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.

I haven't yet updated tests or the changelog.

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

[nicholebarry]

ohhh agreed.