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New version #1347

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merged 2 commits into from
Oct 13, 2023
Merged

New version #1347

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794cb2a
remove deprecation warning that was marked to be removed in 2.4
bhazelton Oct 13, 2023
96b35ed
update the changelog for a new version
bhazelton Oct 13, 2023
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2 changes: 2 additions & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,8 @@ All notable changes to this project will be documented in this file.

## [Unreleased]

## [2.4.1] - 2023-10-13

### Added
- Added a `uvw_track_generator` method within `utils` for calculating the expected
uvws (and a few other values) without needing to instantiate a whole `UVData` object.
Expand Down
9 changes: 1 addition & 8 deletions pyuvdata/uvdata/mwa_corr_fits.py
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Expand Up @@ -1268,7 +1268,7 @@ def read_mwa_corr_fits(
use_aoflagger_flags=None,
remove_dig_gains=True,
remove_coarse_band=True,
correct_cable_len=None,
correct_cable_len=True,
correct_van_vleck=False,
cheby_approx=True,
flag_small_auto_ants=True,
Expand Down Expand Up @@ -1766,13 +1766,6 @@ def read_mwa_corr_fits(
self.data_array *= self.extra_keywords["SCALEFAC"]

# cable delay corrections
if correct_cable_len is None:
correct_cable_len = True
warnings.warn(
"cable length correction is now defaulted to True rather than "
"False. To read in files without applying the correction set "
"correct_cable_len=False. This warning will be removed in v2.4"
)
if correct_cable_len:
self.correct_cable_length(
meta_dict["cable_lens"], ant_1_inds, ant_2_inds
Expand Down
33 changes: 0 additions & 33 deletions pyuvdata/uvdata/tests/test_mwa_corr_fits.py
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Original file line number Diff line number Diff line change
Expand Up @@ -175,7 +175,6 @@ def test_read_mwax_write_uvfits(tmp_path):


@pytest.mark.filterwarnings("ignore:some coarse channel files were not submitted")
@pytest.mark.filterwarnings("ignore:cable length correction is now defaulted to True")
def test_mwax_metafits_keys(tmp_path):
"""Check that mwax keywords are removed from extra_keywords for legacy files"""
meta_spoof_file = str(tmp_path / "spoof_1131733552.metafits")
Expand All @@ -189,7 +188,6 @@ def test_mwax_metafits_keys(tmp_path):


@pytest.mark.filterwarnings("ignore:some coarse channel files were not submitted")
@pytest.mark.filterwarnings("ignore:cable length correction is now defaulted to True")
def test_select_on_read():
mwa_uv = UVData()
mwa_uv2 = UVData()
Expand Down Expand Up @@ -297,7 +295,6 @@ def test_read_mwa_write_uvfits_meta_mod(tmp_path):

@pytest.mark.filterwarnings("ignore:some coarse channel files were not submitted")
@pytest.mark.filterwarnings("ignore:Combined frequencies are separated by more than")
@pytest.mark.filterwarnings("ignore:cable length correction is now defaulted to True")
def test_read_mwa_multi():
"""Test reading in two sets of files."""
set1 = filelist[0:2]
Expand All @@ -309,9 +306,7 @@ def test_read_mwa_multi():
mwa_uv2 = UVData()
messages = [
"some coarse channel files were not submitted",
"cable length correction is now defaulted to True",
"some coarse channel files were not submitted",
"cable length correction is now defaulted to True",
"Combined frequencies are separated by more than their channel width",
]
with uvtest.check_warnings(UserWarning, messages):
Expand All @@ -324,7 +319,6 @@ def test_read_mwa_multi():

@pytest.mark.filterwarnings("ignore:some coarse channel files were not submitted")
@pytest.mark.filterwarnings("ignore:Combined frequencies are separated by more than")
@pytest.mark.filterwarnings("ignore:cable length correction is now defaulted to True")
def test_read_mwa_multi_concat(tmp_path):
"""Test reading in two sets of files with fast concatenation."""
# modify file so that time arrays are matching
Expand All @@ -340,9 +334,7 @@ def test_read_mwa_multi_concat(tmp_path):
mwa_uv2 = UVData()
messages = [
"some coarse channel files were not submitted",
"cable length correction is now defaulted to True",
"some coarse channel files were not submitted",
"cable length correction is now defaulted to True",
"Combined frequencies are separated by more than their channel width",
]
with uvtest.check_warnings(UserWarning, messages):
Expand All @@ -365,7 +357,6 @@ def test_read_mwa_flags():
messages = [
"mwaf files submitted with use_aoflagger_flags=False",
"some coarse channel files were not submitted",
"cable length correction is now defaulted to True",
]
with uvtest.check_warnings(UserWarning, messages):
mwa_uv.read(subfiles, use_aoflagger_flags=False, use_future_array_shapes=True)
Expand Down Expand Up @@ -394,7 +385,6 @@ def test_multiple_coarse():
messages = [
"coarse channels are not contiguous for this observation",
"some coarse channel files were not submitted",
"cable length correction is now defaulted to True",
]
with uvtest.check_warnings(UserWarning, messages):
mwa_uv1.read(order1, use_future_array_shapes=True)
Expand All @@ -405,7 +395,6 @@ def test_multiple_coarse():


@pytest.mark.filterwarnings("ignore:some coarse channel files were not submitted")
@pytest.mark.filterwarnings("ignore:cable length correction is now defaulted to True")
def test_ppds(tmp_path):
"""Test handling of ppds files"""
# turnaround test with just ppds file given
Expand Down Expand Up @@ -562,7 +551,6 @@ def test_misaligned_times(tmp_path):
"ignore:coarse channels are not contiguous for this observation"
)
@pytest.mark.filterwarnings("ignore:some coarse channel files were not submitted")
@pytest.mark.filterwarnings("ignore:cable length correction is now defaulted to True")
def test_flag_nsample_basic():
"""
Test that the flag(without flag_int) and nsample arrays correctly reflect data.
Expand Down Expand Up @@ -606,7 +594,6 @@ def test_flag_nsample_basic():
"ignore:coarse channels are not contiguous for this observation"
)
@pytest.mark.filterwarnings("ignore:some coarse channel files were not submitted")
@pytest.mark.filterwarnings("ignore:cable length correction is now defaulted to True")
def test_flag_init(flag_file_init):
"""
Test that routine MWA flagging works as intended.
Expand Down Expand Up @@ -636,7 +623,6 @@ def test_flag_init(flag_file_init):
"ignore:coarse channels are not contiguous for this observation"
)
@pytest.mark.filterwarnings("ignore:some coarse channel files were not submitted")
@pytest.mark.filterwarnings("ignore:cable length correction is now defaulted to True")
def test_flag_start_flag(flag_file_init):
uv = UVData()
uv.read(
Expand Down Expand Up @@ -686,7 +672,6 @@ def test_flag_start_flag(flag_file_init):
"ignore:coarse channels are not contiguous for this observation"
)
@pytest.mark.filterwarnings("ignore:some coarse channel files were not submitted")
@pytest.mark.filterwarnings("ignore:cable length correction is now defaulted to True")
def test_flag_init_errors(flag_file_init, err_type, read_kwargs, err_msg):
uv = UVData()
# give noninteger multiple inputs
Expand All @@ -711,7 +696,6 @@ def test_read_metadata_only(tmp_path):


@pytest.mark.filterwarnings("ignore:some coarse channel files were not submitted")
@pytest.mark.filterwarnings("ignore:cable length correction is now defaulted to True")
def test_data_array_precision():
uv = UVData()
uv2 = UVData()
Expand All @@ -730,7 +714,6 @@ def test_data_array_precision():


@pytest.mark.filterwarnings("ignore:some coarse channel files were not submitted")
@pytest.mark.filterwarnings("ignore:cable length correction is now defaulted to True")
def test_nsample_array_precision():
uv = UVData()
uv2 = UVData()
Expand Down Expand Up @@ -769,7 +752,6 @@ def test_invalid_precision_errors():


@pytest.mark.filterwarnings("ignore:some coarse channel files were not submitted")
@pytest.mark.filterwarnings("ignore:cable length correction is now defaulted to True")
def test_remove_dig_gains():
"""Test digital gain removal."""
uv1 = UVData()
Expand Down Expand Up @@ -804,7 +786,6 @@ def test_remove_dig_gains():


@pytest.mark.filterwarnings("ignore:some coarse channel files were not submitted")
@pytest.mark.filterwarnings("ignore:cable length correction is now defaulted to True")
def test_remove_coarse_band(tmp_path):
"""Test coarse band removal."""
# generate a spoof file with 32 channels
Expand Down Expand Up @@ -842,7 +823,6 @@ def test_remove_coarse_band(tmp_path):


@pytest.mark.filterwarnings("ignore:some coarse channel files were not submitted")
@pytest.mark.filterwarnings("ignore:cable length correction is now defaulted to True")
@pytest.mark.filterwarnings("ignore:Fixing auto-correlations to be be real-only")
def test_remove_coarse_band_mwax_40(tmp_path):
"""Test coarse band removal for a 40 kHz mwax file."""
Expand Down Expand Up @@ -878,7 +858,6 @@ def test_remove_coarse_band_mwax_40(tmp_path):


@pytest.mark.filterwarnings("ignore:some coarse channel files were not submitted")
@pytest.mark.filterwarnings("ignore:cable length correction is now defaulted to True")
@pytest.mark.filterwarnings("ignore:Fixing auto-correlations to be be real-only")
def test_remove_coarse_band_mwax_80(tmp_path):
"""Test coarse band removal for an 80 kHz mwax file."""
Expand Down Expand Up @@ -914,7 +893,6 @@ def test_remove_coarse_band_mwax_80(tmp_path):


@pytest.mark.filterwarnings("ignore:some coarse channel files were not submitted")
@pytest.mark.filterwarnings("ignore:cable length correction is now defaulted to True")
@pytest.mark.filterwarnings("ignore:Fixing auto-correlations to be be real-only")
def test_remove_coarse_band_mwax_warning(tmp_path):
"""Test coarse band removal for a file we don't have a passband for."""
Expand Down Expand Up @@ -966,7 +944,6 @@ def test_aoflagger_flags():
)
@pytest.mark.filterwarnings("ignore:some coarse channel files were not submitted")
@pytest.mark.filterwarnings("ignore:coarse channel, start time, and end time flagging")
@pytest.mark.filterwarnings("ignore:cable length correction is now defaulted to True")
def test_aoflagger_flags_multiple(tmp_path):
"""Test aoflagger flags with multiple coarse bands"""
mod_mini_6 = str(tmp_path / "mini_gpubox06_01.fits")
Expand Down Expand Up @@ -995,7 +972,6 @@ def test_aoflagger_flags_multiple(tmp_path):

@pytest.mark.filterwarnings("ignore:some coarse channel files were not submitted")
@pytest.mark.filterwarnings("ignore:coarse channel, start time, and end time flagging")
@pytest.mark.filterwarnings("ignore:cable length correction is now defaulted to True")
def test_mismatch_flags():
"""Break by submitting flag and gpubox files from different coarse bands."""
uv = UVData()
Expand All @@ -1009,7 +985,6 @@ def test_mismatch_flags():
"ignore:coarse channels are not contiguous for this observation"
)
@pytest.mark.filterwarnings("ignore:some coarse channel files were not submitted")
@pytest.mark.filterwarnings("ignore:cable length correction is now defaulted to True")
def test_propagate_coarse_flags():
"""
Test that the flag(without flag_int) and nsample arrays correctly reflect data.
Expand All @@ -1025,7 +1000,6 @@ def test_propagate_coarse_flags():


@pytest.mark.filterwarnings("ignore:some coarse channel files were not submitted")
@pytest.mark.filterwarnings("ignore:cable length correction is now defaulted to True")
def test_start_flag(tmp_path):
"""Test the default value of start_flag."""
uv1 = UVData()
Expand Down Expand Up @@ -1061,7 +1035,6 @@ def test_start_flag(tmp_path):


@pytest.mark.filterwarnings("ignore:some coarse channel files were not submitted")
@pytest.mark.filterwarnings("ignore:cable length correction is now defaulted to True")
def test_start_flag_goodtime_ppds():
"""Test that error is thrown using 'goodtime' with only ppds file."""
uv = UVData()
Expand All @@ -1070,7 +1043,6 @@ def test_start_flag_goodtime_ppds():


@pytest.mark.filterwarnings("ignore:some coarse channel files were not submitted")
@pytest.mark.filterwarnings("ignore:cable length correction is now defaulted to True")
def test_start_flag_bad_string():
"""Test that error is thrown if start_flag is given string other than 'goodtime'"""
uv = UVData()
Expand All @@ -1081,7 +1053,6 @@ def test_start_flag_bad_string():


@pytest.mark.filterwarnings("ignore:some coarse channel files were not submitted")
@pytest.mark.filterwarnings("ignore:cable length correction is now defaulted to True")
def test_start_flag_int_time(tmp_path):
"""Test goodtime returning a start_flag smaller than integration time."""
uv = UVData()
Expand Down Expand Up @@ -1194,7 +1165,6 @@ def test_van_vleck_interp(tmp_path):


@pytest.mark.filterwarnings("ignore:some coarse channel files were not submitted")
@pytest.mark.filterwarnings("ignore:cable length correction is now defaulted to True")
def test_remove_flagged_ants(tmp_path):
"""Test remove_flagged_ants."""
uv1 = UVData()
Expand All @@ -1210,7 +1180,6 @@ def test_remove_flagged_ants(tmp_path):

@pytest.mark.filterwarnings("ignore:some coarse channel files were not submitted")
@pytest.mark.filterwarnings("ignore:.*values are being corrected with the van vleck")
@pytest.mark.filterwarnings("ignore:cable length correction is now defaulted to True")
def test_small_sigs(tmp_path):
"""Test flag_small_auto_ants."""
small_sigs = str(tmp_path / "small_sigs07_02.fits")
Expand All @@ -1227,7 +1196,6 @@ def test_small_sigs(tmp_path):
messages = ["values are being corrected with the van vleck integral"]
messages = messages * 8
messages.append("some coarse channel files were not submitted")
messages.append("cable length correction is now defaulted to True")
uv2 = UVData()
with uvtest.check_warnings(UserWarning, messages):
uv2.read(
Expand All @@ -1242,7 +1210,6 @@ def test_small_sigs(tmp_path):


@pytest.mark.filterwarnings("ignore:some coarse channel files were not submitted")
@pytest.mark.filterwarnings("ignore:cable length correction is now defaulted to True")
@pytest.mark.filterwarnings("ignore:Fixing auto-correlations to be be real-only")
def test_bscale(tmp_path):
"""Test that bscale is saved correctly"""
Expand Down
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