Add file reader for autoionization files (#240)

.github/workflows/ci.yml

@@ -18,9 +18,7 @@ jobs:
       posargs: '--ascii-dbase-root ~/.chianti'
       toxdeps: "'tox<4' tox-pypi-filter"
       envs: |
-        - macos: py38
         - macos: py310
-        - windows: py38
         - windows: py310
         - linux: py38
         - linux: py39
@@ -40,6 +38,14 @@ jobs:
         - linux: py310
       cache-path: ~/.chianti
       cache-key: chianti-${{ github.event.number }}
+  test_database_v9:
+    needs: [test]
+    uses: OpenAstronomy/github-actions-workflows/.github/workflows/tox.yml@v1
+    with:
+      posargs: '--ascii-dbase-root ~/.chianti --ascii-dbase-url http://download.chiantidatabase.org/CHIANTI_v9.0.1_database.tar.gz --disable-file-hash --skip-version-check'
+      toxdeps: "'tox<4' tox-pypi-filter"
+      envs: |
+        - linux: py310
   precommit:
     uses: OpenAstronomy/github-actions-workflows/.github/workflows/tox.yml@v1
     with:

docs/references.bib

@@ -404,3 +404,13 @@ @article{zatsarinny_dielectronic_2003
   issn = {0004-6361},
   doi = {10.1051/0004-6361:20031462}
 }
+
+@techreport{dere_chianti_2017,
+  title = {{{CHIANTI Technical Report No}}. 8: {{The CHIANTI}} Autoionization Rate Files (Auto)},
+  author = {Dere, K. P.},
+  year = {2017},
+  month = dec,
+  number = {8},
+  urldate = {2022-08-21},
+  langid = {english}
+}

fiasco/conftest.py

@@ -1,7 +1,7 @@
 import pathlib
 import pytest
 
-from fiasco.util import check_database
+from fiasco.util import check_database, read_chianti_version
 
 # Force MPL to use non-gui backends for testing.
 try:
@@ -148,3 +148,29 @@ def ascii_dbase_root(ascii_dbase_tree, hdf5_dbase_root):
     # but in a worse way. What this means is that the HDF5 database is always built, even
     # when testing the ASCII parsing code, but that is not a huge price to pay.
     return ascii_dbase_tree
+
+
+@pytest.fixture(scope="session")
+def dbase_version(ascii_dbase_root):
+    return read_chianti_version(ascii_dbase_root)
+
+
+@pytest.fixture(autouse=True)
+def requires_dbase_version(request, dbase_version):
+    # NOTE: Fixtures that depend on other fixtures are awkward to implement.
+    # See this SO answer: https://stackoverflow.com/a/28198398
+    if marker := request.node.get_closest_marker('requires_dbase_version'):
+        version_condition = marker.args[0]
+        # NOTE: This currently only works for major versions. If we
+        # need tests that discriminate between minor versions or patches,
+        # this logic will need to be added.
+        conditional = f'{dbase_version["major"]}{version_condition}'
+        allowed_dbase_version = eval(conditional)
+        if not allowed_dbase_version:
+            pytest.skip(f'Test skipped because current dbase version {conditional}.')
+
+
+def pytest_configure(config):
+  config.addinivalue_line(
+        "markers", "requires_dbase_version(dbase_version): Skip tests based on CHIANTI database version requirements.",
+  )

fiasco/io/generic.py

@@ -13,6 +13,7 @@
 import fiasco
 
 from fiasco.util.exceptions import MissingASCIIFileError
+from fiasco.util.util import read_chianti_version
 
 
 class GenericParser:
@@ -32,10 +33,8 @@ def __init__(self, filename, **kwargs):
         if standalone:
             self.chianti_version = ''
         else:
-            version_file = self.ascii_dbase_root / 'VERSION'
-            with version_file.open() as f:
-                lines = f.readlines()
-                self.chianti_version = lines[0].strip()
+            version = read_chianti_version(self.ascii_dbase_root)
+            self.chianti_version = f"{version['major']}.{version['minor']}.{version['patch']}"
         self.full_path = pathlib.Path(filename) if standalone else self.ascii_dbase_root / self.filename
 
     def parse(self):

fiasco/io/sources/ion_sources.py

@@ -7,11 +7,22 @@
 
 from fiasco.io.generic import GenericIonParser
 
-__all__ = ['ElvlcParser', 'FblvlParser', 'ScupsParser',
-           'PsplupsParser', 'EasplomParser', 'EasplupsParser',
-           'WgfaParser', 'CilvlParser', 'ReclvlParser',
-           'RrparamsParser', 'TrparamsParser', 'DrparamsParser',
-           'DiparamsParser']
+__all__ = [
+    'ElvlcParser',
+    'FblvlParser',
+    'ScupsParser',
+    'PsplupsParser',
+    'EasplomParser',
+    'EasplupsParser',
+    'WgfaParser',
+    'CilvlParser',
+    'ReclvlParser',
+    'RrparamsParser',
+    'TrparamsParser',
+    'DrparamsParser',
+    'DiparamsParser',
+    'AutoParser',
+]
 
 
 class ElvlcParser(GenericIonParser):
@@ -416,3 +427,37 @@ def preprocessor(self, table, line, index):
             ionization_potential = tmp[0]
             cs_spline = np.array(tmp[1:], dtype=float)*1e-14
             table[-1] = [ionization_potential] + table[-1] + [cs_spline] + [0.0]
+
+
+class AutoParser(GenericIonParser):
+    """
+    Autoionization rates for each level in an ion.
+
+    The autoionization rate is the rate of decay of atomic level through autoionization to a
+    bound level. It is also needed to calculate the dielectronic recombination rate
+    from the more highly ionized ions, by means of the principle of detailed-balance.
+    For a full description of these files, see :cite:t:`dere_chianti_2017`.
+    """
+    filetype = 'auto'
+    dtypes = [int, int, float, str, str]
+    units = [None, None, 1/u.s, None, None]
+    headings = [
+        'lower_level',
+        'upper_level',
+        'autoionization_rate',
+        'lower_label',
+        'upper_label'
+    ]
+    descriptions = [
+        'lower level index',
+        'upper level index',
+        'autoionization rate',
+        'lower level label',
+        'upper level label'
+    ]
+    fformat = fortranformat.FortranRecordReader('(2I7,E12.2,A30,A30)')
+
+    def preprocessor(self, table, line, index):
+        super().preprocessor(table, line, index)
+        # remove the dash in the second-to-last entry
+        table[-1][-2] = table[-1][-2].split('-')[0].strip()

fiasco/io/sources/tests/test_sources.py

@@ -22,6 +22,7 @@
     'fe_2.trparams',
     'fe_12.drparams',
     'al_3.diparams',
+    pytest.param('fe_23.auto', marks=pytest.mark.requires_dbase_version('>=9')),
 ])
 def test_ion_sources(ascii_dbase_root, filename,):
     parser = fiasco.io.Parser(filename, ascii_dbase_root=ascii_dbase_root)

fiasco/tests/test_ion.py

@@ -244,6 +244,7 @@ def test_level_populations_normalized(pops_no_correction, pops_with_correction):
     assert u.allclose(pops_no_correction.sum(axis=1), 1, atol=None, rtol=1e-15)
 
 
+@pytest.mark.requires_dbase_version('<=8')
 def test_level_populations_correction(fe20, pops_no_correction, pops_with_correction):
     # Test level-resolved correction applied to correct levels
     i_corrected = np.unique(np.concatenate([fe20._cilvl['upper_level'], fe20._reclvl['upper_level']]))

fiasco/util/tests/test_util.py

@@ -3,7 +3,7 @@
 """
 import pytest
 
-from fiasco.util import get_chianti_catalog, parse_ion_name
+from fiasco.util import get_chianti_catalog, parse_ion_name, read_chianti_version
 
 
 @pytest.mark.parametrize('ion_name', [
@@ -35,3 +35,11 @@ def test_get_chianti_catalog(ascii_dbase_root):
     for k in keys:
         assert k in catalog
         assert isinstance(catalog[k], list)
+
+
+def test_chianti_version(ascii_dbase_root):
+    version = read_chianti_version(ascii_dbase_root)
+    assert isinstance(version, dict)
+    for k in ['major', 'minor', 'patch']:
+        assert k in version
+        assert isinstance(version[k], int)

fiasco/util/util.py

@@ -12,7 +12,7 @@
 FIASCO_HOME = pathlib.Path.home() / '.fiasco'
 FIASCO_RC = FIASCO_HOME / 'fiascorc'
 
-__all__ = ['setup_paths', 'get_chianti_catalog', 'parse_ion_name']
+__all__ = ['setup_paths', 'get_chianti_catalog', 'read_chianti_version', 'parse_ion_name']
 
 
 def parse_ion_name(ion_name):
@@ -117,6 +117,28 @@ def walk_sub_dir(subdir):
     return all_files
 
 
+def read_chianti_version(ascii_dbase_root):
+    """
+    Read the CHIANTI version number from the ASCII database.
+    """
+    version_file = pathlib.Path(ascii_dbase_root) / 'VERSION'
+    with version_file.open() as f:
+        lines = f.readlines()
+    version = lines[0].strip().split('.')
+    version_dict = {'major': 0, 'minor': 0, 'patch': 0}
+    n = len(version)
+    if n > 0:
+        version_dict['major'] = int(version[0])
+    if n > 1:
+        version_dict['minor'] = int(version[1])
+    if n > 2:
+        version_dict['patch'] = int(version[2])
+    if n > 3:
+        import fiasco
+        fiasco.log.warning(f'Version {version} has an unexpected number of entries.')
+    return version_dict
+
+
 def query_yes_no(question, default="yes"):
     """
     Ask a yes/no question via raw_input() and return their answer.