Merge pull request #15396 from saimn/fits-deprecation

Remove deprecated code and deprecate a few more things in io.fits

astropy/io/fits/hdu/base.py

@@ -27,6 +27,7 @@
 )
 from astropy.io.fits.verify import _ErrList, _Verify
 from astropy.utils import lazyproperty
+from astropy.utils.decorators import deprecated
 from astropy.utils.exceptions import AstropyUserWarning
 
 __all__ = [
@@ -109,7 +110,11 @@ def _hdu_class_from_header(cls, header):
                     or c in cls._hdu_registry
                 ):
                     continue
-                if c.match_header(header):
+                # skip _NonstandardExtHDU and _ExtensionHDU since those are deprecated
+                if c.match_header(header) and c not in (
+                    _NonstandardExtHDU,
+                    _ExtensionHDU,
+                ):
                     klass = c
                     break
             except NotImplementedError:
@@ -1613,9 +1618,9 @@ def _verify(self, option="warn"):
         return errs
 
 
-# For backwards compatibility, though this needs to be deprecated
-# TODO: Mark this as deprecated
-_ExtensionHDU = ExtensionHDU
+@deprecated("v6.0")
+class _ExtensionHDU(ExtensionHDU):
+    pass
 
 
 class NonstandardExtHDU(ExtensionHDU):
@@ -1662,5 +1667,6 @@ def data(self):
         return self._get_raw_data(self.size, "ubyte", self._data_offset)
 
 
-# TODO: Mark this as deprecated
-_NonstandardExtHDU = NonstandardExtHDU
+@deprecated("v6.0")
+class _NonstandardExtHDU(NonstandardExtHDU):
+    pass

astropy/io/fits/hdu/table.py

@@ -8,7 +8,6 @@
 import re
 import sys
 import textwrap
-import warnings
 from contextlib import suppress
 
 import numpy as np
@@ -38,7 +37,7 @@
 from astropy.io.fits.header import Header, _pad_length
 from astropy.io.fits.util import _is_int, _str_to_num, path_like
 from astropy.utils import lazyproperty
-from astropy.utils.exceptions import AstropyDeprecationWarning
+from astropy.utils.decorators import deprecated
 
 from .base import DELAYED, ExtensionHDU, _ValidHDU
 
@@ -351,40 +350,6 @@ def __init__(
                 else:
                     self.data = self._data_type.from_columns(data)
 
-                # TEMP: Special column keywords are normally overwritten by attributes
-                # from Column objects. In Astropy 3.0, several new keywords are now
-                # recognized as being special column keywords, but we don't
-                # automatically clear them yet, as we need to raise a deprecation
-                # warning for at least one major version.
-                if header is not None:
-                    future_ignore = set()
-                    for keyword in header.keys():
-                        match = TDEF_RE.match(keyword)
-                        try:
-                            base_keyword = match.group("label")
-                        except Exception:
-                            continue  # skip if there is no match
-                        if base_keyword in {
-                            "TCTYP",
-                            "TCUNI",
-                            "TCRPX",
-                            "TCRVL",
-                            "TCDLT",
-                            "TRPOS",
-                        }:
-                            future_ignore.add(base_keyword)
-                    if future_ignore:
-                        keys = ", ".join(x + "n" for x in sorted(future_ignore))
-                        warnings.warn(
-                            "The following keywords are now recognized as special "
-                            "column-related attributes and should be set via the "
-                            f"Column objects: {keys}. In future, these values will be "
-                            "dropped from manually specified headers automatically "
-                            "and replaced with values generated based on the "
-                            "Column objects.",
-                            AstropyDeprecationWarning,
-                        )
-
                 # TODO: Too much of the code in this class uses header keywords
                 # in making calculations related to the data size.  This is
                 # unreliable, however, in cases when users mess with the header
@@ -395,7 +360,7 @@ def __init__(
 
                 self.columns = self.data._coldefs
                 self.columns._add_listener(self.data)
-                self.update()
+                self.update_header()
 
                 with suppress(TypeError, AttributeError):
                     # Make the ndarrays in the Column objects of the ColDefs
@@ -484,7 +449,7 @@ def data(self, data):
 
             self.columns = self.data.columns
             self.columns._add_listener(self.data)
-            self.update()
+            self.update_header()
 
             with suppress(TypeError, AttributeError):
                 # Make the ndarrays in the Column objects of the ColDefs
@@ -517,10 +482,11 @@ def _theap(self):
         size = self._header["NAXIS1"] * self._header["NAXIS2"]
         return self._header.get("THEAP", size)
 
-    # TODO: Need to either rename this to update_header, for symmetry with the
-    # Image HDUs, or just at some point deprecate it and remove it altogether,
-    # since header updates should occur automatically when necessary...
+    @deprecated("v6.0", alternative="update_header")
     def update(self):
+        self.update_header()
+
+    def update_header(self):
         """
         Update header keywords to reflect recent changes of columns.
         """
@@ -702,20 +668,6 @@ def _clear_table_keywords(self, index=None):
                 continue  # skip if there is no match
 
             if base_keyword in KEYWORD_TO_ATTRIBUTE:
-                # TEMP: For Astropy 3.0 we don't clear away the following keywords
-                # as we are first raising a deprecation warning that these will be
-                # dropped automatically if they were specified in the header. We
-                # can remove this once we are happy to break backward-compatibility
-                if base_keyword in {
-                    "TCTYP",
-                    "TCUNI",
-                    "TCRPX",
-                    "TCRVL",
-                    "TCDLT",
-                    "TRPOS",
-                }:
-                    continue
-
                 num = int(match.group("num")) - 1  # convert to zero-base
                 table_keywords.append((idx, match.group(0), base_keyword, num))
 

astropy/io/fits/header.py

@@ -1057,50 +1057,6 @@ def update(self, *args, **kwargs):
 
             header.update({'NAXIS1': 100, 'NAXIS2': 100})
 
-        .. warning::
-            As this method works similarly to `dict.update` it is very
-            different from the ``Header.update()`` method in Astropy v0.1.
-            Use of the old API was
-            **deprecated** for a long time and is now removed. Most uses of the
-            old API can be replaced as follows:
-
-            * Replace ::
-
-                  header.update(keyword, value)
-
-              with ::
-
-                  header[keyword] = value
-
-            * Replace ::
-
-                  header.update(keyword, value, comment=comment)
-
-              with ::
-
-                  header[keyword] = (value, comment)
-
-            * Replace ::
-
-                  header.update(keyword, value, before=before_keyword)
-
-              with ::
-
-                  header.insert(before_keyword, (keyword, value))
-
-            * Replace ::
-
-                  header.update(keyword, value, after=after_keyword)
-
-              with ::
-
-                  header.insert(after_keyword, (keyword, value),
-                                after=True)
-
-            See also :meth:`Header.set` which is a new method that provides an
-            interface similar to the old ``Header.update()`` and may help make
-            transition a little easier.
-
         """
         if args:
             other = args[0]

astropy/io/fits/tests/test_core.py

@@ -25,7 +25,7 @@
     HAS_BZ2,  # NOTE: Python can be built without bz2
 )
 from astropy.utils.data import conf
-from astropy.utils.exceptions import AstropyUserWarning
+from astropy.utils.exceptions import AstropyDeprecationWarning, AstropyUserWarning
 from astropy.utils.misc import _NOT_OVERWRITING_MSG_MATCH
 
 from .conftest import FitsTestCase
@@ -1466,3 +1466,12 @@ def test_error_if_memmap_impossible(self):
         # See https://github.com/astropy/astropy/issues/3766
         with fits.open(pth, memmap=True, do_not_scale_image_data=True) as hdul:
             hdul[0].data  # Just make sure it doesn't crash
+
+
+def test_deprecated_hdu_classes():
+    from astropy.io.fits.hdu.base import _ExtensionHDU, _NonstandardExtHDU
+
+    with pytest.warns(AstropyDeprecationWarning):
+        _ExtensionHDU()
+    with pytest.warns(AstropyDeprecationWarning):
+        _NonstandardExtHDU()

astropy/io/fits/tests/test_table.py

@@ -6,7 +6,6 @@
 import pickle
 import re
 import sys
-import warnings
 
 import numpy as np
 import pytest
@@ -26,7 +25,7 @@
 from astropy.table import Table
 from astropy.units import Unit, UnitsWarning, UnrecognizedUnit
 from astropy.utils.compat import NUMPY_LT_1_22_1
-from astropy.utils.exceptions import AstropyDeprecationWarning, AstropyUserWarning
+from astropy.utils.exceptions import AstropyUserWarning
 
 from .conftest import FitsTestCase
 
@@ -3786,118 +3785,6 @@ def test_regression_scalar_indexing():
     assert all(a == b for a, b in zip(x1a, x1b))
 
 
-def test_new_column_attributes_preserved(tmp_path):
-    # Regression test for https://github.com/astropy/astropy/issues/7145
-    # This makes sure that for now we don't clear away keywords that have
-    # newly been recognized (in Astropy 3.0) as special column attributes but
-    # instead just warn that we might do so in future. The new keywords are:
-    # TCTYP, TCUNI, TCRPX, TCRVL, TCDLT, TRPOS
-
-    col = []
-    col.append(fits.Column(name="TIME", format="1E", unit="s"))
-    col.append(fits.Column(name="RAWX", format="1I", unit="pixel"))
-    col.append(fits.Column(name="RAWY", format="1I"))
-    cd = fits.ColDefs(col)
-
-    hdr = fits.Header()
-
-    # Keywords that will get ignored in favor of these in the data
-    hdr["TUNIT1"] = "pixel"
-    hdr["TUNIT2"] = "m"
-    hdr["TUNIT3"] = "m"
-
-    # Keywords that were added in Astropy 3.0 that should eventually be
-    # ignored and set on the data instead
-    hdr["TCTYP2"] = "RA---TAN"
-    hdr["TCTYP3"] = "ANGLE"
-    hdr["TCRVL2"] = -999.0
-    hdr["TCRVL3"] = -999.0
-    hdr["TCRPX2"] = 1.0
-    hdr["TCRPX3"] = 1.0
-    hdr["TALEN2"] = 16384
-    hdr["TALEN3"] = 1024
-    hdr["TCUNI2"] = "angstrom"
-    hdr["TCUNI3"] = "deg"
-
-    # Other non-relevant keywords
-    hdr["RA"] = 1.5
-    hdr["DEC"] = 3.0
-
-    with pytest.warns(AstropyDeprecationWarning) as warning_list:
-        hdu = fits.BinTableHDU.from_columns(cd, hdr)
-    assert str(warning_list[0].message).startswith(
-        "The following keywords are now recognized as special"
-    )
-
-    # First, check that special keywords such as TUNIT are ignored in the header
-    # We may want to change that behavior in future, but this is the way it's
-    # been for a while now.
-
-    assert hdu.columns[0].unit == "s"
-    assert hdu.columns[1].unit == "pixel"
-    assert hdu.columns[2].unit is None
-
-    assert hdu.header["TUNIT1"] == "s"
-    assert hdu.header["TUNIT2"] == "pixel"
-    assert "TUNIT3" not in hdu.header  # TUNIT3 was removed
-
-    # Now, check that the new special keywords are actually still there
-    # but weren't used to set the attributes on the data
-
-    assert hdu.columns[0].coord_type is None
-    assert hdu.columns[1].coord_type is None
-    assert hdu.columns[2].coord_type is None
-
-    assert "TCTYP1" not in hdu.header
-    assert hdu.header["TCTYP2"] == "RA---TAN"
-    assert hdu.header["TCTYP3"] == "ANGLE"
-
-    # Make sure that other keywords are still there
-
-    assert hdu.header["RA"] == 1.5
-    assert hdu.header["DEC"] == 3.0
-
-    # Now we can write this HDU to a file and re-load. Re-loading *should*
-    # cause the special column attributes to be picked up (it's just that when a
-    # header is manually specified, these values are ignored)
-
-    filename = tmp_path / "test.fits"
-
-    hdu.writeto(filename)
-
-    # Make sure we don't emit a warning in this case
-    with warnings.catch_warnings(record=True) as warning_list:
-        with fits.open(filename) as hdul:
-            hdu2 = hdul[1]
-    assert len(warning_list) == 0
-
-    # Check that column attributes are now correctly set
-
-    assert hdu2.columns[0].unit == "s"
-    assert hdu2.columns[1].unit == "pixel"
-    assert hdu2.columns[2].unit is None
-
-    assert hdu2.header["TUNIT1"] == "s"
-    assert hdu2.header["TUNIT2"] == "pixel"
-    assert "TUNIT3" not in hdu2.header  # TUNIT3 was removed
-
-    # Now, check that the new special keywords are actually still there
-    # but weren't used to set the attributes on the data
-
-    assert hdu2.columns[0].coord_type is None
-    assert hdu2.columns[1].coord_type == "RA---TAN"
-    assert hdu2.columns[2].coord_type == "ANGLE"
-
-    assert "TCTYP1" not in hdu2.header
-    assert hdu2.header["TCTYP2"] == "RA---TAN"
-    assert hdu2.header["TCTYP3"] == "ANGLE"
-
-    # Make sure that other keywords are still there
-
-    assert hdu2.header["RA"] == 1.5
-    assert hdu2.header["DEC"] == 3.0
-
-
 def test_empty_table(tmp_path):
     ofile = tmp_path / "emptytable.fits"
     hdu = fits.BinTableHDU(header=None, data=None, name="TEST")

docs/changes/io.fits/15396.api.rst

@@ -0,0 +1,7 @@
+Deprecate ``_ExtensionHDU`` and ``_NonstandardExtHDU`` (use ``ExtensionHDU`` or
+``NonstandardExtHDU`` instead).
+
+Remove special handling of TCTYP TCUNI TCRPX TCRVL TCDLT TRPOS (#7157)
+
+Rename and deprecate ``TableHDU.update`` to ``TableHDU.update_header``, for
+consistency with ``ImageHDU``.