Trac #30804: Merge branch 'develop' into t/30804/add_standard_sphere_…

…to_manifold_catalog

.github/workflows/tox.yml

@@ -239,13 +239,13 @@ jobs:
         if: contains(matrix.tox_system_factor, 'nobootstrap')
       - name: Move homebrew away
         run: |
-          (cd /usr/local && for a in bin etc include lib opt sbin share; do mv $a $a-moved; done)
+          (cd /usr/local && for a in bin etc include lib opt sbin share; do sudo mv $a $a-moved; done)
       - name: Select Xcode version
         run: |
           if [ ${{ matrix.xcode_version_factor }} != default ]; then sudo xcode-select -s /Applications/Xcode_${{ matrix.xcode_version_factor }}.app; fi
       - name: Install test prerequisites
         run: |
-          /usr/bin/python3 -m pip install --user tox
+          sudo /usr/bin/python3 -m pip install tox
       - name: Install python3 from python.org
         # As of 2020-03-30 (https://github.com/actions/virtual-environments/blob/master/images/macos/macos-10.15-Readme.md),
         # Python 3.7.7 is installed on GitHub Actions runners.  But we install our own copy from the python.org binary package.

.gitignore

@@ -77,6 +77,9 @@ $RECYCLE.BIN/
 # SublimeText
 *.sublime-workspace
 
+# mypy
+**/.mypy_cache/
+
 #################
 # SageMathCloud #
 #################

.zenodo.json

@@ -1,10 +1,10 @@
 {
     "description": "Mirror of the Sage https://sagemath.org/ source tree", 
     "license": "other-open", 
-    "title": "sagemath/sage: 9.2", 
-    "version": "9.2", 
+    "title": "sagemath/sage: 9.3.beta0", 
+    "version": "9.3.beta0", 
     "upload_type": "software", 
-    "publication_date": "2020-10-24", 
+    "publication_date": "2020-11-01", 
     "creators": [
         {
             "affiliation": "SageMath.org", 
@@ -15,7 +15,7 @@
     "related_identifiers": [
         {
             "scheme": "url", 
-            "identifier": "https://github.com/sagemath/sage/tree/9.2", 
+            "identifier": "https://github.com/sagemath/sage/tree/9.3.beta0", 
             "relation": "isSupplementTo"
         }, 
         {

README.md

@@ -173,9 +173,11 @@ Guide](https://doc.sagemath.org/html/en/installation).
 
     - [Git] Alternatively, clone the Sage git repository:
 
-            $ git clone -c core.symlinks=true --branch master git://trac.sagemath.org/sage.git
+            $ git clone -c core.symlinks=true --branch master https://github.com/sagemath/sage.git
 
-      This will create the subdirectory `sage`.
+      This will create the subdirectory `sage`. `cd sage/` and pick the branch you need
+      by doing `git checkout` - typically you want the latest development branch, thus do
+      `git checkout develop`.
 
     - [Windows] The Sage source tree contains symbolic links, and the
       build will not work if Windows line endings rather than UNIX

VERSION.txt

@@ -1 +1 @@
-SageMath version 9.2, Release Date: 2020-10-24
+SageMath version 9.3.beta0, Release Date: 2020-11-01

build/bin/sage-clone-source

@@ -35,6 +35,7 @@ git clone "$SRC" "$DST"
 
 cd "$DST"
 git remote set-url origin "$SAGE_REPO_ANONYMOUS"
+git remote set-url --push origin "$SAGE_REPO_AUTHENTICATED"
 
 # Save space
 git gc --aggressive --prune=now

build/bin/sage-spkg

@@ -489,6 +489,7 @@ export SAGE_ROOT="$SAGE_ROOT"
 export SAGE_SRC="$SAGE_SRC"
 export SAGE_PKG_DIR="$script_dir"
 export SAGE_SPKG_SCRIPTS="$SAGE_SPKG_SCRIPTS"
+export SAGE_SPKG_WHEELS="$SAGE_SPKG_WHEELS"
 
 export PKG_NAME="$PKG_NAME"
 export PKG_BASE="$PKG_BASE"

build/bin/sage-spkg-info

@@ -40,7 +40,7 @@ for system_package_file in "$PKG_DISTROS"/*.txt; do
                 echo "$system:"
                 ;;
         esac
-        echo -n "  "
+        printf "  "
         sage-print-system-package-command $system --prompt --sudo install $system_packages
     fi
 done

build/bin/write-dockerfile.sh

@@ -17,8 +17,8 @@ for PKG_SCRIPTS in build/pkgs/*; do
     if [ -d $PKG_SCRIPTS ]; then
         PKG_BASE=$(basename $PKG_SCRIPTS)
         SYSTEM_PACKAGES_FILE=$PKG_SCRIPTS/distros/$SYSTEM.txt
-        PKG_TYPE=$(cat $PKG_SCRIPTS/type)
-        if [ -f $SYSTEM_PACKAGES_FILE -a -f $PKG_SCRIPTS/spkg-configure.m4 ]; then
+        if [ -f $PKG_SCRIPTS/type -a -f $SYSTEM_PACKAGES_FILE -a -f $PKG_SCRIPTS/spkg-configure.m4 ]; then
+           PKG_TYPE=$(cat $PKG_SCRIPTS/type)
            PKG_SYSTEM_PACKAGES=$(echo $(${STRIP_COMMENTS} $SYSTEM_PACKAGES_FILE))
            if [ -n "PKG_SYSTEM_PACKAGES" ]; then
                case "$PKG_TYPE" in

build/pkgs/_recommended/SPKG.txt

@@ -0,0 +1,6 @@
+= _recommended =
+
+== Description ==
+
+Script package representing a list of system packages recommended
+to be installed for additional functionality.

build/pkgs/_recommended/distros/debian.txt

@@ -0,0 +1,17 @@
+# From https://wiki.sagemath.org/prerequisitesUbuntu
+
+# to generate pdf documentation
+texlive-generic-extra
+# to convert Jupyter notebooks to pdf
+texlive-xetex
+# to generate pdf documentation
+latexmk
+# to convert Jupyter notebooks to pdf
+pandoc
+# to render text with LaTeX in Matplotlib
+dvipng
+# to run the Jmol 3D viewer from the console and generate images for 3D plots in the documentation
+default-jdk
+# to produce animations
+ffmpeg
+libavdevice-dev

build/pkgs/_recommended/distros/homebrew.txt

@@ -0,0 +1,8 @@
+# To convert Jupyter notebooks to pdf:
+pandoc
+# To produce animations:
+ffmpeg
+imagemagick
+# Homebrew's texinfo can be used to build the info files for ecl and
+# maxima but the OS X default version of texinfo cannot.
+texinfo

build/pkgs/_recommended/spkg-configure.m4

@@ -0,0 +1,3 @@
+SAGE_SPKG_CONFIGURE([_recommended], [
+  sage_spkg_install__recommended=yes
+])

build/pkgs/_recommended/spkg-install

@@ -0,0 +1,2 @@
+#! /usr/bin/env bash
+# Nothing to do

build/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=3d2376e9c9035632fac4c1628e63bebb1eb449ed
-md5=e28f30a4b7968339d7d803bf6c1aaa4d
-cksum=2795376077
+sha1=8e62a22481989ce61bb06adab0ce926c555604c5
+md5=3ea78ce307e26ca687652bc8d6bde85d
+cksum=791004627

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-b41abf12c433805c89a6c0fa28485916ef9e6b40
+f1e553872604276da99fb4dc017b515766c38532

build/pkgs/deformation/type

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

build/pkgs/gap_packages/patches/cohomolo-gcc10.patch

@@ -0,0 +1,150 @@
+diff --git a/pkg/cohomolo-1.6.7/standalone/progs.d/crp1.c b/pkg/cohomolo-1.6.7/standalone/progs.d/crp1.c
+index 3bbdc45..7df699f 100644
+--- a/pkg/cohomolo-1.6.7/standalone/progs.d/crp1.c
++++ b/pkg/cohomolo-1.6.7/standalone/progs.d/crp1.c
+@@ -8,9 +8,8 @@ extern short sp[],**mat[],*psp[],**imcos[],**cpco[],lorb[],
+ short *cst,**cpst,***cdpst,**svptr,*cp,*rel;
+ short *spst,**pspst,**pptr,**cpptr,npt,nb,nph,nph2,npg,npg2,
+       rno,orno,coh_index,*invg;
+-FILE  *ip,*op;
+
+-void seeknln (void) { while (getc(ip)!='\n'); }
++void seeknln (FILE *ip) { while (getc(ip)!='\n'); }
+
+ /* This program differs from most other permutation programs in that perms are
+    all stored in the single array sp. Schreier vectors are stored in the short
+@@ -23,13 +22,14 @@ void seeknln (void) { while (getc(ip)!='\n'); }
+ int 
+ crprog1 (void)
+ { short *pc,*qc,ex,neg; int x;
++  FILE  *ip,*op;
+   short i,j,k,l,m,n,cl,rl,*p,ocl,im,pt,pt1,pn,ipt;
+   if ((ip=fopen(inf2,"r"))== 0)
+   { fprintf(stderr,"Cannot open %s.\n",inf2); return(-1);}
+   fscanf(ip,"%hd%hd%hd%hd",&npt,&nph,&nb,&k);
+   if (nb>=mb) {fprintf(stderr,"nb too big. Increase MB.\n"); return(-1);}
+   if (k<=2) {fprintf(stderr,"inf2 has illegal format.\n"); return(-1); }
+-  seeknln(); seeknln();
++  seeknln(ip); seeknln(ip);
+   for (i=1;i<=nb;i++) fscanf(ip,"%hd",lorb+i);
+   pptr=psp-1; pspst=psp+nph; svptr=cpsp-1;  cpst=cpsp+nb;
+   invg=sp; nph2=2*nph; spst=sp+nph2;
+@@ -37,7 +37,7 @@ crprog1 (void)
+   { pptr[i]=spst+(i-1)*npt-1; p=pptr[i];
+     for (j=1;j<=npt;j++) {fscanf(ip,"%hd",&k); p[k]=j; }
+     invg[2*i-2]=2*i-1; invg[2*i-1]=2*i-2;
+-    seeknln();
++    seeknln(ip);
+   }
+   spst+=(npt*nph);
+   for (i=1;i<=nb;i++)
+@@ -75,7 +75,7 @@ crprog1 (void)
+   strcpy(inf1,inf0); strcat(inf1,".rel");
+   if ((ip=fopen(inf1,"r"))==0)
+   { fprintf(stderr,"Cannot open %s.\n",inf1); return(-1);}
+-  fscanf(ip,"%hd%hd",&k,&rno); seeknln();
++  fscanf(ip,"%hd%hd",&k,&rno); seeknln(ip);
+   op=fopen(outft,"w");
+ /* Now we have read everything in, and the computation can start */
+   orno=0;
+diff --git a/pkg/cohomolo-1.6.7/standalone/progs.d/nq+chfns.c b/pkg/cohomolo-1.6.7/standalone/progs.d/nq+chfns.c
+index a7396b2..658496f 100644
+--- a/pkg/cohomolo-1.6.7/standalone/progs.d/nq+chfns.c
++++ b/pkg/cohomolo-1.6.7/standalone/progs.d/nq+chfns.c
+@@ -20,8 +20,6 @@ short  mexp=MEXP,mcl=MCL,no,rel[RSP],wt[MEXP],exp,*rpf,*rpb,
+ extern short  prime,dim,*spv,**spm,mspace[],*vec[],**mat[],cp[],pinv[],opmats,
+         mm,mv;
+ extern int msp;
+-FILE *ip,*op;
+-
+
+ int 
+ calcmats (void)
+@@ -59,7 +57,7 @@ calcmats (void)
+   }
+   for (i=1;i<=exp;i++) trans(mat[i+exp],mat[i]);
+   if (opmats)
+-  { op=fopen(outf,"w");
++  { FILE *op=fopen(outf,"w");
+     fprintf(op,"%4d%4d%4d\n",prime,dim,exp);
+     for (i=1;i<=exp;i++) printmat(mat[i]); 
+     fclose(op);
+@@ -71,6 +69,7 @@ int
+ rdmats (void)
+ /* reads matrices of generators of P */
+ { short i; int quot;
++  FILE *ip;
+   ip=fopen(inf4,"r");
+   if (ip==0)
+   { fprintf(stderr,"Cannot open %s\n ",inf4); return(-1); }
+@@ -90,12 +89,12 @@ rdmats (void)
+   fclose(ip);
+   return(0);
+ }
+-FILE *ip;
+
+ int 
+ ingp (int inp)
+ /* Read in output of respcrun -s */
+ { short i,j,k,l,m,*orpf,**pcp;
++  FILE *ip;
+   ip=fopen(inf3,"r");
+   if (ip==0) { fprintf(stderr,"Cannot open %s\n",inf3); return(-1); }
+   fscanf(ip,"%hd%hd%hd%hd%hd%hd",&prime,&exp,&i,&no,&j,&m);
+diff --git a/pkg/cohomolo-1.6.7/standalone/progs.d/nqmfns.c b/pkg/cohomolo-1.6.7/standalone/progs.d/nqmfns.c
+index 0896551..6841bc8 100644
+--- a/pkg/cohomolo-1.6.7/standalone/progs.d/nqmfns.c
++++ b/pkg/cohomolo-1.6.7/standalone/progs.d/nqmfns.c
+@@ -9,7 +9,6 @@ extern short  intexp,mexp,mng,wksp,
+        spugen[],*tlintg[];
+ extern int ptrsp,rsp;
+ short  fac;
+-FILE *ip,*op;
+
+ int 
+ ingp (void)
+@@ -18,6 +17,7 @@ ingp (void)
+    of nqrun, and tails are also read in.
+ */
+ { short i,j,k,l,m,x,y,no,*orpf,*orpb,**pcp;  char tails;
++  FILE *ip;
+   if ((ip=fopen(inf1,"r"))==0)
+   { fprintf(stderr,"Cannot open %s.\n",inf1); return(-1); }
+   fscanf(ip,"%hd%hd%hd%hd%hd%hd",&prime,&exp,&nng,&no,&class,&m);
+@@ -89,6 +89,7 @@ int
+ outgp (void)
+ /* The PCP is output, together with tails */
+ { short i,k,l,**pcp,*b,*e,*c;
++  FILE *op;
+   op=fopen(outf,"w");
+   fprintf(op,"%4d%4d%4d%4d%4d%4d\n",prime,exp,nng,exp,class,1);
+   for (i=1;i<=exp;i++) fprintf(op,"%4d",wt[i]); fprintf(op,"\n");
+@@ -379,7 +380,7 @@ restart:
+     nng--; mnng--; enexpnt--;
+     if (nng==0)
+     { if (gap)
+-      { op=fopen(outfm,"w"); fprintf(op,"COHOMOLO.Multiplier:=[];\n");
++      { FILE *op=fopen(outfm,"w"); fprintf(op,"COHOMOLO.Multiplier:=[];\n");
+         fclose(op);
+         printf("All new generators eliminated. Multiplier is trivial.\n");
+       }
+diff --git a/pkg/cohomolo-1.6.7/standalone/progs.d/nqmp.c b/pkg/cohomolo-1.6.7/standalone/progs.d/nqmp.c
+index 01cf914..0144883 100644
+--- a/pkg/cohomolo-1.6.7/standalone/progs.d/nqmp.c
++++ b/pkg/cohomolo-1.6.7/standalone/progs.d/nqmp.c
+@@ -9,7 +9,6 @@ extern short  intexp,mng,mexp,wksp,
+        spugen[],*intg[],*imintg[],*tlintg[];
+ extern int ptrsp,rsp;
+ short  *wf,*wc; char norm;
+-FILE *ip,*op;
+
+ /* The data structures for this program and for nqrun are similar.
+    d1 and d2 contain definitions of generators. (Def. comes from commutator
+@@ -35,6 +34,7 @@ nqmprog (void)
+ { short i,j,k,l,m,d,*gi,*gj,*ti,*tj,cl,def,*ps,*pf,**dp,*nrpb,*p,*orpf,*orpb,
+         nb,np,k1,*rno,*covrel,**pgen,tdef,sgn;
+   char nt;
++  FILE *ip,*op;
+   if (ingp() == -1) {fprintf(stderr,"Input error.\n"); return(-1); }
+   eexpnt=expnt+exp; enexpnt=nexpnt+nng;
+

build/pkgs/gap_packages/patches/guava_leon_includes.patch

@@ -0,0 +1,13 @@
+--- a/pkg/guava-3.14/src/leon/src/generate.c	Sat Feb 29 09:02:10 2020
+--- b/pkg/guava-3.14/src/leon/src/generate.c	Thu Sep 24 13:58:36 2020
+***************
+*** 115,120 ****
+--- 115,122 ----
+  #include "groupio.h"
+  #include "enum.h"
+  #include "storage.h"
++ #include "chbase.h"
++ #include "inform.h"
+
+  #ifdef ALT_TIME_HEADER
+  #include "cputime.h"

build/pkgs/gap_packages/spkg-install.in

@@ -68,6 +68,8 @@ install_compiled_pkg()
 for pkg in cohomolo-* crypting-* grape-* guava-* orb-*
 do
     echo "Building GAP package $pkg"
+    CFLAGS="$CFLAGS -Wno-implicit-function-declaration"
+    export CFLAGS
     cd "$PKG_SRC_DIR/$pkg"
     ./configure "$GAP_ROOT"
     sdh_make -j1