Merge branch 't/30383/new_package_type__optional_enabled_by_default' …

…into t/31409/cygwin_standard__r_build_fails_____downgrade_r__rpy2_to_optional
sagemath · Mar 15, 2021 · f04c134 · f04c134
2 parents f0a5fb5 + 4916415
commit f04c134
Show file tree

Hide file tree

Showing 348 changed files with 6,255 additions and 8,464 deletions.
diff --git a/.github/workflows/tox.yml b/.github/workflows/tox.yml
@@ -108,6 +108,15 @@ jobs:
         tox_system_factor: [homebrew-macos, homebrew-macos-python3_xcode, homebrew-macos-python3_xcode-nokegonly, homebrew-macos-python3_pythonorg, homebrew-macos-python3_xcode-gcc_spkg, conda-forge-macos]
         tox_packages_factor: [minimal, standard]
         xcode_version_factor: [11.7, 12.2, default, 12.4]
+        include:
+          - tox_system_factor: conda-forge-macos
+            tox_packages_factor: environment
+            xcode_version_factor: default
+            os: macos-11.0
+          - tox_system_factor: conda-forge-macos
+            tox_packages_factor: environment-optional
+            xcode_version_factor: default
+            os: macos-11.0
     env:
       TOX_ENV: local-${{ matrix.tox_system_factor }}-${{ matrix.tox_packages_factor }}
       LOGS_ARTIFACT_NAME: logs-commit-${{ github.sha }}-tox-local-${{ matrix.tox_system_factor }}-${{ matrix.tox_packages_factor }}-${{ matrix.os }}-xcode_${{ matrix.xcode_version_factor }}
@@ -154,7 +163,7 @@ jobs:
       max-parallel: 1
       matrix:
         tox_system_factor: [conda-forge-ubuntu]
-        tox_packages_factor: [minimal, standard]
+        tox_packages_factor: [minimal, standard, environment, environment-optional]
     env:
       TOX_ENV: local-${{ matrix.tox_system_factor }}-${{ matrix.tox_packages_factor }}
       LOGS_ARTIFACT_NAME: logs-commit-${{ github.sha }}-tox-local-${{ matrix.tox_system_factor }}-${{ matrix.tox_packages_factor }}
@@ -196,7 +205,7 @@ jobs:
       - name: Install bootstrap prerequisites
         run: |
           sudo DEBIAN_FRONTEND=noninteractive apt-get update
-          sudo DEBIAN_FRONTEND=noninteractive apt-get install $(sed "s/#.*//;" build/pkgs/debian-bootstrap.txt)
+          sudo DEBIAN_FRONTEND=noninteractive apt-get install $(build/bin/sage-get-system-packages debian _bootstrap)
       - name: Bootstrap with sage-update-version
         # We set SAGE_ROOT and SAGE_SRC by hand
         # because 'sage -sh' does not work with an unconfigured tree,

diff --git a/.gitignore b/.gitignore
@@ -118,6 +118,7 @@ src/sage/modular/arithgroup/farey_symbol.h
 !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.*/

diff --git a/.homebrew-build-env b/.homebrew-build-env
@@ -23,7 +23,7 @@ export PKG_CONFIG_PATH
 LIBRARY_PATH="$HOMEBREW/lib$LIBRARY_PATH"
 [ -z "$CPATH" ] || CPATH=":${CPATH}"
 CPATH="$HOMEBREW/include$CPATH"
-for l in readline bzip2; do
+for l in readline bzip2 ntl; do
     if [ -d "$HOMEBREW/opt/$l/lib" ]; then
         LIBRARY_PATH="$HOMEBREW/opt/$l/lib:$LIBRARY_PATH"
     fi

diff --git a/.zenodo.json b/.zenodo.json
@@ -1,10 +1,10 @@
 {
     "description": "Mirror of the Sage https://sagemath.org/ source tree", 
     "license": "other-open", 
-    "title": "sagemath/sage: 9.3.beta8", 
-    "version": "9.3.beta8", 
+    "title": "sagemath/sage: 9.3.beta9", 
+    "version": "9.3.beta9", 
     "upload_type": "software", 
-    "publication_date": "2021-03-07", 
+    "publication_date": "2021-03-14", 
     "creators": [
         {
             "affiliation": "SageMath.org", 
@@ -15,7 +15,7 @@
     "related_identifiers": [
         {
             "scheme": "url", 
-            "identifier": "https://github.com/sagemath/sage/tree/9.3.beta8", 
+            "identifier": "https://github.com/sagemath/sage/tree/9.3.beta9", 
             "relation": "isSupplementTo"
         }, 
         {

diff --git a/COPYING.txt b/COPYING.txt
@@ -130,7 +130,6 @@ symmetrica                  MIT-like License (see below)
 sympow                      Modified BSD
 sympy                       Modified BSD
 tachyon                     Modified BSD
-termcap                     GPLv2+
 threejs                     MIT License
 tornado                     Apache License
 zlib                        Custom (Modified BSD)

diff --git a/README.md b/README.md
@@ -219,9 +219,9 @@ Guide](https://doc.sagemath.org/html/en/installation).
    * Build tools: GNU `make`, GNU `m4`, `perl` (including
      ``ExtUtils::MakeMaker``), `ranlib`, `git`, `tar`, `bc`
 
-   * Any version of `python` (full installation including `urllib`),
-     but ideally version 3.7.x or 3.8.x, which will avoid having to build Sage's
-     own copy of Python 3.
+   * Python 3.4 or later, or Python 2.7, a full installation including
+     `urllib`; but ideally version 3.7.x, 3.8.x, or 3.9.x, which will
+     avoid having to build Sage's own copy of Python 3.
 
    We have collected lists of system packages that provide these build
    prerequisites. See [build/pkgs/arch.txt](build/pkgs/arch.txt),

diff --git a/VERSION.txt b/VERSION.txt
@@ -1 +1 @@
-SageMath version 9.3.beta8, Release Date: 2021-03-07
+SageMath version 9.3.beta9, Release Date: 2021-03-14
diff --git a/build/bin/sage-bootstrap-python b/build/bin/sage-bootstrap-python
@@ -17,6 +17,9 @@ fi
 # So it needs to find a python that has the urllib module.
 # For example, on Debian buster, the python3-minimal package does NOT provide it.
 #
+# Also, Trac #20023 removed the vendored argparse library from sage_bootstrap,
+# so we test that python is new enough (>= 2.7) to run it.
+#
 # See https://trac.sagemath.org/ticket/29090
 
 # Trac #29890: Our first choice is "python", not "python3". This is to avoid
@@ -41,7 +44,7 @@ PYTHONS="python python3 python3.8 python3.7 python2.7 python3.6 python2"
 for PY in $PYTHONS; do
     PYTHON="$(PATH="$SAGE_ORIG_PATH" command -v $PY)"
     if [ -n "$PYTHON" ]; then
-        if "$PYTHON" -c "import urllib; from hashlib import sha1; from os import listdir; listdir(\"$(pwd)\");" 2>/dev/null; then
+        if "$PYTHON" -c "import argparse; import urllib; from hashlib import sha1; from os import listdir; listdir(\"$(pwd)\");" 2>/dev/null; then
             exec "$PYTHON" "$@"
         fi
     fi

diff --git a/build/bin/sage-build-env-config.in b/build/bin/sage-build-env-config.in
@@ -106,3 +106,5 @@ export SAGE_FREETYPE_PREFIX="@SAGE_FREETYPE_PREFIX@"
 export SAGE_SUITESPARSE_PREFIX="@SAGE_SUITESPARSE_PREFIX@"
 
 export SAGE_CONFIGURE_FFLAS_FFPACK="@SAGE_CONFIGURE_FFLAS_FFPACK@"
+
+export SAGE_EDITABLE="@SAGE_EDITABLE@"
diff --git a/build/bin/sage-site b/build/bin/sage-site
@@ -162,7 +162,7 @@ if [ "$1" = "-docbuild" -o "$1" = "--docbuild" ]; then
         export OMP_NUM_THREADS=1
     fi
 
-    exec sage-python -m sage_setup.docbuild "$@" </dev/null
+    exec sage-python -m sage_docbuild "$@" </dev/null
 fi
 
 if [ "$1" = '-git-branch' -o "$1" = '--git-branch' ]; then

diff --git a/build/make/Makefile.in b/build/make/Makefile.in
@@ -328,7 +328,7 @@ base: $(inst_patch) $(inst_pkgconf)
 # Building the documentation has many dependencies, because all
 # documented modules are imported and because we use matplotlib to
 # produce plots.
-DOC_DEPENDENCIES = sagelib $(inst_sphinx) \
+DOC_DEPENDENCIES = sagelib sage_docbuild $(inst_sphinx) \
 	| $(SAGERUNTIME) $(inst_maxima) $(inst_networkx) $(inst_scipy) $(inst_sympy) \
 	$(inst_matplotlib) $(inst_pillow) $(inst_mathjax) $(inst_mpmath) \
 	$(inst_ipykernel) $(inst_jupyter_client) $(inst_conway_polynomials) \
@@ -373,11 +373,21 @@ clean:
 	rm -rf "$(SAGE_LOCAL)/var/tmp/sage/build"
 
 # "c_lib", ".cython_version", "build" in $(SAGE_SRC) are from old sage versions
+# Cleaning .so files (and .c and .cpp files associated with .pyx files) is for editable installs.
+# Also cython_debug is for editable installs.
 sagelib-clean:
 	@echo "Deleting Sage library build artifacts..."
-	(cd "$(SAGE_SRC)" && rm -rf c_lib .cython_version; rm -rf build; find . -name '*.pyc' | xargs rm -f; rm -rf sage/ext/interpreters) && (cd "$(SAGE_ROOT)/build/pkgs/sagelib/src/" && rm -rf build)
+	(cd "$(SAGE_SRC)" && \
+	 rm -rf c_lib .cython_version cython_debug; \
+	 rm -rf build; find . -name '*.pyc' -o -name "*.so" | xargs rm -f; \
+	 rm -f $$(find . -name "*.pyx" | sed 's/\(.*\)[.]pyx$$/\1.c \1.cpp/'); \
+	 rm -rf sage/ext/interpreters) \
+	&& (cd "$(SAGE_ROOT)/build/pkgs/sagelib/src/" && rm -rf build)
 
-build-clean: clean doc-clean sagelib-clean
+sage_docbuild-clean:
+	(cd "$(SAGE_ROOT)/build/pkgs/sage_docbuild/src" && rm -rf build)
+
+build-clean: clean doc-clean sagelib-clean sage_docbuild-clean
 
 # Special target for cleaning up a broken GCC install detected by configure
 # This should check for the .clean-broken-gcc stamp, and if found clean

diff --git a/build/pkgs/_prereq/distros/fedora.txt b/build/pkgs/_prereq/distros/fedora.txt
@@ -32,3 +32,5 @@ findutils
 which
 # Needed for pcre configure, see https://trac.sagemath.org/ticket/29129:
 diffutils
+# Needed for openssl 3.0
+perl-IPC-Cmd
diff --git a/build/pkgs/cffi/checksums.ini b/build/pkgs/cffi/checksums.ini
@@ -1,5 +1,5 @@
 tarball=cffi-VERSION.tar.gz
-sha1=45bd57a0903a2d63b93461e096c5d291875a457b
-md5=ad3d8537b1516bad6bcdc36c458788be
-cksum=2426586502
+sha1=21cdeccd7b7b121d35eae1b8e91d78f9ec83da98
+md5=272cb183bf0365530e3c0d8f446cd89d
+cksum=4039836079
 upstream_url=https://pypi.io/packages/source/c/cffi/cffi-VERSION.tar.gz
diff --git a/build/pkgs/cffi/dependencies b/build/pkgs/cffi/dependencies
@@ -1,4 +1,4 @@
-$(PYTHON) | $(PYTHON_TOOLCHAIN)
+$(PYTHON) | $(PYTHON_TOOLCHAIN) pycparser
 
 ----------
 All lines of this file are ignored except the first.

diff --git a/build/pkgs/cffi/package-version.txt b/build/pkgs/cffi/package-version.txt
@@ -1 +1 @@
-1.14.4
+1.14.5
diff --git a/build/pkgs/configure/checksums.ini b/build/pkgs/configure/checksums.ini
@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=c8427caab0d95e76945e11569caa546169cdd249
-md5=a54f3a1b7e2c504eee96f613e93d4844
-cksum=510204214
+sha1=aa0af418219f2789b127a03573f5da64e1444012
+md5=eb6299096db077da054c6f98a60d3e6e
+cksum=1438833545
diff --git a/build/pkgs/configure/package-version.txt b/build/pkgs/configure/package-version.txt
@@ -1 +1 @@
-d6cf85bd5016ee6fc75537d1611bbd154f025b87
+d57188beedceca00617aadbd9ca512d19970a8fe
diff --git a/build/pkgs/e_antic/checksums.ini b/build/pkgs/e_antic/checksums.ini
@@ -1,5 +1,5 @@
 tarball=e-antic-VERSION.tar.gz
-sha1=a210607c184831099619f2af7c0fcc373bf99d75
-md5=0ee15d22f49cd4235f14a5ec0bb1c848
-cksum=1752190215
+sha1=f51d90fcffb2c849eebc1013eb14984f9ad59719
+md5=84ab45f0e1eb3ddbbfb175927506b7bc
+cksum=3161097188
 upstream_url=https://www.labri.fr/perso/vdelecro/e-antic/e-antic-VERSION.tar.gz
diff --git a/build/pkgs/e_antic/package-version.txt b/build/pkgs/e_antic/package-version.txt
@@ -1 +1 @@
-0.1.8
+0.1.9
diff --git a/build/pkgs/ecl/checksums.ini b/build/pkgs/ecl/checksums.ini
@@ -1,5 +1,5 @@
 tarball=ecl-VERSION.tgz
-sha1=96daa970ae31821c44d9e8ee344f62106d6d79a0
-md5=93ba832d2ec609d49132a7076e5c14ae
-cksum=3753868648
+sha1=c41838960964c6e0b9b83a08bca1f717ccc6951e
+md5=0c9e0437dbf3a7f1b00da32b7794a3b0
+cksum=1854014871
 upstream_url=https://common-lisp.net/project/ecl/static/files/release/ecl-VERSION.tgz
diff --git a/build/pkgs/ecl/package-version.txt b/build/pkgs/ecl/package-version.txt
@@ -1 +1 @@
-20.4.24.p1
+21.2.1
diff --git a/build/pkgs/ecl/patches/0001-unicode-fix-ecl_string_case-for-non-ascii-characters.patch b/build/pkgs/ecl/patches/0001-unicode-fix-ecl_string_case-for-non-ascii-characters.patch