Merge branch 'main' into patch-1

corneliusroemer · Dec 2, 2024 · 167f9c9 · 167f9c9
2 parents 2b70c2f + 3f49aa5
commit 167f9c9
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diff --git a/.github/actions/workspace/action.yml b/.github/actions/workspace/action.yml
@@ -28,13 +28,13 @@ runs:
   steps:
     - name: Create workspace
       if: ${{ inputs.action == 'save' }}
-      uses: actions/cache/save@v3
+      uses: actions/cache/save@v4
       with:
         path: ${{ inputs.path }}
         key: ${{ inputs.key_prefix }}-${{ inputs.key_base }}-${{ inputs.key_suffix }}
     - name: Restore workspace
       if: ${{ inputs.action == 'restore' }}
-      uses: actions/cache/restore@v3
+      uses: actions/cache/restore@v4
       with:
         path: ${{ inputs.path }}
         key: ${{ inputs.key_prefix }}-${{ inputs.key_base }}-${{ inputs.key_suffix }}

diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -0,0 +1,15 @@
+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for all configuration options:
+# https://docs.github.com/en/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file
+
+version: 2
+updates:
+  - package-ecosystem: github-actions
+    directory: /
+    schedule:
+      interval: weekly
+  - package-ecosystem: github-actions
+    directory: .github/actions/workspace/
+    schedule:
+      interval: weekly
diff --git a/.github/workflows/brew.yml b/.github/workflows/brew.yml
@@ -0,0 +1,47 @@
+name: Homebrew and Linuxbrew toolchains
+
+on:
+  workflow_call:
+
+jobs:
+  build_linuxbrew:
+    name: Build on linuxbrew
+    runs-on: ubuntu-latest
+    container:
+      image: homebrew/brew:latest
+
+    steps:
+      # v1 required due to permissions error
+      - name: Checkout mamba repository
+        uses: actions/checkout@v1
+
+      - name: Correct the creation permissions
+        run: sudo chown -R linuxbrew .
+
+      - name: Install host and build dependencies
+        run: brew install fmt libarchive libsolv lz4 openssl@3 reproc simdjson xz yaml-cpp zstd cmake cli11 nlohmann-json spdlog tl-expected curl pkgconfig python bzip2 krb5 zlib
+
+      - name: Configure to build mamba
+        run: cmake -S. -Bbuild -DBUILD_LIBMAMBA=ON -DBUILD_MAMBA=ON -DBUILD_SHARED=ON -DBUILD_STATIC=OFF
+
+      - name: Build mamba
+        run: cmake --build build -j4
+
+  build_homebrew:
+    name: Build on homebrew
+    runs-on: macos-13
+
+    steps:
+      - name: Checkout mamba repository
+        uses: actions/checkout@v4
+
+      - name: Install host and build dependencies
+        run: brew install fmt libarchive libsolv lz4 openssl@3 reproc simdjson xz yaml-cpp zstd cmake cli11 nlohmann-json spdlog tl-expected pkgconfig python
+
+      - name: Configure to build mamba
+        run: >
+          cmake -S. -Bbuild -DBUILD_LIBMAMBA=ON -DBUILD_MAMBA=ON -DBUILD_SHARED=ON -DBUILD_STATIC=OFF
+          -DLibArchive_ROOT=$(brew --prefix libarchive)
+
+      - name: Build mamba
+        run: cmake --build build -j4
diff --git a/.github/workflows/conda_canary.yml b/.github/workflows/conda_canary.yml
@@ -52,18 +52,16 @@ jobs:
           restore-keys: conda-canary-
       - name: build libmamba Python bindings
         run: |
-          mkdir build
-          cd build
-          cmake .. -DCMAKE_INSTALL_PREFIX=$CONDA_PREFIX \
-                   -DBUILD_LIBMAMBAPY=ON \
-                   -DBUILD_LIBMAMBA=ON \
-                   -DBUILD_SHARED=ON \
-                   -DBUILD_MAMBA_PACKAGE=ON \
-                   -DCMAKE_CXX_COMPILER_LAUNCHER=sccache \
-                   -DCMAKE_C_COMPILER_LAUNCHER=sccache \
-                   -GNinja
-          ninja
-          ninja install
+          cmake -B build/ -G Ninja \
+            -D CMAKE_INSTALL_PREFIX=$CONDA_PREFIX \
+            -D BUILD_LIBMAMBAPY=ON \
+            -D BUILD_LIBMAMBA=ON \
+            -D BUILD_SHARED=ON \
+            -D BUILD_MAMBA_PACKAGE=ON \
+            -D CMAKE_CXX_COMPILER_LAUNCHER=sccache \
+            -D CMAKE_C_COMPILER_LAUNCHER=sccache
+          cmake --build build/ --parallel
+          cmake --install build/
       - name: install libmambapy
         run: pip install -e ./libmambapy/ --no-deps
       - name: build cache statistics

diff --git a/.github/workflows/label_check.yml b/.github/workflows/label_check.yml
@@ -14,7 +14,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout code
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
 
       - name: Check labels
         run: |

diff --git a/.github/workflows/linters.yml b/.github/workflows/linters.yml
@@ -20,7 +20,7 @@ jobs:
     env:
       PRE_COMMIT_USE_MICROMAMBA: 1
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Install pre-commit
       uses: mamba-org/setup-micromamba@v1
       with:

diff --git a/.github/workflows/static_build.yml b/.github/workflows/static_build.yml
@@ -27,19 +27,24 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          - { os: ubuntu-latest, platform: linux, arch: "64" }
-          - { os: ubuntu-latest, platform: linux, arch: aarch64 }
-          - { os: ubuntu-latest, platform: linux, arch: ppc64le }
-          - { os: macos-latest, platform: osx, arch: "64" }
-          - { os: macos-latest, platform: osx, arch: arm64 }
+          - {os: ubuntu-latest, platform: linux, arch: "64"}
+          - {os: ubuntu-latest, platform: linux, arch: aarch64}
+          - {os: ubuntu-latest, platform: linux, arch: ppc64le}
+          - {os: macos-latest, platform: osx, arch: "64"}
+          - {os: macos-latest, platform: osx, arch: arm64}
     steps:
       - name: Checkout micromamba-feedstock
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           repository: conda-forge/micromamba-feedstock
           path: micromamba-feedstock
+      - name: Disable output validation
+        if: ${{ matrix.platform == 'osx' }}
+        run: |
+          cd micromamba-feedstock/
+          sed -i '' '/conda_forge_output_validation/d' conda-forge.yml
       - name: Checkout mamba branch
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           path: mamba
       - name: Clear mamba git directory and link source
@@ -50,11 +55,11 @@ jobs:
           mv mamba/ micromamba-feedstock/source
           # Prevent irrelevant file permission error
           git -C micromamba-feedstock/ config --local --add safe.directory '*'
-      - uses: mamba-org/setup-micromamba@v1
+      - uses: mamba-org/setup-micromamba@v2
         with:
           environment-name: mambabuild
           create-args: python boa
-          post-cleanup: none  # FIXME the cleanup fails on OSX
+          post-cleanup: none # FIXME the cleanup fails on OSX
       - name: Build conda package (Unix native)
         if: ${{ !(matrix.platform == 'linux' && matrix.arch != '64') }}
         shell: bash -l {0}
@@ -94,29 +99,38 @@ jobs:
             "micromamba-feedstock/build_artifacts/${{ matrix.platform }}-${{ matrix.arch }}/"micromamba-*.tar.bz2 "pkg/"
           mkdir -p "${{ github.workspace }}/artifacts"
           cp pkg/bin/micromamba "${{ github.workspace }}/artifacts"
+
+      - name: Test basic commands
+        if: ${{ matrix.arch != 'aarch64' && matrix.arch != 'ppc64le' }}
+        run: |
+          mkdir test_prefix
+          ${{ github.workspace }}/artifacts/micromamba --version
+          ${{ github.workspace }}/artifacts/micromamba --help
+          ${{ github.workspace }}/artifacts/micromamba env create -y -n testenv -r ./test_prefix "python<3.13"
+          ${{ github.workspace }}/artifacts/micromamba list -n testenv -r ./test_prefix --log-level 1
+
       - name: Archive conda-build artifact
         if: failure()
         run: tar -czf ${{ github.workspace }}/micromamba-conda-build-failed-${{ matrix.platform }}-${{ matrix.arch }}.tar.gz $MAMBA_ROOT_PREFIX/envs/mambabuild/conda-bld/micromamba_*
       - name: Upload conda build artifacts
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         if: failure()
         with:
           name: micromamba-conda-build-failed-${{ matrix.platform }}-${{ matrix.arch }}
           path: ${{ github.workspace }}/micromamba-conda-build-failed-${{ matrix.platform }}-${{ matrix.arch }}.tar.gz
           retention-days: 7
       - name: Upload micromamba
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: micromamba-${{ matrix.platform }}-${{ matrix.arch }}
           path: ${{ github.workspace }}/artifacts/micromamba
-
   micromamba-static-win:
     name: "win-64"
     runs-on: windows-2022
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Cache vcpkg packages
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           # The installed packages are in %VCPKG_INSTALLATION_ROOT%\installed\x64-windows-static
           # and the info which packages are installed is in %VCPKG_INSTALLATION_ROOT%\installed\vcpkg
@@ -133,40 +147,36 @@ jobs:
           key: sccache-${{ github.job }}-win-64
       - name: Set up MSVC
         uses: ilammy/msvc-dev-cmd@v1
-      - uses: mamba-org/setup-micromamba@v1
+      - uses: mamba-org/setup-micromamba@v2
         with:
           environment-name: mambabuild
           init-shell: bash cmd.exe
+          # Constraint on fmt is due to an issue with 11.0.2 (to be fixed in next version)
+          # cf. https://github.com/fmtlib/fmt/issues/4091
           create-args: >-
             cli11>=2.2,<3
             cpp-expected
             nlohmann_json
             simdjson-static>=3.3.0
             spdlog
-            fmt
+            fmt<=11.0.1
             yaml-cpp-static>=0.8.0
             libsolv-static>=0.7.24
             reproc-cpp-static>=14.2.4.post0
       - name: build micromamba
         shell: cmd /C call {0}
-        # Using D_DISABLE_CONSTEXPR_MUTEX_CONSTRUCTOR is a workaround to fix CI failure on win-64
-        # after updating runners to 20240603.1 image
-        # (cf. https://github.com/actions/runner-images/issues/10004#issuecomment-2153445161)
         run: |
           set CMAKE_PREFIX_PATH=.\vcpkg_installed\x64-windows-static-md;%CONDA_PREFIX%\Library
-          cmake -S . ^
-            -B build ^
+          cmake -B build/ -G Ninja ^
             -D CMAKE_CXX_COMPILER_LAUNCHER=sccache ^
             -D CMAKE_C_COMPILER_LAUNCHER=sccache ^
             -D CMAKE_MSVC_RUNTIME_LIBRARY="MultiThreadedDLL" ^
-            -D CMAKE_CXX_FLAGS=" /D_DISABLE_CONSTEXPR_MUTEX_CONSTRUCTOR" ^
             -D CMAKE_BUILD_TYPE="Release" ^
             -D BUILD_LIBMAMBA=ON ^
             -D BUILD_STATIC=ON ^
-            -D BUILD_MICROMAMBA=ON ^
-            -G "Ninja"
+            -D BUILD_MICROMAMBA=ON
           if %errorlevel% neq 0 exit /b %errorlevel%
-          cmake --build build
+          cmake --build build/ --parallel
           if %errorlevel% neq 0 exit /b %errorlevel%
           sccache --show-stats
           if %errorlevel% neq 0 exit /b %errorlevel%
@@ -179,14 +189,23 @@ jobs:
       - name: Archive-build artifact
         if: failure()
         run: tar -czf ${{ github.workspace }}/micromamba-build-failed-win-64.tar.gz ${{ github.workspace }}/build/
+
+      - name: Test basic commands
+        run: |
+          mkdir test_prefix
+          ${{ github.workspace }}/build/micromamba/micromamba.exe --version
+          ${{ github.workspace }}/build/micromamba/micromamba.exe --help
+          ${{ github.workspace }}/build/micromamba/micromamba.exe env create -y -n testenv -r ./test_prefix "python<3.13"
+          ${{ github.workspace }}/build/micromamba/micromamba.exe list -n testenv -r ./test_prefix  --log-level 1
+
       - name: Upload build artifacts
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         if: failure()
         with:
           name: micromamba-build-failed-win-64
           path: ${{ github.workspace }}/micromamba-build-failed-win-64.tar.gz
           retention-days: 7
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
           name: micromamba-win-64
           path: ${{ github.workspace }}/build/micromamba/micromamba.exe
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -42,3 +42,7 @@ jobs:
     with:
       os: ${{ matrix.os }}
       build_type: ${{ matrix.build_type }}
+
+  brew_tests:
+    name: Homebrew and Linuxbrew toolchains
+    uses: ./.github/workflows/brew.yml
diff --git a/.github/workflows/unix_impl.yml b/.github/workflows/unix_impl.yml
@@ -23,7 +23,7 @@ jobs:
       - name: Checkout mamba repository
         uses: actions/checkout@v4
       - name: Create build environment
-        uses: mamba-org/setup-micromamba@v1
+        uses: mamba-org/setup-micromamba@v2
         with:
           environment-file: ./dev/environment-dev.yml
           environment-name: build_env
@@ -40,7 +40,8 @@ jobs:
             --preset mamba-unix-shared-${{ inputs.build_type }}  \
             -D CMAKE_CXX_COMPILER_LAUNCHER=sccache \
             -D CMAKE_C_COMPILER_LAUNCHER=sccache \
-            -D BUILD_LIBMAMBAPY=OFF
+            -D BUILD_LIBMAMBAPY=OFF \
+            -D ENABLE_MAMBA_ROOT_PREFIX_FALLBACK=OFF
           cmake --build build/ --parallel
       - name: Show build cache statistics
         run: sccache --show-stats
@@ -69,7 +70,7 @@ jobs:
           path: build/
           key_suffix: ${{ inputs.os }}-${{ inputs.build_type }}
       - name: Create build environment
-        uses: mamba-org/setup-micromamba@v1
+        uses: mamba-org/setup-micromamba@v2
         with:
           environment-file: ./build/environment.lock
           environment-name: build_env
@@ -95,7 +96,7 @@ jobs:
           path: build/
           key_suffix: ${{ inputs.os }}-${{ inputs.build_type }}
       - name: Create build environment
-        uses: mamba-org/setup-micromamba@v1
+        uses: mamba-org/setup-micromamba@v2
         with:
           environment-file: ./build/environment.lock
           environment-name: build_env
@@ -122,7 +123,7 @@ jobs:
           path: build/
           key_suffix: ${{ inputs.os }}-${{ inputs.build_type }}
       - name: Create build environment
-        uses: mamba-org/setup-micromamba@v1
+        uses: mamba-org/setup-micromamba@v2
         with:
           environment-file: ./build/environment.lock
           environment-name: build_env
@@ -179,7 +180,7 @@ jobs:
           path: build/
           key_suffix: ${{ inputs.os }}-${{ inputs.build_type }}
       - name: Create build environment
-        uses: mamba-org/setup-micromamba@v1
+        uses: mamba-org/setup-micromamba@v2
         with:
           environment-file: ./build/environment.lock
           environment-name: build_env