Public-Health-Bioinformatics / LexMapr / 427
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Merge development into master (#80)

* Various small bug fixes (#74)

* Do not delimit more than once per row

* Also removed InputFileNotFoundError

  * Let's just use FileNotFoundError

* Also raise exception for unreachable code

* Remove comments from test input files

* Increase threshold for calling ``ngrams``

* ``get_gram_chunks`` now calls ``ngrams`` if ``input`` has less than 15
  tokens

  * As opposed to less than 7 tokens

* Clean up matching logic (#75)

* Empty commit

* To create WIP pr

* Made full and non-full output more similar

* Replaced ``Final_Refined_Terms_with_Resource_IDs`` in full format with
  ``Matched_Components``

* Modified tests accordingly

* Clean up ``pipeline.run``, and other things

* ``pipeline.run``

  * Removed a lot of unneccessary variables

  * Output columns now stored in clearly named variables, and all
    columns are populated at the same time

  * Removed reporting of matches when there are no matches

  * General clean-up

* Other things

  * Renamed ``punctuationTreatment`` to ``punctuation_treatment``

  * Modified tests accordingly

* Increased robustness of full term matching

* Now calls new function ``map_term``

* Cleaner

* Attempts suffix addition on synonyms as well, so more robust

* Empty commit

* To test modification of coveralls setting

* Increased robustness of component matching

* Component matching now relies on the more robust ``map_term``

* Removed duplicates in ``micro_status``

* Removed unneccessary variables

* Fixed bug in ``_map_term_helper``

* Modified tests accordingly

* Cleaned up ``genomeTrackerMaster.csv``

* Removed stale code

* Docstrings

* ``match_term``

* ``_match_term_helper``

* Modify matching logic

* We want to consider suffixes last

* Also modifies some code to make adhere to PEP 8

* More transparent matching (#76)

* Less randomness, better reporting and clea... (continued)

977 of 1135 relevant lines covered (86.08%)

0.86 hits per line

Jobs
ID Job ID Ran Files Coverage
1 427.1 (PYTHONHASHSEED=0) 0
86.08
 Travis Job 427.1
Source Files on build 427
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