Merge pull request #180 from ammarhakim/metadata_retrocompatibility_fix

add geqdsk_sign_convention and geometry_type as None in the ctx dict.

Author: manauref

environment.yml

@@ -1,9 +1,8 @@
-name: pgkyl
+name: pgkylSrcH5
 channels:
   - defaults
   - conda-forge
 dependencies:
-  - conda-forge::adios2==2.9.2
   - click>=8.1.7
   - matplotlib>=3.7.0
   - msgpack-python>=1.0.3
@@ -13,3 +12,4 @@ dependencies:
   - python>=3.11
   - scipy>=1.10.1
   - sympy>=1.12
+  - h5py

src/postgkyl/commands/animate.py

@@ -27,24 +27,24 @@ def _update(frame, data, fig, kwargs):
   for i, dat in enumerate(data[frame]):
     kwargs["title"] = ""
     if not kwargs["notitle"]:
-      if dat.ctx["frame"] is not None:
+      if dat.ctx.get("frame"):
         kwargs["title"] = f"{kwargs['title']:s} frame: {dat.ctx['frame']:d} "
       # end
-      if dat.ctx["time"] is not None:
+      if dat.ctx.get("time"):
         kwargs["title"] = f"{kwargs['title']:s} time: {dat.ctx['time']:.4e}"
       # end
     # end
 
     if i == 0:
-      if kwargs["arg"] is not None:
+      if kwargs.get("arg"):
         im = postgkyl.output.plot(dat, kwargs["arg"], **kwargs)
       else:
         im = postgkyl.output.plot(dat, **kwargs)
       # end
     else:
       kwargs_ncb = kwargs.copy()
       kwargs_ncb["colorbar"] = False
-      if kwargs["arg"] is not None:
+      if kwargs.get("arg"):
         im = postgkyl.output.plot(dat, kwargs["arg"], **kwargs_ncb)
       else:
         im = postgkyl.output.plot(dat, **kwargs_ncb)

src/postgkyl/commands/collect.py

@@ -92,7 +92,7 @@ def collect(ctx, **kwargs):
       time[i] = np.array(time[i])
       values[i] = np.array(values[i])
 
-      if kwargs["period"] is not None:
+      if "period" in kwargs.keys():
         time[i] = (time[i] - kwargs["offset"]) % kwargs["period"]
       # end
 

src/postgkyl/commands/differentiate.py

@@ -24,7 +24,7 @@ def differentiate(ctx, **kwargs):
 
   basis_type = None
   is_modal = None
-  if kwargs["basis_type"] is not None:
+  if "basis_type" in kwargs.keys():
     if kwargs["basis_type"] == "ms":
       basis_type = "serendipity"
       is_modal = True

src/postgkyl/commands/gk_energy_balance.py

@@ -233,6 +233,8 @@ def absy_disabled(data_in):
       field_dot_file = block_path_prefix + 'field_energy_dot.gkyl'
 
     has_field_dot, time_field_dot, field_dot_pb, gdat = read_gfile_if_present(field_dot_file)
+    if not has_field_dot or gdat is None:
+      raise FileNotFoundError(f"Required file not found: {field_dot_file}")
     gdat_field_dot = GData(tag="field_dot", label="field_dot", ctx=gdat.ctx)
 
     fdot_pb = None
@@ -247,7 +249,9 @@ def absy_disabled(data_in):
       else:
         fdot_file = block_path_prefix + spec_nm + '_fdot_integrated_moms.gkyl'
 
-      _, time_fdot, fdot_ps, gdat = read_gfile_if_present(fdot_file)
+      has_fdot, time_fdot, fdot_ps, gdat = read_gfile_if_present(fdot_file)
+      if not has_fdot or gdat is None:
+        raise FileNotFoundError(f"Required file not found: {fdot_file}")
       gdat_fdot = GData(tag="fdot", label="fdot", ctx=gdat.ctx)
 
       # Load integrated moments of the source.

src/postgkyl/commands/gk_nodes.py

@@ -19,7 +19,7 @@ def is_geo_mapc2p(gdata):
   gdata_meta = gdata.get_ctx()
   is_mapc2p = True
   if ("geometry_type" in gdata_meta):
-    if gdata_meta["geometry_type"] is not None:
+    if "geometry_type" in gdata_meta.keys():
       mc2p_idx = gkenums.enum_key_to_idx(gkenums.gkyl_geometry_id,"GKYL_GEOMETRY_MAPC2P")
       is_mapc2p = mc2p_idx == gdata_meta["geometry_type"]
     # end

src/postgkyl/commands/gk_particle_balance.py

@@ -218,7 +218,9 @@ def absy_disabled(data_in):
     else:
       fdot_file = block_path_prefix + kwargs["species"] + '_fdot_integrated_moms.gkyl'
 
-    _, time_fdot, fdot_pb, gdat = read_gfile_if_present(fdot_file)
+    has_fdot, time_fdot, fdot_pb, gdat = read_gfile_if_present(fdot_file)
+    if not has_fdot or gdat is None:
+      raise FileNotFoundError(f"Required file not found: {fdot_file}")
     gdat_fdot = GData(tag="fdot", label="fdot", ctx=gdat.ctx)
 
     # Load integrated moments of the source.

src/postgkyl/commands/interpolate.py

@@ -24,7 +24,7 @@ def interpolate(ctx, **kwargs):
 
   basis_type = None
   is_modal = None
-  if kwargs["basis_type"] is not None:
+  if "basis_type" in kwargs.keys():
     if kwargs["basis_type"] == "ms":
       basis_type = "serendipity"
       is_modal = True

src/postgkyl/commands/mask.py

@@ -28,11 +28,11 @@ def mask(ctx, **kwargs):
     if kwargs["filename"]:
       mask_fld_rep = np.repeat(mask_fld, dat.get_num_comps(), axis=-1)
       data.set_values(np.ma.masked_where(mask_fld_rep < 0.0, values))
-    elif kwargs["lower"] is not None and kwargs["upper"] is not None:
+    elif "lower" in kwargs.keys() and "upper" in kwargs.keys():
       dat.set_values(np.ma.masked_outside(values, kwargs["lower"], kwargs["upper"]))
-    elif kwargs["lower"] is not None:
+    elif "lower" in kwargs.keys():
       dat.set_values(np.ma.masked_less(values, kwargs["lower"]))
-    elif kwargs["upper"] is not None:
+    elif "upper" in kwargs.keys():
       dat.set_values(np.ma.masked_greater(values, kwargs["upper"]))
     else:
       data.set_values(values)

src/postgkyl/commands/old/recovery.py

@@ -25,7 +25,7 @@ def recovery(ctx, **kwargs):
   verb_print(ctx, "Starting recovery")
   data = ctx.obj["data"]
 
-  if kwargs["basis_type"] is not None:
+  if "basis_type" in kwargs.keys():
     if kwargs["basis_type"] == "ms" or kwargs["basis_type"] == "ns":
       basis_type = "serendipity"
     elif kwargs["basis_type"] == "mo":