Various fixes

[bhazelton]

Various fixes

This collects a number of bug fixes plus a few doc fixes for things I stumbled on trying to get data through.

fixes #59
fixes #63
fixes #66

progress on #70, but issues remain.

Types of Changes

• Bug Fixes
• New Feature(s)
• Breaking Changes
• Documentation
• Version Change
• Translation from FHD
• Build or CI Change

Changelog

Bug Fixes

• Fixed errors when using ~ in file paths to indicate a user's home directory.
• Fixed a bug that causes errors on current versions of numpy in calibration_utils.py
• Fixed erroneous assumptions of RA/Dec keywords in uvfits.py. This is not really a full fix, but it got me over the problem. There are still lurking issues around handling of telescope locations.
• Fixed checkpointing. It was completely broken because it was trying to read data in from a boolean value.
• Fixed vis_model_transfer.py to handle the standard FHD folder layout.
• Fixed a misspelled option in the example yamls (and therefore the tutorial) for calibration checkpointing.
• Fixed a shape error in calibration_utils that occurs when flagging is present.
• Fixed a KeyError caused by failing to check for key existence
• Fixed an error in image plotting that caused a variable not to be defined.
• Fixed a KeyError and numpy indexing errors in beam_image
• Fixed defaulting of baseline_threshold in dirty_image_generate.

General PR Checklist

• I have the read the contribution guide
• Add all the above to the Changelog into the unreleased section

Existing Tests Checklist

• If some tests fail and they are meant to, have they been changed? if so mention the exact tests that were changed and why here
• Have the changes to existing tests been documented either through comments, changes to the docstring in ether the test or the associated functions?

Bug Fixes Checklist

• Added all bug fixes with any issues associated with them linked.
• Added new tests to cover bugs
• Adjusted existing tests to cover bug, in which case check the Existing Tests Checklist

Documentation Checklist

• The documentation is able to build successfully with any new changes and they are visible in your own build

[nicholebarry]

Is it worth linking the memo here for the uninitiated? Or putting it in the repo somewhere

[bhazelton]

I added information about how to find it either in the pyuvdata repo or on the NRAO website

[nicholebarry]

ohhh agreed.

[codecov]

Codecov Report

❌ Patch coverage is 11.26761% with 63 lines in your changes missing coverage. Please review.
✅ Project coverage is 32.74%. Comparing base (a0cea8d) to head (0266cb6).
⚠️ Report is 22 commits behind head on main.

Files with missing lines	Patch %	Lines
PyFHD/pyfhd.py	0.00%	33 Missing ⚠️
PyFHD/beam_setup/beam_utils.py	0.00%	8 Missing ⚠️
PyFHD/data_setup/uvfits.py	36.36%	4 Missing and 3 partials ⚠️
PyFHD/source_modeling/vis_model_transfer.py	0.00%	7 Missing ⚠️
PyFHD/pyfhd_tools/pyfhd_setup.py	44.44%	2 Missing and 3 partials ⚠️
PyFHD/calibration/calibration_utils.py	0.00%	2 Missing ⚠️
PyFHD/plotting/image.py	0.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #71      +/-   ##
==========================================
- Coverage   32.86%   32.74%   -0.13%     
==========================================
  Files          27       27              
  Lines        5501     5540      +39     
  Branches     1002     1012      +10     
==========================================
+ Hits         1808     1814       +6     
- Misses       3496     3525      +29     
- Partials      197      201       +4     

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

🚀 New features to boost your workflow:

• ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.