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Compute sheaf cohomology of coherent sheaves on toric varieties

GAP 90.09% Makefile 1.23% Shell 0.26% C++ 8.31% Python 0.12%

coherent-sheaves toric-varieties compute-cohomologies

toricvarieties_project's People

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zickgraf herearound lmyreg2017 rosshochwert

toricvarieties_project's Issues

Tests in Julia

Extend test suite to issue

(gap) tests of package Convex in Julia
(gap) tests of package ToricVarieties in Julia.

Tests for TruncationsOfFPGradedModules fail

This is because of kamalsaleh/ComplexesCategories#4 and sunnyquiver/QPA2#37 respectively.

Currently, the runners on github seem to come with outdated certificates. As a consequence, apt-get update cannot be executed, boost cannot be properly installed. Ultimately, this leads to failed tests of the QSMExplorer package.

After spending some serious time on this, I have decided to currently disable any tests of the QSMExplorer package on github. Eventually, a more satisfying resolution to this issue should be achieved, include enabling the tests for the QSMExplorer again.

Merge TopcomInterface into ToricVarieties_project

Bug: DegreeGroup of the Cox ring of a product of varieties is not identical to the SuperObject of degrees of its indeterminates.

The issue has been originally opened in
homalg-project/homalg_project#231

QSM Explorer example

Suggestion:

Add one more command -- LoadPackage( "QSMExplorer" ); at the beginning of each example file.
Recheck the input, shall we keep purely loopwise closed diagrams or allowed diagrams with external legs?

QSM Explorer check input

Suggestion:

Once the input is not corresponding to a realizable diagram, i.e., the length of genus list and degree list do not match, or exists extra unwanted node labels in the edge list, an error warning the incorrect form of input is supposed to be returned.

Improvement on Polymake_V_Rep_command_string (and similar for H_Rep)

As noted by @fingolfin in oscar-system/JToric.jl#38:

However, it also seems as if your function Polymake_V_Rep_command_string constantly creates new Polymake objects? Is there a reason why you don't just create one of these once, and keep it around? Or am I misunderstanding the code?

This should be changed into an attribute.

QSM Explorer Data

Add more information to database:

More about the polytope (e.g. its lattice points and a constructor)
The dual polytope (e.g. its lattice points and a constructor)
A base triangulation including constructor
An X5-triangulation including constructor
Save compute number of root bundles.

Reorder the polytopes in the database

Suggestion: we could reorder the polytopes in the database ascendingly by the triple intersection number Kbar^3.

Remove JuliaEvalString

As suggested by @fingolfin in oscar-system/JToric.jl#38:

Another thing: I noticed that in JConvex, you use JuliaEvalString a lot. That's inefficient and should almost never be necessary. It also leads to hard to debug code.
For example, if one defined pm as in oscar-system/JToric.jl#40, then this works just fine in GAP: pm.polytope.Polytope()

Version mismatch blocks update

Could you please investigate and fix this:

* ToricVarieties - new version 2021.05.04 discovered!!!
  ============================================
  Getting new archives from 
  https://github.com/homalg-project/ToricVarieties_project/releases/download/2021-05-04/ToricVarieties[ ".zip" ]
  unpacking ToricVarieties.zip
Archive:  ToricVarieties.zip
   creating: ToricVarieties/
  inflating: ToricVarieties/read.g   [text]  
...
  inflating: ToricVarieties/tst/toricvarieties05.tst  [text]  
  ERROR (ToricVarieties): PackageInfo.g on web refers to version 2021.05.04, but 
PackageInfo.g in the archive has version 2021.04.25! SKIPPING!!!

Improve test for sheafification

There are other simpler tests for "does sheafify to zero" which can be added before going for the final test here. One of them is to test the dimension of the module using the command AffineDimension.

ToricVarieties: Dependency on Convex is not optional

If I try to load ToricVarieties without NConvex, I get the following error:

Error, Variable: 'IsConvexObject' must have a value
not in any function at ~/.gap/pkg/ToricVarieties_project/ToricVarieties/gap/ToricVarieties.gd:435

Additionally, the version 2021.04-24 of NConvex required by Convex is not available in the homalg CI, since we use the version here: https://github.com/homalg-project/NConvex Maybe we could simply remove ToricVarieties from the homalg CI now that ToricVarieties_project has its own CI?

Build scripts to be integrated into makefiles

QSM Explorer counting capability

The root countings on certain polytopes (especially those polytopes with Kbar^3=30) in the QSM list are not manageable to be done by Plesken within reasonable time. We shall give a warning in the output of "CountLimitRootsOfQSM()", etc if one inputs the index of those polytopes.

ToricVarieties: Add `TestFile` to `PackageInfo.g` ?

See homalg-project/homalg_project#465 for motivation to do so.

Your current testfile tst/testall.g unfortunately can't be used as it loads FreydCategoriesForCAP which is not a deposited package.

New location of distributed gap-package ToricVarieties

@alex-konovalov: After discussion with @mohamed-barakat, we have moved the distributed gap-package ToricVarieties to this new repository. Are further adjustments necessary?

Make TopcomInterface optional in tests

The new tests in 368614e require TopcomInterface, which in turn requires TOPCOM, which is not available on our CI server. Could you wrap the tests in a suitable if block which tests if TopcomInterface is available? Here is an example of such an if block (in FinGSetsForCAP testing if FinSetsForCAP is available): https://github.com/homalg-project/FinGSetsForCAP/blob/master/examples/ReconstructGroup.g#L10-L18

Can't pick up ToricVarieties release - wrong date in the release tag

Hi, I see in check for updates logs:

[/circa/home/gap-jenkins/pkgadmin/pkgcache/toricvarieties/tmp/ToricVarieties.zip]
  End-of-central-directory signature not found.  Either this file is not
  a zipfile, or it constitutes one disk of a multi-part archive.  In the
  latter case the central directory and zipfile comment will be found on
  the last disk(s) of this archive.
unzip:  cannot find zipfile directory in one of /circa/home/gap-jenkins/pkgadmin/pkgcache/toricvarieties/tmp/ToricVarieties.zip or
        /circa/home/gap-jenkins/pkgadmin/pkgcache/toricvarieties/tmp/ToricVarieties.zip.zip, and cannot find /circa/home/gap-jenkins/pkgadmin/pkgcache/toricvarieties/tmp/ToricVarieties.zip.ZIP, period.
  End-of-central-directory signature not found.  Either this file is not
  a zipfile, or it constitutes one disk of a multi-part archive.  In the
  latter case the central directory and zipfile comment will be found on
  the last disk(s) of this archive.
unzip:  cannot find zipfile directory in one of ToricVarieties.zip or
        ToricVarieties.zip.zip, and cannot find ToricVarieties.zip.ZIP, period.

and then

* ToricVarieties - new version 2021.09.05 discovered!!!
  ============================================
  Getting new archives from 
  https://github.com/homalg-project/ToricVarieties_project/releases/download/2\
021-09-05/ToricVarieties[ ".zip" ]
  unpacking ToricVarieties.zip
Archive:  ToricVarieties.zip
ERROR (ToricVarieties): could not unpack archive .... SKIPPING !!!

The link above is

https://github.com/homalg-project/ToricVarieties_project/releases/download/2021-09-05/ToricVarieties.zip

and opening it shows "Not Found".

Now I see what's happening. Going to https://github.com/homalg-project/ToricVarieties_project/releases/tag/2021-09-95 and checking the link to ToricVarieties.zip and copying link address shows almost the same link:

https://github.com/homalg-project/ToricVarieties_project/releases/download/2021-09-95/ToricVarieties.zip

except that the date is the 95th of September! Please fix this!

Archive URLs should have no format extension

Otherwise the following occurs:

* ToricVarieties - new version 2020.08.16 discovered!!!
  ============================================
  Getting new archives from 
  https://github.com/homalg-project/ToricVarieties_project/releases/download/2\
020-08-16/ToricVarieties.zip[ ".zip" ]
  unpacking ToricVarieties.zip.zip
Archive:  ToricVarieties.zip.zip
ERROR (ToricVarieties): could not unpack archive .... SKIPPING !!!

Please see https://github.com/gap-packages/example/blob/master/PackageInfo.g for documentation of these components.

Adding ToricVarieties_project to the homalg CI and "lines of code"

I have added some instructions to homalg_project describing how to do this: https://github.com/zickgraf/homalg_project/blob/56938ec8cb3cb681f784fea91ef751ce01702ae6/README_DEV.md

As a starting point for the tests you can look at the make targets ci-test and test-with-coverage in ToricVarieties/makefile, and my attempt to actually execute ci-test in the CI: zickgraf/homalg_project@207dc2b (the IsPackageMarkedForLoading-part needs gap-system/gap#3931 to work correctly).

If anything is unclear, just ask, then maybe we can improve the instructions :-)

Version number update required

It's not possible to pick it up unless the version is incremented:

Package: ToricVarieties
  changed components: [ "Persons" ]
  ERROR (ToricVarieties): There are changed components in the new info file from
  https://homalg-project.github.io/ToricVarieties_project/ToricVarieties/PackageInfo.g
   but .Version remains the same. This is not allowed, so the info file will not be changed

ToricaVarieties: broken ArchiveURL

PackageInfo.g has ArchiveURL equal to https://github.com/homalg-project/ToricVarieties_project/releases/download/2022-03-23/ToricVarieties-2022.03.23 -- combined with the format suffix .tar.gz this results in a broken download link

https://github.com/homalg-project/ToricVarieties_project/releases/download/2022-03-23/ToricVarieties-2022.03.23.tar.gz

However, the actual release is missing the file extensions, i.e. no .tar.gz suffix, as can be seen here: https://github.com/homalg-project/ToricVarieties_project/releases/tag/2022-03-23

Tests fail with TOPCOM 1.1.1

With TOPCOM 1.1.1 the following errors occur when executing make test in ToricVarieties:

 ┌───────┐   GAP 4.12.0 of 2022-08-18
 │  GAP  │   https://www.gap-system.org/
 └───────┘   Architecture: x86_64-pc-linux-gnu-default64-kv8
 Configuration:  gmp 6.2.1, GASMAN
 Loading the library and packages ...

 Packages:   AClib 1.3.2, Alnuth 3.2.1, AtlasRep 2.1.4, AutoDoc 2022.07.10, 
             AutPGrp 1.11, Browse 1.8.14, CRISP 1.4.5, Cryst 4.1.25, 
             CrystCat 1.1.10, CTblLib 1.3.4, FactInt 1.6.3, FGA 1.4.0, 
             Forms 1.2.8, GAPDoc 1.6.6, genss 1.6.7, IO 4.7.2, IRREDSOL 1.4.3, 
             LAGUNA 3.9.5, orb 4.8.5, Polenta 1.3.10, Polycyclic 2.16, 
             PrimGrp 3.4.2, RadiRoot 2.9, recog 1.3.2, ResClasses 4.7.3, 
             SmallGrp 1.5, Sophus 1.27, SpinSym 1.5.2, TomLib 1.2.9, 
             TransGrp 3.6.3, utils 0.76
 Try '??help' for help. See also '?copyright', '?cite' and '?authors'
Architecture: x86_64-pc-linux-gnu-default64-kv8

testing: /var/lib/jenkins/workspace/lg-project_homalg_project_master/pkg/Toric\
Varieties_project/ToricVarieties//tst/000_LoadPackage.tst
    1610 ms (194 ms GC) and 169MB allocated for 000_LoadPackage.tst
testing: /var/lib/jenkins/workspace/lg-project_homalg_project_master/pkg/Toric\
Varieties_project/ToricVarieties//tst/toricvarieties01.tst
Evaluating Commandline Options ...
Evaluating Commandline Options ...
########> Diff in /var/lib/jenkins/workspace/lg-project_homalg_project_ma\
ster/pkg/ToricVarieties_project/ToricVarieties//tst/toricvarieties01.tst:
81
# Input is:
H5_version2 := DeriveToricVarietiesFromGrading( [[0,1,1,0],[1,0,-5,1]], false \
);
# Expected output:
[ <A toric variety of dimension 2> ]
# But found:
Error, Variable: 'unknown' must have a value
Syntax error: ] expected in stream:1
_EVALSTRINGTMP:=[unknown option --regular  - exiting];
                         ^^^^^^
Error, Could not evaluate string.

########
########> Diff in /var/lib/jenkins/workspace/lg-project_homalg_project_ma\
ster/pkg/ToricVarieties_project/ToricVarieties//tst/toricvarieties01.tst:
83
# Input is:
H5_version3 := ToricVarietyFromGrading( [[0,1,1,0],[1,0,-5,1]] );
# Expected output:
<A toric variety of dimension 2>
# But found:
Error, Variable: 'unknown' must have a value
Syntax error: ] expected in stream:1
_EVALSTRINGTMP:=[unknown option --regular  - exiting];
                         ^^^^^^
Error, Could not evaluate string.

########

The last working version was 0.17.10. (I have downgraded TOPCOM in our CI for now, but will disable the tests the next time TOPCOM is updated automatically, which happens once a week.)

Bug with current GAP master

There seems to be a bug in ToricVarieties with current GAP master, as seen in our CI:

https://github.com/homalg-project/homalg_project/runs/1233928070

2020-10-10T00:16:35.6749594Z gap: src/plist.h:202: ELM_PLIST: Assertion `pos <= CAPACITY_PLIST(list)' failed.
2020-10-10T00:16:35.6750543Z make[1]: Entering directory '/home/gap/.gap/pkg/ToricVarieties_project/ToricVarieties'
2020-10-10T00:16:35.6751273Z Abort
2020-10-10T00:16:35.6752613Z /usr/bin/time --quiet --format="%U %S\n%e" --output=performance.out gap --quitonbreak --cover stats tst/testall.g
2020-10-10T00:16:35.6753492Z /home/gap/inst/gap-master/gap(+0x95540)[0x561b1e9f5540]
2020-10-10T00:16:35.6754134Z /lib/x86_64-linux-gnu/libc.so.6(+0x3efd0)[0x7f553fec6fd0]
2020-10-10T00:16:35.6754803Z /lib/x86_64-linux-gnu/libc.so.6(gsignal+0xc7)[0x7f553fec6f47]
2020-10-10T00:16:35.6755501Z /lib/x86_64-linux-gnu/libc.so.6(abort+0x141)[0x7f553fec88b1]
2020-10-10T00:16:35.6756151Z /lib/x86_64-linux-gnu/libc.so.6(+0x3042a)[0x7f553feb842a]
2020-10-10T00:16:35.6756769Z /lib/x86_64-linux-gnu/libc.so.6(+0x304a2)[0x7f553feb84a2]
2020-10-10T00:16:35.6757613Z /home/gap/inst/gap-master/gap(+0x38018)[0x561b1e998018]
2020-10-10T00:16:35.6758281Z /home/gap/inst/gap-master/gap(+0x134f1b)[0x561b1ea94f1b]
2020-10-10T00:16:35.6759028Z /home/gap/inst/gap-master/gap(DoProperty+0x3d)[0x561b1ea7ca7d]
2020-10-10T00:16:35.6759759Z /home/gap/inst/gap-master/gap(+0xb7751)[0x561b1ea17751]
2020-10-10T00:16:35.6760424Z /home/gap/inst/gap-master/gap(+0xac7fa)[0x561b1ea0c7fa]
2020-10-10T00:16:35.6761081Z /home/gap/inst/gap-master/gap(+0xac17c)[0x561b1ea0c17c]
2020-10-10T00:16:35.6761749Z /home/gap/inst/gap-master/gap(+0xae72d)[0x561b1ea0e72d]
2020-10-10T00:16:35.6762415Z /home/gap/inst/gap-master/gap(+0x171341)[0x561b1ead1341]
2020-10-10T00:16:35.6763074Z /home/gap/inst/gap-master/gap(+0x171a48)[0x561b1ead1a48]
2020-10-10T00:16:35.6763797Z /home/gap/inst/gap-master/gap(EXEC_CURR_FUNC+0x2d)[0x561b1ead3efd]
2020-10-10T00:16:35.6764517Z /home/gap/inst/gap-master/gap(+0xb9fc3)[0x561b1ea19fc3]
2020-10-10T00:16:35.6765186Z /home/gap/inst/gap-master/gap(+0xb80d0)[0x561b1ea180d0]
2020-10-10T00:16:35.6765864Z /home/gap/inst/gap-master/gap(+0x171a9f)[0x561b1ead1a9f]
2020-10-10T00:16:35.6766516Z /home/gap/inst/gap-master/gap(+0x171988)[0x561b1ead1988]
2020-10-10T00:16:35.6767232Z /home/gap/inst/gap-master/gap(EXEC_CURR_FUNC+0x2d)[0x561b1ead3efd]
2020-10-10T00:16:35.6767944Z /home/gap/inst/gap-master/gap(+0xb9fc3)[0x561b1ea19fc3]
2020-10-10T00:16:35.6768856Z /home/gap/inst/gap-master/gap(DoOperation1Args+0xd5)[0x561b1ea7c8f5]
2020-10-10T00:16:35.6769777Z /home/gap/inst/gap-master/gap(DoAttribute+0x68)[0x561b1ea7d938]
2020-10-10T00:16:35.6770424Z /home/gap/inst/gap-master/gap(+0xb7751)[0x561b1ea17751]
2020-10-10T00:16:35.6770884Z /home/gap/inst/gap-master/gap(+0xb77da)[0x561b1ea177da]
2020-10-10T00:16:35.6771356Z /home/gap/inst/gap-master/gap(+0x19ed9d)[0x561b1eafed9d]
2020-10-10T00:16:35.6771826Z /home/gap/inst/gap-master/gap(+0xb77da)[0x561b1ea177da]
2020-10-10T00:16:35.6772281Z /home/gap/inst/gap-master/gap(+0x171a9f)[0x561b1ead1a9f]
2020-10-10T00:16:35.6772947Z /home/gap/inst/gap-master/gap(+0x170305)[0x561b1ead0305]
2020-10-10T00:16:35.6773544Z /home/gap/inst/gap-master/gap(EXEC_CURR_FUNC+0x2d)[0x561b1ead3efd]
2020-10-10T00:16:35.6774046Z /home/gap/inst/gap-master/gap(+0xb9fc3)[0x561b1ea19fc3]
2020-10-10T00:16:35.6774507Z make[1]: *** [test-with-coverage] Error 1
2020-10-10T00:16:35.6774955Z make: *** [ci-test_ToricVarieties] Error 2
2020-10-10T00:16:35.6777406Z make: *** Waiting for unfinished jobs....

Edit: ToricVarieties is now disabled in the CI: homalg-project/homalg_project@2f4f84b

ToricVarieties: Broken `README_URL` and `PackageInfoURL`

The current ToricVarieties release unfortunately has broken README_URL and PackageInfoURL fields. E.g. the former is https://homalg-project.github.io/ToricVarieties_project/ToricVarietiesPackageInfo.g -- note the missing slash.

In addition, the README_URL fields were missing the .md suffix.

I've submitted PR #189 to fix this. No immediate change is needed by you -- but this breakage means that we won't be able to automatically pick up the next ToricVarieties update. So I suggest to leave this issue here open until PR #189 is merged and a new release is made. At that point, just notify me, and I'll import the new package version into the distribution.

QSM explorer index adjustment

The following adjustment needs to be made:

adding the index of each polytope by one in the QSM explorer
modifying the documentation.

IsZeroForObjects( DefiningSerreQuotientObject( sheaf ) );
Error, no method found! For debugging hints type ?Recovery from NoMethodFound
Error, no 1st choice method found for `UnderlyingMatrix' on 1 arguments at /home/kamal/software/gap/lib/methsel2.g:249 called from
UnderlyingMatrix( module

Segfault with Normaliz 3.10.1

With Normaliz 3.10.1, the tests of ToricVarieties_project in our CI segfault.