Merge remote-tracking branch 'upstream/develop' into features

Author: Matthias Koeppe

.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
 ---------------