Merge pull request #969 from aphearin/h5py_warnings

Resolved h5py warnings

Author: aphearin

halotools/sim_manager/cached_halo_catalog.py

@@ -564,7 +564,7 @@ def _bind_additional_metadata(self):
                 self.log_entry.fname + "\n\n")
             raise InvalidCacheLogEntry(msg)
 
-        f = h5py.File(self.log_entry.fname)
+        f = h5py.File(self.log_entry.fname, 'r')
         for attr_key in list(f.attrs.keys()):
             if attr_key == 'redshift':
                 setattr(self, attr_key, float(get_redshift_string(f.attrs[attr_key])))

halotools/sim_manager/download_manager.py

@@ -290,7 +290,7 @@ def download_processed_halo_table(self, simname, halo_finder, redshift,
                 "of the DownloadManager class.\n")
             raise HalotoolsError(msg)
 
-        f = h5py.File(output_fname)
+        f = h5py.File(output_fname, 'a')
         f.attrs['fname'] = str(output_fname)
         f.close()
 
@@ -564,7 +564,7 @@ def download_ptcl_table(self, simname, redshift,
                 "the \ndownload_ptcl_table method "
                 "of the DownloadManager class.\n")
             raise HalotoolsError(msg)
-        f = h5py.File(output_fname)
+        f = h5py.File(output_fname, 'a')
         f.attrs['fname'] = str(output_fname)
         f.close()
 

halotools/sim_manager/halo_table_cache.py

@@ -318,7 +318,7 @@ def determine_log_entry_from_fname(self, fname, overwrite_fname_metadata=False):
             return str(msg)
 
         try:
-            f = h5py.File(fname)
+            f = h5py.File(fname, 'r')
             required_set = set(HaloTableCacheLogEntry.required_metadata)
             actual_set = set(f.attrs.keys())
             assert required_set.issubset(actual_set)
@@ -335,7 +335,7 @@ def determine_log_entry_from_fname(self, fname, overwrite_fname_metadata=False):
             except:
                 pass
 
-        f = h5py.File(fname)
+        f = h5py.File(fname, 'a')
         constructor_kwargs = {}
 
         # We need to get rid of the byte attributes here to avoid failures

halotools/sim_manager/halo_table_cache_log_entry.py

@@ -218,7 +218,7 @@ def _verify_metadata_consistency(self, num_failures):
 
         try:
             import h5py
-            f = h5py.File(self.fname)
+            f = h5py.File(self.fname, 'r')
 
             for key in HaloTableCacheLogEntry.log_attributes:
                 try:
@@ -304,7 +304,7 @@ def _verify_all_positions_inside_box(self, halo_table, num_failures):
         msg = ''
 
         try:
-            f = h5py.File(self.fname)
+            f = h5py.File(self.fname, 'r')
             Lbox = f.attrs['Lbox']
             f.close()
             try:
@@ -401,7 +401,7 @@ def _verify_hdf5_has_complete_metadata(self, num_failures):
         msg = ''
 
         try:
-            f = h5py.File(self.fname)
+            f = h5py.File(self.fname, 'r')
             required_set = set(HaloTableCacheLogEntry.required_metadata)
             actual_set = set(f.attrs.keys())
 

halotools/sim_manager/ptcl_table_cache.py

@@ -288,7 +288,7 @@ def determine_log_entry_from_fname(self, fname, overwrite_fname_metadata=False):
             return str(msg)
 
         try:
-            f = h5py.File(fname)
+            f = h5py.File(fname, 'r')
             required_set = set(PtclTableCacheLogEntry.required_metadata)
             actual_set = set(f.attrs.keys())
             assert required_set.issubset(actual_set)
@@ -305,7 +305,7 @@ def determine_log_entry_from_fname(self, fname, overwrite_fname_metadata=False):
             except:
                 pass
 
-        f = h5py.File(fname)
+        f = h5py.File(fname, 'a')
         constructor_kwargs = {}
 
         # We need to get rid of the byte attributes here to avoid failures

halotools/sim_manager/ptcl_table_cache_log_entry.py

@@ -197,7 +197,7 @@ def _verify_metadata_consistency(self, msg, num_failures):
         """
 
         try:
-            f = h5py.File(self.fname)
+            f = h5py.File(self.fname, 'r')
 
             for key in PtclTableCacheLogEntry.log_attributes:
                 ptcl_log_attr = getattr(self, key)
@@ -261,7 +261,7 @@ def _verify_all_positions_inside_box(self, msg, num_failures):
         """
         try:
             data = Table.read(_passively_decode_string(self.fname), path='data')
-            f = h5py.File(self.fname)
+            f = h5py.File(self.fname, 'r')
             Lbox = np.empty(3)
             Lbox[:] = f.attrs['Lbox']
 
@@ -316,7 +316,7 @@ def _verify_hdf5_has_complete_metadata(self, msg, num_failures):
         """
 
         try:
-            f = h5py.File(self.fname)
+            f = h5py.File(self.fname, 'r')
             required_set = set(PtclTableCacheLogEntry.required_metadata)
             actual_set = set(f.attrs.keys())
 

halotools/sim_manager/rockstar_hlist_reader.py

@@ -707,7 +707,7 @@ def _write_metadata(self):
             raise HalotoolsError(uninstalled_h5py_msg)
 
         # Now add the metadata
-        f = h5py.File(self.output_fname)
+        f = h5py.File(self.output_fname, 'a')
         f.attrs.create('simname', np.string_(self.simname))
         f.attrs.create('halo_finder', np.string_(self.halo_finder))
         redshift_string = np.string_(get_redshift_string(self.redshift))

halotools/sim_manager/tests/test_cached_halo_catalog.py

@@ -108,8 +108,8 @@ def test_halo_ptcl_consistency(self):
                 assert halo_log_entry.simname == ptcl_log_entry.simname
                 assert halo_log_entry.redshift == ptcl_log_entry.redshift
 
-                hf = h5py.File(halo_log_entry.fname)
-                pf = h5py.File(ptcl_log_entry.fname)
+                hf = h5py.File(halo_log_entry.fname, 'r')
+                pf = h5py.File(ptcl_log_entry.fname, 'r')
 
                 assert hf.attrs['simname'] == pf.attrs['simname']
 

halotools/sim_manager/tests/test_halo_table_cache.py

@@ -71,7 +71,7 @@ def setUp(self):
                 'good_simname1', 'good_halo_finder', 'good_version_name',
                 get_redshift_string(0.0), self.good_table_fname)
 
-            f = h5py.File(self.good_table_fname)
+            f = h5py.File(self.good_table_fname, 'a')
             for attr_name in self.good_log_entry.log_attributes:
                 attr = getattr(self.good_log_entry, attr_name).encode('ascii')
                 f.attrs.create(attr_name, attr)
@@ -90,7 +90,7 @@ def setUp(self):
                 'good_simname2', 'good_halo_finder2', 'good_version_name',
                 get_redshift_string(1.0), self.good_table2_fname)
 
-            f = h5py.File(self.good_table2_fname)
+            f = h5py.File(self.good_table2_fname, 'a')
             for attr_name in self.good_log_entry2.log_attributes:
                 attr = getattr(self.good_log_entry2, attr_name).encode('ascii')
                 f.attrs.create(attr_name, attr)
@@ -135,14 +135,14 @@ def test_determine_log_entry_from_fname(self):
 
         entry = self.good_log_entry
         fname = entry.fname
-        f = h5py.File(fname)
+        f = h5py.File(fname, 'a')
         tmp = deepcopy(f.attrs['version_name'])
         del f.attrs['version_name']
         f.close()
         result = cache.determine_log_entry_from_fname(fname)
         assert "The hdf5 file is missing the following metadata:" in result
 
-        f = h5py.File(fname)
+        f = h5py.File(fname, 'a')
         f.attrs.create('version_name', tmp)
         f.close()
 

halotools/sim_manager/tests/test_halo_table_cache_log_entry.py

@@ -185,7 +185,7 @@ def test_scenario2a(self):
             pass
         self.table1.write(self.fnames[num_scenario], path='data')
 
-        f = h5py.File(self.fnames[num_scenario])
+        f = h5py.File(self.fnames[num_scenario], 'r')
         k = list(f.attrs.keys())
         f.close()
 
@@ -206,15 +206,15 @@ def test_scenario2b(self):
 
         log_entry = HaloTableCacheLogEntry(**self.get_scenario_kwargs(num_scenario))
 
-        f = h5py.File(self.fnames[num_scenario])
+        f = h5py.File(self.fnames[num_scenario], 'a')
         for attr in self.hard_coded_log_attrs:
             f.attrs[attr] = getattr(log_entry, attr)
         f.close()
 
         assert log_entry.safe_for_cache is False
         assert "``particle_mass``" in log_entry._cache_safety_message
 
-        f = h5py.File(self.fnames[num_scenario])
+        f = h5py.File(self.fnames[num_scenario], 'a')
         f.attrs['Lbox'] = 100.
         f.attrs['particle_mass'] = 1.e8
         f.close()
@@ -233,7 +233,7 @@ def test_scenario2c(self):
 
         log_entry = HaloTableCacheLogEntry(**self.get_scenario_kwargs(num_scenario))
 
-        f = h5py.File(self.fnames[num_scenario])
+        f = h5py.File(self.fnames[num_scenario], 'a')
         for attr in self.hard_coded_log_attrs:
             if attr != 'redshift':
                 f.attrs[attr] = getattr(log_entry, attr)
@@ -246,13 +246,13 @@ def test_scenario2c(self):
         assert log_entry.safe_for_cache is False
         assert "does not match" in log_entry._cache_safety_message
 
-        f = h5py.File(self.fnames[num_scenario])
+        f = h5py.File(self.fnames[num_scenario], 'a')
         f.attrs['redshift'] = 1.3390001
         f.close()
         assert log_entry.safe_for_cache is False
         assert "does not match" not in log_entry._cache_safety_message
 
-        f = h5py.File(self.fnames[num_scenario])
+        f = h5py.File(self.fnames[num_scenario], 'a')
         f.attrs['redshift'] = '1.3390001'
         f.close()
         assert log_entry.safe_for_cache is False
@@ -270,7 +270,7 @@ def test_scenario3(self):
 
         log_entry = HaloTableCacheLogEntry(**self.get_scenario_kwargs(num_scenario))
 
-        f = h5py.File(self.fnames[num_scenario])
+        f = h5py.File(self.fnames[num_scenario], 'a')
         for attr in self.hard_coded_log_attrs:
             f.attrs[attr] = getattr(log_entry, attr)
         f.attrs['Lbox'] = 100.
@@ -296,7 +296,7 @@ def test_scenario3b(self):
 
         log_entry = HaloTableCacheLogEntry(**self.get_scenario_kwargs(num_scenario))
 
-        f = h5py.File(self.fnames[num_scenario])
+        f = h5py.File(self.fnames[num_scenario], 'a')
         for attr in self.hard_coded_log_attrs:
             f.attrs[attr] = getattr(log_entry, attr)
         f.attrs['Lbox'] = 100.
@@ -324,7 +324,7 @@ def test_scenario3c(self):
         log_entry = HaloTableCacheLogEntry(**self.get_scenario_kwargs(num_scenario))
 
         self.table3.write(self.fnames[num_scenario], path='data')
-        f = h5py.File(self.fnames[num_scenario])
+        f = h5py.File(self.fnames[num_scenario], 'a')
         for attr in self.hard_coded_log_attrs:
             f.attrs[attr] = getattr(log_entry, attr)
         f.attrs['Lbox'] = 100.
@@ -338,7 +338,7 @@ def test_scenario3c(self):
         assert "must contain a unique set of integers" not in log_entry._cache_safety_message
 
         self.table4.write(self.fnames[num_scenario], path='data', overwrite=True)
-        f = h5py.File(self.fnames[num_scenario])
+        f = h5py.File(self.fnames[num_scenario], 'a')
         for attr in self.hard_coded_log_attrs:
             f.attrs[attr] = getattr(log_entry, attr)
         f.attrs['Lbox'] = 100.
@@ -365,7 +365,7 @@ def test_scenario4a(self):
         bad_table['halo_id'] = np.arange(len(bad_table), dtype=float)
         bad_table['halo_id'][0] = 0.1
         bad_table.write(self.fnames[num_scenario], path='data')
-        f = h5py.File(self.fnames[num_scenario])
+        f = h5py.File(self.fnames[num_scenario], 'a')
         for attr in self.hard_coded_log_attrs:
             f.attrs[attr] = getattr(log_entry, attr)
         f.attrs['Lbox'] = 100.
@@ -390,7 +390,7 @@ def test_scenario4b(self):
         bad_table['halo_rvir'] = 0.
         bad_table['halo_rvir'][0] = 51
         bad_table.write(self.fnames[num_scenario], path='data')
-        f = h5py.File(self.fnames[num_scenario])
+        f = h5py.File(self.fnames[num_scenario], 'a')
         for attr in self.hard_coded_log_attrs:
             f.attrs[attr] = getattr(log_entry, attr)
         f.attrs['Lbox'] = 100.
@@ -412,7 +412,7 @@ def test_passing_scenario(self):
         log_entry = HaloTableCacheLogEntry(**self.get_scenario_kwargs(num_scenario))
 
         self.good_table.write(self.fnames[num_scenario], path='data')
-        f = h5py.File(self.fnames[num_scenario])
+        f = h5py.File(self.fnames[num_scenario], 'a')
         for attr in self.hard_coded_log_attrs:
             f.attrs[attr] = getattr(log_entry, attr)
         f.attrs['Lbox'] = 100.