Merge pull request #7 from bio2bel/update-bio2bel-0-2-0

Update for Bio2BEL v0.2.0

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.1.2-dev
+current_version = 0.2.1-dev
 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

@@ -23,6 +23,7 @@ ignore = D105,E501
 # flake8-import-order
 application-import-names =
 	bio2bel_chebi
+    bio2bel
 	tests
 import-order-style = pycharm
 

.travis.yml

@@ -3,27 +3,35 @@ cache: pip
 language: python
 python:
 - 3.6
-matrix:
+stages:
+  - lint
+  - docs
+  - test
+jobs:
   include:
-    - env: TOXENV=py
-    - 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
+    - env: TOXENV=pyroma
+    - env: TOXENV=xenon
+    # docs stage
+    - stage: docs
+      env: TOXENV=doc8
+    - env: TOXENV=readme
+    - env: TOXENV=docs
+    # test stage
+    - stage: test
+      env: TOXENV=py
+matrix:
   allow_failures:
-    - env: TOXENV=flake8
-    - env: TOXENV=doc8
-    - env: TOXENV=pylint
+      - env: TOXENV=flake8
+      - env: TOXENV=xenon
 install:
-- pip install tox
-- pip install codecov
-- pip install coverage
+  - sh -c 'if [ "$TOXENV" = "py" ]; then pip install tox codecov; else pip install tox; fi'
 script:
-- tox
+  - travis_wait 45 tox
 after_success:
-- tox -e coverage-report
-- codecov
+  - sh -c 'if [ "$TOXENV" = "py" ]; then tox -e coverage-report; codecov; fi'
 notifications:
   slack: pybel:n2KbWKBum3musnBg3L76gGwq

README.rst

@@ -2,7 +2,6 @@ Bio2BEL ChEBI |build| |coverage| |docs| |zenodo|
 ================================================
 Convert the ChEBI ontology and related chemical information to BEL.
 
-
 Installation |pypi_version| |python_versions| |pypi_license|
 ------------------------------------------------------------
 ``bio2bel_chebi`` can be installed easily from `PyPI <https://pypi.python.org/pypi/bio2bel_chebi>`_ with
@@ -20,8 +19,8 @@ or from the latest code on `GitHub <https://github.com/bio2bel/chebi>`_ with:
 
 Setup
 -----
-ChEBI can be downloaded and populated from either the Python REPL or the automatically installed command line
-utility.
+ChEBI can be downloaded and populated from either the Python REPL or the automatically
+installed command line utility.
 
 Python REPL
 ~~~~~~~~~~~
@@ -65,4 +64,4 @@ Command Line Utility
 
 .. |zenodo| image:: https://zenodo.org/badge/97003706.svg
     :target: https://zenodo.org/badge/latestdoi/97003706
-    :alt: Zenodo DOI
+    :alt: Zenodo DOI

docs/source/conf.py

@@ -20,7 +20,7 @@
 copyright = '2017-2018, Charles Tapley Hoyt'
 author = 'Charles Tapley Hoyt'
 
-release = '0.1.2-dev'
+release = '0.2.1-dev'
 
 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

@@ -6,7 +6,6 @@ Bio2BEL ChEBI
    :maxdepth: 2
    :caption: Contents:
 
-   enrichment
    manager
    constants
 

setup.py

@@ -10,14 +10,17 @@
 
 PACKAGES = setuptools.find_packages(where='src')
 META_PATH = os.path.join('src', 'bio2bel_chebi', '__init__.py')
+KEYWORDS = ['Biological Expression Language', 'BEL', 'ChEBI', 'Systems Biology', 'Networks Biology']
 CLASSIFIERS = [
     'Development Status :: 4 - Beta',
     'Environment :: Console',
     'Intended Audience :: Developers',
     'Intended Audience :: Science/Research',
     'Operating System :: OS Independent',
     'Programming Language :: Python',
+    'Programming Language :: Python :: 3 :: Only',
     'Programming Language :: Python :: 3.6',
+    'Programming Language :: Python :: 3.7',
     'Topic :: Scientific/Engineering :: Bio-Informatics',
     'License :: OSI Approved :: MIT License',
 ]
@@ -26,11 +29,20 @@
     'pandas',
     'sqlalchemy',
     'tqdm',
-    'bio2bel>=0.1.4',
-    'pybel>=0.11.10',
+    'bio2bel>=0.2.0,<0.3.0',
+    'pybel>=0.12.0,<0.13.0',
 ]
 EXTRAS_REQUIRE = {
-    'web': ['flask', 'flask-admin'],
+    'web': [
+        'flask',
+        'flask-admin',
+    ],
+    'docs': [
+        'sphinx',
+        'sphinx-rtd-theme',
+        'sphinx-click',
+        'sphinx-autodoc-typehints',
+    ],
 }
 ENTRY_POINTS = {
     'bio2bel': [
@@ -84,9 +96,11 @@ def get_long_description():
         maintainer_email=find_meta('email'),
         license=find_meta('license'),
         classifiers=CLASSIFIERS,
+        keywords=KEYWORDS,
         packages=PACKAGES,
         package_dir={'': 'src'},
         install_requires=INSTALL_REQUIRES,
         extras_require=EXTRAS_REQUIRE,
         entry_points=ENTRY_POINTS,
+        zip_safe=False,
     )

src/bio2bel_chebi/__init__.py

@@ -38,15 +38,11 @@
 
 """
 
-from . import enrich, manager, models
-from .enrich import *
 from .manager import *
 from .models import *
 from .utils import get_version
 
-__all__ = (manager.__all__ + enrich.__all__ + models.__all__ + ['get_version'])
-
-__version__ = '0.1.2-dev'
+__version__ = '0.2.1-dev'
 
 __title__ = 'bio2bel_chebi'
 __description__ = "A package for converting ChEBI to BEL"

src/bio2bel_chebi/constants.py

@@ -6,7 +6,7 @@
 
 from bio2bel.utils import get_data_dir
 
-VERSION = '0.1.2-dev'
+VERSION = '0.2.1-dev'
 
 MODULE_NAME = 'chebi'
 DATA_DIR = get_data_dir(MODULE_NAME)

src/bio2bel_chebi/manager.py

@@ -41,7 +41,7 @@ class Manager(AbstractManager, FlaskMixin, BELNamespaceManagerMixin):
 
     namespace_model = Chemical
     identifiers_recommended = 'ChEBI'
-    identifiers_pattern = '^CHEBI:\d+$'
+    identifiers_pattern = r'^CHEBI:\d+$'
     identifiers_miriam = 'MIR:00000002'
     identifiers_namespace = 'chebi'
     identifiers_url = 'http://identifiers.org/chebi/'
@@ -413,7 +413,7 @@ def _create_namespace_entry_from_model(self, chemical: Chemical, namespace: Name
                 encoding=chemical.bel_encoding,
                 name=chemical.name,
                 identifier=chemical.chebi_id,
-                namespace=namespace
+                namespace=namespace,
             )
 
     @staticmethod

src/bio2bel_chebi/models.py

@@ -2,12 +2,14 @@
 
 """SQLAlchemy models for Bio2BEL ChEBI."""
 
+from typing import Mapping
+
 from sqlalchemy import Column, Date, ForeignKey, Index, Integer, String, Text
 from sqlalchemy.ext.declarative import declarative_base
 from sqlalchemy.orm import backref, relationship
 
 from pybel.constants import NAME, PART_OF
-from pybel.dsl import abundance
+import pybel.dsl
 
 __all__ = [
     'Base',
@@ -27,7 +29,7 @@
 
 
 class Chemical(Base):
-    """Represents a chemical"""
+    """Represents a chemical."""
 
     __tablename__ = CHEMICAL_TABLE_NAME
     id = Column(Integer, primary_key=True)
@@ -55,17 +57,14 @@ def __str__(self):
         return self.safe_name or self.chebi_id
 
     @property
-    def safe_name(self):
-        """Either returns this molecule's name, or the parent name
-
-        :rtype: str
-        """
+    def safe_name(self) -> str:
+        """Either returns this molecule's name, or the parent name."""
         return self.name or self.parent.name
 
-    def to_json(self, include_id=False):
-        """
+    def to_json(self, include_id: bool = False) -> Mapping:
+        """Export this chemical as dictionary.
+
         :param bool include_id: Include the database identifier?
-        :rtype: dict
         """
         rv = {
             'chebi_id': self.chebi_id,
@@ -81,10 +80,7 @@ def to_json(self, include_id=False):
         return rv
 
     def to_bel(self) -> pybel.dsl.Abundance:
-        """Makes an abundance PyBEL data dictionary
-
-        :rtype: abundance
-        """
+        """Make an abundance PyBEL data dictionary."""
         if self.parent:
             return self.parent.to_bel()
 
@@ -96,9 +92,9 @@ def to_bel(self) -> pybel.dsl.Abundance:
 
 
 class Relation(Base):
-    """Represents a relation between two chemicals"""
-    __tablename__ = RELATION_TABLE_NAME
+    """Represents a relation between two chemicals."""
 
+    __tablename__ = RELATION_TABLE_NAME
     id = Column(Integer, primary_key=True)
 
     type = Column(String(32), nullable=False, index=True)
@@ -111,7 +107,7 @@ class Relation(Base):
     target = relationship('Chemical', foreign_keys=[target_id], backref=backref('in_edges', lazy='dynamic'))
 
     def add_to_graph(self, graph):
-        """Add this relation to the graph
+        """Add this relation to the graph.
 
         :param pybel.BELGraph graph:
         :rtype: Optional[str]
@@ -134,9 +130,9 @@ def add_to_graph(self, graph):
 
 
 class Synonym(Base):
-    """Represents synonyms of a chemical"""
-    __tablename__ = SYNONYM_TABLE_NAME
+    """Represents synonyms of a chemical."""
 
+    __tablename__ = SYNONYM_TABLE_NAME
     id = Column(Integer, primary_key=True)
 
     chemical_id = Column(Integer, ForeignKey('{}.id'.format(CHEMICAL_TABLE_NAME)), nullable=False)
@@ -156,9 +152,9 @@ def __str__(self):
 
 
 class Accession(Base):
-    """Represents related accession numbers of a chemical"""
-    __tablename__ = ACCESSION_TABLE_NAME
+    """Represents related accession numbers of a chemical."""
 
+    __tablename__ = ACCESSION_TABLE_NAME
     id = Column(Integer, primary_key=True)
 
     chemical_id = Column(Integer, ForeignKey('{}.id'.format(CHEMICAL_TABLE_NAME)), nullable=False)