Fix Pyodide workflow exception flag mismatch (#9909)

The Pyodide `build` job was passing legacy Emscripten exception flags
that conflict with the wasm-exception ABI now used by the Python
packaging configuration. This caused the wheel build to fail before
compilation completed.

- **Align Pyodide workflow flags**
- Remove per-workflow `CFLAGS` / `CXXFLAGS` / `LDFLAGS` overrides from
the Pyodide build step.
- Let the build inherit the canonical wasm-exception / longjmp / bigint
flags from `src/api/python/pyproject.toml`.

- **Apply the fix consistently**
  - Update the standalone Pyodide workflow.
- Update the matching Pyodide build steps in `nightly.yml` and
`release.yml` to avoid the same regression in scheduled and release
builds.

- **Why this fixes the failure**
  - The broken path mixed JS-exception and wasm-exception settings:
    ```yaml
    CFLAGS: "-fexceptions -s DISABLE_EXCEPTION_CATCHING=0 -g2"
    CXXFLAGS: "-fexceptions -s DISABLE_EXCEPTION_CATCHING=0"
    ```
  - The updated workflows now invoke:
    ```yaml
    ~/env/bin/pyodide build --exports whole_archive
    ```
    and rely on the packaging config’s wasm-exception settings instead.

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>

.github/workflows/nightly.yml

@@ -512,11 +512,10 @@ jobs:
         run: |
           source ~/emsdk/emsdk_env.sh
           cd src/api/python
-          CFLAGS="${CFLAGS}" LDFLAGS="${LDFLAGS}" CXXFLAGS="${CXXFLAGS}" ~/env/bin/pyodide build --exports whole_archive
-        env:
-          CFLAGS: "-fexceptions -s DISABLE_EXCEPTION_CATCHING=0 -g2"
-          LDFLAGS: "-fexceptions -s WASM_BIGINT"
-          CXXFLAGS: "-fexceptions -s DISABLE_EXCEPTION_CATCHING=0"
+          # Exception/longjmp/bigint flags are declared in pyproject.toml and
+          # combined with Pyodide's -fwasm-exceptions defaults. Passing the
+          # legacy JS-EH -fexceptions flags here conflicts with the wasm-EH ABI.
+          ~/env/bin/pyodide build --exports whole_archive
 
       - name: Setup env-pyodide
         run: |

.github/workflows/pyodide.yml

@@ -42,11 +42,10 @@ jobs:
       run: |
          source ~/emsdk/emsdk_env.sh 
          cd src/api/python 
-         CFLAGS="${CFLAGS}" LDFLAGS="${LDFLAGS}" CXXFLAG="${CXXFLAGS}" ~/env/bin/pyodide build --exports whole_archive
-      env:
-         CFLAGS: "-fexceptions -s DISABLE_EXCEPTION_CATCHING=0 -g2"
-         LDFLAGS: "-fexceptions -s WASM_BIGINT"     
-         CXXFLAGS: "-fexceptions -s DISABLE_EXCEPTION_CATCHING=0"
+         # Exception/longjmp/bigint flags are declared in pyproject.toml and
+         # combined with Pyodide's -fwasm-exceptions defaults. Passing the
+         # legacy JS-EH -fexceptions flags here conflicts with the wasm-EH ABI.
+         ~/env/bin/pyodide build --exports whole_archive
          
     - name: Setup env-pyodide
       run: |
@@ -65,4 +64,3 @@ jobs:
           name: pyodide-wheel
           path: src/api/python/dist/*.whl
           retention-days: 1         
-

.github/workflows/release.yml

@@ -522,11 +522,10 @@ jobs:
         run: |
           source ~/emsdk/emsdk_env.sh
           cd src/api/python
-          CFLAGS="${CFLAGS}" LDFLAGS="${LDFLAGS}" CXXFLAGS="${CXXFLAGS}" ~/env/bin/pyodide build --exports whole_archive
-        env:
-          CFLAGS: "-fexceptions -s DISABLE_EXCEPTION_CATCHING=0 -g2"
-          LDFLAGS: "-fexceptions -s WASM_BIGINT"
-          CXXFLAGS: "-fexceptions -s DISABLE_EXCEPTION_CATCHING=0"
+          # Exception/longjmp/bigint flags are declared in pyproject.toml and
+          # combined with Pyodide's -fwasm-exceptions defaults. Passing the
+          # legacy JS-EH -fexceptions flags here conflicts with the wasm-EH ABI.
+          ~/env/bin/pyodide build --exports whole_archive
 
       - name: Setup env-pyodide
         run: |