Merge pull request #4021 from pnorbert/fix-python

fix IO.available_attributes(), remove a debug print from Stream, fix …

examples/hello/sstReader/sstReader-bindings.py

@@ -36,7 +36,15 @@
     sstReader.EndStep()
 
     print(
-        "Rank=", rank, "loop index =", loopStep, "stream step =", currentStep, "data =", floatArray
+        "Rank=",
+        rank,
+        "loop index =",
+        loopStep,
+        "stream step =",
+        currentStep,
+        "data =",
+        floatArray,
+        flush=True,
     )
     loopStep = loopStep + 1
 

examples/hello/sstReader/sstReader.py

@@ -34,4 +34,5 @@
             currentStep,
             "data =",
             floatArray,
+            flush=True,
         )

examples/hello/sstWriter/sstWriter-bindings.py

@@ -33,7 +33,7 @@
 
 sstWriter = sstIO.Open("helloSst", adios2.Mode.Write)
 for i in range(4):
-    print("Rank=", rank, "loop index =", i, "data =", myArray)
+    print("Rank=", rank, "loop index =", i, "data =", myArray, flush=True)
     sstWriter.BeginStep()
     sstWriter.Put(ioArray, myArray, adios2.Mode.Sync)
     myArray += increment

examples/hello/sstWriter/sstWriter.py

@@ -34,7 +34,7 @@
         sleep(1.0)
 
         stream.write("bpFloats", myArray, [size * nx], [rank * nx], [nx])
-        print("Rank=", rank, "loop index =", currentStep, "data =", myArray)
+        print("Rank=", rank, "loop index =", currentStep, "data =", myArray, flush=True)
         myArray += increment
         # Warning: the data of the current step is not published until
         # the next loop entry or the exit of the loop

pyproject.toml

@@ -48,6 +48,9 @@ Documentation = "https://adios2.readthedocs.io/"
 Discussions = "https://github.com/ornladios/ADIOS2/discussions"
 Changelog = "https://github.com/ornladios/ADIOS2/releases"
 
+[project.entry-points."xarray.backends"]
+adios = "adios2.xarraybackend:AdiosBackendEntrypoint"
+
 [tool.cibuildwheel]
 # Trigger an install of the package, and run a basic test
 test-command = "python -m unittest adios2.test.simple_read_write.TestSimpleReadWrite"

python/adios2/file_reader.py

@@ -5,7 +5,7 @@
 from functools import singledispatchmethod
 from adios2 import Stream, IO
 
-
+# pylint: disable=W0221
 class FileReader(Stream):
     """High level implementation of the FileReader class for read Random access mode"""
 
@@ -19,7 +19,7 @@ def __init__(self, path, comm=None):
     # e.g. FileReader(io: adios2.IO, path, mode)
     # pylint: disable=E1121
     @__init__.register(IO)
-    def _(self, io: IO, path, mode, comm=None):
+    def _(self, io: IO, path, comm=None):
         super().__init__(io, path, "rra", comm)
 
     # pylint: enable=E1121

python/adios2/io.py

@@ -66,7 +66,15 @@ def define_attribute(
                 e.g. variable_name + separator + name ("var/attr")
                 Not used if variable_name is empty
         """
-        return Attribute(self.impl, name, content, variable_name, separator)
+
+        # string or list of strings passed on as is
+        if isinstance(content, list) and len(content) > 0 and isinstance(content[0], str):
+            return Attribute(self.impl, name, content, variable_name, separator)
+        if isinstance(content, str):
+            return Attribute(self.impl, name, content, variable_name, separator)
+
+        # python values (single or list) needs to be passed as a numpy array
+        return Attribute(self.impl, name, np.asarray(content), variable_name, separator)
 
     def inquire_attribute(self, name, variable_name="", separator="/"):
         """
@@ -103,10 +111,7 @@ def available_attributes(self):
                 value
                     attribute information dictionary
         """
-        attributes = {}
-        for name, attr in self.impl.AvailableAttributes():
-            attributes[name] = Attribute(attr, name)
-        return attributes
+        return self.impl.AvailableAttributes()
 
     def remove_attribute(self, name):
         """

python/adios2/stream.py

@@ -202,6 +202,27 @@ def inquire_variable(self, name):
         """
         return self._io.inquire_variable(name)
 
+    def inquire_attribute(self, name, variable_name="", separator="/"):
+        """
+        Inquire an attribute
+
+        Parameters
+            name
+                attribute name
+
+            variable_name
+                if attribute is associated with a variable
+
+            separator
+                concatenation string between variable_name and attribute
+                e.g. variable_name + separator + name ("var/attr")
+                Not used if variable_name is empty
+
+        Returns
+            The attribute if it is defined, otherwise None
+        """
+        return self._io.inquire_attribute(name, variable_name, separator)
+
     @singledispatchmethod
     def write(self, variable: Variable, content):
         """
@@ -311,10 +332,6 @@ def read(self, variable: Variable):
 
             output_shape = np.array(count)
             output_shape[0] *= steps
-            print(
-                f"Stream.read variable {variable.name()} dtype = {dtype} "
-                f"shape = {output_shape}, steps = {variable.steps()}"
-            )
         else:
             # scalar
             output_shape = (variable.selection_size(),)

scripts/ci/images/Dockerfile.ci-el8-intel

@@ -27,7 +27,7 @@ RUN dnf install -y \
         patch \
         patchelf \
         python39-devel \
-        python3-pip \
+        python39-pip \
         tar \
         tcl \
         unzip \

testing/adios2/bindings/python/TestBPWriteReadTypes.py

@@ -38,7 +38,7 @@ def check_array(np1, np2, hint):
 Nx = 8
 
 # list of tested attributes and variables
-attr_names = ["attrString", "attrI8", "attrI16", "attrI32", "attrI64",
+attr_names = ["attrString", "attrStringArray", "attrI8", "attrI16", "attrI32", "attrI64",
               "attrU8", "attrU16", "attrU32", "attrU64", "attrR32", "attrR64"]
 var_names = ["varStr", "varI8", "varI16", "varI32", "varI64",
              "varU8", "varU16", "varU32", "varU64",
@@ -82,7 +82,8 @@ def check_array(np1, np2, hint):
 varR64 = ioWriter.DefineVariable(
     "varR64", data.R64, shape, start, count, adios2.ConstantDims)
 
-attString = ioWriter.DefineAttribute("attrString", ["one", "two", "three"])
+attString = ioWriter.DefineAttribute("attrString", "one")
+attStringArray = ioWriter.DefineAttribute("attrStringArray", ["one", "two", "three"])
 attI8 = ioWriter.DefineAttribute("attrI8", data.I8)
 attI16 = ioWriter.DefineAttribute("attrI16", data.I16)
 attI32 = ioWriter.DefineAttribute("attrI32", data.I32)
@@ -146,6 +147,7 @@ def check_array(np1, np2, hint):
 reader = ioReader.Open("npTypes.bp", adios2.Mode.ReadRandomAccess)
 
 attrString = ioReader.InquireAttribute("attrString")
+attrStringArray = ioReader.InquireAttribute("attrStringArray")
 attrI8 = ioReader.InquireAttribute("attrI8")
 attrI16 = ioReader.InquireAttribute("attrI16")
 attrI32 = ioReader.InquireAttribute("attrI32")
@@ -158,6 +160,7 @@ def check_array(np1, np2, hint):
 attrR64 = ioReader.InquireAttribute("attrR64")
 
 check_object(attrString, "attrString")
+check_object(attrStringArray, "attrStringArray")
 check_object(attrI8, "attrI8")
 check_object(attrI16, "attrI16")
 check_object(attrI32, "attrI32")
@@ -170,6 +173,12 @@ def check_array(np1, np2, hint):
 check_object(attrR64, "attrR64")
 
 attrStringData = attrString.DataString()
+print(f"attrString = {attrStringData}", flush=True)
+if attrStringData[0] != "one":
+    raise ValueError('attrString failed')
+
+attrStringData = attrStringArray.DataString()
+print(f"attrStringArray = {attrStringData}", flush=True)
 if attrStringData[0] != "one":
     raise ValueError('attrStringData[0] failed')
 if attrStringData[1] != "two":

testing/adios2/python/TestIO.py

@@ -24,13 +24,22 @@ def test_io_inquire_attribute(self):
         self.assertNotEqual(ts, coords)
         self.assertNotEqual(ts, x)
         self.assertEqual(coords, x)
+        self.assertIs(io.inquire_attribute("notanattribute"), None)
 
-    def test_available_attribute(self):
+    def test_available_attributes(self):
         adios = Adios()
         io = adios.declare_io("BPWriter")
         io.define_attribute("timestamp", "20231122")
-        io.inquire_attribute("timestamp")
-        self.assertIs(io.inquire_attribute("coords"), None)
+        io.define_attribute("stringarray", ["one", "two", "three"])
+        io.define_attribute("afloat", 3.14)
+        io.define_attribute("floatarray", [3.14, 6.28])
+        attrs = io.available_attributes()
+        print("Available attributes:")
+        for aname, ainfo in attrs.items():
+            print(f"    {aname}:\t{ainfo}")
+        self.assertEqual(attrs["timestamp"]["Value"], '"20231122"')
+        self.assertEqual(attrs["stringarray"]["Value"], '{ "one", "two", "three" }')
+        self.assertFalse("coords" in attrs)
 
     def test_remove_attribute(self):
         adios = Adios()
@@ -96,6 +105,7 @@ def test_open_engine(self):
         io.add_transport("File", {"Library": "POSIX"})
         engine = io.open("pythontest.bp", bindings.Mode.Write)
         self.assertNotEqual(engine, None)
+        engine.close()
 
 
 if __name__ == "__main__":