avoid setting read mode to 'r' as it became the default in 3.0.0 and now raises a deprecation warning

Author: sjanssen2

qiita_files/util.py

@@ -7,13 +7,17 @@
 # -----------------------------------------------------------------------------
 
 from contextlib import contextmanager
+from packaging import version
 
 import h5py
 
 
-# not present in all 2.x series
-if hasattr(h5py.get_config(), 'default_file_mode'):
-    h5py.get_config().default_file_mode = 'r'
+# Setting h5py.default_file_mode is deprecated.
+# 'r' (read-only) is the default from h5py 3.0.
+if version.Version(h5py.__version__) <= version.Version("3.0"):
+    # not present in all 2.x series
+    if hasattr(h5py.get_config(), 'default_file_mode'):
+        h5py.get_config().default_file_mode = 'r'
 
 
 def _is_string_or_bytes(s):

setup.py

@@ -43,6 +43,6 @@
                 'qiita_files/format',
                 'qiita_files/parse'],
       extras_require={'test': ["nose >= 0.10.1", "pep8"]},
-      install_requires=['numpy', 'h5py', 'joblib'],
+      install_requires=['numpy', 'h5py', 'joblib', 'packaging'],
       classifiers=classifiers
       )