Merge branch 'develop'

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.5.3
+current_version = 0.6.1
 commit = True
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(?:-(?P<release>[0-9A-Za-z-]+(?:\.[0-9A-Za-z-]+)*))?(?:\+(?P<build>[0-9A-Za-z-]+(?:\.[0-9A-Za-z-]+)*))?

.flake8

@@ -0,0 +1,24 @@
+#########################
+# Flake8 Configuration  #
+# (.flake8)             #
+# (formerly in tox.ini) #
+#########################
+
+[flake8]
+ignore = E501
+exclude =
+    .tox,
+    .git,
+    __pycache__,
+    docs/source/conf.py,
+    build,
+    dist,
+    tests/fixtures/*,
+    *.pyc,
+    *.egg-info,
+    .cache,
+    .eggs
+max-complexity = 10
+import-order-style = google
+application-import-names = flake8
+format = ${cyan}%(path)s${reset}:${yellow_bold}%(row)d${reset}:${green_bold}%(col)d${reset}: ${red_bold}%(code)s${reset} %(text)s

.travis.yml

@@ -6,21 +6,33 @@ language: python
 python:
     - 3.6
     - 3.4
+
+stages:
+  - lint
+  - docs
+  - test
+
 env:
   - TOXENV=py
 
-matrix:
+jobs:
   include:
-    - env: TOXENV=docs
-    - env: TOXENV=manifest
-    - env: TOXENV=rst-lint
+    # lint stage
+    - stage: lint
+      env: TOXENV=manifest
     - env: TOXENV=flake8
-    - env: TOXENV=doc8
     - env: TOXENV=pylint
+
+    # docs stage
+    - stage: docs
+      env: TOXENV=doc8
+    - env: TOXENV=readme
+    - env: TOXENV=docs
+
+matrix:
   allow_failures:
-    - env: TOXENV=flake8
-    - env: TOXENV=doc8
-    - env: TOXENV=pylint
+      - env: TOXENV=flake8
+      - env: TOXENV=pylint
 
 before_install:
     - pip install codecov coverage

MANIFEST.in

@@ -9,4 +9,4 @@ global-exclude docs/*
 global-exclude *.py[cod] __pycache__ *.so *.dylib .DS_Store
 
 exclude .bumpversion.cfg
-include *.rst *.txt LICENSE tox.ini *.yml docs/Makefile .coveragerc .codecov.yml .codeclimate.yml
+include *.rst *.txt *.ini *.yml LICENSE docs/Makefile .coveragerc .codecov.yml .codeclimate.yml .flake8

README.rst

@@ -88,4 +88,4 @@ Links
     :alt: Apache 2.0 License
 
 .. |zenodo| image:: https://zenodo.org/badge/70473008.svg
-    :target: https://zenodo.org/badge/latestdoi/70473008
+    :target: https://zenodo.org/badge/latestdoi/70473008

doc8.ini

@@ -0,0 +1,2 @@
+[doc8]
+max-line-length = 120

docs/source/algorithms.rst

@@ -0,0 +1,21 @@
+Algorithms
+==========
+NeuroMMSig
+----------
+.. automodule:: pybel_tools.analysis.neurommsig.algorithm
+    :members:
+
+EpiCom
+------
+.. automodule:: pybel_tools.analysis.epicom.algorithm
+    :members:
+
+Reverse Causal Reasoning
+------------------------
+.. automodule:: pybel_tools.analysis.rcr
+    :members:
+
+Sample of Spanning Trees
+------------------------
+.. automodule:: pybel_tools.analysis.sst
+    :members:

docs/source/conf.py

@@ -47,7 +47,7 @@
 #
 
 # The full version, including alpha/beta/rc tags.
-release = '0.5.3'
+release = '0.6.1'
 
 parsed_version = re.match(
     '(?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(?:-(?P<release>[0-9A-Za-z-]+(?:\.[0-9A-Za-z-]+)*))?(?:\+(?P<build>[0-9A-Za-z-]+(?:\.[0-9A-Za-z-]+)*))?',

docs/source/index.rst

@@ -40,13 +40,7 @@ Links
    integration
    mutation
    visualization
-
-.. toctree::
-   :maxdepth: 2
-   :caption: Graph Queries
-   :name: graphquery
-
-   pipeline
+   query
 
 .. toctree::
    :caption: Workflows
@@ -56,6 +50,7 @@ Links
    expansion
    generation
    heat
+   algorithms
 
 .. toctree::
    :caption: Other Utilities
@@ -73,4 +68,4 @@ Indices and tables
 * :ref:`modindex`
 * :ref:`search`
 
-.. _PyPI: https://pypi.python.org/pypi/pybel_tools
+.. _PyPI: https://pypi.python.org/pypi/pybel_tools

docs/source/query.rst

@@ -0,0 +1,4 @@
+Query Builder
+=============
+.. automodule:: pybel_tools.query
+    :members:

docs/source/visualization.rst

@@ -1,5 +1,4 @@
 Visualization
 =============
-
 .. automodule:: pybel_tools.visualization
     :members:

requirements.txt

@@ -1,11 +1,10 @@
-pybel>=0.11.2
+pybel>=0.11.11
 pybel-artifactory
-pandas==0.20.3
+pandas
 networkx==1.11
 sqlalchemy
 requests
 click
 scipy
 numpy
-jinja2
 tqdm

setup.cfg

@@ -1,5 +1,5 @@
 [bdist_wheel]
-universal = 1
+universal = 0
 
 [metadata]
 license_file = LICENSE

setup.py

@@ -1,5 +1,7 @@
 # -*- coding: utf-8 -*-
 
+"""Setup.py for PyBEL-Tools."""
+
 import codecs
 import os
 import re
@@ -24,24 +26,19 @@
     'Topic :: Scientific/Engineering :: Bio-Informatics'
 ]
 INSTALL_REQUIRES = [
-    'pybel>=0.11.2',
+    'pybel>=0.11.11',
     'pybel-artifactory',
-    'pandas==0.20.3',
+    'pandas',
     'networkx==1.11',
     'requests',
     'sqlalchemy',
     'click',
     'scipy',
     'numpy',
-    'jinja2',
     'tqdm',
 ]
 
-EXTRAS_REQUIRE = {
-    'ipython': [
-        'ipython',  # Enable inline viewing in Jupyter notebooks
-    ],
-}
+EXTRAS_REQUIRE = {}
 TESTS_REQUIRE = []
 ENTRY_POINTS = {
     'console_scripts': [

src/pybel_tools/__init__.py

@@ -46,10 +46,11 @@
 
 from . import io, utils
 from .io import *
+from .utils import get_version
 
-__all__ = io.__all__
+__all__ = io.__all__ + ['get_version']
 
-__version__ = '0.5.3'
+__version__ = '0.6.1'
 
 __title__ = 'pybel_tools'
 __description__ = 'Tools for using BEL documents in Python'

src/pybel_tools/analysis/concordance.py

@@ -2,22 +2,20 @@
 
 """Performs concordance analysis"""
 
+from collections import defaultdict
+
 import enum
 import logging
-from collections import defaultdict
 from functools import partial
 
 from pybel.constants import (
+    CAUSAL_DECREASE_RELATIONS, CAUSAL_INCREASE_RELATIONS, CAUSES_NO_CHANGE, NEGATIVE_CORRELATION, POSITIVE_CORRELATION,
     RELATION,
-    CAUSAL_DECREASE_RELATIONS,
-    CAUSAL_INCREASE_RELATIONS,
-    CAUSES_NO_CHANGE,
-    POSITIVE_CORRELATION,
-    NEGATIVE_CORRELATION,
 )
-from ..mutation import collapse_all_variants, collapse_by_central_dogma_to_genes_out_place
-from ..mutation.random import random_by_edges, shuffle_relations, shuffle_node_data
-from ..grouping import get_subgraphs_by_annotation
+from pybel.struct import get_subgraphs_by_annotation
+from pybel.struct.mutation import collapse_to_genes
+from ..mutation import collapse_all_variants
+from ..mutation.random import random_by_edges, shuffle_node_data, shuffle_relations
 
 __all__ = [
     'Concordance',
@@ -221,7 +219,8 @@ def calculate_concordance_probability(graph, key, cutoff=None, permutations=None
     else:
         raise ValueError
 
-    graph = collapse_by_central_dogma_to_genes_out_place(graph)
+    graph = graph.copy()
+    collapse_to_genes(graph)
     collapse_all_variants(graph)
 
     score = calculate_concordance(graph, key, cutoff=cutoff)

src/pybel_tools/analysis/epicom/algorithm.py

@@ -1,36 +1,40 @@
 # -*- coding: utf-8 -*-
 
-"""This algorithm has multiple steps
+"""An implementation of chemical-based mechanism enrichment with NeuroMMSig [HoytDomingoFernandez2018]_.
+
+This algorithm has multiple steps:
 
 1. Select NeuroMMSig networks for AD, PD, and epilepsy
 2. Select drugs from DrugBank, and their targets
 3. Run NeuroMMSig algorithm on target list for each network and each mechanism
 4. Store in database
+
+.. [HoytDomingoFernandez2018] Charles Tapley Hoyt, Daniel Domingo-Fernández, Nora Balzer, Anka Güldenpfennig,
+    Martin Hofmann-Apitius; `A systematic approach for identifying shared mechanisms in epilepsy and its comorbidities
+    <https://doi.org/10.1093/database/bay050>`_, Database, Volume 2018, 1 January 2018, bay050
 """
 
 import itertools as itt
 import logging
 import os
 
-import bio2bel_drugbank
-from bio2bel_drugbank.constants import DATA_DIR as DRUGBANK_DATA_DIR
 from tqdm import tqdm
 
 from pybel.dsl import gene as gene_dsl
+from pybel.struct.grouping import get_subgraphs_by_annotation
+from pybel.struct.summary import get_annotation_values
 from pybel_tools.analysis.neurommsig import get_neurommsig_score, neurommsig_graph_preprocessor
-from pybel_tools.grouping import get_subgraphs_by_annotation
-from pybel_tools.summary import get_annotation_values
 
 log = logging.getLogger(__name__)
 
-_dti_cache_path = os.path.join(DRUGBANK_DATA_DIR, 'drug_to_gene_symbols.json')
-
 
 def _get_drug_target_interactions():
     """Gets a mapping from drugs to their list of gene
 
     :rtype: dict[str,list[str]]
     """
+    import bio2bel_drugbank
+
     drugbank_manager = bio2bel_drugbank.Manager()
     if not drugbank_manager.is_populated():
         drugbank_manager.populate()