fix pkg_resources DeprecationWarning

.devcontainer/onCreate-conda.sh

@@ -10,4 +10,4 @@ mamba env create -y --file environment-3.11-linux.yml || mamba env update --file
 conda init bash
 
 # Build sage
-conda run -n sage-dev pip install --no-build-isolation -v -v -e . --config-settings=build-dir="build/conda-cp311"
+conda run -n sage-dev pip install --no-build-isolation -v -v --config-settings=build-dir="build/conda-cp311" --editable .

.github/workflows/build.yml

@@ -74,6 +74,8 @@ env:
   FROM_DOCKER_TARGET:     "with-targets"
   FROM_DOCKER_TAG:        ${{ github.event.inputs.docker_tag || 'dev'}}
   EXTRA_CONFIGURE_ARGS:   --enable-fat-binary
+  # Enable editable installs for faster incremental builds
+  SAGE_EDITABLE:          yes
 
 jobs:
   test-long:

.github/workflows/ci-meson.yml

@@ -101,6 +101,30 @@ jobs:
           activate-environment: sage-dev
           environment-file: environment-${{ matrix.python }}-${{ startsWith(matrix.os, 'macos') && (startsWith(runner.arch, 'ARM') && 'macos' || 'macos-x86_64') || startsWith(matrix.os, 'ubuntu') && 'linux' || 'win' }}.yml
 
+      - name: Install build dependencies
+        if: runner.os == 'Linux'
+        shell: bash -l {0}
+        run: |
+          # Ensure essential build tools are available for Linux builds
+          sudo apt-get update
+          sudo apt-get install -y build-essential gfortran libtool-bin
+
+      - name: Install build dependencies (macOS)
+        if: runner.os == 'macOS'
+        shell: bash -l {0}
+        run: |
+          # Ensure build dependencies are properly installed on macOS
+          # First update conda and pip to latest versions
+          conda update -n base –y conda 
+          # Install/update essential build tools in the correct order
+          conda activate sage-dev
+          pip install --upgrade pip
+          pip install --upgrade setuptools wheel
+          pip install --upgrade meson-python
+          # Verify installations
+          python -c "import setuptools; print(f'setuptools: {setuptools.__version__}')"
+          python -c "import mesonpy; print(f'meson-python: {mesonpy.__version__}')"
+
       # Sometimes the conda setup fails due to network issues.
       # This is a workaround to retry the setup step if it fails.
       # Workaround for https://github.com/conda-incubator/setup-miniconda/issues/129
@@ -123,33 +147,91 @@ jobs:
           conda info
           conda list
 
+      - name: Clean build artifacts
+        shell: bash -l {0}
+        run: |
+          # Clean any previous build artifacts that might cause issues
+          rm -rf build/ dist/ *.egg-info builddir/
+          find . -name "*.pyc" -delete
+          find . -name "__pycache__" -type d -exec rm -rf {} + 2>/dev/null || true
+
+      - name: Verify Python environment
+        shell: bash -l {0}
+        run: |
+          # Verify the Python environment is correctly set up
+          python --version
+          pip --version
+          python -c "import sys; print(f'Python executable: {sys.executable}')"
+          python -c "import sysconfig; print(f'Python include: {sysconfig.get_path(\"include\")}')"
+          # Test that we can import required build dependencies
+          python -c "import setuptools, wheel, mesonpy; print('Build dependencies OK')" || {
+            echo "Build dependencies missing, installing..."
+            pip install --upgrade setuptools wheel meson-python
+          }
+
       - name: Build
         shell: bash -l {0}
         run: |
           if [[ "$RUNNER_OS" != "Windows" ]]; then
+            # Clean environment to avoid conflicts
+            unset CFLAGS CXXFLAGS LDFLAGS
+            # Set up ccache for faster builds
             export PATH="/usr/lib/ccache:/usr/local/opt/ccache/libexec:$PATH"
-            export CC="ccache $CC"
-            export CXX="ccache $CXX"
+            # Only use ccache if the base compilers are available
+            if command -v gcc >/dev/null 2>&1; then
+              export CC="ccache gcc"
+            fi
+            if command -v g++ >/dev/null 2>&1; then
+              export CXX="ccache g++"
+            fi
           else
             export LIB="$LIB;$CONDA_PREFIX\\Library\\lib"
             export INCLUDE="$INCLUDE;$CONDA_PREFIX\\Library\\include"
           fi
 
+          # Debug: Show environment before build
+          echo "=== Build Environment ==="
+          echo "Python: $(python --version)"
+          echo "Pip: $(pip --version)"
+          echo "Working directory: $(pwd)"
+          echo "Python path: $PYTHONPATH"
+
           # Use --no-deps and pip check below to verify that all necessary dependencies are installed via conda
-          pip install --no-build-isolation --no-deps --config-settings=builddir=builddir ${{ matrix.editable && '--editable' || '' }} . -v
+          if [[ "${{ matrix.editable }}" == "true" ]]; then
+            echo "Building in editable mode..."
+            pip install --no-build-isolation --no-deps --config-settings=builddir=builddir --editable . -v
+          else
+            echo "Building in standard mode..."
+            pip install --no-build-isolation --no-deps --config-settings=builddir=builddir . -v
+          fi
 
       - name: Check update-meson
         # this step must be after build, because meson.build creates a number of __init__.py files
         # that is needed to make tools/update-meson.py run correctly
         shell: bash -l {0}
         if: matrix.tests == 'all'
         run: |
+          # Store current git state
+          git add .
+          git stash push -m "Pre-update-meson state"
+
+          # Run update-meson
           python tools/update-meson.py
-          if ! ./tools/test-git-no-uncommitted-changes; then
-            git add --intent-to-add .  # also show newly created files in git diff
-            git status
-            git diff
-            false
+
+          # Check if update-meson made any changes to tracked files
+          if ! git diff --quiet HEAD; then
+            echo "update-meson.py made changes to tracked files:"
+            git diff HEAD
+            echo "Please run 'python tools/update-meson.py' and commit the changes."
+            exit 1
+          fi
+
+          # Check for new untracked files that should be committed
+          if [ -n "$(git ls-files --others --exclude-standard)" ]; then
+            echo "update-meson.py created new files that may need to be committed:"
+            git ls-files --others --exclude-standard
+            echo "If these files should be tracked, please add and commit them."
+            # Don't fail for new files, just warn
           fi
 
       - name: Verify dependencies

.github/workflows/ci.yml

@@ -67,15 +67,16 @@ jobs:
           # Install build dependencies manually as workaround for https://github.com/astral-sh/uv/issues/1516
           uv pip install \
             meson-python \
+            "setuptools >=68.1.1" \
             "cypari2 >=2.2.1" \
             "cysignals >=1.11.2, != 1.12.0" \
             "cython >=3.0, != 3.0.3, < 3.1.0" \
             "gmpy2 ~=2.1.b999" \
             memory_allocator \
             "numpy >=1.25" \
-            jinja2 \
-            setuptools
-          uv sync --frozen --inexact --no-build-isolation -v
+            jinja2
+          # Use editable install for faster incremental builds
+          MESONPY_EDITABLE_VERBOSE=1 uv sync --frozen --inexact --no-build-isolation -v
 
       - name: Test
         run: |

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

@@ -28,6 +28,8 @@ env:
   FROM_DOCKER_TARGET:     "with-targets"
   FROM_DOCKER_TAG:        ${{ github.event.inputs.docker_tag || 'dev'}}
   EXTRA_CONFIGURE_ARGS:   --enable-fat-binary
+  # Enable editable installs for faster incremental builds
+  SAGE_EDITABLE:          yes
 
 jobs:
   build-doc-pdf:

.github/workflows/doc-build.yml

@@ -62,14 +62,30 @@ jobs:
           channel-priority: true
           activate-environment: sage-dev
           environment-file: environment-${{ env.PYTHON_VERSION }}-linux.yml
+
+      - name: Install build dependencies
+        shell: bash -l {0}
+        run: |
+          # Ensure essential build tools are available
+          sudo apt-get update
+          sudo apt-get install -y build-essential gfortran libtool-bin
 
       - name: Build Sage
         shell: bash -l {0}
         run: |
+          # Clean environment to avoid conflicts
+          unset CFLAGS CXXFLAGS LDFLAGS
+          # Set up ccache for faster builds
           export PATH="/usr/lib/ccache:/usr/local/opt/ccache/libexec:$PATH"
-          export CC="ccache $CC"
-          export CXX="ccache $CXX"
-          pip install --no-build-isolation --config-settings=builddir=builddir . -v
+          # Only use ccache if the base compilers are available
+          if command -v gcc >/dev/null 2>&1; then
+            export CC="ccache gcc"
+          fi
+          if command -v g++ >/dev/null 2>&1; then
+            export CXX="ccache g++"
+          fi
+          # Use editable install for faster incremental builds
+          MESONPY_EDITABLE_VERBOSE=1 pip install --no-build-isolation --config-settings=builddir=builddir --editable . -v
 
       #
       # For pull requests

.github/workflows/docker.yml

@@ -121,6 +121,8 @@ jobs:
       FROM_DOCKER_TAG:    ${{ inputs.from_docker_tag }}
       EXTRA_CONFIGURE_ARGS: --enable-fat-binary
       EXTRA_SAGE_PACKAGES:  ${{ inputs.extra_sage_packages }}
+      # Enable editable installs for faster incremental builds
+      SAGE_EDITABLE:      yes
     steps:
       - name: Maximize build disk space
         uses: easimon/maximize-build-space@v10

.github/workflows/macos.yml

@@ -136,7 +136,7 @@ jobs:
                              ;;
           esac
           (sleep ${{ inputs.timeout }}; pkill make) &
-          MAKE="make -j12" EXTRA_SAGE_PACKAGES="${{ inputs.extra_sage_packages }}" "${{ steps.python.outputs.python-path }}" -m pipx run tox -e $TOX_ENV -- SAGE_NUM_THREADS=6 $TARGETS
+          MAKE="make -j12" EXTRA_SAGE_PACKAGES="${{ inputs.extra_sage_packages }}" SAGE_EDITABLE=yes "${{ steps.python.outputs.python-path }}" -m pipx run tox -e $TOX_ENV -- SAGE_NUM_THREADS=6 $TARGETS
       - name: Prepare logs artifact
         run: |
           mkdir -p "artifacts/$LOGS_ARTIFACT_NAME"; cp -r .tox/*/log "artifacts/$LOGS_ARTIFACT_NAME"

.gitpod.yml

@@ -11,7 +11,7 @@ tasks:
       && conda config --append envs_dirs $(pwd)
       && conda activate $(pwd)/venv
       && ./bootstrap
-      && pip install --no-build-isolation -v -v -e ./src
+      && pip install --no-build-isolation -v -v --editable ./src
     # Activate conda environment, set up Trac remote
     # RestructuredText extension recommends python extension, although we have already installed it
     # So disable the recommendation dialog

.vscode/settings.json

@@ -119,5 +119,15 @@
     // Use the Meson build system for C/C++ files
     "C_Cpp.default.configurationProvider": "mesonbuild.mesonbuild",
     // Use the compile_commands.json file generated by Meson for IntelliSense
-    "C_Cpp.default.compileCommands": "${workspaceFolder}/builddir/compile_commands.json"
+    "C_Cpp.default.compileCommands": "${workspaceFolder}/builddir/compile_commands.json",
+    // Environment variables for SageMath development
+    "terminal.integrated.env.linux": {
+        "MESONPY_EDITABLE_VERBOSE": "1"
+    },
+    "terminal.integrated.env.osx": {
+        "MESONPY_EDITABLE_VERBOSE": "1"
+    },
+    "terminal.integrated.env.windows": {
+        "MESONPY_EDITABLE_VERBOSE": "1"
+    }
 }

build/bin/sage-spkg

@@ -177,7 +177,7 @@ fi
 . sage-build-env-config
 . sage-build-env || exit_with_error_msg "Error setting environment variables by sourcing sage-build-env"
 
-# Remove '.' from PYTHONPATH, to avoid trouble with setuptools / easy_install
+# Remove '.' from PYTHONPATH, to avoid trouble with setuptools / pip
 # (cf. #10192, #10176):
 if [ -n "$PYTHONPATH" ]; then
     # We also collapse multiple slashs into a single one (first substitution),

build/pkgs/beniget/checksums.ini

@@ -1,4 +1,4 @@
 tarball=beniget-VERSION.tar.gz
-sha1=0167f16d17fbd61b91e620bca07e4ec7054ce51d
-sha256=75554b3b8ad0553ce2f607627dad3d95c60c441189875b98e097528f8e23ac0c
+sha1=95233c191f0ea8486a8ef0cf40d9c5a9838f2439
+sha256=a0258537e65e7e14ec33a86802f865a667f949bb6c73646d55e42f7c45a052ae
 upstream_url=https://files.pythonhosted.org/packages/source/b/beniget/beniget-VERSION.tar.gz

build/pkgs/beniget/package-version.txt

@@ -1 +1 @@
-0.4.1
+0.4.2.post1

build/pkgs/cysignals/checksums.ini

@@ -1,4 +1,4 @@
 tarball=cysignals-VERSION.tar.gz
-sha1=e285e209a3a5f9469cb5ade746c518cd3a600a9b
-sha256=89f7626dbf29db5ab3d6eff15a89978f4eb5193c320e9099bcc157dacdefd1eb
+sha1=d3f23d9d82aab06939996f8cbc881a1c529cab98
+sha256=4aefa3b35eb036cb40b2b948df84725976b987895338204f64550e2d63891f5f
 upstream_url=https://files.pythonhosted.org/packages/source/c/cysignals/cysignals-VERSION.tar.gz

build/pkgs/cysignals/package-version.txt

@@ -1 +1 @@
-1.12.3
+1.12.4

build/pkgs/cython/checksums.ini

@@ -1,4 +1,4 @@
 tarball=cython-VERSION.tar.gz
-sha1=f692b0c6f209b75b6bbd69bdbd57fac23785c23e
-sha256=7146dd2af8682b4ca61331851e6aebce9fe5158e75300343f80c07ca80b1faff
+sha1=3bd5a99e283297a423bb9bb1ab9765bb4bfde86e
+sha256=10ee785e42328924b78f75a74f66a813cb956b4a9bc91c44816d089d5934c089
 upstream_url=https://files.pythonhosted.org/packages/source/c/cython/cython-VERSION.tar.gz

build/pkgs/cython/package-version.txt

@@ -1 +1 @@
-3.0.11
+3.1.3

build/pkgs/gast/checksums.ini

@@ -1,4 +1,4 @@
 tarball=gast-VERSION.tar.gz
-sha1=6c113cf8d33cc654d33210335103485ab41d3dbb
-sha256=9c270fe5f4b130969b54174de7db4e764b09b4f7f67ccfc32480e29f78348d97
+sha1=6ff8b1105c331ac55d1f9fa389b7486b9f8c9c07
+sha256=88fc5300d32c7ac6ca7b515310862f71e6fdf2c029bbec7c66c0f5dd47b6b1fb
 upstream_url=https://files.pythonhosted.org/packages/source/g/gast/gast-VERSION.tar.gz

build/pkgs/gast/package-version.txt

@@ -1 +1 @@
-0.5.4
+0.6.0

build/pkgs/pip/SPKG.rst

@@ -1,12 +1,12 @@
-pip: Tool for installing and managing Python packages
-=====================================================
+pip
+===
 
 Description
 -----------
 
-This package installs pip, the tool for installing and managing Python
-packages, such as those found in the Python Package Index. It’s a
-replacement for easy_install.
+This package installs pip, the standard tool for installing and managing Python
+packages, such as those found in the Python Package Index. It has replaced
+the deprecated easy_install tool.
 
 License
 -------
@@ -23,4 +23,3 @@ Upstream Contact
 - Bug Tracking: https://github.com/pypa/pip/issues
 - Mailing list: http://groups.google.com/group/python-virtualenv
 - Docs: https://pip.pypa.io/
-

build/pkgs/pythran/checksums.ini

@@ -1,4 +1,4 @@
 tarball=pythran-VERSION-py3-none-any.whl
-sha1=2341d42c014f88318f447083c62e8d3953b04ac2
-sha256=be569cc2817b625ccd2c8f74fa3c93806f245c65fadc282c26a9f546ebd34cfa
+sha1=5e68b54f525e1f7de6e73aa3e897f5f21652bd1d
+sha256=405ecf2100d4926d1a15640c36bd1b19a560386653d0ee4d5234f9421ef4034b
 upstream_url=https://files.pythonhosted.org/packages/py3/p/pythran/pythran-VERSION-py3-none-any.whl

build/pkgs/pythran/package-version.txt

@@ -1 +1 @@
-0.17.0
+0.18.0

build/pkgs/setuptools/checksums.ini

@@ -1,4 +1,4 @@
 tarball=setuptools-VERSION-py3-none-any.whl
-sha1=3756539d45341ca5cec9e2dfe11539faa066f5cd
-sha256=b208925fcb9f7af924ed2dc04708ea89791e24bde0d3020b27df0e116088b34e
+sha1=f82aabaab9ae429e91d2b0d748ecd2c0b07c5de8
+sha256=062d34222ad13e0cc312a4c02d73f059e86a4acbfbdea8f8f76b28c99f306922
 upstream_url=https://files.pythonhosted.org/packages/py3/s/setuptools/setuptools-VERSION-py3-none-any.whl

build/pkgs/setuptools/package-version.txt

@@ -1 +1 @@
-73.0.1
+80.9.0

build/pkgs/setuptools_scm/checksums.ini

@@ -1,4 +1,4 @@
 tarball=setuptools_scm-VERSION-py3-none-any.whl
-sha1=be606b6acb67714b96e9e1e9a9944feaca504e44
-sha256=897a3226a6fd4a6eb2f068745e49733261a21f70b1bb28fce0339feb978d9af3
+sha1=29b1eb2fa08075564f062c354eab106380ad16e6
+sha256=332ca0d43791b818b841213e76b1971b7711a960761c5bea5fc5cdb5196fbce3
 upstream_url=https://files.pythonhosted.org/packages/py3/s/setuptools_scm/setuptools_scm-VERSION-py3-none-any.whl

build/pkgs/setuptools_scm/package-version.txt

@@ -1 +1 @@
-8.1.0
+8.3.1

docker/Dockerfile

@@ -189,6 +189,9 @@ ENV SAGE_FAT_BINARY yes
 # Just to be sure Sage doesn't try to build its own GCC (even though
 # it shouldn't with a recent GCC package from the system and with gfortran)
 ENV SAGE_INSTALL_GCC no
+# Enable editable installs for faster incremental builds
+ARG SAGE_EDITABLE="yes"
+ENV SAGE_EDITABLE $SAGE_EDITABLE
 # Set MAKEFLAGS and SAGE_NUM_THREADS to build things in parallel during the
 # docker build. Note that these do not leak into the sagemath and sagemath-dev
 # images.
@@ -197,8 +200,8 @@ ENV MAKEFLAGS $MAKEFLAGS
 ARG SAGE_NUM_THREADS="2"
 ENV SAGE_NUM_THREADS $SAGE_NUM_THREADS
 RUN make configure
-# Old default before https://github.com/sagemath/sage/issues/32406
-RUN ./configure --disable-editable
+# Enable editable installs by default (SAGE_EDITABLE=yes is the default in configure.ac)
+RUN ./configure
 RUN make build
 
 ################################################################################