Merge pull request astropy#11903 from nstarman/dependency-pyyaml

make PyYaml a runtime dependency

astropy/coordinates/tests/test_regression.py

@@ -29,7 +29,7 @@
 from astropy.table import Table
 
 from astropy.tests.helper import assert_quantity_allclose
-from astropy.utils.compat.optional_deps import HAS_SCIPY, HAS_YAML  # noqa
+from astropy.utils.compat.optional_deps import HAS_SCIPY  # noqa
 from astropy.units import allclose as quantity_allclose
 
 
@@ -519,7 +519,6 @@ def test_gcrs_itrs_cartesian_repr():
     gcrs.transform_to(ITRS())
 
 
-@pytest.mark.skipif('not HAS_YAML')
 def test_regression_6446():
     # this succeeds even before 6446:
     sc1 = SkyCoord([1, 2], [3, 4], unit='deg')
@@ -538,23 +537,6 @@ def test_regression_6446():
     assert sio1.getvalue() == sio2.getvalue()
 
 
-def test_regression_6448():
-    """
-    This tests the more narrow problem reported in 6446 that 6448 is meant to
-    fix. `test_regression_6446` also covers this, but this test is provided
-    so that this is still tested even if YAML isn't installed.
-    """
-    sc1 = SkyCoord([1, 2], [3, 4], unit='deg')
-    # this should always succeed even prior to 6448
-    assert sc1.galcen_v_sun is None
-
-    c1 = SkyCoord(1, 3, unit='deg')
-    c2 = SkyCoord(2, 4, unit='deg')
-    sc2 = SkyCoord([c1, c2])
-    # without 6448 this fails
-    assert sc2.galcen_v_sun is None
-
-
 def test_regression_6597():
     frame_name = 'galactic'
     c1 = SkyCoord(1, 3, unit='deg', frame=frame_name)

astropy/coordinates/tests/test_spectral_coordinate.py

@@ -840,9 +840,6 @@ def test_spectral_coord_from_sky_coord_without_distance():
 @pytest.mark.parametrize('specsys', list(EXPECTED_VELOCITY_FRAMES))
 def test_spectralcoord_accuracy(specsys):
 
-    # PyYAML is needed to read in the ecsv table
-    pytest.importorskip('yaml')
-
     # This is a test to check the numerical results of transformations between
     # different velocity frames in SpectralCoord. This compares the velocity
     # shifts determined with SpectralCoord to those determined from the rv

astropy/io/ascii/ecsv.py

@@ -14,11 +14,9 @@
 from . import core, basic
 from astropy.table import meta, serialize
 from astropy.utils.data_info import serialize_context_as
-from astropy.utils.exceptions import AstropyUserWarning, AstropyWarning
+from astropy.utils.exceptions import AstropyUserWarning
 from astropy.io.ascii.core import convert_numpy
 
-__doctest_requires__ = {'Ecsv': ['yaml']}
-
 ECSV_VERSION = '1.0'
 DELIMITERS = (' ', ',')
 ECSV_DATATYPES = (
@@ -135,13 +133,6 @@ def get_cols(self, lines):
 
         try:
             header = meta.get_header_from_yaml(lines)
-        except ImportError as exc:
-            if 'PyYAML package is required' in str(exc):
-                warnings.warn("file looks like ECSV format but PyYAML is not installed "
-                              "so it cannot be parsed as ECSV",
-                              AstropyWarning)
-            raise core.InconsistentTableError('unable to parse yaml in meta header'
-                                              ' (PyYAML package is required)')
         except meta.YamlParseError:
             raise core.InconsistentTableError('unable to parse yaml in meta header')
 

astropy/io/ascii/tests/test_connect.py

@@ -5,7 +5,7 @@
 
 from astropy.table.table_helpers import simple_table
 from astropy.utils.data import get_pkg_data_filename
-from astropy.utils.compat.optional_deps import HAS_BS4, HAS_YAML  # noqa
+from astropy.utils.compat.optional_deps import HAS_BS4  # noqa
 
 import numpy as np
 
@@ -136,7 +136,6 @@ def test_write_csv(tmpdir):
     t.write(path)
 
 
-@pytest.mark.skipif('not HAS_YAML')
 def test_auto_identify_ecsv(tmpdir):
     tbl = simple_table()
     tmpfile = str(tmpdir.join('/tmpFile.ecsv'))

astropy/io/ascii/tests/test_ecsv.py

@@ -3,8 +3,6 @@
 """
 This module tests some of the methods related to the ``ECSV``
 reader/writer.
-
-Requires `pyyaml <https://pyyaml.org/>`_ to be installed.
 """
 from astropy.table.column import MaskedColumn
 import os
@@ -15,6 +13,7 @@
 
 import pytest
 import numpy as np
+import yaml
 
 from astropy.table import Table, Column, QTable, NdarrayMixin
 from astropy.table.table_helpers import simple_table
@@ -25,17 +24,14 @@
 from astropy.units import allclose as quantity_allclose
 from astropy.units import QuantityInfo
 
-from astropy.utils.exceptions import AstropyUserWarning, AstropyWarning
+from astropy.utils.exceptions import AstropyUserWarning
 
 from astropy.io.ascii.ecsv import DELIMITERS
 from astropy.io import ascii
 from astropy import units as u
-from astropy.utils.compat.optional_deps import HAS_YAML  # noqa
 
 from .common import TEST_DIR
 
-pytestmark = pytest.mark.skipif(not HAS_YAML, reason='YAML required')
-
 DTYPES = ['bool', 'int8', 'int16', 'int32', 'int64', 'uint8', 'uint16', 'uint32',
           'uint64', 'float16', 'float32', 'float64', 'float128',
           'str']
@@ -370,7 +366,6 @@ def assert_objects_equal(obj1, obj2, attrs, compare_class=True):
 }
 
 
-@pytest.mark.skipif('not HAS_YAML')
 def test_ecsv_mixins_ascii_read_class():
     """Ensure that ascii.read(ecsv_file) returns the correct class
     (QTable if any Quantity subclasses, Table otherwise).
@@ -392,7 +387,6 @@ def test_ecsv_mixins_ascii_read_class():
     assert type(t2) is QTable
 
 
-@pytest.mark.skipif('not HAS_YAML')
 def test_ecsv_mixins_qtable_to_table():
     """Test writing as QTable and reading as Table.  Ensure correct classes
     come out.
@@ -423,7 +417,6 @@ def test_ecsv_mixins_qtable_to_table():
         assert_objects_equal(col, col2, attrs, compare_class)
 
 
-@pytest.mark.skipif('not HAS_YAML')
 @pytest.mark.parametrize('table_cls', (Table, QTable))
 def test_ecsv_mixins_as_one(table_cls):
     """Test write/read all cols at once and validate intermediate column names"""
@@ -493,7 +486,6 @@ def make_multidim(col, ndim):
     return col
 
 
-@pytest.mark.skipif('not HAS_YAML')
 @pytest.mark.parametrize('name_col', list(mixin_cols.items()))
 @pytest.mark.parametrize('table_cls', (Table, QTable))
 @pytest.mark.parametrize('ndim', (1, 2, 3))
@@ -524,23 +516,6 @@ def test_ecsv_mixins_per_column(table_cls, name_col, ndim):
         assert t2[name]._time.jd2.__class__ is np.ndarray
 
 
-def test_ecsv_but_no_yaml_warning(monkeypatch):
-    """
-    Test that trying to read an ECSV without PyYAML installed when guessing
-    emits a warning, but reading with guess=False gives an exception.
-    """
-    monkeypatch.setitem(sys.modules, 'yaml', None)
-
-    with pytest.warns(AstropyWarning, match=r'file looks like ECSV format but '
-                      'PyYAML is not installed') as w:
-        ascii.read(SIMPLE_LINES)
-    assert len(w) == 1
-
-    with pytest.raises(ascii.InconsistentTableError, match='unable to parse yaml'), \
-            pytest.warns(AstropyWarning, match=r'PyYAML is not installed'):
-        ascii.read(SIMPLE_LINES, format='ecsv')
-
-
 def test_round_trip_masked_table_default(tmpdir):
     """Test (mostly) round-trip of MaskedColumn through ECSV using default serialization
     that uses an empty string "" to mark NULL values.  Note:
@@ -574,7 +549,6 @@ def test_round_trip_masked_table_default(tmpdir):
         assert not np.all(t2[name] == t[name])  # Expected diff
 
 
-@pytest.mark.skipif('not HAS_YAML')
 def test_round_trip_masked_table_serialize_mask(tmpdir):
     """Same as prev but set the serialize_method to 'data_mask' so mask is written out"""
     filename = str(tmpdir.join('test.ecsv'))
@@ -601,7 +575,6 @@ def test_round_trip_masked_table_serialize_mask(tmpdir):
         assert np.all(t2[name] == t[name])
 
 
-@pytest.mark.skipif('not HAS_YAML')
 @pytest.mark.parametrize('table_cls', (Table, QTable))
 def test_ecsv_round_trip_user_defined_unit(table_cls, tmpdir):
     """Ensure that we can read-back enabled user-defined units."""
@@ -822,7 +795,6 @@ def test_full_repr_roundtrip():
 
 # First here is some helper code used to make the expected outputs code.
 def _get_ecsv_header_dict(text):
-    import yaml
     lines = [line.strip() for line in text.splitlines()]
     lines = [line[2:] for line in lines if line.startswith('#')]
     lines = lines[2:]  # Get rid of the header

astropy/io/ascii/tests/test_write.py

@@ -748,7 +748,7 @@ def test_roundtrip_masked(fmt_name_class):
     fast = fmt_name in ascii.core.FAST_CLASSES
     try:
         ascii.write(t, out, format=fmt_name, fast_writer=fast)
-    except ImportError:  # Some failed dependency, e.g. PyYAML, skip test
+    except ImportError:  # Some failed dependency, skip test
         return
 
     # No-header formats need to be told the column names

astropy/io/fits/connect.py

@@ -11,9 +11,8 @@
 from astropy.io import registry as io_registry
 from astropy import units as u
 from astropy.table import Table, serialize, meta, Column, MaskedColumn
-from astropy.table.table import has_info_class
 from astropy.time import Time
-from astropy.utils.data_info import MixinInfo, serialize_context_as
+from astropy.utils.data_info import serialize_context_as
 from astropy.utils.exceptions import (AstropyUserWarning,
                                       AstropyDeprecationWarning)
 from . import HDUList, TableHDU, BinTableHDU, GroupsHDU, append as fits_append
@@ -92,20 +91,7 @@ def _decode_mixins(tbl):
     if not tbl.meta['comments']:
         del tbl.meta['comments']
 
-    try:
-        info = meta.get_header_from_yaml(lines)
-    except ImportError as exc:
-        if 'PyYAML package is required' in str(exc):
-            warnings.warn(
-                "the file contains information about Astropy native objects "
-                "(mixin columns) that have been serialized when writing it, "
-                "but the PyYAML package is required to read those. Without "
-                "this package some information will be missing in the table",
-                AstropyUserWarning
-            )
-            return tbl
-        else:
-            raise
+    info = meta.get_header_from_yaml(lines)
 
     # Add serialized column information to table meta for use in constructing mixins
     tbl.meta['__serialized_columns__'] = info['meta']['__serialized_columns__']
@@ -324,30 +310,6 @@ def _encode_mixins(tbl):
                         for attr in ('description', 'meta'))
                     for col in tbl.itercols())
 
-    # If PyYAML is not available then check to see if there are any mixin cols
-    # that *require* YAML serialization.  FITS already has support for Time,
-    # Quantity, so if those are the only mixins the proceed without doing the
-    # YAML bit, for backward compatibility (i.e. not requiring YAML to write
-    # Time or Quantity).  In this case other mixin column meta (e.g.
-    # description or meta) will be silently dropped, consistent with astropy <=
-    # 2.0 behavior.
-    try:
-        import yaml  # noqa
-    except ImportError:
-        for col in tbl.itercols():
-            if (has_info_class(col, MixinInfo) and
-                    col.__class__ not in (u.Quantity, Time)):
-                raise TypeError("cannot write type {} column '{}' "
-                                "to FITS without PyYAML installed."
-                                .format(col.__class__.__name__, col.info.name))
-        else:
-            if info_lost:
-                warnings.warn("table contains column(s) with defined 'format',"
-                              " 'description', or 'meta' info attributes. These"
-                              " will be dropped unless you install PyYAML.",
-                              AstropyUserWarning)
-            return tbl
-
     # Convert the table to one with no mixins, only Column objects.  This adds
     # meta data which is extracted with meta.get_yaml_from_table.  This ignores
     # Time-subclass columns and leave them in the table so that the downstream

astropy/io/fits/convenience.py

@@ -551,10 +551,9 @@ def table_to_hdu(table, character_as_bytes=False):
                         "though one has to enable the unit before reading.")
                 else:
                     warning += (
-                        "and cannot be recovered in reading. If pyyaml is "
-                        "installed, it can roundtrip within astropy by "
-                        "using QTable both to write and read back, "
-                        "though one has to enable the unit before reading.")
+                        "and cannot be recovered in reading. It can roundtrip "
+                        "within astropy by using QTable both to write and read "
+                        "back, though one has to enable the unit before reading.")
                 warnings.warn(warning, AstropyUserWarning)
 
             else: