Merge branch 'sagemath:develop' into sync_labels

Author: soehms

.codecov.yml

@@ -0,0 +1,18 @@
+# https://docs.codecov.com/docs/pull-request-comments#disable-comment
+comment: false
+# https://docs.codecov.com/docs/codecovyml-reference#codecov
+codecov:
+  require_ci_to_pass: 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

@@ -23,7 +23,7 @@ concurrency:
 jobs:
   build:
     runs-on: ubuntu-latest
-    container: ghcr.io/sagemath/sage/sage-docker-${{ github.event.inputs.platform || 'ubuntu-focal-standard' }}-with-targets:${{ github.event.inputs.docker_tag || 'dev'}}
+    container: ghcr.io/sagemath/sage/sage-${{ github.event.inputs.platform || 'ubuntu-focal-standard' }}-with-targets:${{ github.event.inputs.docker_tag || 'dev'}}
     steps:
       - name: Checkout
         id: checkout
@@ -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

@@ -6,6 +6,9 @@ on:
       - '*'
     branches:
       - 'public/build/**-runci'
+  pull_request:
+    types:
+      - labeled
   workflow_dispatch:
     # Allow to run manually
 
@@ -19,11 +22,18 @@ jobs:
     name: Conda
     runs-on: ${{ matrix.os }}
 
+    # Run on push, workflow dispatch and when certain labels are added 
+    if: |
+      github.event.action != 'labeled' ||
+      github.event.label.name == 'c: packages: optional' || 
+      github.event.label.name == 'c: packages: standard' || 
+      github.event.label.name == 's: run conda ci'
+
     strategy:
       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 +51,18 @@ 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:
@@ -77,13 +94,22 @@ jobs:
           echo "::remove-matcher owner=configure-system-package-warning::"
           echo "::remove-matcher owner=configure-system-package-error::"
 
+          # Manually install ptyprocess for now, until https://github.com/sagemath/sage/issues/32147 is fixed
+          pip install --no-build-isolation -v -v ptyprocess==0.5.1
+
       - 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
+          # Use --no-deps and pip check below to verify that all necessary dependencies are installed via conda.
+          pip install --no-build-isolation --no-deps -v -v -e ./pkgs/sage-conf ./pkgs/sage-setup
+          pip install --no-build-isolation --no-deps -v -v -e ./src
         env:
           SAGE_NUM_THREADS: 2
+        
+      - name: Verify dependencies
+        if: always()
+        shell: bash -l {0}
+        run: pip check
 
       - name: Test
         shell: bash -l {0}

.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-build.yml

@@ -14,7 +14,7 @@ concurrency:
 jobs:
   build-docs:
     runs-on: ubuntu-latest
-    container: ghcr.io/sagemath/sage/sage-docker-ubuntu-focal-standard-with-targets:dev
+    container: ghcr.io/sagemath/sage/sage-ubuntu-focal-standard-with-targets:dev
     steps:
       - name: Checkout
         uses: actions/checkout@v3

.github/workflows/doc-publish.yml

@@ -28,18 +28,18 @@ 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({
+            var artifacts = await github.rest.actions.listWorkflowRunArtifacts({
                owner: context.repo.owner,
                repo: context.repo.repo,
                run_id: ${{github.event.workflow_run.id }},
             });
             var matchArtifact = artifacts.data.artifacts.filter((artifact) => {
               return artifact.name == "docs"
             })[0];
-            var download = await github.actions.downloadArtifact({
+            var download = await github.rest.actions.downloadArtifact({
                owner: context.repo.owner,
                repo: context.repo.repo,
                artifact_id: matchArtifact.id,

.zenodo.json

@@ -1,10 +1,10 @@
 {
     "description": "Mirror of the Sage https://sagemath.org/ source tree", 
     "license": "other-open", 
-    "title": "sagemath/sage: 10.0.beta5", 
-    "version": "10.0.beta5", 
+    "title": "sagemath/sage: 10.0.beta8", 
+    "version": "10.0.beta8", 
     "upload_type": "software", 
-    "publication_date": "2023-03-19", 
+    "publication_date": "2023-04-06", 
     "creators": [
         {
             "affiliation": "SageMath.org", 
@@ -15,7 +15,7 @@
     "related_identifiers": [
         {
             "scheme": "url", 
-            "identifier": "https://github.com/sagemath/sage/tree/10.0.beta5", 
+            "identifier": "https://github.com/sagemath/sage/tree/10.0.beta8", 
             "relation": "isSupplementTo"
         }, 
         {

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
 

VERSION.txt

@@ -1 +1 @@
-SageMath version 10.0.beta5, Release Date: 2023-03-19
+SageMath version 10.0.beta8, Release Date: 2023-04-06

bootstrap-conda

@@ -11,7 +11,6 @@ STRIP_COMMENTS="sed s/#.*//;"
 shopt -s extglob
 
 DEVELOP_SPKG_PATTERN="@(_develop$(for a in $(head -n 1 build/pkgs/_develop/dependencies); do echo -n "|"$a; done))"
-
 BOOTSTRAP_PACKAGES=$(echo $(${STRIP_COMMENTS} build/pkgs/_bootstrap/distros/conda.txt))
 SYSTEM_PACKAGES=
 OPTIONAL_SYSTEM_PACKAGES=
@@ -37,10 +36,13 @@ for PKG_BASE in $(sage-package list --has-file distros/conda.txt); do
                     ;;
             esac
         else
-            case "$PKG_TYPE" in
-                standard)
+            case "$PKG_BASE:$PKG_TYPE" in
+                *:standard)
                     SAGELIB_SYSTEM_PACKAGES+=" $PKG_SYSTEM_PACKAGES"
                     ;;
+                $DEVELOP_SPKG_PATTERN:*)
+                    DEVELOP_SYSTEM_PACKAGES+=" $PKG_SYSTEM_PACKAGES"
+                    ;;
                 *)
                     SAGELIB_OPTIONAL_SYSTEM_PACKAGES+=" $PKG_SYSTEM_PACKAGES"
                     ;;

build/bin/sage-clone-source

@@ -31,11 +31,13 @@ CONFBALL="$SRC/upstream/configure-$CONFVERSION.tar.gz"
 rm -rf "$DST"
 mkdir -p "$DST"
 
-git clone --origin trac "$SRC" "$DST"
+git clone --origin upstream "$SRC" "$DST"
 
 cd "$DST"
-git remote set-url trac "$SAGE_REPO_ANONYMOUS"
-git remote set-url --push trac "$SAGE_REPO_AUTHENTICATED"
+git remote set-url upstream "$SAGE_REPO_ANONYMOUS"
+git remote set-url --push upstream "do not push to upstream"
+git remote add trac https://github.com/sagemath/sagetrac-mirror.git
+git remote set-url --push trac "do not push to trac"
 
 # Save space
 git gc --aggressive --prune=now

build/pkgs/argon2_cffi/dependencies

@@ -1,4 +1,4 @@
-$(PYTHON) six | $(PYTHON_TOOLCHAIN) cffi
+$(PYTHON) argon2_cffi_bindings | $(PYTHON_TOOLCHAIN) flit_core
 
 ----------
 All lines of this file are ignored except the first.

build/pkgs/argon2_cffi/spkg-install.in

@@ -1,6 +1,2 @@
 cd src
-if [ "$SAGE_FAT_BINARY" = "yes" ]; then
-   # https://argon2-cffi.readthedocs.io/en/stable/installation.html
-   export ARGON2_CFFI_USE_SSE2=0
-fi
 sdh_pip_install .

build/pkgs/argon2_cffi_bindings/SPKG.rst

@@ -0,0 +1,18 @@
+argon2_cffi_bindings: Low-level CFFI bindings for Argon2
+========================================================
+
+Description
+-----------
+
+Low-level CFFI bindings for Argon2
+
+License
+-------
+
+MIT
+
+Upstream Contact
+----------------
+
+https://pypi.org/project/argon2-cffi-bindings/
+

build/pkgs/argon2_cffi_bindings/checksums.ini

@@ -0,0 +1,5 @@
+tarball=argon2-cffi-bindings-VERSION.tar.gz
+sha1=5a9b8906d9ca73c53c2bf0a2f0a8127fda69e965
+md5=f1591e1af7dea9ef3e5b982e2c196c1d
+cksum=2420586823
+upstream_url=https://pypi.io/packages/source/a/argon2_cffi_bindings/argon2-cffi-bindings-VERSION.tar.gz

build/pkgs/argon2_cffi_bindings/dependencies

@@ -0,0 +1,4 @@
+$(PYTHON) | $(PYTHON_TOOLCHAIN) cffi setuptools_scm
+
+----------
+All lines of this file are ignored except the first.

build/pkgs/argon2_cffi_bindings/install-requires.txt

@@ -0,0 +1 @@
+argon2-cffi-bindings

build/pkgs/argon2_cffi_bindings/package-version.txt

@@ -0,0 +1 @@
+21.2.0

build/pkgs/argon2_cffi_bindings/spkg-install.in

@@ -0,0 +1,6 @@
+cd src
+if [ "$SAGE_FAT_BINARY" = "yes" ]; then
+   # https://argon2-cffi.readthedocs.io/en/stable/installation.html
+   export ARGON2_CFFI_USE_SSE2=0
+fi
+sdh_pip_install .

build/pkgs/argon2_cffi_bindings/type

@@ -0,0 +1 @@
+standard

build/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=0ea92e19072c843aa21527e051eff0a0f97eb9ad
-md5=44e659f4d263acad8194e16952762a82
-cksum=3343113057
+sha1=c809622a8c0b706231b5c8e02c0fb96b940e2a10
+md5=4ab2cb23636289210afe4a6743b36183
+cksum=1470715760

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-49c2cd323e638cdfb0444d72daad21b4ddbd1887
+adaf3af26892f4a3720cc09d0e21c35281b472a3