Refactor podo

[GenevieveBuckley]

Unit tests, and more organised validation code that takes CellCounter xml files as input.

[pep8speaks]

Hello @GenevieveBuckley! Thanks for updating the PR.

• There are no PEP8 issues in the file podocytes/__init__.py !

• There are no PEP8 issues in the file podocytes/_version.py !

• In the file podocytes/cellcounter_xml.py, following are the PEP8 issues :

  Line 22:1: E302 expected 2 blank lines, found 0

• There are no PEP8 issues in the file podocytes/image_processing.py !

• In the file podocytes/main.py, following are the PEP8 issues :

  Line 18:1: E402 module level import not at top of file Line 25:1: E402 module level import not at top of file Line 26:1: E402 module level import not at top of file Line 31:1: E402 module level import not at top of file Line 39:1: E402 module level import not at top of file Line 83:17: E128 continuation line under-indented for visual indent Line 85:17: E128 continuation line under-indented for visual indent

• There are no PEP8 issues in the file podocytes/statistics.py !

• There are no PEP8 issues in the file podocytes/test/test_cellcounter_xml.py !

• There are no PEP8 issues in the file podocytes/test/test_image_processing.py !

• There are no PEP8 issues in the file podocytes/test/test_main.py !

• In the file podocytes/test/test_statistics.py, following are the PEP8 issues :

  Line 26:9: E128 continuation line under-indented for visual indent Line 28:9: E128 continuation line under-indented for visual indent

• There are no PEP8 issues in the file podocytes/test/test_util.py !

• There are no PEP8 issues in the file podocytes/test/test_validate.py !

• There are no PEP8 issues in the file podocytes/util.py !

• In the file podocytes/validate.py, following are the PEP8 issues :

  Line 14:1: E402 module level import not at top of file Line 15:1: E402 module level import not at top of file Line 17:1: E402 module level import not at top of file Line 18:1: E402 module level import not at top of file Line 24:1: E402 module level import not at top of file Line 64:1: E302 expected 2 blank lines, found 0 Line 99:80: E501 line too long (81 > 79 characters) Line 106:80: E501 line too long (80 > 79 characters)

Comment last updated on November 21, 2018 at 06:28 Hours UTC

[GenevieveBuckley]

• closes https://github.com/monashmicroimaging/podocytes/issues/21 (Need to filter out hidden files)
• closes https://github.com/monashmicroimaging/podocytes/issues/27 (Log file needs to report which version of the Podo program was used)
• closes https://github.com/monashmicroimaging/podocytes/issues/32 (Create _version.py file to track version numbers of podo, loci_tools.jar, etc. in a central place)