Merge #32116

Author: Matthias Koeppe

.github/workflows/ci-cygwin-minimal.yml

@@ -13,7 +13,7 @@ env:
   MAKE: make -j8
   SAGE_NUM_THREADS: 3
   CYGWIN: winsymlinks:native
-  CONFIGURE_ARGS: --enable-experimental-packages --enable-download-from-upstream-url --enable-fat-binary
+  EXTRA_CONFIGURE_ARGS: --enable-fat-binary
   SAGE_LOCAL: /opt/sage-${{ github.sha }}
 
 jobs:

.github/workflows/ci-cygwin-standard.yml

@@ -13,7 +13,7 @@ env:
   MAKE: make -j8
   SAGE_NUM_THREADS: 3
   CYGWIN: winsymlinks:native
-  CONFIGURE_ARGS: --enable-experimental-packages --enable-download-from-upstream-url --enable-fat-binary
+  EXTRA_CONFIGURE_ARGS: --enable-fat-binary
   SAGE_LOCAL: /opt/sage-${{ github.sha }}
 
 jobs:

.gitignore

@@ -1,4 +1,6 @@
-*.pyc
+## We use this file both as .gitignore and .dockerignore,
+## which have different semantics.
+
 /dist
 /local
 /logs
@@ -33,15 +35,21 @@
 
 # Various editors
 *~
+**/*~
 
 # Emacs
 \#*\#
+**/\#*\#
 .\#*
+**/.\#*
 
 # Vim
 *.swp
+**/*.swp
 *.swo
+**/*.swo
 *.swn
+**/*.swn
 *.un~
 .netrwhist
 
@@ -51,6 +59,7 @@
 
 # VSCode
 .vscode/*
+**/.vscode/*
 
 # XCode
 xcuserdata/
@@ -61,6 +70,7 @@ xcuserdata/
 .metadata
 *.tmp
 *.bak
+**/*.bak
 *.swp
 *~.nib
 .classpath
@@ -72,6 +82,7 @@ xcuserdata/
 
 # OSX specific temporary files
 .DS_Store
+**/.DS_Store
 ._*
 .AppleDouble
 .LSOverride
@@ -98,44 +109,55 @@ gitlab-build-docker.log
 
 # Byte-compiled / optimized / DLL files
 __pycache__/
+**/__pycache__
 *.py[cod]
+**/*.py[cod]
 *$py.class
 
 # Generated by sage_setup.autogen
 /src/sage/ext/interpreters
 
 # Generated Cython files
 *.so
-src/sage/**/*.c
-src/sage/**/*.cpp
-src/sage/modular/arithgroup/farey_symbol.h
-!src/sage/cpython/debugimpl.c
-!src/sage/graphs/base/boost_interface.cpp
-!src/sage/graphs/cliquer/cl.c
-!src/sage/graphs/graph_decompositions/sage_tdlib.cpp
-!src/sage/libs/eclib/wrap.cpp
-!src/sage/libs/linkages/padics/relaxed/flint_helper.c
-!src/sage/misc/inherit_comparison_impl.c
-!src/sage/modular/arithgroup/farey.cpp
-!src/sage/modular/arithgroup/sl2z.cpp
-!src/sage/rings/bernmm/bern_modp.cpp
-!src/sage/rings/bernmm/bern_modp_util.cpp
-!src/sage/rings/bernmm/bern_rat.cpp
-!src/sage/rings/bernmm/bernmm-test.cpp
-!src/sage/rings/padics/transcendantal.c
-!src/sage/rings/polynomial/weil/power_sums.c
-!src/sage/schemes/hyperelliptic_curves/hypellfrob/hypellfrob.cpp
-!src/sage/schemes/hyperelliptic_curves/hypellfrob/recurrences_ntl.cpp
-!src/sage/schemes/hyperelliptic_curves/hypellfrob/recurrences_zn_poly.cpp
-!src/sage/stats/distributions/dgs_bern.c
-!src/sage/stats/distributions/dgs_gauss_dp.c
-!src/sage/stats/distributions/dgs_gauss_mp.c
+**/*.so
+/src/sage/**/*.c
+/src/sage/**/*.cpp
+/src/sage/modular/arithgroup/farey_symbol.h
+!/src/sage/cpython/debugimpl.c
+!/src/sage/graphs/base/boost_interface.cpp
+!/src/sage/graphs/cliquer/cl.c
+!/src/sage/graphs/graph_decompositions/sage_tdlib.cpp
+!/src/sage/libs/eclib/wrap.cpp
+!/src/sage/libs/linkages/padics/relaxed/flint_helper.c
+!/src/sage/misc/inherit_comparison_impl.c
+!/src/sage/modular/arithgroup/farey.cpp
+!/src/sage/modular/arithgroup/sl2z.cpp
+!/src/sage/rings/bernmm/bern_modp.cpp
+!/src/sage/rings/bernmm/bern_modp_util.cpp
+!/src/sage/rings/bernmm/bern_rat.cpp
+!/src/sage/rings/bernmm/bernmm-test.cpp
+!/src/sage/rings/padics/transcendantal.c
+!/src/sage/rings/polynomial/weil/power_sums.c
+!/src/sage/schemes/hyperelliptic_curves/hypellfrob/hypellfrob.cpp
+!/src/sage/schemes/hyperelliptic_curves/hypellfrob/recurrences_ntl.cpp
+!/src/sage/schemes/hyperelliptic_curves/hypellfrob/recurrences_zn_poly.cpp
+!/src/sage/stats/distributions/dgs_bern.c
+!/src/sage/stats/distributions/dgs_gauss_dp.c
+!/src/sage/stats/distributions/dgs_gauss_mp.c
 /src/cython_debug
 
 # Temporary build files
 build/temp.*/
 build/bin/sage-build-env-config
 
+# Generated files in the top-level source trees
+/pkgs/*/build
+/pkgs/*/dist
+/pkgs/*/MANIFEST
+/pkgs/*/*.egg-info
+/pkgs/*/.tox
+
+# same for old locations - before Trac #31577
 /build/pkgs/*/src/build
 /build/pkgs/*/src/dist
 /build/pkgs/*/src/MANIFEST
@@ -173,7 +195,9 @@ src/venv.bak/
 # tox generated files
 /.tox
 /build/.tox
+**/.tox
 /prefix
 
 # git worktree
 worktree*
+**/worktree*

.zenodo.json

@@ -1,10 +1,10 @@
 {
     "description": "Mirror of the Sage https://sagemath.org/ source tree", 
     "license": "other-open", 
-    "title": "sagemath/sage: 9.4.beta4", 
-    "version": "9.4.beta4", 
+    "title": "sagemath/sage: 9.4.beta5", 
+    "version": "9.4.beta5", 
     "upload_type": "software", 
-    "publication_date": "2021-07-01", 
+    "publication_date": "2021-07-18", 
     "creators": [
         {
             "affiliation": "SageMath.org", 
@@ -15,7 +15,7 @@
     "related_identifiers": [
         {
             "scheme": "url", 
-            "identifier": "https://github.com/sagemath/sage/tree/9.4.beta4", 
+            "identifier": "https://github.com/sagemath/sage/tree/9.4.beta5", 
             "relation": "isSupplementTo"
         }, 
         {

Makefile

@@ -41,7 +41,7 @@ sageruntime: base-toolchain
 
 # CONFIG_FILES lists all files that appear in AC_CONFIG_FILES in configure.ac;
 # except for build/make/Makefile-auto, which is unused by the build system
-CONFIG_FILES = build/make/Makefile src/bin/sage-env-config build/bin/sage-build-env-config build/pkgs/sage_conf/src/sage_conf.py build/pkgs/sage_conf/src/setup.cfg
+CONFIG_FILES = build/make/Makefile src/bin/sage-env-config build/bin/sage-build-env-config pkgs/sage-conf/sage_conf.py pkgs/sage-conf/setup.cfg
 
 # SPKG_COLLECT_FILES contains all files that influence the SAGE_SPKG_COLLECT macro
 SPKG_COLLECT_FILES = build/pkgs/*/type build/pkgs/*/package-version.txt build/pkgs/*/dependencies build/pkgs/*/requirements.txt build/pkgs/*/checksums.ini build/pkgs/*/spkg-install

README.md

@@ -360,16 +360,31 @@ SAGE_ROOT                 Root directory (sage-x.y.z in Sage tarball)
 │       ├── atlas
 │       …
 │       └── zn_poly
+├── configure             Top-level configure script
 ├── COPYING.txt           Copyright information
-├── local                 Compiled packages are installed here
+├── pkgs                  Source trees of Python distribution packages
+│   ├── sage-conf
+│   │   ├── sage_conf.py
+│   │   └── setup.py
+│   ├── sage-docbuild
+│   │   ├── sage_docbuild
+│   │   └── setup.py
+│   ├── sage-sws2rst
+│   │   ├── sage_sws2rst
+│   │   └── setup.py
+│   └── sagemath-standard
+│       ├── bin
+│       ├── sage
+│       └── setup.py
+├── local  (SAGE_LOCAL)   Compiled packages are installed here
 │   ├── bin               Executables
 │   ├── include           C/C++ headers
 │   ├── lib               Shared libraries
 │   ├── share             Databases, architecture-independent data, docs
-│       └── doc           Viewable docs of Sage and of some components
+│   │   └── doc           Viewable docs of Sage and of some components
 │   └── var
-│       ├── sage          List of installed packages
-│       └── tmp           Temporary files when building Sage
+│       ├── lib/sage      List of installed packages
+│       └── tmp/sage      Temporary files when building Sage
 ├── logs
 │   ├── dochtml.log       Log of the documentation build
 │   ├── install.log       Full install log
@@ -382,7 +397,7 @@ SAGE_ROOT                 Root directory (sage-x.y.z in Sage tarball)
 ├── Makefile              Running "make" uses this file
 ├── README.md             This file
 ├── sage                  Script to start Sage
-├── src                   All of Sage source (not third-party packages)
+├── src                   Monolithic Sage library source tree
 │   ├── bin               Scripts that Sage uses internally
 │   ├── doc               Sage documentation sources
 │   └── sage              The Sage library source code

VERSION.txt

@@ -1 +1 @@
-SageMath version 9.4.beta4, Release Date: 2021-07-01
+SageMath version 9.4.beta5, Release Date: 2021-07-18