Merge branch 'develop' into fix_E303_in_folders_defghi

.codecov.yml

@@ -0,0 +1,15 @@
+# https://docs.codecov.com/docs/pull-request-comments#disable-comment
+comment: false
+# https://docs.codecov.com/docs/commit-status
+coverage:
+  status:
+    project:
+      default:
+        target: auto
+        threshold: 0%
+        base: auto
+    patch:
+      default:
+        target: auto
+        threshold: 0%
+        base: auto

.devcontainer/portability-Dockerfile

@@ -5,4 +5,4 @@ ARG SYSTEM_FACTOR="ubuntu-jammy"
 ARG PACKAGE_FACTOR="standard"
 ARG DOCKER_TARGET="with-system-packages"
 ARG DOCKER_TAG="dev"
-FROM ghcr.io/sagemath/sage/sage-docker-${SYSTEM_FACTOR}-${PACKAGE_FACTOR}-${DOCKER_TARGET}:${DOCKER_TAG}
+FROM ghcr.io/sagemath/sage/sage-${SYSTEM_FACTOR}-${PACKAGE_FACTOR}-${DOCKER_TARGET}:${DOCKER_TAG}

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,29 +1,29 @@
-<!-- ^^^^^
-Please provide a concise, informative and self-explanatory title.
-Don't put issue numbers in there, do this in the PR body below.
-For example, instead of "Fixes #1234" use "Introduce new method to calculate 1+1"
--->
-### 📚 Description
+<!-- Please provide a concise, informative and self-explanatory title. -->
+<!-- Don't put issue numbers in the title. Put it in the Description below. -->
+<!-- For example, instead of "Fixes #12345", use "Add a new method to multiply two integers" -->
+
+### :books: Description
 
-<!-- Describe your changes here in detail -->
+<!-- Describe your changes here in detail. -->
 <!-- Why is this change required? What problem does it solve? -->
-<!-- If it resolves an open issue, please link to the issue here. For example "Closes #1337" -->
+<!-- If this PR resolves an open issue, please link to it here. For example "Fixes #12345". -->
+<!-- If your change requires a documentation PR, please link it appropriately. -->
 
-### 📝 Checklist
+### :memo: Checklist
 
-<!-- Put an `x` in all the boxes that apply. -->
-<!-- If your change requires a documentation PR, please link it appropriately -->
-<!-- If you're unsure about any of these, don't hesitate to ask. We're here to help! -->
+<!-- Put an `x` in all the boxes that apply. It should be `[x]` not `[x ]`. -->
 
-- [ ] I have made sure that the title is self-explanatory and the description concisely explains the PR.
-- [ ] I have linked an issue or discussion.
+- [ ] The title is concise, informative, and self-explanatory.
+- [ ] The description explains in detail what this PR is about.
+- [ ] I have linked a relevant issue or discussion.
 - [ ] I have created tests covering the changes.
 - [ ] I have updated the documentation accordingly.
 
-### ⌛ Dependencies
-<!-- List all open pull requests that this PR logically depends on -->
-<!--
-- #xyz: short description why this is a dependency
-- #abc: ...
+### :hourglass: Dependencies
+
+<!-- List all open PRs that this PR logically depends on
+- #12345: short description why this is a dependency
+- #34567: ...
 -->
 
+<!-- If you're unsure about any of these, don't hesitate to ask. We're here to help! -->

.github/workflows/build.yml

@@ -103,6 +103,6 @@ jobs:
       
       - name: Upload coverage to codecov
         if: always() && steps.build.outcome == 'success'
-        uses: codecov/codecov-action@v2
+        uses: codecov/codecov-action@v3
         with:
           files: ./coverage.xml

.github/workflows/ci-conda.yml

@@ -23,7 +23,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, macos-latest]
-        python: [3.8, 3.9]
+        python: ['3.9', '3.10', '3.11']
         conda-env: [environment, environment-optional]
 
     steps:
@@ -41,11 +41,18 @@ jobs:
           bash ~/miniconda.sh -b -p $HOME/miniconda
           echo "CONDA=$HOME/miniconda" >> $GITHUB_ENV
 
+      # Workaround for /~https://github.com/actions/runner-images/issues/6910 / /~https://github.com/conda/conda/issues/12303
+      - name: Downgrade conda
+        if: matrix.os == 'ubuntu-latest'
+        run: |
+          conda config --set allow_conda_downgrades true
+          conda install conda=4.12.0 -y
+
       - name: Create conda environment files
         run: ./bootstrap-conda
 
       - name: Cache conda packages
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         with:
           path: ~/conda_pkgs_dir
           key:

.github/workflows/doc-build-pdf.yml

@@ -0,0 +1,51 @@
+name: Build documentation (PDF)
+
+on:
+  pull_request:
+  push:
+  workflow_dispatch:
+    # Allow to run manually
+
+concurrency:
+  # Cancel previous runs of this workflow for the same branch
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  build-docs:
+    runs-on: ubuntu-latest
+    # Use "maximal" so that texlive is installed
+    # Use "fedora-31" for build diversity
+    container: ghcr.io/sagemath/sage/sage-docker-fedora-31-maximal-with-targets:dev
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+
+      - name: Prepare
+        run: |
+          apt-get update && apt-get install -y zip
+          # Reuse built SAGE_LOCAL contained in the Docker image
+          ./bootstrap
+          ./configure --enable-build-as-root --prefix=/sage/local --with-sage-venv --enable-download-from-upstream-url
+
+      - name: Build
+        run: make build V=0 && make doc-pdf
+        env:
+          MAKE: make -j2
+          SAGE_NUM_THREADS: 2
+          TEXMFHOME: /sage/texmf
+
+      - name: Copy docs
+        run: |
+          # For some reason the deploy step below cannot find /sage/...
+          # So copy everything from there to local folder
+          mkdir -p ./docs
+          cp -r -L /sage/local/share/doc/sage/pdf/en/* ./docs
+          # Zip everything for increased performance
+          zip -r docs-pdf.zip docs
+
+      - name: Upload docs
+        uses: actions/upload-artifact@v3
+        with:
+          name: docs-pdf
+          path: docs-pdf.zip

.github/workflows/doc-publish.yml

@@ -28,7 +28,7 @@ jobs:
       # Once /~https://github.com/actions/download-artifact/issues/172 and/or /~https://github.com/actions/download-artifact/issues/60 is implemented, we can use the official download-artifact action
       # For now use the solution from https://docs.github.com/en/actions/using-workflows/events-that-trigger-workflows#using-data-from-the-triggering-workflow
       - name: Download docs
-        uses: actions/github-script@v3.1.0
+        uses: actions/github-script@v6.4.0
         with:
           script: |
             var artifacts = await github.actions.listWorkflowRunArtifacts({

.zenodo.json

@@ -1,10 +1,10 @@
 {
     "description": "Mirror of the Sage https://sagemath.org/ source tree", 
     "license": "other-open", 
-    "title": "sagemath/sage: 10.0.beta3", 
-    "version": "10.0.beta3", 
+    "title": "sagemath/sage: 10.0.beta6", 
+    "version": "10.0.beta6", 
     "upload_type": "software", 
-    "publication_date": "2023-03-02", 
+    "publication_date": "2023-03-26", 
     "creators": [
         {
             "affiliation": "SageMath.org", 
@@ -15,7 +15,7 @@
     "related_identifiers": [
         {
             "scheme": "url", 
-            "identifier": "/~https://github.com/sagemath/sage/tree/10.0.beta3", 
+            "identifier": "/~https://github.com/sagemath/sage/tree/10.0.beta6", 
             "relation": "isSupplementTo"
         }, 
         {

Makefile

@@ -80,42 +80,6 @@ download:
 dist: build/make/Makefile
 	./sage --sdist
 
-pypi-sdists: sage_setup
-	./sage --sh build/pkgs/sage_conf/spkg-src
-	./sage --sh build/pkgs/sage_sws2rst/spkg-src
-	./sage --sh build/pkgs/sage_docbuild/spkg-src
-	./sage --sh build/pkgs/sage_setup/spkg-src
-	./sage --sh build/pkgs/sagelib/spkg-src
-	./sage --sh build/pkgs/sagemath_objects/spkg-src
-	./sage --sh build/pkgs/sagemath_categories/spkg-src
-	./sage --sh build/pkgs/sagemath_environment/spkg-src
-	./sage --sh build/pkgs/sagemath_repl/spkg-src
-	@echo "Built sdists are in upstream/"
-
-# Ensuring wheels are present, even for packages that may have been installed
-# as editable. Until we have better uninstallation of script packages, we
-# just remove the timestamps, which will lead to rebuilds of the packages.
-PYPI_WHEEL_PACKAGES = sage_sws2rst sage_setup sagemath_environment sagemath_objects sagemath_repl sagemath_categories
-pypi-wheels:
-	for a in $(PYPI_WHEEL_PACKAGES); do \
-	    rm -f venv/var/lib/sage/installed/$$a-*; \
-	done
-	for a in $(PYPI_WHEEL_PACKAGES); do \
-	    $(MAKE) SAGE_EDITABLE=no SAGE_WHEELS=yes $$a; \
-	done
-	@echo "Built wheels are in venv/var/lib/sage/wheels/"
-
-# sage_docbuild is here, not in PYPI_WHEEL_PACKAGES, because it depends on sagelib
-WHEEL_PACKAGES = $(PYPI_WHEEL_PACKAGES) sage_conf sagelib sage_docbuild
-wheels:
-	for a in $(WHEEL_PACKAGES); do \
-	    rm -f venv/var/lib/sage/installed/$$a-*; \
-	done
-	for a in $(WHEEL_PACKAGES); do \
-	    $(MAKE) SAGE_EDITABLE=no SAGE_WHEELS=yes $$a; \
-	done
-	@echo "Built wheels are in venv/var/lib/sage/wheels/"
-
 ###############################################################################
 # Cleaning up
 ###############################################################################
@@ -380,7 +344,6 @@ list:
 	@$(MAKE) --silent -f build/make/Makefile SAGE_PKGCONFIG=dummy $@
 
 .PHONY: default build dist install micro_release \
-	pypi-sdists pypi-wheels wheels \
 	misc-clean bdist-clean distclean bootstrap-clean maintainer-clean \
 	test check testoptional testall testlong testoptionallong testallong \
 	ptest ptestoptional ptestall ptestlong ptestoptionallong ptestallong \

README.md

@@ -1,4 +1,9 @@
-<a href="https://sagemath.org"><img src="src/doc/common/themes/sage/static/logo_sagemath_black.svg" height="60" align="right" /></a>
+<a href="https://sagemath.org">
+  <picture>
+    <source media="(prefers-color-scheme: dark)" srcset="src/doc/common/static/logo_sagemath_white.svg">
+    <img src="src/doc/common/static/logo_sagemath_black.svg" height="60" align="left">
+  </picture>
+</a>
 
 # Sage: Open Source Mathematical Software
 
@@ -394,6 +399,20 @@ in the Installation Guide.
     or JupyterLab installation, as described in [section
     "Launching SageMath"](https://doc.sagemath.org/html/en/installation/launching.html)
     in the installation manual.
+
+Alternative Installation using PyPI
+---------------
+
+For installation of `sage` in python using `pip` you need to install `sagemath-standard`. First, activate your python virtual environment and follow these steps:
+
+            $ python3 -m pip install sage_conf
+            $ ls $(sage-config SAGE_SPKG_WHEELS)
+            $ python3 -m pip install $(sage-config SAGE_SPKG_WHEELS)/*.whl 
+            $ python3 -m pip install sagemath-standard
+
+You need to install `sage_conf`, a wheelhouse of various python packages. You can list the wheels using `ls $(sage-config SAGE_SPKG_WHEELS)`. After manual installation of these wheels, you can install the sage library, `sagemath-standard`. 
+
+**NOTE:** You can find `sage` and `sagemath` pip packages but with these packages, you will encounter `ModuleNotFoundError`.
 
 Troubleshooting
 ---------------

VERSION.txt

@@ -1 +1 @@
-SageMath version 10.0.beta3, Release Date: 2023-03-02
+SageMath version 10.0.beta6, Release Date: 2023-03-26

build/make/Makefile.in

@@ -128,7 +128,23 @@ PIP_PACKAGES = @SAGE_PIP_PACKAGES@
 # Packages that use the 'script' package build rules
 SCRIPT_PACKAGES = @SAGE_SCRIPT_PACKAGES@
 
-
+# Packages for which we build wheels for PyPI
+PYPI_WHEEL_PACKAGES =				\
+	sage_sws2rst				\
+	sage_setup				\
+	sagemath_environment			\
+	sagemath_objects			\
+	sagemath_repl				\
+	sagemath_categories
+
+# sage_docbuild is here, not in PYPI_WHEEL_PACKAGES, because it depends on sagelib
+WHEEL_PACKAGES = $(PYPI_WHEEL_PACKAGES)		\
+	sage_conf				\
+	sagelib					\
+	sage_docbuild
+
+# Packages for which build sdists for PyPI
+PYPI_SDIST_PACKAGES = $(WHEEL_PACKAGES)
 
 # Generate the actual inst_<pkgname> variables; for each package that is
 # actually built this generates a line like:
@@ -198,6 +214,7 @@ SAGE_I_TARGETS = sagelib doc
 # Tell make not to look for files with these names:
 .PHONY: all all-sage all-toolchain all-build all-sageruntime \
 	all-start build-start base toolchain toolchain-deps base-toolchain \
+	pypi-sdists pypi-wheels wheels \
 	sagelib \
 	doc doc-html doc-html-jsmath doc-html-mathjax doc-pdf \
 	doc-uninstall \
@@ -418,6 +435,25 @@ list-broken-packages: auditwheel_or_delocate
 	    echo >&2 "$$fix_broken_packages"; \
 	fi
 
+pypi-sdists: $(PYPI_SDIST_PACKAGES:%=%-sdist)
+	@echo "Built sdists are in upstream/"
+
+# Ensuring wheels are present, even for packages that may have been installed
+# as editable. Until we have better uninstallation of script packages, we
+# just remove the timestamps, which will lead to rebuilds of the packages.
+pypi-wheels:
+	for a in $(PYPI_WHEEL_PACKAGES); do \
+	    rm -f $(SAGE_VENV)/var/lib/sage/installed/$$a-*; \
+	done
+	$(MAKE_REC) SAGE_EDITABLE=no SAGE_WHEELS=yes $(PYPI_WHEEL_PACKAGES)
+	@echo "Built wheels are in venv/var/lib/sage/wheels/"
+
+wheels:
+	for a in $(WHEEL_PACKAGES); do \
+	    rm -f $(SAGE_VENV)/var/lib/sage/installed/$$a-*; \
+	done
+	$(MAKE_REC) SAGE_EDITABLE=no SAGE_WHEELS=yes $(WHEEL_PACKAGES)
+	@echo "Built wheels are in venv/var/lib/sage/wheels/"
 
 #==============================================================================
 # Setting SAGE_CHECK... variables
@@ -711,6 +747,13 @@ $(1)-uninstall: $(1)-$(4)-uninstall
 
 $(1)-clean: $(1)-uninstall
 
+$(1)-sdist: FORCE python_build sage_setup cython
+	$(AM_V_at) cd '$$(SAGE_ROOT)' && \
+		. '$$(SAGE_ROOT)/src/bin/sage-src-env-config' && \
+		. '$$(SAGE_ROOT)/src/bin/sage-env-config' && \
+		. '$$(SAGE_ROOT)/src/bin/sage-env' && \
+		'$$(SAGE_ROOT)/build/pkgs/$(1)/spkg-src'
+
 # Recursive tox invocation (note - we do not set the environment here).
 # Setting SAGE_SPKG_WHEELS is for the benefit of sagelib's tox.ini
 $(1)-tox-%: FORCE

build/pkgs/_prereq/distros/fedora.txt

@@ -30,7 +30,6 @@ gcc-c++
 # The need for which comes [...] from MPIR's configure script
 findutils
 which
-# Needed for pcre configure, see /~https://github.com/sagemath/sage/issues/29129:
 diffutils
 # Needed for openssl 3.0
 perl-IPC-Cmd

build/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=b9a6c30f4f1c828ca611527d104643d8c0b89ed9
-md5=37a7a99a528efa8a4eea1beff33985db
-cksum=1112286999
+sha1=c9dfa61ff70a2dceec85ad01fc37ee42232402c0
+md5=7479fb53c1b9fd56aea37f83a34cdac3
+cksum=3525422540

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-a822a2132aa0e85069ec8b6efa48ad6db08cc044
+4452928a1a41758883e2f0e3a445b015dfa0e593

build/pkgs/cvxpy/SPKG.rst

@@ -0,0 +1,18 @@
+cvxpy: A domain-specific language for modeling convex optimization problems in Python.
+======================================================================================
+
+Description
+-----------
+
+A domain-specific language for modeling convex optimization problems in Python.
+
+License
+-------
+
+Apache License, Version 2.0
+
+Upstream Contact
+----------------
+
+https://pypi.org/project/cvxpy/
+

build/pkgs/cvxpy/checksums.ini

@@ -0,0 +1,5 @@
+tarball=cvxpy-VERSION.tar.gz
+sha1=8c87f8f8c2177f917ec2fad7d2b510787ffdf72d
+md5=408b0a3140750299207f61de95b4ed6e
+cksum=3643150234
+upstream_url=https://pypi.io/packages/source/c/cvxpy/cvxpy-VERSION.tar.gz

build/pkgs/cvxpy/dependencies

@@ -0,0 +1,4 @@
+$(PYTHON) numpy scipy glpk cvxopt osqp_python ecos_python scs | $(PYTHON_TOOLCHAIN)
+
+----------
+All lines of this file are ignored except the first.