jsdillon: Thanks for a super quick review @bhazelton!
diff --git a/CHANGELOG.md b/CHANGELOG.md
index bf6fdbd7..1b3a4981 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -8,6 +8,7 @@ All notable changes to this project will be documented in this file.
 - `utils.apply_uvflag` for applying UVFlag objects to UVData objects
 
 ### Fixed
+- A bug in `UVCal` objects that prevented them from properly getting data with `ee`/`nn`-style polarizations.
 - a bug in `UVFlag` where `x_orientation` was not set during initialization.
 - A bug in `UVCal.read_fhd_cal` that caused calibration solutions to be approximately doubled.
 - A bug in UVFlag where polarization array states were not updated when using `force_pol` keyword in `to_antenna` and `to_baseline`
diff --git a/ci/pyuvdata_linting.yml b/ci/pyuvdata_linting.yml
index 2313fca0..f1a7a055 100644
--- a/ci/pyuvdata_linting.yml
+++ b/ci/pyuvdata_linting.yml
@@ -4,6 +4,7 @@ channels:
   - conda-forge
 dependencies:
   - flake8
+  - pip
   - pip:
     - flake8-docstrings
     - flake8-pytest
diff --git a/pyuvdata/uvcal.py b/pyuvdata/uvcal.py
index 94943034..e04d1ab8 100644
--- a/pyuvdata/uvcal.py
+++ b/pyuvdata/uvcal.py
@@ -761,7 +761,7 @@ class UVCal(UVBase):
             Index in data arrays
         """
         if isinstance(jpol, (str, np.str)):
-            jpol = uvutils.jstr2num(jpol)
+            jpol = uvutils.jstr2num(jpol, x_orientation=self.x_orientation)
 
         if not self._has_key(jpol=jpol):
             raise ValueError("{} not found in jones_array".format(jpol))
@@ -777,7 +777,7 @@ class UVCal(UVBase):
                 return False
         if jpol is not None:
             if isinstance(jpol, (str, np.str)):
-                jpol = uvutils.jstr2num(jpol)
+                jpol = uvutils.jstr2num(jpol, x_orientation=self.x_orientation)
             if jpol not in self.jones_array:
                 return False
 

UVCal objects don't use x_orientation properly
This occurs twice.

https://github.com/RadioAstronomySoftwareGroup/pyuvdata/blob/fb15b4a3f1546da06ba2531e04455eb3e6d9a7ea/pyuvdata/uvcal.py#L764

https://github.com/RadioAstronomySoftwareGroup/pyuvdata/blob/fb15b4a3f1546da06ba2531e04455eb3e6d9a7ea/pyuvdata/uvcal.py#L780

Both times, `jstr2num` should use `self.x_orientation` to allow for queries with `Jee` or `Jnn` in `get_gains()`, `get_flags()`, and `get_qualities()`.
diff --git a/pyuvdata/tests/test_uvcal.py b/pyuvdata/tests/test_uvcal.py
index 012e72f6..42455da1 100644
--- a/pyuvdata/tests/test_uvcal.py
+++ b/pyuvdata/tests/test_uvcal.py
@@ -1443,7 +1443,7 @@ def test_uvcal_get_methods():
     uvc.read_calfits(os.path.join(DATA_PATH, 'zen.2457698.40355.xx.gain.calfits'))
 
     # test get methods: add in a known value and make sure it is returned
-    key = (10, 'Jxx')
+    key = (10, 'Jee')
     uvc.gain_array[1] = 0.0
     d, f, q = uvc.get_gains(key), uvc.get_flags(key), uvc.get_quality(key)
 
@@ -1470,14 +1470,14 @@ def test_uvcal_get_methods():
 
     # check has_key
     assert uvc._has_key(antnum=10)
-    assert uvc._has_key(jpol='Jxx')
-    assert uvc._has_key(antnum=10, jpol='Jxx')
-    assert not uvc._has_key(antnum=10, jpol='Jyy')
-    assert not uvc._has_key(antnum=101, jpol='Jxx')
+    assert uvc._has_key(jpol='Jee')
+    assert uvc._has_key(antnum=10, jpol='Jee')
+    assert not uvc._has_key(antnum=10, jpol='Jnn')
+    assert not uvc._has_key(antnum=101, jpol='Jee')
 
     # test exceptions
     pytest.raises(ValueError, uvc.get_gains, 1)
-    pytest.raises(ValueError, uvc.get_gains, (10, 'Jyy'))
+    pytest.raises(ValueError, uvc.get_gains, (10, 'Jnn'))
     uvc.cal_type = 'delay'
     pytest.raises(ValueError, uvc.get_gains, 10)
 

pip install -e .
parse_log_pytest
requirements.txt
pytest pytest-cov pytest-xdist pytest-mock pytest-asyncio pypandoc
apt-get update apt-get install -y gcc g++
3.6
docs/requirements.txt
pytest --no-header -rA --tb=line --color=no -p no:cacheprovider -W ignore::DeprecationWarning
alabaster==0.7.13
astropy==4.1
attrs==22.2.0
Babel==2.11.0
cached-property==1.5.2
certifi==2021.5.30
charset-normalizer==2.0.12
coverage==6.2
docutils==0.18.1
execnet==1.9.0
h5py==3.1.0
idna==3.10
imagesize==1.4.1
importlib-metadata==4.8.3
iniconfig==1.1.1
Jinja2==3.0.3
MarkupSafe==2.0.1
numpy==1.19.5
packaging==21.3
pluggy==1.0.0
py==1.11.0
Pygments==2.14.0
pypandoc==1.14
pyparsing==3.1.4
pytest==7.0.1
pytest-asyncio==0.16.0
pytest-cov==4.0.0
pytest-mock==3.6.1
pytest-xdist==3.0.2
pytz==2025.2
-e git+https://github.com/RadioAstronomySoftwareGroup/pyuvdata.git@fb15b4a3f1546da06ba2531e04455eb3e6d9a7ea#egg=pyuvdata
requests==2.27.1
scipy==1.5.4
six==1.17.0
snowballstemmer==2.2.0
Sphinx==5.3.0
sphinxcontrib-applehelp==1.0.2
sphinxcontrib-devhelp==1.0.2
sphinxcontrib-htmlhelp==2.0.0
sphinxcontrib-jsmath==1.0.1
sphinxcontrib-qthelp==1.0.3
sphinxcontrib-serializinghtml==1.1.5
tomli==1.2.3
typing_extensions==4.1.1
urllib3==1.26.20
zipp==3.6.0

name: pyuvdata
channels:
  - defaults
  - https://repo.anaconda.com/pkgs/main
  - https://repo.anaconda.com/pkgs/r
  - conda-forge
dependencies:
  - _libgcc_mutex=0.1=main
  - _openmp_mutex=5.1=1_gnu
  - ca-certificates=2025.2.25=h06a4308_0
  - certifi=2021.5.30=py36h06a4308_0
  - ld_impl_linux-64=2.40=h12ee557_0
  - libffi=3.3=he6710b0_2
  - libgcc-ng=11.2.0=h1234567_1
  - libgomp=11.2.0=h1234567_1
  - libstdcxx-ng=11.2.0=h1234567_1
  - ncurses=6.4=h6a678d5_0
  - openssl=1.1.1w=h7f8727e_0
  - pip=21.2.2=py36h06a4308_0
  - python=3.6.13=h12debd9_1
  - readline=8.2=h5eee18b_0
  - setuptools=58.0.4=py36h06a4308_0
  - sqlite=3.45.3=h5eee18b_0
  - tk=8.6.14=h39e8969_0
  - wheel=0.37.1=pyhd3eb1b0_0
  - xz=5.6.4=h5eee18b_1
  - zlib=1.2.13=h5eee18b_1
  - pip:
      - alabaster==0.7.13
      - astropy==4.1
      - attrs==22.2.0
      - babel==2.11.0
      - cached-property==1.5.2
      - charset-normalizer==2.0.12
      - coverage==6.2
      - docutils==0.18.1
      - execnet==1.9.0
      - h5py==3.1.0
      - idna==3.10
      - imagesize==1.4.1
      - importlib-metadata==4.8.3
      - iniconfig==1.1.1
      - jinja2==3.0.3
      - markupsafe==2.0.1
      - numpy==1.19.5
      - packaging==21.3
      - pluggy==1.0.0
      - py==1.11.0
      - pygments==2.14.0
      - pypandoc==1.14
      - pyparsing==3.1.4
      - pytest==7.0.1
      - pytest-asyncio==0.16.0
      - pytest-cov==4.0.0
      - pytest-mock==3.6.1
      - pytest-xdist==3.0.2
      - pytz==2025.2
      - requests==2.27.1
      - scipy==1.5.4
      - six==1.17.0
      - snowballstemmer==2.2.0
      - sphinx==5.3.0
      - sphinxcontrib-applehelp==1.0.2
      - sphinxcontrib-devhelp==1.0.2
      - sphinxcontrib-htmlhelp==2.0.0
      - sphinxcontrib-jsmath==1.0.1
      - sphinxcontrib-qthelp==1.0.3
      - sphinxcontrib-serializinghtml==1.1.5
      - tomli==1.2.3
      - typing-extensions==4.1.1
      - urllib3==1.26.20
      - zipp==3.6.0
prefix: /opt/conda/envs/pyuvdata

pyuvdata/tests/test_uvcal.py::test_uvcal_get_methods
pyuvdata/tests/test_uvcal.py::test_parameter_iter pyuvdata/tests/test_uvcal.py::test_required_parameter_iter pyuvdata/tests/test_uvcal.py::test_unexpected_parameters pyuvdata/tests/test_uvcal.py::test_unexpected_attributes pyuvdata/tests/test_uvcal.py::test_properties pyuvdata/tests/test_uvcal.py::test_equality pyuvdata/tests/test_uvcal.py::test_check pyuvdata/tests/test_uvcal.py::test_nants_data_telescope_larger pyuvdata/tests/test_uvcal.py::test_ant_array_not_in_antnums pyuvdata/tests/test_uvcal.py::test_set_gain pyuvdata/tests/test_uvcal.py::test_set_delay pyuvdata/tests/test_uvcal.py::test_set_unknown pyuvdata/tests/test_uvcal.py::test_convert_filetype pyuvdata/tests/test_uvcal.py::test_convert_to_gain pyuvdata/tests/test_uvcal.py::test_select_antennas pyuvdata/tests/test_uvcal.py::test_select_times pyuvdata/tests/test_uvcal.py::test_select_frequencies pyuvdata/tests/test_uvcal.py::test_select_freq_chans pyuvdata/tests/test_uvcal.py::test_select_polarizations pyuvdata/tests/test_uvcal.py::test_select pyuvdata/tests/test_uvcal.py::test_select_antennas_delay pyuvdata/tests/test_uvcal.py::test_select_times_delay pyuvdata/tests/test_uvcal.py::test_select_frequencies_delay pyuvdata/tests/test_uvcal.py::test_select_freq_chans_delay pyuvdata/tests/test_uvcal.py::test_select_polarizations_delay pyuvdata/tests/test_uvcal.py::test_select_delay pyuvdata/tests/test_uvcal.py::test_add_antennas pyuvdata/tests/test_uvcal.py::test_add_frequencies pyuvdata/tests/test_uvcal.py::test_add_times pyuvdata/tests/test_uvcal.py::test_add_jones pyuvdata/tests/test_uvcal.py::test_add pyuvdata/tests/test_uvcal.py::test_add_multiple_axes pyuvdata/tests/test_uvcal.py::test_add_errors pyuvdata/tests/test_uvcal.py::test_jones_warning pyuvdata/tests/test_uvcal.py::test_frequency_warnings pyuvdata/tests/test_uvcal.py::test_parameter_warnings pyuvdata/tests/test_uvcal.py::test_multi_files pyuvdata/tests/test_uvcal.py::test_add_antennas_delay pyuvdata/tests/test_uvcal.py::test_add_times_delay pyuvdata/tests/test_uvcal.py::test_add_jones_delay pyuvdata/tests/test_uvcal.py::test_add_errors_delay pyuvdata/tests/test_uvcal.py::test_multi_files_delay pyuvdata/tests/test_uvcal.py::test_write_read_optional_attrs pyuvdata/tests/test_uvcal.py::test_deprecated_x_orientation
pyuvdata/uvcal.py CHANGELOG.md ci/pyuvdata_linting.yml
pyuvdata/uvcal.py CHANGELOG.md ci/pyuvdata_linting.yml