From 7d29312b75fdd5bd43346ab2d954e1d370b9c2e2 Mon Sep 17 00:00:00 2001
From: Oscar Benjamin <oscar.j.benjamin@gmail.com>
Date: Mon, 23 Mar 2026 20:15:37 +0000
Subject: [PATCH 01/18] Use cibuildwheel to build pyodide wheels

---
 .github/workflows/ci-emscripten.yml | 77 +++++------------------------
 bin/build_dependencies_unix.sh      |  1 +
 bin/build_variables.sh              |  8 ++-
 bin/build_wheel.sh                  |  1 +
 bin/cibw_before_all_pyodide.sh      | 18 +++++++
 bin/pyodide_build_dependencies.sh   |  9 +++-
 pyproject.toml                      | 18 +++++++
 7 files changed, 61 insertions(+), 71 deletions(-)
 create mode 100755 bin/cibw_before_all_pyodide.sh

diff --git a/.github/workflows/ci-emscripten.yml b/.github/workflows/ci-emscripten.yml
index 27f1741b..55c66a89 100644
--- a/.github/workflows/ci-emscripten.yml
+++ b/.github/workflows/ci-emscripten.yml
@@ -15,93 +15,42 @@ jobs:
   build:
     runs-on: ubuntu-latest
     env:
-      PYODIDE_VERSION: "https://github.com/pyodide/pyodide-build-environment-nightly/releases/download/20250523-emscripten_4.0.9/xbuildenv.tar.bz2"
       PYTHON_VERSION: 3.13 # any 3.13.x version works
-      EMSCRIPTEN_VERSION: 4.0.9
       NODE_VERSION: 22
     steps:
-      - uses: actions/checkout@0c366fd6a839edf440554fa01a7085ccba70ac98 # v4.2.2
+      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd  # v6.0.2
 
       - name: Set up Python ${{ env.PYTHON_VERSION }}
-        uses: actions/setup-python@2e3e4b15a884dc73a63f962bff250a855150a234 # v5.4.0
+        uses: actions/setup-python@v6
         with:
           python-version: ${{ env.PYTHON_VERSION }}
 
-      - name: Set up Emscripten toolchain
-        uses: mymindstorm/setup-emsdk@6ab9eb1bda2574c4ddb79809fc9247783eaf9021 # v14
-        with:
-          version: ${{ env.EMSCRIPTEN_VERSION }}
-          actions-cache-folder: emsdk-cache
-
       - name: Set up Node.js
-        uses: actions/setup-node@6044e13b5dc448c55e2357c09f80417699197238 # v6.2.0
+        uses: actions/setup-node@v6
         with:
           node-version: ${{ env.NODE_VERSION }}
 
-      - name: Install pyodide-build
-        run: |
-          pip install pyodide-build
-          pyodide xbuildenv install --url ${{ env.PYODIDE_VERSION }}
-
       - name: Restore WASM library directory from cache
         id: cache-wasm-library-dir
         uses: actions/cache/restore@cdf6c1fa76f9f475f3d7449005a359c84ca0f306 # v5.0.3
         with:
           path: ${{ github.workspace }}/wasm-library-dir
-          key: wasm-library-dir-${{ hashFiles('bin/pyodide_build_dependencies.sh', 'bin/build_variables.sh') }}-0
+          key: wasm-library-dir-${{ hashFiles('pyproject.toml', 'bin/cibw_before_all_pyodide.sh', 'bin/pyodide_build_dependencies.sh', 'bin/build_variables.sh') }}-0
 
-      - name: Build GMP, MPFR and FLINT
-        if: steps.cache-wasm-library-dir.outputs.cache-hit != 'true'
+      - name: Build and test Pyodide wheel
+        uses: pypa/cibuildwheel@298ed2fb2c105540f5ed055e8a6ad78d82dd3a7e # v3.3.1
         env:
-          CFLAGS: "-fPIC"
-        run: bin/pyodide_build_dependencies.sh --wasm-library-dir ${{ github.workspace }}/wasm-library-dir
+          CIBW_PLATFORM: pyodide
+          CIBW_BUILD: cp313-*
 
       - name: Persist WASM library directory to cache
+        if: steps.cache-wasm-library-dir.outputs.cache-hit != 'true'
         uses: actions/cache/save@cdf6c1fa76f9f475f3d7449005a359c84ca0f306 # v5.0.3
         with:
           path: ${{ github.workspace }}/wasm-library-dir
-          key: wasm-library-dir-${{ hashFiles('bin/pyodide_build_dependencies.sh', 'bin/build_variables.sh') }}-0
-
-      - name: Restore python-flint build directory from cache
-        uses: actions/cache/restore@cdf6c1fa76f9f475f3d7449005a359c84ca0f306 # v5.0.3
-        with:
-          path: ${{ github.workspace }}/flint_wasm_build
-          key: flint-wasm-build-${{ hashFiles('**/meson.build', '**/pyproject.toml', '**/setup.py') }}
-
-      - name: Build python-flint
-        env:
-          WASM_LIBRARY_DIR: ${{ github.workspace }}/wasm-library-dir
-        run: |
-          export PKG_CONFIG_PATH="${{ env.WASM_LIBRARY_DIR }}/lib/pkgconfig:${PKG_CONFIG_PATH}"
-          export CFLAGS="-I${{ env.WASM_LIBRARY_DIR }}/include ${CFLAGS:-}"
-          export LDFLAGS="-L${{ env.WASM_LIBRARY_DIR }}/lib -lflint -lmpfr -lgmp ${LDFLAGS:-}"
-
-          echo "PKG_CONFIG_PATH=${PKG_CONFIG_PATH}"
-          echo "CFLAGS=${CFLAGS}"
-          echo "LDFLAGS=${LDFLAGS}"
-
-          pkg-config --modversion python3
-          pkg-config --modversion mpfr
-          pkg-config --modversion flint
+          key: wasm-library-dir-${{ hashFiles('pyproject.toml', 'bin/cibw_before_all_pyodide.sh', 'bin/pyodide_build_dependencies.sh', 'bin/build_variables.sh') }}-0
 
-          pyodide build -Cbuild-dir=flint_wasm_build -Csetup-args="-Dflint_version_check=false"
-
-      - name: Persist python-flint build directory to cache
-        uses: actions/cache/save@cdf6c1fa76f9f475f3d7449005a359c84ca0f306 # v5.0.3
+      - uses: actions/upload-artifact@v7
         with:
-          path: ${{ github.workspace }}/flint_wasm_build
-          key: flint-wasm-build-${{ hashFiles('**/meson.build', '**/pyproject.toml', '**/setup.py') }}
-
-      - name: Set up Pyodide virtual environment and test python-flint
-        run: |
-          pyodide venv .venv-pyodide
-
-          source .venv-pyodide/bin/activate
-          pip install dist/*.whl
-
-          cd doc
-
-          pip install pytest hypothesis
-          # Don't use the cache provider plugin, as it doesn't work with Pyodide
-          # right now: https://github.com/pypa/cibuildwheel/issues/1966
-          pytest -svra -p no:cacheprovider --pyargs flint
+          name: wheels-pyodide
+          path: wheelhouse/*.whl
diff --git a/bin/build_dependencies_unix.sh b/bin/build_dependencies_unix.sh
index d7a9d33d..7a38f8c0 100755
--- a/bin/build_dependencies_unix.sh
+++ b/bin/build_dependencies_unix.sh
@@ -140,6 +140,7 @@ done
 
 source bin/build_variables.sh
 
+mkdir -p "$PREFIX"
 cd $PREFIX
 mkdir -p src
 cd src
diff --git a/bin/build_variables.sh b/bin/build_variables.sh
index cf7bb143..256f4d84 100644
--- a/bin/build_variables.sh
+++ b/bin/build_variables.sh
@@ -1,9 +1,8 @@
 #!/usr/bin/env bash
 #
-# Create a local directory .local to be used as --prefix when building
-# local installs of python-flint's dependencies. This also sets the PREFIX
-# shell variable and environment variables giving the versions to use for each
-# dependency. This script should be sourced rather than executed e.g.:
+# Set the PREFIX shell variable and environment variables giving the versions
+# to use for each dependency. This script should be sourced rather than
+# executed e.g.:
 #
 #    $ source bin/build_variables.sh
 #
@@ -11,7 +10,6 @@
 # executed directly.
 
 PREFIX=$(pwd)/.local
-mkdir -p $PREFIX
 
 ARBVER=2.23.0 # Not needed with flint >= 3.0.0 (Arb is included in flint)
 
diff --git a/bin/build_wheel.sh b/bin/build_wheel.sh
index e881dda6..8d5d39da 100755
--- a/bin/build_wheel.sh
+++ b/bin/build_wheel.sh
@@ -7,6 +7,7 @@ set -o errexit
 
 source bin/build_variables.sh
 
+mkdir -p "$PREFIX"
 python3 -m venv $PREFIX/venv
 source $PREFIX/venv/bin/activate
 pip install -U pip
diff --git a/bin/cibw_before_all_pyodide.sh b/bin/cibw_before_all_pyodide.sh
new file mode 100755
index 00000000..15e4e2bf
--- /dev/null
+++ b/bin/cibw_before_all_pyodide.sh
@@ -0,0 +1,18 @@
+#!/bin/bash
+
+set -euo pipefail
+
+SCRIPT_DIR=$(cd -- "$(dirname -- "${BASH_SOURCE[0]}")" && pwd)
+PROJECT_DIR=$(cd -- "$SCRIPT_DIR/.." && pwd)
+WASM_LIBRARY_DIR=${WASM_LIBRARY_DIR:-"$PROJECT_DIR/wasm-library-dir"}
+
+if [ -f "$WASM_LIBRARY_DIR/lib/pkgconfig/flint.pc" ]; then
+  echo "Using cached Pyodide dependencies from $WASM_LIBRARY_DIR"
+  exit 0
+fi
+
+mkdir -p "$WASM_LIBRARY_DIR"
+
+export CFLAGS="-fPIC ${CFLAGS:-}"
+
+"$SCRIPT_DIR/pyodide_build_dependencies.sh" --wasm-library-dir "$WASM_LIBRARY_DIR"
diff --git a/bin/pyodide_build_dependencies.sh b/bin/pyodide_build_dependencies.sh
index dd594d45..d58af513 100755
--- a/bin/pyodide_build_dependencies.sh
+++ b/bin/pyodide_build_dependencies.sh
@@ -2,6 +2,8 @@
 
 set -e
 
+SCRIPT_DIR=$(cd -- "$(dirname -- "${BASH_SOURCE[0]}")" && pwd)
+
 while [[ $# -gt 0 ]]
 do
   key="$1"
@@ -43,9 +45,12 @@ if [ -z "$WASM_LIBRARY_DIR" ]; then
   exit 1
 fi
 
+mkdir -p "$WASM_LIBRARY_DIR/src"
+cd "$WASM_LIBRARY_DIR/src"
+
 # Sets versions of GMP, MPFR and FLINT:
 
-source bin/build_variables.sh
+source "$SCRIPT_DIR/build_variables.sh"
 
 # Download mirrored copy of source distributions for GMP and MPFR
 
@@ -106,7 +111,7 @@ fi
 
     # Patch needed for FLINT == 3.4.0
     # This is https://github.com/flintlib/flint/pull/2594
-    patch -N -Z -p1 < ../bin/patch-flint-emscripten-profiler.diff
+    patch -N -Z -p1 < "$SCRIPT_DIR/patch-flint-emscripten-profiler.diff"
 
     ./bootstrap.sh
 
diff --git a/pyproject.toml b/pyproject.toml
index 399b0e23..9899fb11 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -176,3 +176,21 @@ repair-wheel-command = [
 """,
 "delvewheel repair -w {dest_dir} {wheel} --add-path .local/bin",
 ]
+
+[tool.cibuildwheel.pyodide]
+before-all = "bin/cibw_before_all_pyodide.sh"
+pyodide-version = "0.28.2"
+# GMP, MPFR, and FLINT are built as static libraries for Pyodide.
+repair-wheel-command = ""
+test-command = "python -m pytest -svra -p no:cacheprovider --pyargs flint"
+test-requires = ["pytest", "hypothesis"]
+
+[tool.cibuildwheel.pyodide.environment]
+WASM_LIBRARY_DIR = "$(pwd)/wasm-library-dir"
+PKG_CONFIG_PATH = "$(pwd)/wasm-library-dir/lib/pkgconfig:$PKG_CONFIG_PATH"
+CFLAGS = "-I$(pwd)/wasm-library-dir/include $CFLAGS"
+LDFLAGS = "-L$(pwd)/wasm-library-dir/lib -lflint -lmpfr -lgmp $LDFLAGS"
+
+[tool.cibuildwheel.pyodide.config-settings]
+build-dir = "flint_wasm_build"
+setup-args = ["-Dflint_version_check=false"]

From 6d15e42954cb3632b1b5c4883c15e9f81627352f Mon Sep 17 00:00:00 2001
From: Oscar Benjamin <oscar.j.benjamin@gmail.com>
Date: Mon, 23 Mar 2026 20:26:00 +0000
Subject: [PATCH 02/18] Add back the emscripten toolchain

---
 .github/workflows/ci-emscripten.yml | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/.github/workflows/ci-emscripten.yml b/.github/workflows/ci-emscripten.yml
index 55c66a89..62e8cf2e 100644
--- a/.github/workflows/ci-emscripten.yml
+++ b/.github/workflows/ci-emscripten.yml
@@ -16,6 +16,7 @@ jobs:
     runs-on: ubuntu-latest
     env:
       PYTHON_VERSION: 3.13 # any 3.13.x version works
+      EMSCRIPTEN_VERSION: 4.0.9
       NODE_VERSION: 22
     steps:
       - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd  # v6.0.2
@@ -25,6 +26,12 @@ jobs:
         with:
           python-version: ${{ env.PYTHON_VERSION }}
 
+      - name: Set up Emscripten toolchain
+        uses: mymindstorm/setup-emsdk@6ab9eb1bda2574c4ddb79809fc9247783eaf9021 # v14
+        with:
+          version: ${{ env.EMSCRIPTEN_VERSION }}
+          actions-cache-folder: emsdk-cache
+
       - name: Set up Node.js
         uses: actions/setup-node@v6
         with:

From 568d91dc438fac6bd0351f2fa88320cafb72ffee Mon Sep 17 00:00:00 2001
From: Oscar Benjamin <oscar.j.benjamin@gmail.com>
Date: Mon, 23 Mar 2026 20:40:00 +0000
Subject: [PATCH 03/18] Unset comiler flags for before_all

---
 bin/cibw_before_all_pyodide.sh | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/bin/cibw_before_all_pyodide.sh b/bin/cibw_before_all_pyodide.sh
index 15e4e2bf..a1cc8707 100755
--- a/bin/cibw_before_all_pyodide.sh
+++ b/bin/cibw_before_all_pyodide.sh
@@ -13,6 +13,13 @@ fi
 
 mkdir -p "$WASM_LIBRARY_DIR"
 
-export CFLAGS="-fPIC ${CFLAGS:-}"
+# The Pyodide cibuildwheel environment for building python-flint itself sets
+# include/library flags that reference libgmp/libmpfr/libflint. Those libraries
+# do not exist yet while bootstrapping the static dependencies here, so letting
+# them leak into configure would break link tests such as "does the C compiler
+# work?" for GMP. Use a minimal environment for the bootstrap step.
+unset PKG_CONFIG_PATH
+unset LDFLAGS
+export CFLAGS="-fPIC"
 
 "$SCRIPT_DIR/pyodide_build_dependencies.sh" --wasm-library-dir "$WASM_LIBRARY_DIR"

From 5794e26191369699da7cfa9d1e255627294c96d1 Mon Sep 17 00:00:00 2001
From: Oscar Benjamin <oscar.j.benjamin@gmail.com>
Date: Mon, 23 Mar 2026 21:00:41 +0000
Subject: [PATCH 04/18] Add a meson.cross file for pyodide cross-build.

---
 bin/emscripten.meson.cross | 15 +++++++++++++++
 pyproject.toml             |  2 +-
 2 files changed, 16 insertions(+), 1 deletion(-)
 create mode 100644 bin/emscripten.meson.cross

diff --git a/bin/emscripten.meson.cross b/bin/emscripten.meson.cross
new file mode 100644
index 00000000..4e59690c
--- /dev/null
+++ b/bin/emscripten.meson.cross
@@ -0,0 +1,15 @@
+# compiler paths are omitted intentionally so pyodide-build can override them
+# with its pywasmcross wrappers.
+[binaries]
+exe_wrapper = 'node'
+pkgconfig = 'pkg-config'
+
+[properties]
+needs_exe_wrapper = true
+skip_sanity_check = true
+
+[host_machine]
+system = 'emscripten'
+cpu_family = 'wasm32'
+cpu = 'wasm'
+endian = 'little'
diff --git a/pyproject.toml b/pyproject.toml
index 9899fb11..2249d473 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -193,4 +193,4 @@ LDFLAGS = "-L$(pwd)/wasm-library-dir/lib -lflint -lmpfr -lgmp $LDFLAGS"
 
 [tool.cibuildwheel.pyodide.config-settings]
 build-dir = "flint_wasm_build"
-setup-args = ["-Dflint_version_check=false"]
+setup-args = ["--cross-file=$PWD/bin/emscripten.meson.cross", "-Dflint_version_check=false"]

From afe2b144dbfaa69e68477fa4520310154a625536 Mon Sep 17 00:00:00 2001
From: Oscar Benjamin <oscar.j.benjamin@gmail.com>
Date: Mon, 23 Mar 2026 22:00:14 +0000
Subject: [PATCH 05/18] Try to get meson to find the pyodide Python headers...

---
 meson.build | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/meson.build b/meson.build
index 63323bb9..e126d3c6 100644
--- a/meson.build
+++ b/meson.build
@@ -21,7 +21,13 @@ cython_lower = '>=3.0.11'
 cython_upper = '<3.3'
 
 py = import('python').find_installation(pure: false)
-dep_py = py.dependency()
+if meson.is_cross_build() and host_machine.system() == 'emscripten'
+  # Avoid picking up the runner's host python.pc via pkg-config.
+  # For Pyodide, use the interpreter sysconfig data from pyodide-build instead.
+  dep_py = py.dependency(method: 'system')
+else
+  dep_py = py.dependency()
+endif
 
 cc = meson.get_compiler('c')
 cy = meson.get_compiler('cython')

From feaa3544283313bd3c3d2be752cf4749b63e1a1c Mon Sep 17 00:00:00 2001
From: Oscar Benjamin <oscar.j.benjamin@gmail.com>
Date: Mon, 23 Mar 2026 22:35:51 +0000
Subject: [PATCH 06/18] Add license files to pyodide wheels

---
 pyproject.toml | 14 +++++++++++++-
 1 file changed, 13 insertions(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 2249d473..a2b0be88 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -179,9 +179,21 @@ repair-wheel-command = [
 
 [tool.cibuildwheel.pyodide]
 before-all = "bin/cibw_before_all_pyodide.sh"
+before-build = "pip install wheel"
 pyodide-version = "0.28.2"
 # GMP, MPFR, and FLINT are built as static libraries for Pyodide.
-repair-wheel-command = ""
+repair-wheel-command = [
+"""python bin/cibw_repair_wheel_licenses.py "{wheel}" \
+    --license LGPL-3.0-or-later \
+    --license-file 'wasm-library-dir/src/gmp-*/COPYING:python-flint.libs/gmp-*/COPYING' \
+    --license-file 'wasm-library-dir/src/gmp-*/COPYING.LESSERv3:python-flint.libs/gmp-*/COPYING.LESSERv3' \
+    --license-file 'wasm-library-dir/src/mpfr-*/COPYING:python-flint.libs/mpfr-*/COPYING' \
+    --license-file 'wasm-library-dir/src/mpfr-*/COPYING.LESSER:python-flint.libs/mpfr-*/COPYING.LESSER' \
+    --license-file 'wasm-library-dir/src/flint-*/COPYING:python-flint.libs/flint-*/COPYING' \
+    --license-file 'wasm-library-dir/src/flint-*/COPYING.LESSER:python-flint.libs/flint-*/COPYING.LESSER' \
+""",
+"cp \"{wheel}\" \"{dest_dir}\"",
+]
 test-command = "python -m pytest -svra -p no:cacheprovider --pyargs flint"
 test-requires = ["pytest", "hypothesis"]
 

From 415dafe292d97445131f73142573b9e130851080 Mon Sep 17 00:00:00 2001
From: Oscar Benjamin <oscar.j.benjamin@gmail.com>
Date: Mon, 23 Mar 2026 23:00:37 +0000
Subject: [PATCH 07/18] Remove unneeded github actions in ci-emscripten.yml

---
 .github/workflows/ci-emscripten.yml | 14 ++------------
 pyproject.toml                      |  7 +++++++
 2 files changed, 9 insertions(+), 12 deletions(-)

diff --git a/.github/workflows/ci-emscripten.yml b/.github/workflows/ci-emscripten.yml
index 62e8cf2e..760eada5 100644
--- a/.github/workflows/ci-emscripten.yml
+++ b/.github/workflows/ci-emscripten.yml
@@ -15,28 +15,17 @@ jobs:
   build:
     runs-on: ubuntu-latest
     env:
-      PYTHON_VERSION: 3.13 # any 3.13.x version works
+      # This needs to be kept in sync with pyodide-version in pyproject.toml
       EMSCRIPTEN_VERSION: 4.0.9
-      NODE_VERSION: 22
     steps:
       - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd  # v6.0.2
 
-      - name: Set up Python ${{ env.PYTHON_VERSION }}
-        uses: actions/setup-python@v6
-        with:
-          python-version: ${{ env.PYTHON_VERSION }}
-
       - name: Set up Emscripten toolchain
         uses: mymindstorm/setup-emsdk@6ab9eb1bda2574c4ddb79809fc9247783eaf9021 # v14
         with:
           version: ${{ env.EMSCRIPTEN_VERSION }}
           actions-cache-folder: emsdk-cache
 
-      - name: Set up Node.js
-        uses: actions/setup-node@v6
-        with:
-          node-version: ${{ env.NODE_VERSION }}
-
       - name: Restore WASM library directory from cache
         id: cache-wasm-library-dir
         uses: actions/cache/restore@cdf6c1fa76f9f475f3d7449005a359c84ca0f306 # v5.0.3
@@ -48,6 +37,7 @@ jobs:
         uses: pypa/cibuildwheel@298ed2fb2c105540f5ed055e8a6ad78d82dd3a7e # v3.3.1
         env:
           CIBW_PLATFORM: pyodide
+          # This needs to be kept in sync with pyodide-version in pyproject.toml
           CIBW_BUILD: cp313-*
 
       - name: Persist WASM library directory to cache
diff --git a/pyproject.toml b/pyproject.toml
index a2b0be88..e8760cfe 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -180,7 +180,14 @@ repair-wheel-command = [
 [tool.cibuildwheel.pyodide]
 before-all = "bin/cibw_before_all_pyodide.sh"
 before-build = "pip install wheel"
+
+# This needs to be kept in sync with EMSCRIPTEN_VERSION and CIBW_BUILD in
+# .github.workflows/ci-emscripten.yml. The pyodide version pins both an
+# emscripten version and a CPython minor version. Not sure what is a good link
+# to see a table of versions but the command pyodide xbuildenv search --all
+# shows this.
 pyodide-version = "0.28.2"
+
 # GMP, MPFR, and FLINT are built as static libraries for Pyodide.
 repair-wheel-command = [
 """python bin/cibw_repair_wheel_licenses.py "{wheel}" \

From 920ced0e7221bf7b702b6cacb1b15e3f1168a6c0 Mon Sep 17 00:00:00 2001
From: Oscar Benjamin <oscar.j.benjamin@gmail.com>
Date: Mon, 23 Mar 2026 23:42:22 +0000
Subject: [PATCH 08/18] Remove unneeded cross file

---
 bin/emscripten.meson.cross | 15 ---------------
 pyproject.toml             |  2 +-
 2 files changed, 1 insertion(+), 16 deletions(-)
 delete mode 100644 bin/emscripten.meson.cross

diff --git a/bin/emscripten.meson.cross b/bin/emscripten.meson.cross
deleted file mode 100644
index 4e59690c..00000000
--- a/bin/emscripten.meson.cross
+++ /dev/null
@@ -1,15 +0,0 @@
-# compiler paths are omitted intentionally so pyodide-build can override them
-# with its pywasmcross wrappers.
-[binaries]
-exe_wrapper = 'node'
-pkgconfig = 'pkg-config'
-
-[properties]
-needs_exe_wrapper = true
-skip_sanity_check = true
-
-[host_machine]
-system = 'emscripten'
-cpu_family = 'wasm32'
-cpu = 'wasm'
-endian = 'little'
diff --git a/pyproject.toml b/pyproject.toml
index e8760cfe..2a7da7fa 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -212,4 +212,4 @@ LDFLAGS = "-L$(pwd)/wasm-library-dir/lib -lflint -lmpfr -lgmp $LDFLAGS"
 
 [tool.cibuildwheel.pyodide.config-settings]
 build-dir = "flint_wasm_build"
-setup-args = ["--cross-file=$PWD/bin/emscripten.meson.cross", "-Dflint_version_check=false"]
+setup-args = ["-Dflint_version_check=false"]

From 4dfaf9a72224bdd2871aa1787e76d2ef653078bd Mon Sep 17 00:00:00 2001
From: Oscar Benjamin <oscar.j.benjamin@gmail.com>
Date: Mon, 23 Mar 2026 23:50:38 +0000
Subject: [PATCH 09/18] Make ci-emscripten.yml match the other wheel jobs

---
 .github/workflows/ci-emscripten.yml | 26 +++++++++-----------------
 1 file changed, 9 insertions(+), 17 deletions(-)

diff --git a/.github/workflows/ci-emscripten.yml b/.github/workflows/ci-emscripten.yml
index 760eada5..8bb47acc 100644
--- a/.github/workflows/ci-emscripten.yml
+++ b/.github/workflows/ci-emscripten.yml
@@ -1,24 +1,16 @@
-name: Run Pyodide CI
+name: Build Pyodide
 
-on:
-  pull_request:
-  workflow_dispatch:
-
-env:
-  FORCE_COLOR: 3
-
-concurrency:
-  group: ${{ github.workflow }}-${{ github.head_ref || github.run_id }}
-  # cancel-in-progress: true
+on: [push, pull_request]
 
 jobs:
-  build:
-    runs-on: ubuntu-latest
+  build_wheels:
+    name: Build Pyodide wheel
+    runs-on: ubuntu-22.04
     env:
       # This needs to be kept in sync with pyodide-version in pyproject.toml
       EMSCRIPTEN_VERSION: 4.0.9
     steps:
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd  # v6.0.2
+      - uses: actions/checkout@v6.0.2
 
       - name: Set up Emscripten toolchain
         uses: mymindstorm/setup-emsdk@6ab9eb1bda2574c4ddb79809fc9247783eaf9021 # v14
@@ -31,9 +23,9 @@ jobs:
         uses: actions/cache/restore@cdf6c1fa76f9f475f3d7449005a359c84ca0f306 # v5.0.3
         with:
           path: ${{ github.workspace }}/wasm-library-dir
-          key: wasm-library-dir-${{ hashFiles('pyproject.toml', 'bin/cibw_before_all_pyodide.sh', 'bin/pyodide_build_dependencies.sh', 'bin/build_variables.sh') }}-0
+          key: wasm-library-dir-${{ env.EMSCRIPTEN_VERSION }}-${{ hashFiles('pyproject.toml', 'bin/cibw_before_all_pyodide.sh', 'bin/pyodide_build_dependencies.sh', 'bin/build_variables.sh') }}-0
 
-      - name: Build and test Pyodide wheel
+      - name: Build wheels
         uses: pypa/cibuildwheel@298ed2fb2c105540f5ed055e8a6ad78d82dd3a7e # v3.3.1
         env:
           CIBW_PLATFORM: pyodide
@@ -45,7 +37,7 @@ jobs:
         uses: actions/cache/save@cdf6c1fa76f9f475f3d7449005a359c84ca0f306 # v5.0.3
         with:
           path: ${{ github.workspace }}/wasm-library-dir
-          key: wasm-library-dir-${{ hashFiles('pyproject.toml', 'bin/cibw_before_all_pyodide.sh', 'bin/pyodide_build_dependencies.sh', 'bin/build_variables.sh') }}-0
+          key: wasm-library-dir-${{ env.EMSCRIPTEN_VERSION }}-${{ hashFiles('pyproject.toml', 'bin/cibw_before_all_pyodide.sh', 'bin/pyodide_build_dependencies.sh', 'bin/build_variables.sh') }}-0
 
       - uses: actions/upload-artifact@v7
         with:

From a6ef189b5357b1ea0bcc2053a671040f29bb35f5 Mon Sep 17 00:00:00 2001
From: Oscar Benjamin <oscar.j.benjamin@gmail.com>
Date: Tue, 24 Mar 2026 01:01:58 +0000
Subject: [PATCH 10/18] Merge the pyodide CI workflow into the main workflow

---
 .github/workflows/buildwheel.yml    | 114 +++++++++++++++++++++++++---
 .github/workflows/ci-emscripten.yml |  45 -----------
 pyproject.toml                      |  11 +--
 3 files changed, 106 insertions(+), 64 deletions(-)
 delete mode 100644 .github/workflows/ci-emscripten.yml

diff --git a/.github/workflows/buildwheel.yml b/.github/workflows/buildwheel.yml
index 2b45a59f..98dad1de 100644
--- a/.github/workflows/buildwheel.yml
+++ b/.github/workflows/buildwheel.yml
@@ -4,55 +4,114 @@ on: [push, pull_request]
 
 jobs:
   build_wheels:
-    name: Build wheels for ${{ matrix.os }}
+    name: ${{ matrix.name }}
     runs-on: ${{ matrix.os }}
     continue-on-error: true
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-22.04, ubuntu-22.04-arm, windows-2022, windows-11-arm, macos-15-intel, macos-14]
+        include:
+          - name: Build manylinux x86-64 wheels
+            os: ubuntu-22.04
+            kind: native
+            artifact_name: wheels-ubuntu-22.04
+            cibw_platform: auto
+            cibw_build: "*"
+          - name: Build manylinux arm64 wheels
+            os: ubuntu-22.04-arm
+            kind: native
+            artifact_name: wheels-ubuntu-22.04-arm
+            cibw_platform: auto
+            cibw_build: "*"
+          - name: Build Windows x86-64 wheels
+            os: windows-2022
+            kind: native
+            artifact_name: wheels-windows-2022
+            cibw_platform: auto
+            cibw_build: "*"
+          - name: Build Windows arm64 wheels
+            os: windows-11-arm
+            kind: native
+            artifact_name: wheels-windows-11-arm
+            cibw_platform: auto
+            cibw_build: "*"
+          - name: Build macOS x86-64 wheels
+            os: macos-15-intel
+            kind: native
+            artifact_name: wheels-macos-15-intel
+            cibw_platform: auto
+            cibw_build: "*"
+          - name: Build macOS arm64 wheels
+            os: macos-14
+            kind: native
+            artifact_name: wheels-macos-14
+            cibw_platform: auto
+            cibw_build: "*"
+          - name: Build Pyodide wheels
+            os: ubuntu-22.04
+            kind: pyodide
+            artifact_name: wheels-pyodide
+            emscripten_version: 4.0.9
+            cibw_platform: pyodide
+            cibw_build: cp313-*
 
     steps:
       - uses: actions/checkout@v6.0.2
 
-      - uses: actions/setup-python@v6
+      - if: ${{ matrix.kind == 'native' }}
+        uses: actions/setup-python@v6
         with:
           python-version: '3.13'
 
-      - uses: msys2/setup-msys2@v2.30.0
+        # -------------- Windows stuff ---------------- #
+
+      - if: ${{ matrix.os == 'windows-2022' }}
+        uses: msys2/setup-msys2@v2.30.0
         with:
           msystem: ucrt64
           update: true
-        if: ${{ matrix.os == 'windows-2022' }}
 
-      - uses: msys2/setup-msys2@v2.30.0
+      - if: ${{ matrix.os == 'windows-11-arm' }}
+        uses: msys2/setup-msys2@v2.30.0
         with:
           msystem: clangarm64
           update: true
-        if: ${{ matrix.os == 'windows-11-arm' }}
 
         # Install pkgconfig on Windows from choco rather than from msys and
         # avoid using the Strawberry one.
-      - run: choco install -y --stoponfirstfailure --checksum 6004DF17818F5A6DBF19CB335CC92702 pkgconfiglite
-        if: ${{ startsWith( matrix.os , 'windows' ) }}
+      - if: ${{ startsWith( matrix.os , 'windows' ) }}
+        run: choco install -y --stoponfirstfailure --checksum 6004DF17818F5A6DBF19CB335CC92702 pkgconfiglite
 
         # We have to set this here rather than in the cibuildwheel config
         # This is probably something to do with \ vs / in paths...
-      - run: |
+      - if: ${{ startsWith( matrix.os , 'windows' ) }}
+        run: |
           $pkgConfigPath = "${{ github.workspace }}/.local/lib/pkgconfig"
           $pkgConfigPath = $pkgConfigPath.Replace('\', '/')
           echo "PKG_CONFIG_PATH=$pkgConfigPath" >> $env:GITHUB_ENV
-        if: ${{ startsWith( matrix.os , 'windows' ) }}
+
+        # ------------- pyodide ------------- #
+
+      - if: ${{ matrix.kind == 'pyodide' }}
+        name: Set up Emscripten toolchain
+        uses: mymindstorm/setup-emsdk@6ab9eb1bda2574c4ddb79809fc9247783eaf9021 # v14
+        with:
+          version: ${{ matrix.emscripten_version }}
+          actions-cache-folder: emsdk-cache
+
+        # ------------- actual build ------------- #
 
       - name: Build wheels
         uses: pypa/cibuildwheel@298ed2fb2c105540f5ed055e8a6ad78d82dd3a7e # v3.3.1
         env:
+          CIBW_PLATFORM: ${{ matrix.cibw_platform }}
+          CIBW_BUILD: ${{ matrix.cibw_build }}
           # override setting in pyproject.toml to use msys2 instead of msys64 bash
           CIBW_BEFORE_ALL_WINDOWS: ${{ matrix.os == 'windows-11-arm' && 'msys2 -c bin/cibw_before_all_windows_arm64.sh' || 'msys2 -c bin/cibw_before_all_windows_amd64.sh' }}
 
       - uses: actions/upload-artifact@v7
         with:
-          name: wheels-${{ matrix.os }}
+          name: ${{ matrix.artifact_name }}
           path: wheelhouse/*.whl
 
   build_sdist:
@@ -120,6 +179,37 @@ jobs:
 
       - run: python -m flint.test --verbose
 
+  test_pyodide:
+    needs: build_wheels
+    name: Test Pyodide wheel
+    runs-on: ubuntu-22.04
+    env:
+      PYODIDE_VERSION: 0.28.2
+
+    steps:
+      - uses: actions/setup-python@v6
+        with:
+          python-version: '3.13'
+
+      - uses: actions/setup-node@v6
+        with:
+          node-version: '22'
+
+      - run: pip install "pyodide-build==${{ env.PYODIDE_VERSION }}"
+      - run: pyodide xbuildenv install "${{ env.PYODIDE_VERSION }}"
+
+      - uses: actions/download-artifact@v8
+        with:
+          name: wheels-pyodide
+          path: wheelhouse
+
+      - run: |
+          pyodide venv .venv-pyodide
+          source .venv-pyodide/bin/activate
+          pip install wheelhouse/*.whl
+          pip install pytest hypothesis
+          python -m pytest -svra -p no:cacheprovider --pyargs flint
+
   # On new enough Ubuntu we can build against the system deb.
   test_pip_flint_deb:
     name: Build on ${{ matrix.os }}
diff --git a/.github/workflows/ci-emscripten.yml b/.github/workflows/ci-emscripten.yml
deleted file mode 100644
index 8bb47acc..00000000
--- a/.github/workflows/ci-emscripten.yml
+++ /dev/null
@@ -1,45 +0,0 @@
-name: Build Pyodide
-
-on: [push, pull_request]
-
-jobs:
-  build_wheels:
-    name: Build Pyodide wheel
-    runs-on: ubuntu-22.04
-    env:
-      # This needs to be kept in sync with pyodide-version in pyproject.toml
-      EMSCRIPTEN_VERSION: 4.0.9
-    steps:
-      - uses: actions/checkout@v6.0.2
-
-      - name: Set up Emscripten toolchain
-        uses: mymindstorm/setup-emsdk@6ab9eb1bda2574c4ddb79809fc9247783eaf9021 # v14
-        with:
-          version: ${{ env.EMSCRIPTEN_VERSION }}
-          actions-cache-folder: emsdk-cache
-
-      - name: Restore WASM library directory from cache
-        id: cache-wasm-library-dir
-        uses: actions/cache/restore@cdf6c1fa76f9f475f3d7449005a359c84ca0f306 # v5.0.3
-        with:
-          path: ${{ github.workspace }}/wasm-library-dir
-          key: wasm-library-dir-${{ env.EMSCRIPTEN_VERSION }}-${{ hashFiles('pyproject.toml', 'bin/cibw_before_all_pyodide.sh', 'bin/pyodide_build_dependencies.sh', 'bin/build_variables.sh') }}-0
-
-      - name: Build wheels
-        uses: pypa/cibuildwheel@298ed2fb2c105540f5ed055e8a6ad78d82dd3a7e # v3.3.1
-        env:
-          CIBW_PLATFORM: pyodide
-          # This needs to be kept in sync with pyodide-version in pyproject.toml
-          CIBW_BUILD: cp313-*
-
-      - name: Persist WASM library directory to cache
-        if: steps.cache-wasm-library-dir.outputs.cache-hit != 'true'
-        uses: actions/cache/save@cdf6c1fa76f9f475f3d7449005a359c84ca0f306 # v5.0.3
-        with:
-          path: ${{ github.workspace }}/wasm-library-dir
-          key: wasm-library-dir-${{ env.EMSCRIPTEN_VERSION }}-${{ hashFiles('pyproject.toml', 'bin/cibw_before_all_pyodide.sh', 'bin/pyodide_build_dependencies.sh', 'bin/build_variables.sh') }}-0
-
-      - uses: actions/upload-artifact@v7
-        with:
-          name: wheels-pyodide
-          path: wheelhouse/*.whl
diff --git a/pyproject.toml b/pyproject.toml
index 2a7da7fa..40e638db 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -181,11 +181,10 @@ repair-wheel-command = [
 before-all = "bin/cibw_before_all_pyodide.sh"
 before-build = "pip install wheel"
 
-# This needs to be kept in sync with EMSCRIPTEN_VERSION and CIBW_BUILD in
-# .github.workflows/ci-emscripten.yml. The pyodide version pins both an
-# emscripten version and a CPython minor version. Not sure what is a good link
-# to see a table of versions but the command pyodide xbuildenv search --all
-# shows this.
+# This needs to be kept in sync with the Pyodide row in
+# .github/workflows/buildwheel.yml. The Pyodide version pins both an
+# Emscripten version and a CPython minor version. The command
+# `pyodide xbuildenv search --all` shows the compatible combinations.
 pyodide-version = "0.28.2"
 
 # GMP, MPFR, and FLINT are built as static libraries for Pyodide.
@@ -201,8 +200,6 @@ repair-wheel-command = [
 """,
 "cp \"{wheel}\" \"{dest_dir}\"",
 ]
-test-command = "python -m pytest -svra -p no:cacheprovider --pyargs flint"
-test-requires = ["pytest", "hypothesis"]
 
 [tool.cibuildwheel.pyodide.environment]
 WASM_LIBRARY_DIR = "$(pwd)/wasm-library-dir"

From 33f9617f286f56b1c5bf68e5fe228c2fb98b394d Mon Sep 17 00:00:00 2001
From: Oscar Benjamin <oscar.j.benjamin@gmail.com>
Date: Tue, 24 Mar 2026 01:53:26 +0000
Subject: [PATCH 11/18] Don't pin pyodide-build version

---
 .github/workflows/buildwheel.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/buildwheel.yml b/.github/workflows/buildwheel.yml
index 98dad1de..826d52d4 100644
--- a/.github/workflows/buildwheel.yml
+++ b/.github/workflows/buildwheel.yml
@@ -195,7 +195,7 @@ jobs:
         with:
           node-version: '22'
 
-      - run: pip install "pyodide-build==${{ env.PYODIDE_VERSION }}"
+      - run: pip install pyodide-build
       - run: pyodide xbuildenv install "${{ env.PYODIDE_VERSION }}"
 
       - uses: actions/download-artifact@v8

From e5dc59362ba12aacb0aed1b5ea20a2d0cf26fd5e Mon Sep 17 00:00:00 2001
From: Oscar Benjamin <oscar.j.benjamin@gmail.com>
Date: Tue, 24 Mar 2026 16:59:41 +0000
Subject: [PATCH 12/18] Use shared libraries for dependencies in pyodide

---
 bin/pyodide_build_dependencies.sh | 15 +++++++++++++++
 pyproject.toml                    |  7 ++++---
 2 files changed, 19 insertions(+), 3 deletions(-)

diff --git a/bin/pyodide_build_dependencies.sh b/bin/pyodide_build_dependencies.sh
index d58af513..ee6e22f9 100755
--- a/bin/pyodide_build_dependencies.sh
+++ b/bin/pyodide_build_dependencies.sh
@@ -129,3 +129,18 @@ fi
     emmake make install
 
 cd ..
+
+
+# ----------------Build shared libraries from static archives --------------#
+
+
+emcc -shared -sSIDE_MODULE=2 -o "$WASM_LIBRARY_DIR/lib/libgmp.so" \
+    -Wl,--whole-archive "$WASM_LIBRARY_DIR/lib/libgmp.a" -Wl,--no-whole-archive
+
+emcc -shared -sSIDE_MODULE=2 -o "$WASM_LIBRARY_DIR/lib/libmpfr.so" \
+    -Wl,--whole-archive "$WASM_LIBRARY_DIR/lib/libmpfr.a" -Wl,--no-whole-archive \
+    -L"$WASM_LIBRARY_DIR/lib" -lgmp
+
+emcc -shared -sSIDE_MODULE=2 -o "$WASM_LIBRARY_DIR/lib/libflint.so" \
+    -Wl,--whole-archive "$WASM_LIBRARY_DIR/lib/libflint.a" -Wl,--no-whole-archive \
+    -L"$WASM_LIBRARY_DIR/lib" -lmpfr -lgmp
diff --git a/pyproject.toml b/pyproject.toml
index 40e638db..4c869699 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -179,7 +179,7 @@ repair-wheel-command = [
 
 [tool.cibuildwheel.pyodide]
 before-all = "bin/cibw_before_all_pyodide.sh"
-before-build = "pip install wheel"
+before-build = "pip install wheel auditwheel_emscripten"
 
 # This needs to be kept in sync with the Pyodide row in
 # .github/workflows/buildwheel.yml. The Pyodide version pins both an
@@ -187,7 +187,8 @@ before-build = "pip install wheel"
 # `pyodide xbuildenv search --all` shows the compatible combinations.
 pyodide-version = "0.28.2"
 
-# GMP, MPFR, and FLINT are built as static libraries for Pyodide.
+# GMP, MPFR, and FLINT are built as shared libraries for Pyodide and bundled
+# into the wheel.
 repair-wheel-command = [
 """python bin/cibw_repair_wheel_licenses.py "{wheel}" \
     --license LGPL-3.0-or-later \
@@ -198,7 +199,7 @@ repair-wheel-command = [
     --license-file 'wasm-library-dir/src/flint-*/COPYING:python-flint.libs/flint-*/COPYING' \
     --license-file 'wasm-library-dir/src/flint-*/COPYING.LESSER:python-flint.libs/flint-*/COPYING.LESSER' \
 """,
-"cp \"{wheel}\" \"{dest_dir}\"",
+"pyodide auditwheel repair --libdir wasm-library-dir --output-dir {dest_dir} {wheel}",
 ]
 
 [tool.cibuildwheel.pyodide.environment]

From 57f4aec9e898acb76aa05efac98a615edb3393c5 Mon Sep 17 00:00:00 2001
From: Oscar Benjamin <oscar.j.benjamin@gmail.com>
Date: Tue, 24 Mar 2026 17:43:01 +0000
Subject: [PATCH 13/18] Don't strip the libraries

---
 bin/pyodide_build_dependencies.sh | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/bin/pyodide_build_dependencies.sh b/bin/pyodide_build_dependencies.sh
index ee6e22f9..d8b776e8 100755
--- a/bin/pyodide_build_dependencies.sh
+++ b/bin/pyodide_build_dependencies.sh
@@ -134,13 +134,13 @@ cd ..
 # ----------------Build shared libraries from static archives --------------#
 
 
-emcc -shared -sSIDE_MODULE=2 -o "$WASM_LIBRARY_DIR/lib/libgmp.so" \
+emcc -shared -sSIDE_MODULE=1 -o "$WASM_LIBRARY_DIR/lib/libgmp.so" \
     -Wl,--whole-archive "$WASM_LIBRARY_DIR/lib/libgmp.a" -Wl,--no-whole-archive
 
-emcc -shared -sSIDE_MODULE=2 -o "$WASM_LIBRARY_DIR/lib/libmpfr.so" \
+emcc -shared -sSIDE_MODULE=1 -o "$WASM_LIBRARY_DIR/lib/libmpfr.so" \
     -Wl,--whole-archive "$WASM_LIBRARY_DIR/lib/libmpfr.a" -Wl,--no-whole-archive \
     -L"$WASM_LIBRARY_DIR/lib" -lgmp
 
-emcc -shared -sSIDE_MODULE=2 -o "$WASM_LIBRARY_DIR/lib/libflint.so" \
+emcc -shared -sSIDE_MODULE=1 -o "$WASM_LIBRARY_DIR/lib/libflint.so" \
     -Wl,--whole-archive "$WASM_LIBRARY_DIR/lib/libflint.a" -Wl,--no-whole-archive \
     -L"$WASM_LIBRARY_DIR/lib" -lmpfr -lgmp

From c8b7323495570a120a5a2361e2d10281c46bb32e Mon Sep 17 00:00:00 2001
From: Oscar Benjamin <oscar.j.benjamin@gmail.com>
Date: Tue, 24 Mar 2026 19:10:24 +0000
Subject: [PATCH 14/18] Don't upload pyodide wheels to PyPI

---
 .github/workflows/buildwheel.yml | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/buildwheel.yml b/.github/workflows/buildwheel.yml
index 826d52d4..634e9d5a 100644
--- a/.github/workflows/buildwheel.yml
+++ b/.github/workflows/buildwheel.yml
@@ -428,7 +428,11 @@ jobs:
           merge-multiple: true
 
       - name: Copy the PyPI files into dist
-        run: mkdir dist && cp wheelhouse/*.whl wheelhouse/*.tar.gz dist
+        # pyodide wheels cannot be uploaded to PyPI
+        run: |
+          mkdir dist
+          rm wheelhouse/*pyodide*.whl
+          cp wheelhouse/*.whl wheelhouse/*.tar.gz dist
 
       - name: Publish package on PyPI
         # It is recommended to pin a commit hash here for security but it

From a79fa74ddb1958958c001dc1ec958c0a15b293d5 Mon Sep 17 00:00:00 2001
From: Oscar Benjamin <oscar.j.benjamin@gmail.com>
Date: Tue, 24 Mar 2026 22:59:58 +0000
Subject: [PATCH 15/18] Apply pyodide emscripten patches

---
 .github/workflows/buildwheel.yml | 17 +++++++++++++++--
 bin/cibw_before_build_pyodide.sh | 12 ++++++++++++
 pyproject.toml                   | 12 +++---------
 3 files changed, 30 insertions(+), 11 deletions(-)
 create mode 100755 bin/cibw_before_build_pyodide.sh

diff --git a/.github/workflows/buildwheel.yml b/.github/workflows/buildwheel.yml
index 634e9d5a..8842634a 100644
--- a/.github/workflows/buildwheel.yml
+++ b/.github/workflows/buildwheel.yml
@@ -2,6 +2,9 @@ name: Build
 
 on: [push, pull_request]
 
+env:
+  PYODIDE_VERSION: 0.28.2
+
 jobs:
   build_wheels:
     name: ${{ matrix.name }}
@@ -99,6 +102,16 @@ jobs:
           version: ${{ matrix.emscripten_version }}
           actions-cache-folder: emsdk-cache
 
+      - if: ${{ matrix.kind == 'pyodide' }}
+        name: Check out Emscripten patches for Pyodide
+        uses: actions/checkout@v6.0.2
+        with:
+          repository: pyodide/pyodide
+          ref: ${{ env.PYODIDE_VERSION }}
+          path: pyodide-patches
+          sparse-checkout: |
+            emsdk/patches/
+
         # ------------- actual build ------------- #
 
       - name: Build wheels
@@ -106,6 +119,8 @@ jobs:
         env:
           CIBW_PLATFORM: ${{ matrix.cibw_platform }}
           CIBW_BUILD: ${{ matrix.cibw_build }}
+          CIBW_PYODIDE_VERSION: ${{ env.PYODIDE_VERSION }}
+          PYODIDE_EMSCRIPTEN_VERSION: ${{ matrix.kind == 'pyodide' && matrix.emscripten_version || '' }}
           # override setting in pyproject.toml to use msys2 instead of msys64 bash
           CIBW_BEFORE_ALL_WINDOWS: ${{ matrix.os == 'windows-11-arm' && 'msys2 -c bin/cibw_before_all_windows_arm64.sh' || 'msys2 -c bin/cibw_before_all_windows_amd64.sh' }}
 
@@ -183,8 +198,6 @@ jobs:
     needs: build_wheels
     name: Test Pyodide wheel
     runs-on: ubuntu-22.04
-    env:
-      PYODIDE_VERSION: 0.28.2
 
     steps:
       - uses: actions/setup-python@v6
diff --git a/bin/cibw_before_build_pyodide.sh b/bin/cibw_before_build_pyodide.sh
new file mode 100755
index 00000000..847a07ac
--- /dev/null
+++ b/bin/cibw_before_build_pyodide.sh
@@ -0,0 +1,12 @@
+#!/bin/bash
+
+set -euo pipefail
+
+python -m pip install wheel auditwheel_emscripten
+
+EMSCRIPTEN_DIR="$HOME/.cache/cibuildwheel/emsdk-$PYODIDE_EMSCRIPTEN_VERSION/emsdk-$PYODIDE_EMSCRIPTEN_VERSION/upstream/emscripten"
+
+for patch_file in pyodide-patches/emsdk/patches/*.patch; do
+  echo "Applying Pyodide Emscripten patch $(basename "$patch_file")"
+  patch -p1 --verbose -d "$EMSCRIPTEN_DIR" < "$patch_file"
+done
diff --git a/pyproject.toml b/pyproject.toml
index 4c869699..17be866a 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -179,16 +179,10 @@ repair-wheel-command = [
 
 [tool.cibuildwheel.pyodide]
 before-all = "bin/cibw_before_all_pyodide.sh"
-before-build = "pip install wheel auditwheel_emscripten"
+before-build = "bin/cibw_before_build_pyodide.sh"
+# The pyodide version is set in .github/workflows/buildwheel.yml as
+# CIBW_PYODIDE_VERSION because it is needed also for other things there.
 
-# This needs to be kept in sync with the Pyodide row in
-# .github/workflows/buildwheel.yml. The Pyodide version pins both an
-# Emscripten version and a CPython minor version. The command
-# `pyodide xbuildenv search --all` shows the compatible combinations.
-pyodide-version = "0.28.2"
-
-# GMP, MPFR, and FLINT are built as shared libraries for Pyodide and bundled
-# into the wheel.
 repair-wheel-command = [
 """python bin/cibw_repair_wheel_licenses.py "{wheel}" \
     --license LGPL-3.0-or-later \

From 1e1a88321111240eaf66fd1bff21c35590f9d032 Mon Sep 17 00:00:00 2001
From: Oscar Benjamin <oscar.j.benjamin@gmail.com>
Date: Tue, 24 Mar 2026 23:03:01 +0000
Subject: [PATCH 16/18] Use pyodide's fork of emsdk

---
 .github/workflows/buildwheel.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/buildwheel.yml b/.github/workflows/buildwheel.yml
index 8842634a..af2275e3 100644
--- a/.github/workflows/buildwheel.yml
+++ b/.github/workflows/buildwheel.yml
@@ -97,7 +97,7 @@ jobs:
 
       - if: ${{ matrix.kind == 'pyodide' }}
         name: Set up Emscripten toolchain
-        uses: mymindstorm/setup-emsdk@6ab9eb1bda2574c4ddb79809fc9247783eaf9021 # v14
+        uses: pyodide/setup-emsdk@ca2dd8aef8c2a0e11743c5c36f0b430ddb694b5c # v15
         with:
           version: ${{ matrix.emscripten_version }}
           actions-cache-folder: emsdk-cache

From 5b9460d3c0811f662fe60ec5ecb22a2c557af55d Mon Sep 17 00:00:00 2001
From: Oscar Benjamin <oscar.j.benjamin@gmail.com>
Date: Tue, 24 Mar 2026 23:35:44 +0000
Subject: [PATCH 17/18] Bump pyodide version 0.28.2 -> 0.29.3

---
 .github/workflows/buildwheel.yml | 18 ++++++++++--------
 pyproject.toml                   |  3 +--
 2 files changed, 11 insertions(+), 10 deletions(-)

diff --git a/.github/workflows/buildwheel.yml b/.github/workflows/buildwheel.yml
index af2275e3..e921dc14 100644
--- a/.github/workflows/buildwheel.yml
+++ b/.github/workflows/buildwheel.yml
@@ -3,7 +3,12 @@ name: Build
 on: [push, pull_request]
 
 env:
-  PYODIDE_VERSION: 0.28.2
+  # These four values need to be kept in sync. Each pyodide version pins an
+  # emscripten version and a CPython version.
+  PYODIDE_VERSION: '0.29.3'
+  PYODIDE_EMSCRIPTEN_VERSION: '4.0.9'
+  PYODIDE_PYTHON_VERSION: '3.13'
+  PYODIDE_CIBW_BUILD: 'cp313-*'
 
 jobs:
   build_wheels:
@@ -54,9 +59,7 @@ jobs:
             os: ubuntu-22.04
             kind: pyodide
             artifact_name: wheels-pyodide
-            emscripten_version: 4.0.9
             cibw_platform: pyodide
-            cibw_build: cp313-*
 
     steps:
       - uses: actions/checkout@v6.0.2
@@ -99,7 +102,7 @@ jobs:
         name: Set up Emscripten toolchain
         uses: pyodide/setup-emsdk@ca2dd8aef8c2a0e11743c5c36f0b430ddb694b5c # v15
         with:
-          version: ${{ matrix.emscripten_version }}
+          version: ${{ env.PYODIDE_EMSCRIPTEN_VERSION }}
           actions-cache-folder: emsdk-cache
 
       - if: ${{ matrix.kind == 'pyodide' }}
@@ -118,9 +121,8 @@ jobs:
         uses: pypa/cibuildwheel@298ed2fb2c105540f5ed055e8a6ad78d82dd3a7e # v3.3.1
         env:
           CIBW_PLATFORM: ${{ matrix.cibw_platform }}
-          CIBW_BUILD: ${{ matrix.cibw_build }}
+          CIBW_BUILD: ${{ matrix.kind == 'pyodide' && env.PYODIDE_CIBW_BUILD || matrix.cibw_build }}
           CIBW_PYODIDE_VERSION: ${{ env.PYODIDE_VERSION }}
-          PYODIDE_EMSCRIPTEN_VERSION: ${{ matrix.kind == 'pyodide' && matrix.emscripten_version || '' }}
           # override setting in pyproject.toml to use msys2 instead of msys64 bash
           CIBW_BEFORE_ALL_WINDOWS: ${{ matrix.os == 'windows-11-arm' && 'msys2 -c bin/cibw_before_all_windows_arm64.sh' || 'msys2 -c bin/cibw_before_all_windows_amd64.sh' }}
 
@@ -138,7 +140,7 @@ jobs:
 
       - uses: actions/setup-python@v6
         with:
-          python-version: '3.13'
+          python-version: ${{ env.PYODIDE_PYTHON_VERSION }}
 
       - run: bin/install_latest_flint_ubuntu.sh
       - run: pip install build
@@ -202,7 +204,7 @@ jobs:
     steps:
       - uses: actions/setup-python@v6
         with:
-          python-version: '3.13'
+          python-version: ${{ env.PYODIDE_PYTHON_VERSION }}
 
       - uses: actions/setup-node@v6
         with:
diff --git a/pyproject.toml b/pyproject.toml
index 17be866a..2745e333 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -178,10 +178,9 @@ repair-wheel-command = [
 ]
 
 [tool.cibuildwheel.pyodide]
+# pyodide version is set in .github/workflows/buildwheel.yml as PYODIDE_VERSION
 before-all = "bin/cibw_before_all_pyodide.sh"
 before-build = "bin/cibw_before_build_pyodide.sh"
-# The pyodide version is set in .github/workflows/buildwheel.yml as
-# CIBW_PYODIDE_VERSION because it is needed also for other things there.
 
 repair-wheel-command = [
 """python bin/cibw_repair_wheel_licenses.py "{wheel}" \

From 877a6a52077f1c95b178ec5d778090cacc26834f Mon Sep 17 00:00:00 2001
From: Oscar Benjamin <oscar.j.benjamin@gmail.com>
Date: Tue, 24 Mar 2026 23:44:16 +0000
Subject: [PATCH 18/18] Remove dep_py from the meson.build files

---
 meson.build | 9 +--------
 1 file changed, 1 insertion(+), 8 deletions(-)

diff --git a/meson.build b/meson.build
index e126d3c6..fbabce65 100644
--- a/meson.build
+++ b/meson.build
@@ -21,13 +21,6 @@ cython_lower = '>=3.0.11'
 cython_upper = '<3.3'
 
 py = import('python').find_installation(pure: false)
-if meson.is_cross_build() and host_machine.system() == 'emscripten'
-  # Avoid picking up the runner's host python.pc via pkg-config.
-  # For Pyodide, use the interpreter sysconfig data from pyodide-build instead.
-  dep_py = py.dependency(method: 'system')
-else
-  dep_py = py.dependency()
-endif
 
 cc = meson.get_compiler('c')
 cy = meson.get_compiler('cython')
@@ -85,7 +78,7 @@ else
   have_acb_theta = true
 endif
 
-pyflint_deps = [dep_py, gmp_dep, mpfr_dep, flint_dep]
+pyflint_deps = [gmp_dep, mpfr_dep, flint_dep]
 
 add_project_arguments(
     '-X', 'embedsignature=True',