Merge #33866

.github/workflows/ci-conda.yml

@@ -43,15 +43,8 @@ jobs:
           bash ~/miniconda.sh -b -p $HOME/miniconda
           echo "CONDA=$HOME/miniconda" >> $GITHUB_ENV
 
-      - name: Install bootstrap prerequisites
-        run: |
-          export PATH="$(pwd)/build/bin:$PATH"
-          SYSTEM=$(sage-guess-package-system)
-          eval $(sage-print-system-package-command $SYSTEM --sudo install $(sage-get-system-packages $SYSTEM _bootstrap))
-
-      # Create conda environment file
-      - name: Bootstrap
-        run: ./bootstrap
+      - name: Create conda environment files
+        run: ./bootstrap-conda
 
       - name: Cache conda packages
         uses: actions/cache@v2
@@ -80,6 +73,7 @@ jobs:
         shell: bash -l {0}
         continue-on-error: true
         run: |
+          ./bootstrap
           echo "::add-matcher::.github/workflows/configure-systempackage-problem-matcher.json"
           ./configure --enable-build-as-root --with-python=$CONDA_PREFIX/bin/python --prefix=$CONDA_PREFIX $(for pkg in $(./sage -package list :standard: --has-file spkg-configure.m4 --has-file distros/conda.txt); do echo --with-system-$pkg=force; done)
           echo "::remove-matcher owner=configure-system-package-warning::"
@@ -88,8 +82,8 @@ jobs:
       - name: Build
         shell: bash -l {0}
         run: |
-          pip install --no-build-isolation -v -v -e pkgs/sage-conf pkgs/sage-setup 
-          pip install --no-build-isolation -v -v -e src
+          pip install --no-build-isolation -v -v -e ./pkgs/sage-conf ./pkgs/sage-setup
+          pip install --no-build-isolation -v -v -e ./src
         env:
           SAGE_NUM_THREADS: 2
 

.gitignore

@@ -23,6 +23,7 @@
 /environment.yml
 /environment-optional.yml
 /src/environment.yml
+/src/environment-dev.yml
 /src/environment-optional.yml
 
 /src/setup.cfg

.lgtm.yml

@@ -6,6 +6,7 @@ queries:
 path_classifiers:
   imports_only:
     - "**/all.py"
+    - "**/all_*.py"
     - "**/*catalog*.py"
     - "**/species/library.py"
     - "**/categories/basic.py"

.vscode/launch.json

@@ -1,6 +1,17 @@
 {
     "version": "0.2.0",
     "configurations": [
+        {
+            "name": "Sage: Pytest",
+            "type": "python",
+            "request": "launch",
+            "module": "pytest",
+            "args": [
+                "${file}"
+            ],
+            "console": "integratedTerminal",
+            "justMyCode": false
+        },
         {
             "name": "Python: Current File",
             "type": "python",
@@ -22,4 +33,4 @@
             "justMyCode": false
         }
     ],
-}
+}

.vscode/settings.json

@@ -16,7 +16,13 @@
     },
     "python.testing.pytestEnabled": true,
     "python.testing.pytestArgs": [
-        "src"
+        "--rootdir=src/sage",
+        "-c=src/tox.ini",
+        "--doctest-modules",
     ],
     "python.testing.unittestEnabled": false,
+    "cSpell.words": [
+        "Conda",
+        "Cython"
+    ],
 }

.zenodo.json

@@ -1,10 +1,10 @@
 {
     "description": "Mirror of the Sage https://sagemath.org/ source tree", 
     "license": "other-open", 
-    "title": "sagemath/sage: 9.6", 
-    "version": "9.6", 
+    "title": "sagemath/sage: 9.7.beta1", 
+    "version": "9.7.beta1", 
     "upload_type": "software", 
-    "publication_date": "2022-05-15", 
+    "publication_date": "2022-05-26", 
     "creators": [
         {
             "affiliation": "SageMath.org", 
@@ -15,7 +15,7 @@
     "related_identifiers": [
         {
             "scheme": "url", 
-            "identifier": "https://github.com/sagemath/sage/tree/9.6", 
+            "identifier": "https://github.com/sagemath/sage/tree/9.7.beta1", 
             "relation": "isSupplementTo"
         }, 
         {

Makefile

@@ -171,6 +171,7 @@ bootstrap-clean:
 	rm -f src/doc/en/reference/repl/*.txt
 	rm -f environment.yml
 	rm -f src/environment.yml
+	rm -f src/environment-dev.yml
 	rm -f environment-optional.yml
 	rm -f src/environment-optional.yml
 	rm -f src/Pipfile
@@ -196,7 +197,7 @@ micro_release:
 	@echo "Removing unnecessary files & directories - make will not be functional afterwards anymore"
 	@# We keep src/sage for some doctests that it expect it to be there and
 	@# also because it does not add any weight with rdfind below.
-	@# We need src/sage/bin/ for the scripts that invoke Sage
+	@# We need src/bin/ for the scripts that invoke Sage
 	@# We need sage, the script to start Sage
 	@# We need local/, the dependencies and the built Sage library itself.
 	@# We keep VERSION.txt.

README.md

@@ -413,15 +413,18 @@ in the Installation Guide.
     get a list by typing  `./sage --optional` or by visiting the
     [packages documentation page](https://doc.sagemath.org/html/en/reference/spkg/).
 
-18. Optional: Create a symlink to the `sage` executable somewhere in your
-    `PATH`, so you can start Sage by typing `sage` from anywhere rather
-    than having to either type the full path or navigate to the Sage
+18. Optional: Create a symlink to the installed `sage` script in a
+    directory in your `PATH`, for example ``/usr/local``. This will
+    allow you to start Sage by typing `sage` from anywhere rather than
+    having to either type the full path or navigate to the Sage
     directory and type `./sage`. This can be done by running:
 
-        $ ln -s $HOME/sage/sage-x.y/sage /usr/local/bin
+        $ sudo ln -s $(./sage -sh -c 'ls $SAGE_ROOT/venv/bin/sage') /usr/local/bin
 
-    The `$HOME/sage/sage-x.y/` part may need adapting. One way to decide
-    how to adapt it is to run `print(SAGE_ROOT)` in a Sage session.
+19. Optional: Set up SageMath as a Jupyter kernel in an existing Jupyter notebook
+    or JupyterLab installation, as described in [section
+    "Launching SageMath"](https://doc.sagemath.org/html/en/installation/launching.html)
+    in the installation manual.
 
 Troubleshooting
 ---------------
@@ -580,17 +583,10 @@ Relocation
 
 It is not supported to move the `SAGE_ROOT` or `SAGE_LOCAL` directory
 after building Sage.  If you do move the directories, you will have to
-build Sage again from scratch.
-
-If you copy the `sage` script or make a symbolic link to it, you
-should modify the script to reflect this (as instructed at the top of
-the script). It is important that the path to Sage does not have any
-spaces and non-ASCII characters in it.
+run ``make distclean`` and build Sage again from scratch.
 
 For a system-wide installation, you have to build Sage as a "normal" user
-and then as root you can change permissions. Afterwards, you need to start up
-Sage as root at least once prior to using the system-wide Sage as a
-normal user. See the [Installation Guide](https://doc.sagemath.org/html/en/installation/source.html#installation-in-a-multiuser-environment)
+and then as root you can change permissions. See the [Installation Guide](https://doc.sagemath.org/html/en/installation/source.html#installation-in-a-multiuser-environment)
 for further information.
 
 Redistribution

VERSION.txt

@@ -1 +1 @@
-SageMath version 9.6, Release Date: 2022-05-15
+SageMath version 9.7.beta1, Release Date: 2022-05-26

bootstrap

@@ -158,6 +158,7 @@ SAGE_SPKG_FINALIZE([$pkgname], [$pkgtype], [$SPKG_SOURCE], [$SPKG_TREE_VAR])"
     # ONLY stderr, and to re-output the results back to stderr leaving
     # stdout alone. Basically we swap the two descriptors using a
     # third, filter, and then swap them back.
+    ./bootstrap-conda && \
     src/doc/bootstrap && \
     install_config_rpath && \
     aclocal -I m4 && \

bootstrap-conda

@@ -0,0 +1,78 @@
+#!/usr/bin/env bash
+
+########################################################################
+# Generate auto-generated conda environment files
+#########################################################################
+
+STRIP_COMMENTS="sed s/#.*//;"
+RECOMMENDED_SPKG_PATTERN="@(_recommended$(for a in $(head -n 1 build/pkgs/_recommended/dependencies); do echo -n "|"$a; done))"
+
+BOOTSTRAP_PACKAGES=$(echo $(${STRIP_COMMENTS} build/pkgs/_bootstrap/distros/conda.txt))
+SYSTEM_PACKAGES=
+OPTIONAL_SYSTEM_PACKAGES=
+SAGELIB_SYSTEM_PACKAGES=
+SAGELIB_OPTIONAL_SYSTEM_PACKAGES=
+RECOMMENDED_SYSTEM_PACKAGES=
+for PKG_BASE in $(./sage --package list --has-file distros/conda.txt); do
+    PKG_SCRIPTS=build/pkgs/$PKG_BASE
+    SYSTEM_PACKAGES_FILE=$PKG_SCRIPTS/distros/conda.txt
+    PKG_TYPE=$(cat $PKG_SCRIPTS/type)
+    PKG_SYSTEM_PACKAGES=$(echo $(${STRIP_COMMENTS} $SYSTEM_PACKAGES_FILE))
+    if [ -n "PKG_SYSTEM_PACKAGES" ]; then
+        if [ -f $PKG_SCRIPTS/spkg-configure.m4 ]; then
+            case "$PKG_BASE:$PKG_TYPE" in
+                *:standard)
+                    SYSTEM_PACKAGES+=" $PKG_SYSTEM_PACKAGES"
+                    ;;
+                $RECOMMENDED_SPKG_PATTERN:*)
+                    RECOMMENDED_SYSTEM_PACKAGES+=" $PKG_SYSTEM_PACKAGES"
+                    ;;
+                *)
+                    OPTIONAL_SYSTEM_PACKAGES+=" $PKG_SYSTEM_PACKAGES"
+                    ;;
+            esac
+        else
+            case "$PKG_TYPE" in
+                standard)
+                    SAGELIB_SYSTEM_PACKAGES+=" $PKG_SYSTEM_PACKAGES"
+                    ;;
+                *)
+                    SAGELIB_OPTIONAL_SYSTEM_PACKAGES+=" $PKG_SYSTEM_PACKAGES"
+                    ;;
+            esac
+        fi
+    fi
+done
+echo >&2 $0:$LINENO: generate conda enviroment files
+echo "name: sage-build" >  environment.yml
+echo "channels:"        >> environment.yml
+echo "  - conda-forge"  >> environment.yml
+echo "  - nodefaults"   >> environment.yml
+echo "dependencies:"    >> environment.yml
+for pkg in $SYSTEM_PACKAGES; do
+    echo "  - $pkg" >> environment.yml
+done
+echo "  # Packages needed for ./bootstrap" >> environment.yml
+for pkg in $BOOTSTRAP_PACKAGES; do
+    echo "  - $pkg" >> environment.yml
+done
+sed 's/name: sage-build/name: sage/' environment.yml > src/environment.yml
+for pkg in $SAGELIB_SYSTEM_PACKAGES; do
+    echo "  - $pkg" >> src/environment.yml
+done
+sed 's/name: sage/name: sage-dev/' src/environment.yml > src/environment-dev.yml
+echo "  # Additional dev tools" >> src/environment-dev.yml
+echo "  - openssh" >> src/environment-dev.yml
+echo "  - pycodestyle" >> src/environment-dev.yml
+echo "  - pytest" >> src/environment-dev.yml
+
+cp environment.yml environment-optional.yml
+    echo "  # optional packages" >> environment-optional.yml
+for pkg in $OPTIONAL_SYSTEM_PACKAGES; do
+    echo "  - $pkg" >> environment-optional.yml
+    done
+cp src/environment.yml src/environment-optional.yml
+    echo "  # optional packages" >> src/environment-optional.yml
+for pkg in $OPTIONAL_SYSTEM_PACKAGES $SAGELIB_OPTIONAL_SYSTEM_PACKAGES; do
+    echo "  - $pkg" >> src/environment-optional.yml
+done

build/make/install

@@ -137,16 +137,3 @@ fi
 
 # Build succeeded.
 echo "Sage build/upgrade complete!"
-
-if [ "$1" = "all" ]; then
-    echo
-    echo "To install small scripts to directly run Sage's versions of GAP,"
-    echo "the PARI/GP interpreter, Maxima, or Singular etc. (by typing e.g."
-    echo "just 'gap' or 'gp') into a standard 'bin' directory, start Sage"
-    echo "by typing 'sage' (or './sage') and enter something like"
-    echo
-    echo "    install_scripts('/usr/local/bin')"
-    echo
-    echo "at the Sage command prompt ('sage:')."
-    echo
-fi

build/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=f0ab7c18b3a169fdf7238fe8d70f8bce29373ef4
-md5=37b7220d90d9ec624e126ebb12cc8547
-cksum=3498005086
+sha1=e147a1128d59e97feef980eb3847798d1838565b
+md5=134802b2602846ef70dba2d0740be18c
+cksum=2068092591

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-888d18eb851f892097a0a683c01e3a95db863495
+8501c7398215556ff4a4c8b05c6699949c8dfca3

build/pkgs/ecm/SPKG.rst

@@ -6,7 +6,7 @@ Description
 
 GMP-ECM - Elliptic Curve Method for Integer Factorization
 
-Sources can be obtained from http://gforge.inria.fr/projects/ecm/
+Sources can be obtained from https://gitlab.inria.fr/zimmerma/ecm
 
 License
 -------

build/pkgs/ecm/checksums.ini

@@ -1,4 +1,5 @@
 tarball=ecm-VERSION.tar.gz
-sha1=407e41af6f93214509810b954b88251e4b89e82b
-md5=559b13454b2094fbf26b33ff4fc824b7
-cksum=3785569195
+sha1=f35d225d1d44f9b8ad420bf9b50a92582f681337
+md5=cfbb789d76cf538fc4dbb99d8e6e4b81
+cksum=2195620014
+upstream_url=https://gitlab.inria.fr/zimmerma/ecm/uploads/89f6f0d65d3e980cef33dc922004e4b2/ecm-VERSION.tar.gz

build/pkgs/ecm/package-version.txt

@@ -1 +1 @@
-7.0.4.p2
+7.0.5