Opened 12 years ago
Closed 12 years ago
#4470 closed defect (fixed)
[with patch, positive review] Merge Jon Hanke's qudratic forms code into Sage
Reported by: | mabshoff | Owned by: | tornaria |
---|---|---|---|
Priority: | major | Milestone: | sage-3.4 |
Component: | quadratic forms | Keywords: | |
Cc: | justin, cremona, tornaria | Merged in: | |
Authors: | Reviewers: | ||
Report Upstream: | Work issues: | ||
Branch: | Commit: | ||
Dependencies: | Stopgaps: |
Description
Jon Hanke wrote some substantial amount of code that is still based on Sage 2.8.14. Get the code ready for review and merge it
#4120 is relevant here since Justin works on binary quadratic forms.
Cheers,
Michael
Attachments (4)
Change History (20)
comment:1 Changed 12 years ago by
- Component changed from algebra to quadratic forms
- Owner changed from tbd to justin
comment:2 Changed 12 years ago by
comment:3 Changed 12 years ago by
Some more remaks:
- commit 10629 is mostly the AUTO code by Bernd Souvignier - the code has been made available under a GPL V2+ compatible license, but that needs to be formalized. It is called via pexpect, but probably can be called via Cython directly. It is only one file. If we keep using the pexpect interface it should be moved into its own spkg.
- commit 10630 are the tables, which should not go into the history. As mentioned above these should be moved into its own database spkg and probably already be pickled
Cheers,
Michael
comment:4 Changed 12 years ago by
For the four extracted patches from Jon's code see
http://sage.math.washington.edu/home/mabshoff/hanke-qf-merge/
There is also some comments in the thread at
http://groups.google.com/group/sage-devel/t/17612419fefaf4d9
Cheers,
Michael
comment:5 Changed 12 years ago by
I've attached a diff with the changed files between stock 2.8.14 and Jon's quadratic forms branch. Note there are several new files in sage/quadratic_forms/
directory which are not included in this patch. The plan was to pick the relevant changes from this patch, but most of it is already included in 3.1.4 with the following exceptions:
setup.py
: adds extension modules for new filessage/quadratic_forms/all.py
: adds imports for new filessage/quadratic_forms/binary_qf.py
: adds comment/todo in docstring for the fileinteger_mod.{pxd,pyx
}: implement classesIntegerMod_gmp_power_of_2
,IntegerMod_int_power_of_2
andIntegerMod_int64_power_of_2
, but this are not used in quadratic forms code, so it's irrelevant and can be ignored.
comment:6 Changed 12 years ago by
- Cc cremona added
Coverage definitely needs to be improved:
sage [sage-3.1.2]> ./sage -coverageall devel//sage/sage/quadratic_forms/ binary_qf.py: 100% (16 of 16) count_local_2.pyx: 0% (0 of 1) cython_testing.pyx: 0% (0 of 4) extras.py: 25% (2 of 8) genera/genus.py: 0% (0 of 34) mass_testing.py: 0% (0 of 3) quadratic_form__automorphisms2.py: 60% (3 of 5) quadratic_form__automorphisms.py: 75% (6 of 8) quadratic_form__count_local_2.py: 0% (0 of 9) quadratic_form__equivalence_testing.py: 25% (1 of 4) quadratic_form__evaluate.pyx: 0% (0 of 2) quadratic_form__genus.py: 0% (0 of 3) quadratic_form__local_density_congruence.py: 9% (1 of 11) quadratic_form__local_density_interfaces.py: 14% (1 of 7) quadratic_form__local_field_invariants.py: 57% (8 of 14) quadratic_form__local_normal_form.py: 75% (3 of 4) quadratic_form__local_representation_conditions.py: 12% (2 of 16) quadratic_form__mass__Conway_Sloane_masses.py: 26% (4 of 15) quadratic_form__mass.py: 0% (0 of 3) quadratic_form__mass__Siegel_densities.py: 20% (1 of 5) quadratic_form__neighbors.py: 75% (3 of 4) quadratic_form.py: 43% (14 of 32) quadratic_form__reduction_theory.py: 40% (2 of 5) quadratic_form__siegel_product.py: 100% (1 of 1) quadratic_form__split_local_covering.py: 100% (3 of 3) quadratic_form__ternary_Tornaria.py: 0% (0 of 17) quadratic_form__theta.py: 50% (2 of 4) quadratic_form__variable_substitutions.py: 71% (5 of 7) random_quadraticform.py: 100% (2 of 2) special_values.py: 60% (3 of 5) table_conversion.py: 100% (4 of 4) table_creation.py: 0% (0 of 2) table_hanke.py: 12% (4 of 32) table_hanke.pyx: 12% (4 of 32) tables.py: 15% (5 of 33) ternary_table_creation.py: 0% (0 of 7) ternary_table.pyx: 0% (0 of 15) Overall weighted coverage score: 26.3% Total number of functions: 377
There are a bunch of doctest failures, but a lot of those will be sorted out hopefully by Sunday night:
The following tests failed: sage -t devel/sage/sage/quadratic_forms/quadratic_form__local_field_invariants.py sage -t devel/sage/sage/quadratic_forms/quadratic_form__local_normal_form.py sage -t devel/sage/sage/quadratic_forms/table_hanke.py sage -t devel/sage/sage/quadratic_forms/special_values.py sage -t devel/sage/sage/quadratic_forms/quadratic_form__neighbors.py sage -t devel/sage/sage/quadratic_forms/quadratic_form__reduction_theory.py sage -t devel/sage/sage/quadratic_forms/quadratic_form__automorphisms.py sage -t devel/sage/sage/quadratic_forms/quadratic_form__local_representation_conditions.py sage -t devel/sage/sage/quadratic_forms/quadratic_form.py sage -t devel/sage/sage/quadratic_forms/table_hanke.pyx sage -t devel/sage/sage/quadratic_forms/quadratic_form__split_local_covering.py sage -t devel/sage/sage/quadratic_forms/quadratic_form__mass__Conway_Sloane_masses.py sage -t devel/sage/sage/quadratic_forms/quadratic_form__local_density_congruence.py sage -t devel/sage/sage/quadratic_forms/quadratic_form__equivalence_testing.py sage -t devel/sage/sage/quadratic_forms/random_quadraticform.py sage -t devel/sage/sage/quadratic_forms/table_conversion.py sage -t devel/sage/sage/quadratic_forms/quadratic_form__siegel_product.py sage -t devel/sage/sage/quadratic_forms/tables.py sage -t devel/sage/sage/quadratic_forms/quadratic_form__local_density_interfaces.py sage -t devel/sage/sage/quadratic_forms/quadratic_form__automorphisms2.py Total time for all tests: 129.5 seconds
Cheers,
Michael
comment:7 Changed 12 years ago by
- Summary changed from Merge Jon Hanke's qudratic forms code into Sage to [with patch, not ready for review] Merge Jon Hanke's qudratic forms code into Sage
Justin,
a preliminary diff can be found at http://sage.math.washington.edu/home/mabshoff/john-hanke-qf.diff
There still are renames to be done, but I should have something in the next 24 hours. Feel free to start the review despite the comment in the summary.
Cheers,
Michael
comment:8 Changed 12 years ago by
- Owner changed from justin to tornaria
- Status changed from new to assigned
comment:9 Changed 12 years ago by
- Milestone changed from sage-3.4.1 to sage-3.4
- Summary changed from [with patch, not ready for review] Merge Jon Hanke's qudratic forms code into Sage to [with patch] Merge Jon Hanke's qudratic forms code into Sage
Attached patches:
- attachment:patch.4470.01-inital_hanke_code: applies Jon Hanke's quadratic forms code into sage. The merge is based in mabshoff work during SD Austin, with some minor updates.
- attachment:patch.4470.02-fixes_and_doctest: fixes and lots of doctests and documentation to be applied on top of the initial patch. This patch raises the doctest coverage from 33% to over 60%.
The patches apply cleanly on a 3.3 tree, all tests pass in sage.math and my core2 debian/64 laptop.
comment:10 Changed 12 years ago by
- Cc tornaria added
comment:11 Changed 12 years ago by
- Summary changed from [with patch] Merge Jon Hanke's qudratic forms code into Sage to [with patch, needs review] Merge Jon Hanke's qudratic forms code into Sage
Hi Gonzalo, Jon,
this patch needs a formal review, so either one of you can give a positive review to the other person's work. We will give an exception to the coverage requirements in this case, but I will open a followup ticket to get coverage up to 100%.
Cheers,
Michael
comment:12 Changed 12 years ago by
- Summary changed from [with patch, needs review] Merge Jon Hanke's qudratic forms code into Sage to [with patch, positive review] Merge Jon Hanke's qudratic forms code into Sage
Jon Hanke and I have been working on reviewing the initial patch last week, improving and doctesting the code. Although the coverage is not 100%, and there's most certainly still bugs in the code, it is completely orthogonal to the rest of sage so it won't affect anything else. Given SD13 and AWS soon, we expect to improve it in the next couple of weeks.
I strongly recommend inclusion of this patch into sage.
comment:13 Changed 12 years ago by
Ok, everything works, but some doctests need to be marked optional since they depend on ISOM:
sage -t devel/sage/sage/quadratic_forms/quadratic_form__equivalence_testing.py # 8 doctests failed sage -t devel/sage/sage/quadratic_forms/quadratic_form__automorphisms.py # 6 doctests failed
Cheers,
Michael
Changed 12 years ago by
comment:14 Changed 12 years ago by
Merged
- patch.4470.01-inital_hanke_code
- patch.4470.02-fixes_and_doctest
- trac_4770-reviewer.patch
in Sage 3.4.alpha0.
Cheers,
Michael
comment:15 Changed 12 years ago by
As mentioned above this code was merged in Sage 3.4.alpha0.
Cheers,
Michael
comment:16 Changed 12 years ago by
- Resolution set to fixed
- Status changed from assigned to closed
As mentioned above this code was merged in Sage 3.4.alpha0.
Cheers,
Michael
There are large tables in Jon's commit:
These should be moved into its own database spkg.
Cheers,
Michael