Feature/beta (#8)

* exporting beta values for methQC to use

* exporting beta values for methQC to use

* consolidate_scores function

* consolidate function now part of pipeline --betas

* consolidate part of pipeline

* added 27k manifest

note: structure of this 27k manifest was missing Strand (F/R) and Infinium_Design_Type (I or II). added columns; left blank.

* added 27K ArrayType

* bug fixes: ArrayTYpe to ArrayType and m_factor to m_value

* CLI tweaks

* Update README.md

* Feature/create sample sheet (#4)

* added function to create sample sheet, optional argument in run_pipeline

* improved create_sample_sheet

- don't rename builtin variables like `dict`
- doesn't require GSM_ID to work
- better logger info

* added flag to allow process to work without a samplesheet.

* make_sample_sheet flag

* create_sample_sheet bug fixes

* pipeline processing bugs fixed

* added readthedocs embed and classifiers

* Update setup.py

* Full tutorial (#6)

* tutorial and figures

* added links in references

* Update index.rst

* Update index.rst

* tutorial revisions

* had to redo footnotes, github doesn't support default markdown footnotes

* more revisions, focusing ease of use

* updated links

* 27k test was wrong

* Update test_array.py

* Update test_array.py

* Update test_array.py

* Update config.yml

* permissions error on pipenv install --dev

.circleci/config.yml

@@ -15,7 +15,7 @@ jobs:
           command: |
             pip install pipenv
             pipenv install --dev # --ignore-pipfile
-            pip install -e . # pytest recommends this: install your package in "editable" mode by running this from the same directory
+            pipenv install -e . # pytest recommends this: install your package in "editable" mode by running this from the same directory
             # pipenv will use requirements.txt with these params.
             # conda env create --name methpypeenv -f=conda-env.yml
             # activate methpypeenv