small updates on seissolxdmf and seissolxdmfwriter

seissolxdmf/seissolxdmf/__init__.py

@@ -1,2 +1,11 @@
 from .seissolxdmf import *
-__version__ = '0.1.3'
+try:
+    from importlib.metadata import version, PackageNotFoundError
+except ImportError:
+    from importlib_metadata import version, PackageNotFoundError
+
+try:
+    __version__ = version("seissolxdmf")
+except PackageNotFoundError:
+    # If the package is not installed, don't add __version__
+    pass

seissolxdmf/seissolxdmf/seissolxdmf.py

@@ -128,7 +128,7 @@ def get(prop):
                     if path is not None:
                         ref = tree.xpath(path)[0]
                         return get(ref)
-        raise NameError("%s not found in dataset" % (dataName))
+        raise NameError(f"{dataName} not found in dataset, available variables are {self.ReadAvailableDataFields()}")
 
     def ReadTopologyOrGeometry(self, attribute):
         """ Common function to read either connect or geometry """
@@ -282,5 +282,5 @@ def LoadData(self, dataName, nElements, idt=0, oneDtMem=False, firstElement=-1):
             idt = -1
         if firstElement == -1:
             firstElement = 0
-        myData = ReadDataChunk(dataName, firstElement, nElements, idt)
+        myData = self.ReadDataChunk(dataName, firstElement, nElements, idt)
         return [myData, data_prec]

seissolxdmfwriter/pyproject.toml

@@ -0,0 +1,26 @@
+[build-system]
+requires = ["setuptools", "setuptools-scm"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "seissolxdmfwriter"
+version = "0.4.2"
+authors = [
+    {name = "SeisSol Group"},
+]
+description = "A python writer for SeisSol xdmf output"
+readme = {file = "README.md", content-type = "text/markdown"}
+requires-python = ">=3.6"
+keywords = ["SeisSol"]
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "Operating System :: OS Independent",
+]
+dependencies = [
+    "numpy", "h5py" ,"seissolxdmf>=0.1.2", "tqdm"
+]
+[project.urls]
+Repository = "https://github.com/SeisSol/Visualization/seissolxdmfwriter"
+
+[project.scripts]
+seissol_output_extractor = "seissolxdmfwriter.seissol_output_extractor:main"

seissolxdmfwriter/seissolxdmfwriter/__init__.py

@@ -1,2 +1,11 @@
 from .seissolxdmfwriter import *
-__version__ = '0.4.1'
+try:
+    from importlib.metadata import version, PackageNotFoundError
+except ImportError:
+    from importlib_metadata import version, PackageNotFoundError
+
+try:
+    __version__ = version("seissolxdmfwriter")
+except PackageNotFoundError:
+    # If the package is not installed, don't add __version__
+    pass

seissolxdmfwriter/seissolxdmfwriter/seissolxdmfwriter.py

@@ -50,13 +50,13 @@ def write_timeseries_xdmf(
     xdmf = """<?xml version="1.0" ?>
 <!DOCTYPE Xdmf SYSTEM "Xdmf.dtd" []>
 <Xdmf Version="2.0">
- <Domain>"""
+ <Domain>
+  <Grid Name="TimeSeries" GridType="Collection" CollectionType="Temporal">"""
     geometry_location = dataLocation(bn_prefix, "geometry", backend)
     connect_location = dataLocation(bn_prefix, "connect", backend)
 
     for i, ctime in enumerate(timeValues):
         xdmf += f"""
-  <Grid Name="TimeSeries" GridType="Collection" CollectionType="Temporal">
    <Grid Name="step_{i}" GridType="Uniform">
     <Topology TopologyType="{topology}" NumberOfElements="{nCells}">
      <DataItem NumberType="Int" Precision="8" Format="{data_format}" Dimensions="{nCells} {node_per_element}">{connect_location}</DataItem>
@@ -82,9 +82,9 @@ def write_timeseries_xdmf(
      </DataItem>
     </Attribute>"""
         xdmf += """
-   </Grid>
-  </Grid>"""
+   </Grid>"""
     xdmf += """
+  </Grid>
  </Domain>
 </Xdmf>
 """
@@ -225,9 +225,9 @@ def read_non_temporal(sx, ar_name, filtered_cells):
                         my_array = sx.ReadData(ar_name, idt)[filtered_cells]
                     except IndexError:
                         print(
-                            f"time step {idt} of {ar_name} is corrupted, replacing with 0s"
+                            f"time step {idt} of {ar_name} is corrupted, replacing with nans"
                         )
-                        my_array = np.zeros(nel)
+                        my_array = np.full(nel, np.nan)
                     if i == 0:
                         h5f.create_dataset(
                             f"/{ar_name}",
@@ -237,9 +237,9 @@ def read_non_temporal(sx, ar_name, filtered_cells):
                         )
                     if my_array.shape[0] == 0:
                         print(
-                            f"time step {idt} of {ar_name} is corrupted, replacing with 0s"
+                            f"time step {idt} of {ar_name} is corrupted, replacing with nans"
                         )
-                        my_array = np.zeros(nel)
+                        my_array = np.full(nel, np.nan)
                     h5f[f"/{ar_name}"][i, :] = my_array[:]
         print(f"done writing {prefix}.h5")
     else:
@@ -259,9 +259,9 @@ def read_non_temporal(sx, ar_name, filtered_cells):
                     my_array = sx.ReadData(ar_name, idt)[filtered_cells]
                     if my_array.shape[0] == 0:
                         print(
-                            f"time step {idt} of {ar_name} is corrupted, replacing with 0s"
+                            f"time step {idt} of {ar_name} is corrupted, replacing with nans"
                         )
-                        my_array = np.zeros(nel)
+                        my_array = np.full(nel, np.nan)
                     if i == 0:
                         mydtype = output_type(my_array, reduce_precision)
                     my_array[:].astype(mydtype).tofile(fid)
@@ -277,8 +277,9 @@ def write_data(
     backend,
     compression_level,
 ):
-    time_indices = list(dictTime.values())
-    if not time_indices:
+    if dictTime:
+        time_indices = list(dictTime.values())
+    else:
         time_indices = [0]
     if backend == "hdf5":
         import h5py