Merge pull request #35 from apriha/develop

v0.6.0

.gitignore

@@ -118,3 +118,4 @@ tests/input/discrepant_snps[12].csv
 tests/input/empty.txt
 tests/input/ftdna.csv.gz
 tests/input/generic.fa.gz
+tests/input/testvcf.vcf.gz

Pipfile

@@ -7,6 +7,9 @@ verify_ssl = true
 pytest = "*"
 pytest-cov = "*"
 pytest-watch = "*"
+sphinx = "*"
+sphinx-rtd-theme = "*"
+black = "==19.10b0"
 
 [packages]
 snps = {editable = true,path = "."}

README.rst

@@ -34,7 +34,6 @@ Dependencies
 - `numpy <http://www.numpy.org>`_
 - `pandas <http://pandas.pydata.org>`_
 - `atomicwrites <https://github.com/untitaker/python-atomicwrites>`_
-- `PyVCF <https://github.com/jamescasbon/PyVCF>`_
 
 Installation
 ------------
@@ -48,7 +47,14 @@ Examples
 --------
 Download Example Data
 `````````````````````
-Let's download some example data from `openSNP <https://opensnp.org>`_:
+First, let's setup logging to get some helpful output:
+
+>>> import logging, sys
+>>> logger = logging.getLogger()
+>>> logger.setLevel(logging.DEBUG)
+>>> logger.addHandler(logging.StreamHandler(sys.stdout))
+
+Now we're ready to download some example data from `openSNP <https://opensnp.org>`_:
 
 >>> from snps.resources import Resources
 >>> r = Resources()
@@ -63,7 +69,8 @@ Load a `23andMe <https://www.23andme.com>`_ raw data file:
 >>> from snps import SNPs
 >>> s = SNPs('resources/662.23andme.340.txt.gz')
 
-The loaded SNPs are available via a ``pandas.DataFrame``:
+The ``SNPs`` class accepts a path to a file or a bytes object. A ``Reader`` class attempts to
+infer the data source and load the SNPs. The loaded SNPs are available via a ``pandas.DataFrame``:
 
 >>> df = s.snps
 >>> df.columns.values

docs/conf.py

@@ -126,7 +126,7 @@ def __getattr__(cls, name):
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ["_static"]
+html_static_path = []
 
 # Custom sidebar templates, must be a dictionary that maps document names
 # to template names.

docs/index.rst

@@ -15,6 +15,7 @@
    README <readme>
    output_files
    snps_banner
+   snps
 
 Indices and tables
 ==================

docs/snps.rst

@@ -1,46 +1,45 @@
 snps package
 ============
 
+Module
+------
+
+.. automodule:: snps
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
 Submodules
 ----------
 
 snps\.ensembl module
---------------------
+~~~~~~~~~~~~~~~~~~~~
 
 .. automodule:: snps.ensembl
     :members:
     :undoc-members:
     :show-inheritance:
 
 snps\.io module
----------------
+~~~~~~~~~~~~~~~
 
 .. automodule:: snps.io
     :members:
     :undoc-members:
     :show-inheritance:
 
 snps\.resources module
-----------------------
+~~~~~~~~~~~~~~~~~~~~~~
 
 .. automodule:: snps.resources
     :members:
     :undoc-members:
     :show-inheritance:
 
 snps\.utils module
-------------------
+~~~~~~~~~~~~~~~~~~
 
 .. automodule:: snps.utils
     :members:
     :undoc-members:
     :show-inheritance:
-
-
-Module contents
----------------
-
-.. automodule:: snps
-    :members:
-    :undoc-members:
-    :show-inheritance:

setup.cfg

@@ -21,16 +21,8 @@ addopts =
     --tb=short
 
 # http://coverage.readthedocs.io/en/latest/
-[coverage:paths]
-source =
-    src
-    */site-packages
-
 [coverage:run]
 branch = true
-source =
-    src
-    tests
 omit = */snps/_version.py
 
 [coverage:report]

setup.py

@@ -118,7 +118,7 @@
         "Issue Tracker": "https://github.com/apriha/snps/issues",
     },
     keywords="snps dna chromosomes bioinformatics",
-    install_requires=["numpy", "pandas", "atomicwrites", "PyVCF"],
+    install_requires=["numpy", "pandas", "atomicwrites"],
     python_requires=">=3.5",
     platforms=["any"],
 )