Merge tag '9.3.beta8' into t/31409/cygwin_standard__r_build_fails_____downgrade_r__rpy2_to_optional

SageMath version 9.3.beta8, Release Date: 2021-03-07

Author: Matthias Koeppe

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

@@ -1,26 +1,27 @@
 #!/usr/bin/env bash
 # to be run from $SAGE_ROOT, with arguments sage-local-${{ env.PREVIOUS_STAGES }}.tar
 
+if [ -z "$SAGE_LOCAL" ]; then
+    SAGE_LOCAL=$(pwd)/local
+fi
+
 # Show all tar files
 ls -l $*
 
 # We specifically use the cygwin tar so that symlinks are saved/restored correctly on Windows.
 for a in $*; do
     echo Extracting $a
-    tar xf $a
+    (cd / && tar xf -) < $a
     rm -f $a
 done
 
-# Also get rid of the stages that were not extracted
-rm -f sage-local-*.tar
-
 # We set the installation records to the same mtime so that no rebuilds due to dependencies
 # among these packages are triggered.
-(cd local/var/lib/sage/installed/ && touch .dummy && touch --reference=.dummy *)
+(cd "$SAGE_LOCAL"/var/lib/sage/installed/ && touch .dummy && touch --reference=.dummy *)
 
 # Show what has been built already.
-ls -l local local/var/lib/sage/installed/
+ls -l "$SAGE_LOCAL" "$SAGE_LOCAL"/var/lib/sage/installed/
 df -h
 
 # Rebase!
-src/bin/sage-rebase.sh local
+src/bin/sage-rebase.sh "$SAGE_LOCAL"

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

@@ -62,7 +62,7 @@ jobs:
       - name: Install test prerequisites
         run: |
           sudo DEBIAN_FRONTEND=noninteractive apt-get update
-          sudo DEBIAN_FRONTEND=noninteractive apt-get install python-tox
+          sudo DEBIAN_FRONTEND=noninteractive apt-get install tox
       - name: Try to login to docker.pkg.github.com
         # https://docs.github.com/en/actions/reference/workflow-commands-for-github-actions#setting-an-environment-variable
         run: |

.github/workflows/extract-sage-local.sh

@@ -60,7 +60,7 @@ jobs:
       - name: Install test prerequisites
         run: |
           sudo DEBIAN_FRONTEND=noninteractive apt-get update
-          sudo DEBIAN_FRONTEND=noninteractive apt-get install python-tox
+          sudo DEBIAN_FRONTEND=noninteractive apt-get install tox
       - name: Try to login to docker.pkg.github.com
         # https://docs.github.com/en/actions/reference/workflow-commands-for-github-actions#setting-an-environment-variable
         run: |
@@ -114,7 +114,7 @@ jobs:
       - name: Install test prerequisites
         run: |
           sudo DEBIAN_FRONTEND=noninteractive apt-get update
-          sudo DEBIAN_FRONTEND=noninteractive apt-get install python-tox
+          sudo DEBIAN_FRONTEND=noninteractive apt-get install tox
       - name: Build and test with tox
         # We use a high parallelization on purpose in order to catch possible parallelization bugs in the build scripts.
         # For doctesting, we use a lower parallelization to avoid timeouts.

.github/workflows/tox-experimental.yml

@@ -64,7 +64,7 @@ jobs:
       - name: Install test prerequisites
         run: |
           sudo DEBIAN_FRONTEND=noninteractive apt-get update
-          sudo DEBIAN_FRONTEND=noninteractive apt-get install python-tox
+          sudo DEBIAN_FRONTEND=noninteractive apt-get install tox
       - name: Try to login to docker.pkg.github.com
         # https://docs.github.com/en/actions/reference/workflow-commands-for-github-actions#setting-an-environment-variable
         run: |

.github/workflows/tox-gcc_spkg.yml

@@ -60,7 +60,7 @@ jobs:
       - name: Install test prerequisites
         run: |
           sudo DEBIAN_FRONTEND=noninteractive apt-get update
-          sudo DEBIAN_FRONTEND=noninteractive apt-get install python-tox
+          sudo DEBIAN_FRONTEND=noninteractive apt-get install tox
       - name: Try to login to docker.pkg.github.com
         # https://docs.github.com/en/actions/reference/workflow-commands-for-github-actions#setting-an-environment-variable
         run: |
@@ -107,7 +107,7 @@ jobs:
         os: [ macos-10.15, macos-11.0 ]
         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, default, 12.3]
+        xcode_version_factor: [11.7, 12.2, default, 12.4]
     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_${{ matrix.xcode_version_factor }}
@@ -163,7 +163,7 @@ jobs:
       - name: Install test prerequisites
         run: |
           sudo DEBIAN_FRONTEND=noninteractive apt-get update
-          sudo DEBIAN_FRONTEND=noninteractive apt-get install python-tox
+          sudo DEBIAN_FRONTEND=noninteractive apt-get install tox
       - name: Build and test with tox
         # We use a high parallelization on purpose in order to catch possible parallelization bugs in the build scripts.
         # For doctesting, we use a lower parallelization to avoid timeouts.
@@ -225,7 +225,7 @@ jobs:
         os: [ macos-10.15, macos-11.0 ]
         tox_system_factor: [macos-nobootstrap, macos-nobootstrap-python3_pythonorg]
         tox_packages_factor: [minimal]
-        xcode_version_factor: [default, 12]
+        xcode_version_factor: [11.7, 12.2, default, 12.4]
     env:
       TOX_ENV: local-${{ 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 }}-xcode_${{ matrix.xcode_version_factor }}

.github/workflows/tox-optional.yml

@@ -101,7 +101,7 @@ 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/tdlib/sage_tdlib.cpp
+!src/sage/graphs/graph_decompositions/sage_tdlib.cpp
 !src/sage/libs/eclib/wrap.cpp
 !src/sage/misc/inherit_comparison_impl.c
 !src/sage/modular/arithgroup/farey.cpp

.github/workflows/tox.yml

@@ -1,10 +1,10 @@
 {
     "description": "Mirror of the Sage https://sagemath.org/ source tree", 
     "license": "other-open", 
-    "title": "sagemath/sage: 9.3.beta7", 
-    "version": "9.3.beta7", 
+    "title": "sagemath/sage: 9.3.beta8", 
+    "version": "9.3.beta8", 
     "upload_type": "software", 
-    "publication_date": "2021-02-07", 
+    "publication_date": "2021-03-07", 
     "creators": [
         {
             "affiliation": "SageMath.org", 
@@ -15,7 +15,7 @@
     "related_identifiers": [
         {
             "scheme": "url", 
-            "identifier": "https://github.com/sagemath/sage/tree/9.3.beta7", 
+            "identifier": "https://github.com/sagemath/sage/tree/9.3.beta8", 
             "relation": "isSupplementTo"
         }, 
         {

.gitignore

@@ -1 +1 @@
-SageMath version 9.3.beta7, Release Date: 2021-02-07
+SageMath version 9.3.beta8, Release Date: 2021-03-07