Rebuild netcdf4; Rebuild libnetcdf; fix runtime failure due to missing listxattr

recipes/recipes_emscripten/h5py/build.sh

@@ -1,11 +1,4 @@
 
-# add ad-hoc code to load the shared libs
-tmp_file="$(mktemp)"
-printf 'import ctypes;ctypes.CDLL("/lib/libhdf5.so");ctypes.CDLL("/lib/libhdf5_hl.so")\n' > "$tmp_file"
-cat "h5py/__init__.py" >> "$tmp_file"
-mv "$tmp_file" "h5py/__init__.py"
-
-
 # remove the emcc symlink in the $BUILD_PREFIX/bin
 rm $BUILD_PREFIX/bin/emcc
 
@@ -30,7 +23,7 @@ export H5PY_DIRECT_VFD='0'
 export HDF5_MPI=OFF
 
 # Explitly set HDF5 version
-export HDF5_VERSION=1.12.3
+export HDF5_VERSION=1.14.6
 
 ${PYTHON} -m pip install . -vvv
 

recipes/recipes_emscripten/h5py/recipe.yaml

@@ -13,7 +13,7 @@ source:
   - patches/configure.patch
 
 build:
-  number: 1
+  number: 2
 
 requirements:
   build:

recipes/recipes_emscripten/h5py/test_h5py.py

@@ -34,4 +34,20 @@ def test_usage():
         assert dset2.name == "/subgroup/another_dataset"
 
     f = h5py.File("mytestfile.hdf5", "r")
-    assert sorted(list(f.keys())) == ["mydataset", "subgroup"]
+    assert sorted(list(f.keys())) == ["mydataset", "subgroup"]
+
+
+def test_dimscales(tmp_path):
+    """Exercises the HL dimscale reopen path across a File close/open cycle."""
+    import h5py
+
+    path = str(tmp_path / "dimscales.h5")
+    with h5py.File(path, "w") as f:
+        scale = f.create_dataset("x", data=[0.0, 1.0, 2.0, 3.0])
+        scale.make_scale("x")
+        data = f.create_dataset("temp", data=[10.0, 20.0, 30.0, 40.0])
+        data.dims[0].attach_scale(scale)
+
+    with h5py.File(path, "r") as f:
+        assert h5py.h5ds.is_scale(f["x"].id)
+        assert f["temp"].dims[0][0].name == "/x"

recipes/recipes_emscripten/hdf5/build.sh

@@ -3,8 +3,6 @@ cd build
 
 export LDFLAGS="-sNODERAWFS=1 -sUSE_ZLIB=1 -sFORCE_FILESYSTEM=1"
 
-cp ${RECIPE_DIR}/settings/* ../src/
-
 emcmake cmake .. \
     -DCMAKE_INSTALL_PREFIX=${PREFIX} \
     -DH5_HAVE_GETPWUID=OFF \
@@ -21,13 +19,11 @@ emcmake cmake .. \
     -DHDF5_BUILD_EXAMPLES=OFF \
     -DHDF5_BUILD_TOOLS=OFF \
     -DHDF5_BUILD_UTILS=OFF \
+    -DHDF5_BUILD_HL_LIB=ON \
     -DHDF5_ENABLE_Z_LIB_SUPPORT=ON \
     -DHDF5_ENABLE_ROS3_VFD=OFF \
     -DZLIB_INCLUDE_DIR=${PREFIX}/include \
     -DZLIB_LIBRARY=${PREFIX}/lib/libz.a
 
-cp ${RECIPE_DIR}/settings/* ../src/
-cp ${RECIPE_DIR}/settings/* src/
-
 emmake make -j 4
 emmake make install

recipes/recipes_emscripten/hdf5/patches/0001-fenv-fe-invalid-guard.patch

@@ -0,0 +1,19 @@
+Emscripten's <bits/fenv.h> defines only rounding modes and FE_ALL_EXCEPT=0;
+FE_INVALID is not defined because WASM has no floating-point exception
+flags. Guard the FE_INVALID clear so the build proceeds; under WASM there
+are no FP exceptions to clear, so the guarded branch is a legitimate no-op.
+
+--- a/src/H5Tinit_float.c
++++ b/src/H5Tinit_float.c
+@@ -608,9 +608,11 @@
+ #endif
+
+ done:
++#ifdef FE_INVALID
+     /* Clear any FE_INVALID exceptions from NaN handling */
+     if (feclearexcept(FE_INVALID) != 0)
+         HSYS_GOTO_ERROR(H5E_DATATYPE, H5E_CANTSET, FAIL, "can't clear floating-point exceptions");
++#endif
+
+     /* Restore the original environment */
+     if (feupdateenv(&saved_fenv) != 0)

recipes/recipes_emscripten/hdf5/patches/0002-drop-soversion.patch

@@ -0,0 +1,28 @@
+Under emscripten the loader dedupes shared libraries by string identity of
+their NEEDED entry, not by realpath. When libhdf5_hl links against libhdf5
+with SOVERSION set, it records NEEDED "libhdf5.so.310.5.1", while consumers
+like h5py link with bare "-lhdf5" and record NEEDED "libhdf5.so". Both paths
+resolve to the same file via symlinks, but the loader sees them as two
+distinct libraries and creates two separate instances — each with its own
+copy of libhdf5.so's file-static globals (H5CX_head_g etc.), which breaks
+the metadata cache when calls cross between the instances.
+
+Skip VERSION/SOVERSION for emscripten builds so every consumer records the
+bare "libhdf5.so" NEEDED entry and the loader deduplicates properly.
+
+--- a/config/cmake/HDF5Macros.cmake
++++ b/config/cmake/HDF5Macros.cmake
+@@ -22,10 +22,10 @@
+     else ()
+       set (LIBHDF_VERSION ${HDF5_${libpackage}_PACKAGE_SOVERSION_MAJOR})
+     endif ()
+-    set_target_properties (${libtarget} PROPERTIES VERSION ${PACKAGE_SOVERSION})
++    if (NOT EMSCRIPTEN)
++      set_target_properties (${libtarget} PROPERTIES VERSION ${PACKAGE_SOVERSION})
++    endif ()
+     if (WIN32)
+         set (${LIB_OUT_NAME} "${LIB_OUT_NAME}-${LIBHDF_VERSION}")
+-    else ()
++    elseif (NOT EMSCRIPTEN)
+         set_target_properties (${libtarget} PROPERTIES SOVERSION ${LIBHDF_VERSION})
+     endif ()

recipes/recipes_emscripten/hdf5/recipe.yaml

@@ -1,14 +1,17 @@
 context:
-  version: 1.12.3
-  maj_min_ver: 1.12
+  version: 1.14.6
+  maj_min_ver: 1.14
 
 package:
   name: hdf5
   version: ${{ version }}
 
 source:
-  url: https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-${{ maj_min_ver }}/hdf5-${{version }}/src/hdf5-${{ version }}.tar.gz
-  sha256: c15adf34647918dd48150ea1bd9dffd3b32a3aec5298991d56048cc3d39b4f6f
+  url: https://support.hdfgroup.org/releases/hdf5/v${{ maj_min_ver | replace(".", "_") }}/v${{ version | replace(".", "_") }}/downloads/hdf5-${{ version }}.tar.gz
+  sha256: e4defbac30f50d64e1556374aa49e574417c9e72c6b1de7a4ff88c4b1bea6e9b
+  patches:
+  - patches/0001-fenv-fe-invalid-guard.patch
+  - patches/0002-drop-soversion.patch
 
 build:
   number: 0
@@ -21,6 +24,14 @@ requirements:
   host:
   - zlib
 
+tests:
+- package_contents:
+    files:
+    - include/hdf5.h
+    - include/hdf5_hl.h
+    - lib/libhdf5.so
+    - lib/libhdf5_hl.so
+
 about:
   homepage: https://www.hdfgroup.org/solutions/hdf5/
   license: BSD-3-Clause

recipes/recipes_emscripten/libnetcdf/patches/skip-daos-emscripten.patch

@@ -0,0 +1,25 @@
+DAOS container detection uses listxattr/getxattr which are declared in
+Emscripten's <sys/xattr.h> but not implemented at runtime — the built .so
+fails to load with "cannot resolve symbol listxattr". DAOS makes no sense
+in a WASM sandbox anyway. Short-circuit isdaoscontainer() under
+__EMSCRIPTEN__ so the xattr code is never reached.
+
+--- a/libdispatch/dinfermodel.c
++++ b/libdispatch/dinfermodel.c
+@@ -1594,6 +1594,10 @@
+ static int
+ isdaoscontainer(const char* path)
+ {
++#ifdef __EMSCRIPTEN__
++    (void)path;
++    return NC_ENOTNC;
++#else
+     int stat = NC_ENOTNC; /* default is that this is not a DAOS container */
+ #ifndef _WIN32
+ #ifdef USE_HDF5
+@@ -1669,6 +1673,7 @@
+ #endif
+     errno = 0; /* reset */
+     return stat;
++#endif /* __EMSCRIPTEN__ */
+ }

recipes/recipes_emscripten/libnetcdf/recipe.yaml

@@ -12,9 +12,10 @@ source:
   patches:
   - patches/parallel-disable.patch
   - patches/hdf5-parallel-disable.patch
+  - patches/skip-daos-emscripten.patch
 
 build:
-  number: 0
+  number: 1
 
   files:
     exclude:

recipes/recipes_emscripten/netcdf4/recipe.yaml

@@ -13,9 +13,9 @@ source:
   - patches/0001-Fix-unknown-arg-R-PREFIX-lib.patch
 
 build:
-  number: 2
+  number: 3
   script:
-  - export LDFLAGS="-L$PREFIX/lib -lhdf5 $LDFLAGS"
+  - export LDFLAGS="-L$PREFIX/lib -lhdf5 -lhdf5_hl $LDFLAGS"
   - ${PYTHON} -m pip install . -vvv
 
   files:

recipes/recipes_emscripten/netcdf4/test_netcdf4.py

@@ -1,7 +1,33 @@
-def test_netcdf4():
-  from netCDF4 import Dataset
-  rootgrp = Dataset("test.nc", "w", format="NETCDF4")
-  rootgrp.data_model == "NETCDF4"
-  rootgrp.close()
+import numpy as np
+import netCDF4
+from netCDF4 import Dataset
 
 
+def test_versions():
+    print("netCDF4:", netCDF4.__version__)
+    print("libnetcdf:", netCDF4.__netcdf4libversion__)
+    print("libhdf5:", netCDF4.__hdf5libversion__)
+
+
+def test_netcdf3_write_read(tmp_path):
+    path = str(tmp_path / "c.nc")
+    with Dataset(path, "w", format="NETCDF3_CLASSIC") as ds:
+        ds.createDimension("x", 4)
+        v = ds.createVariable("temp", "f8", ("x",))
+        v[:] = np.arange(4.0)
+    with Dataset(path, "r") as ds:
+        assert ds.variables["temp"].shape == (4,)
+
+
+def test_netcdf4_roundtrip(tmp_path):
+    """End-to-end netcdf-4 round-trip: dim + variable + attribute."""
+    path = str(tmp_path / "v.nc")
+    with Dataset(path, "w", format="NETCDF4") as ds:
+        ds.title = "hello"
+        ds.createDimension("x", 4)
+        v = ds.createVariable("temp", "f8", ("x",))
+        v[:] = np.arange(4.0)
+    with Dataset(path, "r") as ds:
+        assert ds.title == "hello"
+        assert "x" in ds.dimensions
+        np.testing.assert_array_equal(ds.variables["temp"][:], np.arange(4.0))

variant.yaml

@@ -383,7 +383,7 @@ harfbuzz:
 hdf4:
   - 4.2
 hdf5:
-  - 1.12.3
+  - 1.14.6
 icu:
   - '73'
 ipopt:
@@ -449,7 +449,7 @@ libmatio:
 libmicrohttpd:
   - 0.9
 libnetcdf:
-  - 4.9.3
+  - 4.10.1
 libopencv:
   - 4.5.5
 libpcap: