Trac #30787: package modular_resolution: Split out from p_group_cohom…

…ology

As discussed in https://trac.sagemath.org/ticket/28711#comment:64:

We split the current `p_group_cohomology` spkg:

In this ticket, we create the package `modular_resolution`, depending on
meataxe-the-C-library, that installs:
 - a standalone C library `libmodres.so` in `$SAGE_LOCAL/lib`
 - some executables in `$SAGE_LOCAL/bin`, linked against `libmodres`
 - database of cohomology rings

This also fixes the build problems of `p_group_cohomology`.

Fixing the doctest failures of `p_group_cohomology` is outside of the
scope of this ticket. That's #34333.

New upstream:
- https://github.com/sagemath/modular_resolution

URL: https://trac.sagemath.org/30787
Reported by: mkoeppe
Ticket author(s): Matthias Koeppe, Dima Pasechnik, John Palmieri
Reviewer(s): John Palmieri, Matthias Koeppe, Dima Pasechnik, Travis
Scrimshaw

build/pkgs/modular_resolution/SPKG.rst

@@ -0,0 +1,115 @@
+p_group_cohomology: Modular cohomology rings of finite groups
+=============================================================
+
+Description
+-----------
+
+Modular Cohomology Rings of Finite Groups
+
+The package is located at http://users.fmi.uni-jena.de/cohomology/,
+that's to say the tarball p_group_cohomology-x.y.tar.xz can be found
+there and the documentation of the package is provided at
+http://users.fmi.uni-jena.de/cohomology/documentation/
+
+License
+-------
+
+Copyright (C) 2018 Simon A. King <simon.king@uni-jena.de> Copyright (C)
+2011 Simon A. King <simon.king@uni-jena.de> Copyright (C) 2009 Simon A.
+King <simon.king@nuigalway.ie> and
+
+   David J. Green <david.green@uni-jena.de>
+
+Distributed under the terms of the GNU General Public License (GPL),
+version 2 or later (at your choice).
+
+   This code is distributed in the hope that it will be useful,
+   but WITHOUT ANY WARRANTY; without even the implied warranty of
+   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+   General Public License for more details.
+
+The full text of the GPL is available at:
+
+   http://www.gnu.org/licenses/
+
+The package includes a data base of cohomology rings of the groups of
+order 64 and provides access to a data base of cohomology rings of the
+groups of order 128 and 243, located at
+
+   http://cohomology.uni-jena.de/db/
+
+These data bases are distributed under the Creative Commons
+Attribution-Share Alike 3.0 License. The full text of this licence is
+available at
+
+   http://creativecommons.org/licenses/by-sa/3.0/
+
+
+SPKG Maintainers
+----------------
+
+Simon A. King <simon.king@uni-jena.de>
+
+
+Upstream Contact
+----------------
+
+Simon A. King <simon.king@uni-jena.de> David J. Green
+<david.green@uni-jena.de>
+
+Acknowledgements
+----------------
+
+The development of the initial version of this SPKG was funded by the
+German Science Foundation, DFG project GR 1585/4.1, and was accomplished
+at the Friedrich Schiller University Jena.
+
+Since version 1.0.1, the further work on this SPKG was funded by Marie
+Curie grant MTKD-CT-2006-042685 and was pursued at the National
+University of Ireland, Galway. Since Novermber 2010, it is moved back to
+Jena.
+
+We thank William Stein for giving us access to various computers on
+which we could build test the SPKG and on which some huge computations
+could be completed, and acknowledge the support by National Science
+Foundation Grant No. DMS-0821725.
+
+We thank Mathieu Dutour Sikirić for hints on how to use GAP more
+efficiently.
+
+We owe Peter Symonds the idea of using the Poincaré series in a rather
+efficient completeness criterion.
+
+We are greatful to John Palmieri for his help on making
+p_group_cohomology work with python-3.
+
+Dependencies
+------------
+
+-  The SharedMeatAxe needs to be installed, as a build time dependency.
+
+   This can be met by installing the meataxe spkg
+
+Testing
+-------
+
+Our package provides a very short test suite for David Green's routines
+for the computation of minimal projective resolutions. The majority of
+this package's tests is formed by doc tests in the Cython code. In fact,
+any class, method and function is covered by tests.
+
+Note that internet access is required for these tests, as it is
+attempted to download cohomology rings from a public data base in the
+web.
+
+The script ``spkg-check`` calls ``sage -t --force_lib`` on the files
+in ``pGroupCohomology``.
+
+Documentation
+-------------
+
+The documentation of this package is automatically built, if the
+environment variable SAGE_SPKG_INSTALL_DOCS is yes (do "export
+SAGE_SPKG_INSTALL_DOCS=yes" on the command line before installation).
+The documents are put into
+SAGE_ROOT/local/share/doc/p_group_cohomology/.

build/pkgs/modular_resolution/checksums.ini

@@ -0,0 +1,5 @@
+tarball=modular_resolution-VERSION.tar.gz
+sha1=09ee61b1f9a33fb3e9bf0b658f81d3ede5748328
+md5=0e59e69a46014b8935c5e081d3bfc57a
+cksum=2981185519
+upstream_url=https://github.com/sagemath/modular_resolution/releases/download/VERSION/modular_resolution-VERSION.tar.gz

build/pkgs/modular_resolution/dependencies

@@ -0,0 +1 @@
+singular meataxe

build/pkgs/modular_resolution/package-version.txt

@@ -0,0 +1 @@
+1.1

build/pkgs/modular_resolution/spkg-check.in

@@ -0,0 +1,3 @@
+cd src
+
+$MAKE check || sdh_die "Error testing modular_resolution"

build/pkgs/modular_resolution/spkg-install.in

@@ -0,0 +1,5 @@
+cd src
+
+# build and install modular_resolution
+sdh_configure
+sdh_make_install

build/pkgs/modular_resolution/type

@@ -0,0 +1 @@
+optional

build/pkgs/p_group_cohomology/checksums.ini

@@ -1,5 +1,5 @@
 tarball=p_group_cohomology-VERSION.tar.xz
-sha1=110a6dbe26ae6d7aa1227e1ff2338d7c8b38daa9
-md5=d4fad2cde21c275aed753ccbd467616a
-cksum=1676569830
+sha1=d1d9a54f212a6de7d6a7e3afff80ffc3475264ad
+md5=9a57cd7dd045dfd5e014473d543060c2
+cksum=2489285741
 upstream_url=https://github.com/sagemath/p_group_cohomology/releases/download/vVERSION/p_group_cohomology-VERSION.tar.xz

build/pkgs/p_group_cohomology/dependencies

@@ -1 +1 @@
-$(PYTHON) cython cysignals singular meataxe $(SAGE_SRC)/sage/matrix/matrix_gfpn_dense.pxd $(SAGE_SRC)/sage/structure/element.pxd $(SAGE_SRC)/sage/matrix/matrix_gfpn_dense.pxd $(SAGE_SRC)/sage/matrix/matrix0.pxd $(SAGE_SRC)/sage/libs/meataxe.pxd $(SAGE_SRC)/sage/rings/morphism.pxd | $(PYTHON_TOOLCHAIN) matplotlib gap xz $(SAGERUNTIME) ipywidgets
+$(PYTHON) cython cysignals singular meataxe modular_resolution $(SAGE_SRC)/sage/matrix/matrix_gfpn_dense.pxd $(SAGE_SRC)/sage/structure/element.pxd $(SAGE_SRC)/sage/matrix/matrix_gfpn_dense.pxd $(SAGE_SRC)/sage/matrix/matrix0.pxd $(SAGE_SRC)/sage/libs/meataxe.pxd $(SAGE_SRC)/sage/rings/morphism.pxd | $(PYTHON_TOOLCHAIN) matplotlib gap xz $(SAGERUNTIME) ipywidgets

build/pkgs/p_group_cohomology/package-version.txt

@@ -1 +1 @@
-3.3.2
+3.3.3.p1

build/pkgs/p_group_cohomology/patches/7.patch

@@ -0,0 +1,23 @@
+From dde5d18ff0a0b8d1f9e88806bb9bb4b694b4666c Mon Sep 17 00:00:00 2001
+From: Matthias Koeppe <mkoeppe@math.ucdavis.edu>
+Date: Tue, 9 Aug 2022 10:09:22 -0700
+Subject: [PATCH] pGroupCohomology-3.3.3/pGroupCohomology/cohomology.pyx: Update import of
+ instancedoc for Sage 9.7
+
+---
+ pGroupCohomology-3.3.3/pGroupCohomology/cohomology.pyx | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/pGroupCohomology-3.3.3/pGroupCohomology/cohomology.pyx b/pGroupCohomology-3.3.3/pGroupCohomology/cohomology.pyx
+index 3a7dc77..ae1458d 100644
+--- a/pGroupCohomology-3.3.3/pGroupCohomology/cohomology.pyx
++++ b/pGroupCohomology-3.3.3/pGroupCohomology/cohomology.pyx
+@@ -68,7 +68,7 @@ from sage.all import mul
+ from sage.env import DOT_SAGE, SAGE_ROOT
+ from sage.misc.sageinspect import sage_getargspec
+ from sage.misc.lazy_attribute import lazy_attribute
+-from sage.docs.instancedoc import instancedoc
++from sage.misc.instancedoc import instancedoc
+ from sage.structure.richcmp import richcmp, richcmp_method, op_LT, op_NE, op_GT
+
+ # Sage rings etc.

build/pkgs/p_group_cohomology/spkg-check.in

@@ -1,9 +1,3 @@
 cd src
 
-# testing modular_resolution-1.1
-cd `ls -d modular_resolution*`
-$MAKE check || sdh_die "Error testing modular_resolution-1.1"
-cd ..
-
-# testing pGroupCohomology
 sage -tp 0 --long --force_lib --warn-long 80 --timeout=0 `ls -d pGroupCohomology*`/pGroupCohomology/ || sdh_die "Error testing pGroupCohomology"

build/pkgs/p_group_cohomology/spkg-install.in

@@ -1,19 +1,3 @@
-# Check if meataxe was properly installed
-sage -c "import sage.libs.meataxe" || sdh_die "sage.libs.meataxe cannot be imported. To solve this, it is enough to retry installation of p_group_cohomology"
-
-cd src
-
-# build and install modular_resolution
-cd `ls -d modular_resolution*`
-sdh_configure || sdh_die "Error configuring modular_resolution"
-# sdh_make install got broken by trac ticket #24106
-$MAKE install || sdh_die "Error installing modular_resolution"
-cd ..
-
-# install helper modules
-sdh_install gap_helper "$SAGE_SHARE/gap/pkg/p_group_cohomology_helper" || sdh_die "Error installing GAP helper module"
-sdh_install singular_helper/dickson.lib "$SAGE_SHARE/singular/LIB/" || sdh_die "Error installing Singular helper module"
-
 # building pGroupCohomology
-cd `ls -d pGroupCohomology*`
+cd `ls -d src/pGroupCohomology*`
 sdh_pip_install .

build/pkgs/p_group_cohomology/spkg-postinst.in

@@ -1,7 +1,9 @@
+cd src
+
 # building pGroupCohomology's documentation
 
 if [ "x$SAGE_SPKG_INSTALL_DOCS" = xyes ] ; then
-    cd `ls -d src/pGroupCohomology*/doc`
+    cd `ls -d pGroupCohomology*/doc`
     $MAKE html || sdh_die "Error building documentation"
     sdh_install build/html/* "$SAGE_SHARE/doc/p_group_cohomology/" || sdh_die "Error moving documentation to $SAGE_SHARE/doc/p_group_cohomology"
 fi

build/pkgs/p_group_cohomology/type

@@ -1 +1 @@
-experimental
+optional

src/sage/tests/modular_group_cohomology.py

@@ -52,7 +52,7 @@
     sage: H.essential_ideal()                           # optional - p_group_cohomology
     a_1_0*a_1_1,
     a_1_1*a_3_1
-    sage: ascii_art(H.bar_code('LowerCentralSeries')[2])# optional - p_group_cohomology
+    sage: ascii_art(H.bar_code('LowerCentralSeries')[2]) # known bug (possibly, the output might be correct) # optional - p_group_cohomology
         *
       *-*
       *-*