parameter min and max values

[KatyBrown]

Hi Lotti,

I have:

• Set it up so that we can give default, minimum and maximum values to all the numeric parameters for the cleaning functions by editing the file "ranges.txt" in the CIAlign/CIAlign folder. This is just for us to use, not the users - so we can set the range of values which are valid. When we change them the --help and the range which the program will accept will automatically update. I also set up the manual to automatically include these by running the update_manual.py script - which replaces the old update_manual.sh script. Instead of updating user_guide.md we should now update user_guide_template.md.

• Moved all the argument parser stuff from CIAlign.py to a separate file - argP.py

• Fixed a couple of small errors with the testing - I think these were just due to differences between our machines.

  • Instead of checking the images for the mini alignments are identical it now checks that they are highly similar - because there were minor differences in the rendering between the test image and the one I made - different shades of the same colour or tiny differences in where the borders of the colours are.
  • The tests for cropSeq.py were raising the warning you added in https://github.com/KatyBrown/CIAlign/commit/195f043284a358e463315a05cf29b218b67c3820 so I made mingap_perc for the tests a bit bigger and some of the sequences a bit longer - please check it's still testing what you wanted it to test.
  • the listFonts function was raising a few "glyph error" warnings on my computer - I just made it skip the fonts that cause these warnings

Please merge this in if it's all OK with you!

Katy

[KatyBrown]

Superceded by my later pull request