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Parse the files with the new functions that return error objects
instead of raising exceptions
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This commit adds a number of functions that return the error object
when an error is found, or `None` otherwise. It avoids the use of
exceptions as control flow constructs.
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- Use a way faster way of parsing the strains file
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Advance the seek position, once we have yielded up an error to causing
an infinite loop in certain conditions, where the `parse_errors`
function ends up resuming the gile in the same position once it
experiences an error.
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To avoid processing all the items in an iterable, the `take` function
is added in this commit. It realised a limited number (specified at
call time) of items from the iterable given.
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Build a function to collect all the parsing errors into a "sequence"
of dict objects containing the issues found.
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Derive a "correct" sample file from an existing sample file with
errors for testing with large files.
Fix issue caught by test.
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* Implement remaining file parsing tests and some helpers functions
needed for ensuring the tests work.
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* Improve tests that ensure parsing fails in case the file has errors
* Add strains.csv file
* Implement minimum viable functionality that passes the implemented tests
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Add dummy failing tests and a stub for the parsing of the files
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Change the exception name to be more descriptive.
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Add some sample files to be used for testing that the parsing works as
expected.
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Without the `tests/__init__.py` file, the tests directory was not
considered a package and therefore, running:
$ pytest
would fail with import error notifications. This fixes that.
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* Add tests to check for validity of the headers
* Add stubs for the tests
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