CLI betas, Methpype full tutorial (#7)

* 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

.circleci/config.yml

@@ -30,12 +30,12 @@ jobs:
           name: Running tests and test coverage
           command: |
             # pipenv run python setup.py test
-            pipenv install coveralls # for coveralls.io -- this can be in pipefile [dev] instead.
+            # set COVERALLS_REPO_TOKEN=<...> in ENVIRONMENT variables in circleci
+            pipenv install coveralls # for coveralls.io -- this can be in Pipfile [dev] instead.
             pipenv run coverage run setup.py test
             pipenv run coverage report
-            pipenv run coverage html
-            # set COVERALLS_REPO_TOKEN=<...> in ENVIRONMENT variables in circleci
-            sudo pipenv run coveralls # pushes report to coveralls.io
+            pipenv run coverage html            
+            pipenv run coveralls # -- pushes report to coveralls.io
       - store_artifacts:
           path: htmlcov # specific folder name where coverage always stores HTML reports
           destination: methpype

README.md

@@ -1,9 +1,9 @@
 `methpype` is a python package for processing Illumina methylation array data.
-View on [ReadTheDocs.](https://life-epigenetics-methpype-dev.readthedocs-hosted.com/en/latest/)
+View on [ReadTheDocs.](https://life-epigenetics-methpype.readthedocs-hosted.com/en/latest/)
 
-[![Readthedocs](https://readthedocs.com/projects/life-epigenetics-methpype-dev/badge/?version=latest)](https://life-epigenetics-methpype-dev.readthedocs-hosted.com/en/latest/) [![image](https://img.shields.io/pypi/l/pipenv.svg)](https://python.org/pypi/pipenv)
+[![Readthedocs](https://readthedocs.com/projects/life-epigenetics-methpype/badge/?version=latest)](https://life-epigenetics-methpype.readthedocs-hosted.com/en/latest/) [![image](https://img.shields.io/pypi/l/pipenv.svg)](https://python.org/pypi/pipenv)
 Linux/OSX
-[![CircleCI](https://circleci.com/gh/LifeEGX/methpype-dev.svg?style=shield&circle-token=28f0bca658e0752a3096432063f2c2ef260d3a84)](https://circleci.com/gh/LifeEGX/methpype-dev) Windows [![Build status](https://ci.appveyor.com/api/projects/status/7vdji73odyc2cate/branch/master?svg=true)](https://ci.appveyor.com/project/life_epigenetics/methpype/branch/master)
+[![CircleCI](https://circleci.com/gh/LifeEGX/methpype.svg?style=shield&circle-token=28f0bca658e0752a3096432063f2c2ef260d3a84)](https://circleci.com/gh/LifeEGX/methpype) Windows [![Build status](https://ci.appveyor.com/api/projects/status/7vdji73odyc2cate/branch/master?svg=true)](https://ci.appveyor.com/project/life_epigenetics/methpype/branch/master)
 [![Codacy Badge](https://api.codacy.com/project/badge/Grade/9e4e03c5cbf54c8aa16dd2cf1a440e2f)](https://www.codacy.com?utm_source=github.com&utm_medium=referral&utm_content=LifeEGX/methpype&utm_campaign=Badge_Grade)
 [![Coverage Status](https://coveralls.io/repos/github/LifeEGX/methpype/badge.svg?t=mwigt8)](https://coveralls.io/github/LifeEGX/methpype)
 

index.rst

@@ -16,11 +16,8 @@ Getting Started
    :maxdepth: 2
    :caption: Contents:
 
+   docs/methpype_tutorial.md
    docs/source/methpype
-   docs/source/methpype.arrays
-   docs/source/methpype.preprocess
-   docs/source/methpype.samples
-   docs/source/methpype.utils
    docs/source/modules
 
 Indices and tables

setup.py

@@ -3,9 +3,25 @@
 
 setup(
     name='methpype',
-    version='1.0.2',
+    version='1.0.3',
     description='Python-based Illumina methylation array preprocessing software',
-    long_description='Python-based Illumina methylation array preprocessing software',
+    long_description=open('README.md').read(),
+    long_description_content_type='text/markdown',  
+    classifiers=[
+        'Development Status :: 4 - Beta',
+        'Environment :: Console',
+        'License :: OSI Approved :: MIT License',
+        'Programming Language :: Python :: 3.7',
+        'Topic :: Scientific/Engineering :: Bio-Informatics',
+        'Topic :: Scientific/Engineering :: Medical Science Apps.',
+        'Framework :: Jupyter',
+        'Intended Audience :: Science/Research',
+        'Intended Audience :: Financial and Insurance Industry',
+        'Operating System :: MacOS :: MacOS X',
+        'Operating System :: Microsoft :: Windows',
+        'Operating System :: POSIX :: Linux',
+      ],
+    keywords='methylation dna data processing epigenetics illumina',    
     url='https://github.com/LifeEGX/methpype',
     license='MIT',
     author='Life Epigenetics',

tests/models/test_array.py

@@ -14,6 +14,7 @@ def test_inits_correctly(self):
 class TestArrayType():
     def test_enum_has_correct_values(self):
         assert ArrayType.CUSTOM.value == 'custom'
+        assert ArrayType.ILLUMINA_27K.value == '27k'
         assert ArrayType.ILLUMINA_450K.value == '450k'
         assert ArrayType.ILLUMINA_EPIC.value == 'epic'
         assert ArrayType.ILLUMINA_EPIC_PLUS.value == 'epic+'
@@ -32,21 +33,13 @@ def test_out_of_range_probe_counts_throws(self, capsys):
             captured = capsys.readouterr()
             assert captured.out == 'Unknown array type\n'
 
-    def test_27k_probe_counts_lower_bound_throws(self, capsys):
-        with pytest.raises(ValueError):
-            results = ArrayType.from_probe_count(54000)
-            assert results is None
-
-            captured = capsys.readouterr()
-            assert captured.out == 'Unsupported array type: Illumina Human Methylation 27k\n'
+    def test_27k_probe_counts_lower_bound(self):
+        array_type = ArrayType.from_probe_count(54000)
+        assert array_type == ArrayType.ILLUMINA_27K
 
-    def test_27k_probe_counts_upper_bound_throws(self, capsys):
-        with pytest.raises(ValueError):
-            results = ArrayType.from_probe_count(56000)
-            assert results is None
-
-            captured = capsys.readouterr()
-            assert captured.out == 'Unsupported array type: Illumina Human Methylation 27k\n'
+    def test_27k_probe_counts_upper_bound(self):
+        array_type = ArrayType.from_probe_count(56000)
+        assert array_type == ArrayType.ILLUMINA_27K
 
     def test_450k_probe_counts_lower_bound(self):
         array_type = ArrayType.from_probe_count(622000)