Merge pull request #102 from apriha/develop

v4.1.3

.github/workflows/ci.yml

@@ -23,7 +23,7 @@ jobs:
     - uses: actions/setup-python@v2
     - name: Install Black
       run: |
-        pip install black==19.10b0
+        pip install black
     - name: Lint with Black
       run: |
         black --check --diff .
@@ -47,24 +47,21 @@ jobs:
     strategy:
       matrix:
         include:
-          - os: ubuntu-latest
-            python-version: 3.6
-            job_id: 0
           - os: ubuntu-latest
             python-version: 3.7
-            job_id: 1
+            job_id: 0
           - os: ubuntu-latest
             python-version: 3.8
-            job_id: 2
+            job_id: 1
           - os: ubuntu-latest
             python-version: 3.9
-            job_id: 3
+            job_id: 2
           - os: macos-latest
             python-version: 3.9
-            job_id: 4
+            job_id: 3
           - os: windows-latest
             python-version: 3.9
-            job_id: 5
+            job_id: 4
 
     steps:
     - uses: actions/checkout@v2
@@ -80,7 +77,7 @@ jobs:
       # so this ensures all Python versions will be periodically integration tested with the
       # resource servers
       env:
-        NUM_JOBS: 6
+        NUM_JOBS: 5
         JOB_ID: ${{ matrix.job_id }}
       if: ${{ github.event_name == 'pull_request' || github.ref == 'refs/heads/master' }}
       shell: bash

.readthedocs.yaml

@@ -0,0 +1,20 @@
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+version: 2
+
+build:
+  os: ubuntu-20.04
+  tools:
+    python: "3.9"
+
+sphinx:
+  configuration: docs/conf.py
+
+formats: all
+
+python:
+   install:
+   - requirements: docs/requirements.txt
+   - method: pip
+     path: .

Pipfile

@@ -8,7 +8,7 @@ pytest = "*"
 pytest-cov = "*"
 sphinx = "*"
 sphinx-rtd-theme = "*"
-black = "==19.10b0"
+black = "==21.12b0"
 
 [packages]
 lineage = {editable = true,path = "."}

README.rst

@@ -31,7 +31,7 @@ Also see the `installation documentation <https://lineage.readthedocs.io/en/stab
 
 Dependencies
 ------------
-``lineage`` requires `Python <https://www.python.org>`_ 3.6.1+ and the following Python packages:
+``lineage`` requires `Python <https://www.python.org>`_ 3.7.1+ and the following Python packages:
 
 - `numpy <https://numpy.org>`_
 - `pandas <https://pandas.pydata.org>`_
@@ -74,9 +74,9 @@ Create an ``Individual`` in the context of the ``lineage`` framework to interact
 ``User662`` dataset:
 
 >>> user662 = l.create_individual('User662', ['resources/662.23andme.340.txt.gz', 'resources/662.ftdna-illumina.341.csv.gz'])
-Loading SNPs('resources/662.23andme.340.txt.gz')
-Merging SNPs('resources/662.ftdna-illumina.341.csv.gz')
-SNPs('resources/662.ftdna-illumina.341.csv.gz') has Build 36; remapping to Build 37
+Loading SNPs('662.23andme.340.txt.gz')
+Merging SNPs('662.ftdna-illumina.341.csv.gz')
+SNPs('662.ftdna-illumina.341.csv.gz') has Build 36; remapping to Build 37
 Downloading resources/NCBI36_GRCh37.tar.gz
 27 SNP positions were discrepant; keeping original positions
 151 SNP genotypes were discrepant; marking those as null
@@ -113,7 +113,7 @@ Compare Individuals
 Let's create another ``Individual`` for the ``User663`` dataset:
 
 >>> user663 = l.create_individual('User663', 'resources/663.23andme.305.txt.gz')
-Loading SNPs('resources/663.23andme.305.txt.gz')
+Loading SNPs('663.23andme.305.txt.gz')
 
 Now we can perform some analysis between the ``User662`` and ``User663`` datasets.
 
@@ -201,10 +201,10 @@ For this example, let's create two more ``Individuals`` for the ``User4583`` and
 datasets:
 
 >>> user4583 = l.create_individual('User4583', 'resources/4583.ftdna-illumina.3482.csv.gz')
-Loading SNPs('resources/4583.ftdna-illumina.3482.csv.gz')
+Loading SNPs('4583.ftdna-illumina.3482.csv.gz')
 
 >>> user4584 = l.create_individual('User4584', 'resources/4584.ftdna-illumina.3483.csv.gz')
-Loading SNPs('resources/4584.ftdna-illumina.3483.csv.gz')
+Loading SNPs('4584.ftdna-illumina.3483.csv.gz')
 
 Now let's find the shared genes, specifying a
 `population-specific <https://www.internationalgenome.org/faq/which-populations-are-part-your-study/>`_

docs/requirements.txt

@@ -0,0 +1,2 @@
+sphinx==4.4.0
+sphinx-rtd-theme==1.0.0

setup.py

@@ -97,7 +97,6 @@
         "License :: OSI Approved :: MIT License",
         "Natural Language :: English",
         "Operating System :: OS Independent",
-        "Programming Language :: Python :: 3.6",
         "Programming Language :: Python :: 3.7",
         "Programming Language :: Python :: 3.8",
         "Programming Language :: Python :: 3.9",
@@ -115,6 +114,6 @@
     keywords="dna genes genetics genealogy snps chromosomes genotype "
     "bioinformatics ancestry",
     install_requires=["numpy", "pandas", "matplotlib", "atomicwrites", "snps"],
-    python_requires=">=3.6.1",
+    python_requires=">=3.7.1",
     platforms=["any"],
 )

src/lineage/__init__.py

@@ -52,7 +52,7 @@
 
 
 class Lineage:
-    """ Object used to interact with the `lineage` framework. """
+    """Object used to interact with the `lineage` framework."""
 
     def __init__(
         self,
@@ -61,7 +61,7 @@ def __init__(
         parallelize=False,
         processes=os.cpu_count(),
     ):
-        """ Initialize a ``Lineage`` object.
+        """Initialize a ``Lineage`` object.
 
         Parameters
         ----------
@@ -80,7 +80,7 @@ def __init__(
         self._parallelizer = Parallelizer(parallelize=parallelize, processes=processes)
 
     def create_individual(self, name, raw_data=(), **kwargs):
-        """ Initialize an individual in the context of the `lineage` framework.
+        """Initialize an individual in the context of the `lineage` framework.
 
         Parameters
         ----------
@@ -104,7 +104,7 @@ def create_individual(self, name, raw_data=(), **kwargs):
         return Individual(name, raw_data, **kwargs)
 
     def download_example_datasets(self):
-        """ Download example datasets from `openSNP <https://opensnp.org>`_.
+        """Download example datasets from `openSNP <https://opensnp.org>`_.
 
         Per openSNP, "the data is donated into the public domain using `CC0 1.0
         <http://creativecommons.org/publicdomain/zero/1.0/>`_."
@@ -130,7 +130,7 @@ def download_example_datasets(self):
     def find_discordant_snps(
         self, individual1, individual2, individual3=None, save_output=False
     ):
-        """ Find discordant SNPs between two or three individuals.
+        """Find discordant SNPs between two or three individuals.
 
         Parameters
         ----------
@@ -282,7 +282,7 @@ def find_shared_dna(
         save_output=True,
         genetic_map="HapMap2",
     ):
-        """ Find the shared DNA between individuals.
+        """Find the shared DNA between individuals.
 
         Computes the genetic distance in centiMorgans (cMs) between SNPs using the specified genetic
         map. Applies thresholds to determine the shared DNA. Plots shared DNA. Optionally determines
@@ -696,7 +696,7 @@ def _is_one_individual_male(self, individuals):
         return False
 
     def _compute_snp_distances(self, task):
-        """ Compute genetic distance in cMs between SNPs.
+        """Compute genetic distance in cMs between SNPs.
 
         Parameters
         ----------

src/lineage/individual.py

@@ -31,7 +31,7 @@
 
 
 class Individual(SNPs):
-    """ Object used to represent and interact with an individual.
+    """Object used to represent and interact with an individual.
 
     The ``Individual`` object maintains information about an individual. The object provides
     methods for loading an individual's genetic data (SNPs) and normalizing it for use with the
@@ -42,7 +42,7 @@ class Individual(SNPs):
     """
 
     def __init__(self, name, raw_data=(), **kwargs):
-        """ Initialize an ``Individual`` object.
+        """Initialize an ``Individual`` object.
 
         Parameters
         ----------
@@ -85,7 +85,7 @@ def __repr__(self):
 
     @property
     def name(self):
-        """ Get this ``Individual``'s name.
+        """Get this ``Individual``'s name.
 
         Returns
         -------