Fix string handling in h5py 3.0 (#977)

* Fix string handling in h5py 3.0

* Add runtimeerror to valueerror catches

* Explicit tuple

* More runtimeerrors when it used to raise a different exception

CHANGELOG.md

@@ -12,6 +12,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/).
 - Return min and max when file is read only
 - try/except the os.close call for tempfile (may already be gone in SWMR mode)
 - data objects retain units of individual axes when copied
+- h5py 3.0 string handling
 
 ## [3.3.1]
 

WrightTools/_dataset.py

@@ -195,7 +195,7 @@ def f(dataset, s):
                 arr = dataset[s]
                 try:
                     amin = np.nanargmax(arr)
-                except ValueError:
+                except (ValueError, RuntimeError):
                     amin = 0
                 idx = np.unravel_index(amin, arr.shape)
                 val = arr[idx]
@@ -215,7 +215,7 @@ def f(dataset, s):
                 arr = dataset[s]
                 try:
                     amin = np.nanargmin(arr)
-                except ValueError:
+                except (ValueError, RuntimeError):
                     amin = 0
                 idx = np.unravel_index(amin, arr.shape)
                 val = arr[idx]
@@ -378,7 +378,7 @@ def f(dataset, s):
             max_ = np.nanmax(list(self.chunkwise(f).values()))
             try:
                 self.attrs["max"] = max_
-            except OSError:
+            except (OSError, RuntimeError):
                 # Cannot write file, just return, can't cache
                 return max_
 
@@ -395,7 +395,7 @@ def f(dataset, s):
             min_ = np.nanmin(list(self.chunkwise(f).values()))
             try:
                 self.attrs["min"] = min_
-            except OSError:
+            except (OSError, RuntimeError):
                 # Cannot write file, just return, can't cache
                 return min_
 

WrightTools/data/_data.py

@@ -47,7 +47,8 @@ def __init__(self, *args, **kwargs):
         Group.__init__(self, *args, **kwargs)
         # populate axes, constants from attrs string
         for identifier in self.attrs.get("axes", []):
-            identifier = identifier.decode()
+            if hasattr(identifier, "decode"):
+                identifier = identifier.decode()
             expression, units = identifier.split("{")
             units = units.replace("}", "").strip()
             if units == "None":
@@ -59,7 +60,8 @@ def __init__(self, *args, **kwargs):
             axis = Axis(self, expression, units)
             self._axes.append(axis)
         for identifier in self.attrs.get("constants", []):
-            identifier = identifier.decode()
+            if hasattr(identifier, "decode"):
+                identifier = identifier.decode()
             expression, units = identifier.split("{")
             units = units.replace("}", "").strip()
             if units == "None":

setup.py

@@ -35,7 +35,7 @@ def read(fname):
     package_data=extra_files,
     python_requires=">=3.6",
     install_requires=[
-        "h5py<3",
+        "h5py",
         "imageio",
         "matplotlib>=3.3.0",
         "numexpr",