revert a sage commit, fixing some docbuild segfaults
Whilst we're at it, revert other crap that depends on Python patches
Add a separate clean-docbuild target, helpful for debugging/testing
Expand temp-disable-parallel-sphinx to other docs
Fixup some test cases (very carefully!) so that they pass
Bump singular build-dep; we rebuilt it against libflint
Fix two more trivial test cases
Alternative way of fixing a test that might be more acceptable to upstream
Unpatch a doctest, GAPDoc is correct in Debian now
Remove instruction about rebuilding linbox, no longer needed
Doesn't yet work with fplll 5
Update note about making sage work with fplll 5
Fix some more singular-4-related tests, but there are 2 left
Add a Build-Dep on singular-doc to prepare for using the .hlp file
Add some more info about failing tests in README.Debian
Dynamically get the multiarch path for Singular
Reminder that we have a preliminary patch for planarity 3
Upstream Singular dev suggests to use -t instead of -b
Add patch for cddlib 094h, fixes 6 tests, still 1 failing
Note that 2 tests are fixed in sympy git
Clean up debian-temp-userdir.patch and disable a failing qepcad test that we're not using
Fix another 3 singular-related tests; takes effect after next Singular upload
Classify more test failures
Link to system mathjax, fixing 1 test
Override 1 failing test, it expects an error that is fixed in Debian's ipython
Backport some upstream commits, fixes 2 more tests
Fix 11 GLPK tests and document the incompatibility between Sage vs upstream
Install everything to debian/tmp instead of $HOME
Hardcode more Debian system paths, avoiding some runtime symlinking
Drop a manual override of some doctests, those now pass
Fix jupyter path
Fix more graph paths
Fix some more paths
Note that we're timing out on R currently
Move some patches to more suitable locations
Confirm 8 total timeouts including in integer.pyx
Add some notes on how to reduce these patches making them generic and forwarding them upstream
Pass -l ecl when running `sage --maxima`
Add a script to help detect which build dependencies changed recently
Add the possibility to show deps for other packages too
Pass --no-readline to R otherwise Pexpect hangs
Document the deeper details of the issue
Some minor fixes to tests and build-deps
Automatically generate rules for per-language doc packages
Install .pxd and other data files into the right place
We have lift-off baby!
Better way of fixing paths, should work even if there is another system-wide install
Fix another paths: this one helps Jupyter not crash at runtime
Update test summaries
Don't (yet) auto-detect system planarity, that one is currently fake from sagemath-deps
Don't compress some documentation files
Use dh_sphinxdoc (must patch it locally) to symlink some embedded JS; and:
Debian binary policy: use LD_LIBRARY_PATH instead of rpath
Add dh_python2 to auto-generate some python helper infrastructure
Move more arch-indep files to sagemath-common, and:
Fix paths patch: don't rewrite SAGE_ROOT after auto-detecting it in /usr/bin
Update todo-stretch.md
Bump build-dependencies
No longer need to manually symlink PARI, mention currently-failing tests
Link directly to dh_sphinxdoc patch
Mention Sage upstream ticket for the runtime doc issue
Add some more rules to count failed tests with
Add rules to print/count failures by their error or stack trace
Lower pari dependants' Build-Dep version constraints
Update todo-stretch.md
Don't fail plot.py doctest if DISPLAY is unset
Don't output pip warnings, otherwise some doctests fail
Remove scary warning about heisenbugs; I think they were due to some bad RAM that I had
Fix more doctests failing because of no DISPLAY
Update expected test results
Restore some notes on test failures from before, deleted accidentally
Update todo-stretch.md with more JS related research
Some more doc updates
Update todo-stretch.md with more scheduling and dates
Add some more ideas for Jmol
Update widgetsnbextension situation
Clean debian/build when cleaning
Better way of preserving the docs
Fix planarity 3 patch and re-enable it
We no longer need "deps" packages (but still install some stuff to ~/.sage, cough cough)
Update todo-stretch.md
Only allow <80 tests to fail, feel free to change this number
d/rules: minor clean-up
d/rules: Clean-up and some corrections, for dpkg-buildpackage to work
Better way of disabling test failures, that will automatically get re-enabled on upload
Use Debian's ipywidgets and widgetsnbextension
Fix syntax error, this made make(1) think it's part of the previous recipe
Don't mention arch/indep targets otherwise debhelper tries to run things twice
Don't try to rmdir debian/build if it's a mountpoint
Fix up test instructions
Fix the recipe for d/control: don't clobber the doc.control inputs
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