Milestone 1p0

pyfive/dataobjects.py

@@ -527,7 +527,11 @@ def _get_chunk_params(self):
             dims, address = struct.unpack_from(
                 '<BQ', self.msg_data, property_offset)
             data_offset = property_offset + struct.calcsize('<BQ')
-        assert (version >= 1) and (version <= 3)
+        supported_version = (version >= 1) and (version <= 3)
+        if not supported_version:
+            # Note that implementation of layout class version 4 will need to deal with
+            # assumption that btree is of type V1 (see chunk_btree = ... in h5d.py).
+            raise RuntimeError(f'Pyfive cannot yet read HDF5 files with layout class {version}')
 
         fmt = '<' + 'I' * (dims-1)
         chunk_shape = struct.unpack_from(fmt, self.msg_data, data_offset)

tests/test_chunk_index_options.py

@@ -29,7 +29,7 @@ def test_lazy_index():
         assert dset1.attrs['attr1'] == 130
 
         # test we have no index yet 
-        assert dset1.id._DatasetID__index_built==False
+        assert not dset1.id._DatasetID__index_built
 
         # this should force an index build
         assert_array_equal(dset1[:], np.arange(21*16).reshape((21, 16)))
@@ -42,13 +42,13 @@ def simpler_check(x,y):
         """ Expect this to be visited and instantiated without an index """
         print(x,y.name)
         assert y.attrs['attr1'] == 130
-        assert y.id._DatasetID__index_built==False
+        assert not y.id._DatasetID__index_built
 
     def simplest_check(x,y):
         """ Expect this to be visited and instantiated with an index """
         print(x,y.name)
         assert y.attrs['attr1'] == 130
-        assert y.id._DatasetID__index_built==True
+        assert y.id._DatasetID__index_built
 
 
     with pyfive.File(DATASET_CHUNKED_HDF5_FILE) as hfile:
@@ -68,7 +68,7 @@ def test_get_chunk_info_chunked():
             open(DATASET_CHUNKED_HDF5_FILE, "rb") as f:
 
         ds = hfile.get_lazy_view('dataset1')
-        assert ds.id._DatasetID__index_built==False
+        assert not ds.id._DatasetID__index_built 
 
         si = StoreInfo((0,0), 0, 4016, 16)
         info = ds.id.get_chunk_info(0)
@@ -92,7 +92,7 @@ def test_get_chunk_methods_contiguous():
     with pyfive.File(NOT_CHUNKED_FILE) as hfile:
 
         ds = hfile.get_lazy_view('q')
-        assert ds.id._DatasetID__index_built==False
+        assert not ds.id._DatasetID__index_built
 
         with pytest.raises(TypeError):
             ds.id.get_chunk_info(0)

tests/test_chunked.py

@@ -53,6 +53,19 @@ def test_chunked_dataset():
         assert dset1.chunks == (2, 2)
 
 
+def test_recognise_btree(name, data):
+    """ 
+    At this point we want to raise an error if we find a chunked variable
+    with a b-tree v2 index, as we don't know how to read it ... yet.
+    It seems that can only come with layoutclass = 4. 
+    """
+    with pytest.raises(RuntimeError):
+        with pyfive.File(name) as hfile:
+            dset1 = hfile['btreev2']
+            print(dset1)
+
+
+
 @pytest.mark.skip(reason="Not implemented yet, see https://github.com/NCAS-CMS/pyfive/issues/137")
 def test_chunked_dataset_btreev2(name, data):
     with pyfive.File(name) as hfile:

tests/test_p5ncdump.py

@@ -1,10 +1,11 @@
 """Test the p5dump executable via p5ncdump utility."""
 import os
 import shutil
-
 import pyfive
-import pytest
+import subprocess 
+import tempfile
 
+DIRNAME = os.path.dirname(__file__)
 
 def test_which_p5dump():
     """Run the basic which p5dump."""
@@ -13,16 +14,46 @@ def test_which_p5dump():
 
 
 def test_p5dump_cmd():
-    """Run a basic p5dump with no/yes file arg."""
-    s1 = os.system("p5dump")
-    assert s1 != 0
-    s2 = os.system("p5dump tests/data/groups.hdf5")
-    assert s2 == 0
+    """
+    Run p5dump on a test HDF5 file safely, capturing output.
+    This currently works fine with pytest from the command
+    line but breaks inside visual studio code with a wierd
+    numpy error. This lengthy version is en route to debugging
+    """
+
+    p5dump = shutil.which("p5dump")
+    assert p5dump, "p5dump not found in PATH"
+    assert os.access(p5dump, os.X_OK), f"{p5dump} is not executable"
+
+    dfile = os.path.join(os.path.dirname(__file__), 'data', 'groups.hdf5')
+    assert os.path.exists(dfile), f"Test file does not exist: {dfile}"
+
+    with tempfile.TemporaryDirectory() as tmpdir:
+
+        # Copy environment and remove PYTHONPATH to avoid NumPy source tree detection
+        env = os.environ.copy()
+        env.pop("PYTHONPATH", None)
+
+        result = subprocess.run(
+            [p5dump, dfile],
+            stdout=subprocess.PIPE,
+            stderr=subprocess.PIPE,
+            text=True,
+            cwd=tmpdir,
+            env=env
+        )
+
+        print("cmd:", result.args)
+        print("returncode:", result.returncode)
+        print("stdout:\n", result.stdout)
+        print("stderr:\n", result.stderr)
+
+        assert result.returncode == 0
 
 
 def test_hdf5(capsys):
     """Run p5dump on a local HDF5 file."""
-    hdf5_file = "./tests/data/groups.hdf5"
+    hdf5_file = DIRNAME+'/data/groups.hdf5'
     pyfive.p5ncdump(hdf5_file)
 
     captured = capsys.readouterr()