Backport PR #210: Fix version checking (#211)

Co-authored-by: Will Barnes <[email protected]>

conftest.py

@@ -12,3 +12,5 @@ def pytest_addoption(parser):
     parser.addoption('--idl-executable', action='store', default=None)
     parser.addoption('--idl-codebase-root', action='store', default=None)
     parser.addoption('--include-all-files', action='store', default=False)
+    parser.addoption('--skip-version-check', action='store_true', default=False,
+                     help='Do not check CHIANTI version')

fiasco/conftest.py

@@ -115,12 +115,15 @@ def hdf5_dbase_root(ascii_dbase_tree, tmpdir_factory, request):
             test_files = TEST_FILES
     # Optionally use a different URL for the database (e.g. for testing different versions)
     ascii_dbase_url = request.config.getoption('--ascii-dbase-url')
+    # Optionally disable version checking. This is useful when testing newer/older versions
+    # of CHIANTI
+    check_chianti_version = not request.config.getoption('--skip-version-check')
     # Finally, run the database setup
     check_database(path,
                    ascii_dbase_root=ascii_dbase_tree,
                    ask_before=False,
                    ascii_dbase_url=ascii_dbase_url,
-                   check_chianti_version=False,
+                   check_chianti_version=check_chianti_version,
                    files=test_files)
     return path
 

fiasco/io/factory.py

@@ -40,7 +40,7 @@ def __call__(cls, *args, **kwargs):
         elif filetype_name in subclass_dict:
             return subclass_dict[filetype_name](*args, **kwargs)
         else:
-            log.warning(f'Unrecognized filename and extension {args[0]}', stacklevel=2)
+            log.debug(f'Unrecognized filename and extension {args[0]}', stacklevel=2)
             return type.__call__(cls, *args, **kwargs)
 
 

fiasco/io/generic.py

@@ -1,13 +1,15 @@
 """
 Base class for file parser
 """
+import astropy
 import astropy.units as u
 import h5py
 import numpy as np
-import os
 import pathlib
+import warnings
 
 from astropy.table import QTable
+from astropy.utils.exceptions import AstropyUserWarning
 
 import fiasco
 
@@ -55,9 +57,14 @@ def parse(self):
                 self.preprocessor(table, line, i)
 
         df = QTable(data=list(map(list, zip(*table))), names=self.headings)
-        for name, unit, dtype in zip(self.headings, self.units, self.dtypes):
-            df[name].unit = unit
-            df[name] = df[name].astype(dtype)
+        # This cataches a warning thrown when we convert a staggered array into
+        # a unitful column. This happens in several of the scups files for the
+        # bt_t, bt_type, bt_upsilon columns.
+        with warnings.catch_warnings():
+            warnings.filterwarnings('ignore', category=AstropyUserWarning)
+            for name, unit, dtype in zip(self.headings, self.units, self.dtypes):
+                df[name].unit = unit
+                df[name] = df[name].astype(dtype)
 
         df.meta['footer'] = self.extract_footer(lines)
         df.meta['chianti_version'] = self.chianti_version

fiasco/ions.py

@@ -89,7 +89,7 @@ def __repr__(self):
 Number of Levels: {n_levels}
 Number of Transitions: {n_transitions}
 
-Temperature range: [{self.temperature[0].to(u.MK):.3f}, {self.temperature[-1].to(u.MK)}:.3f]
+Temperature range: [{self.temperature[0].to(u.MK):.3f}, {self.temperature[-1].to(u.MK):.3f}]
 
 HDF5 Database: {self.hdf5_dbase_root}
 Using Datasets:

fiasco/util/setup_db.py

@@ -92,7 +92,7 @@ def check_database(hdf5_dbase_root, **kwargs):
 
 
 def check_database_version(hdf5_dbase_root):
-    dl = DataIndexer.create_indexer(hdf5_dbase_root, '/')
+    dl = DataIndexer.create_indexer(hdf5_dbase_root, '/h/h_1/elvlc')
     if dl.version not in SUPPORTED_VERSIONS:
         raise UnsupportedVersionError(
             f'CHIANTI {dl.version} is not in the list of supported versions {SUPPORTED_VERSIONS}.')