Update for Bio2BEL v0.2.0 (#10)

* Update for bio2bel v0.2.0

* Update .travis.yml

* Update formatting

* Update .flake8

[skip ci]

* Update BEL export

* Update MANIFEST.in

* Update src/bio2bel_reactome/manager.py

* Update tests/test_all.py

.flake8

@@ -0,0 +1,26 @@
+[flake8]
+ignore =
+	C901 # too complex methods
+max-line-length = 120
+exclude =
+    .tox,
+    .git,
+    __pycache__,
+    docs/source/conf.py,
+    build,
+    dist,
+    tests/fixtures/*,
+    *.pyc,
+    *.egg-info,
+    .cache,
+    .eggs
+max-complexity = 10
+import-order-style = pycharm
+application-import-names =
+    bio2bel_reactome
+    bio2bel_hgnc
+    bio2bel
+	compath_utils
+    pybel
+    tests
+format = ${cyan}%(path)s${reset}:${yellow_bold}%(row)d${reset}:${green_bold}%(col)d${reset}: ${red_bold}%(code)s${reset} %(text)s

.travis.yml

@@ -3,27 +3,41 @@ cache: pip
 language: python
 python:
 - 3.6
-matrix:
+stages:
+  - lint
+  - docs
+  - test
+env:
+  - TOXENV=py
+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=vulture
+    - env: TOXENV=mypy
+    - 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=vulture
+      - env: TOXENV=mypy
+      - env: TOXENV=flake8
+      - env: TOXENV=xenon
 install:
-- pip install tox
-- pip install codecov
-- pip install coverage
+    - sh -c 'if [ "$TOXENV" = "py" ]; then pip install tox codecov; else pip install tox; fi'
 script:
 - tox
 after_success:
-- tox -e coverage-report
-- codecov
+    - sh -c 'if [ "$TOXENV" = "py" ]; then tox -e coverage-report; codecov; fi'
 notifications:
   slack: pybel:n2KbWKBum3musnBg3L76gGwq

MANIFEST.in

@@ -8,4 +8,4 @@ recursive-include docs Makefile
 global-exclude *.py[cod] __pycache__ *.so *.dylib .DS_Store *.gpickle
 
 exclude .bumpversion.cfg
-include *.rst *.txt *.yml LICENSE tox.ini .coveragerc
+include *.rst *.txt *.yml LICENSE *.ini .coveragerc .flake8

README.rst

@@ -1,14 +1,16 @@
 Bio2BEL Reactome |build| |coverage| |documentation| |zenodo|
 ============================================================
 This package allows the enrichment of BEL networks with Reactome information by wrapping its RESTful API.
-Furthermore, it is integrated in the `ComPath environment <https://github.com/ComPath>`_ for pathway database comparison.
+Furthermore, it is integrated in the `ComPath environment <https://github.com/ComPath>`_ for pathway database
+comparison.
 
 Installation
 ------------
 This code can be installed with :code:`pip3 install git+https://github.com/bio2bel/reactome.git`
 
 
-These two resources will be installed together with this package and can be quickly loaded by running the following commands in your terminal:
+These two resources will be installed together with this package and can be quickly loaded by running the following
+commands in your terminal:
 
 - :code:`python3 -m bio2bel_hgnc populate`
 - :code:`python3 -m bio2bel_chebi populate`
@@ -60,8 +62,10 @@ Other Command Line Utilities
 
 Citation
 --------
-- Fabregat, Antonio et al. “The Reactome Pathway Knowledgebase.” Nucleic Acids Research 44.Database issue (2016): D481–D487. PMC. Web. 6 Oct. 2017.
-- Croft, David et al. “The Reactome Pathway Knowledgebase.” Nucleic Acids Research 42.Database issue (2014): D472–D477. PMC. Web. 6 Oct. 2017.
+- Fabregat, Antonio et al. “The Reactome Pathway Knowledgebase.” Nucleic Acids Research 44.Database issue (2016):
+  D481–D487. PMC. Web. 6 Oct. 2017.
+- Croft, David et al. “The Reactome Pathway Knowledgebase.” Nucleic Acids Research 42.Database issue (2014): D472–D477.
+  PMC. Web. 6 Oct. 2017.
 
 .. |build| image:: https://travis-ci.org/bio2bel/reactome.svg?branch=master
     :target: https://travis-ci.org/bio2bel/reactome

doc8.ini

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

docs/source/cli.rst

@@ -2,8 +2,16 @@ Command Line Interface
 ======================
 The command line interface allows you to communicate with the package and perform basic functions such as:
 
-* Populate the database: :code:`python3 -m bio2bel_reactome populate`. By default this command populates the database only with human information. In order to populate all species pathway information you can add the "--not-only-human" argument. By default the database is reset every time is populated. However, another optional parameter "--reset-db=False", allows you to avoid the reset. More logging can be activated by added "-vv" or "-v" as an argument.
+* Populate the database: :code:`python3 -m bio2bel_reactome populate`. By default this command populates the database
+  only with human information. In order to populate all species pathway information you can add the "--not-only-human"
+  argument. By default the database is reset every time is populated. However, another optional parameter
+  "--reset-db=False", allows you to avoid the reset. More logging can be activated by added "-vv" or "-v" as an
+  argument.
 
-* Drop the database: :code:`python3 -m bio2bel_reactome drop`. More logging can be activated by added "-vv" or "-v" as an argument.
+* Drop the database: :code:`python3 -m bio2bel_reactome drop`. More logging can be activated by added "-vv" or "-v" as
+  an argument.
 
-* Export gene sets as an excel file: :code:`python3 -m bio2bel_reactome export`. By default, the excel will contain all pathways from all species. However, you can add the argument "species" and type the name of a particular one to get only those pathways (e.g., "--species='Homo sapiens'""). Since Reactome has a hierarchy pathway structure, you can get only the major pathways with the optional parameter "--top-hierarchy".
+* Export gene sets as an excel file: :code:`python3 -m bio2bel_reactome export`. By default, the excel will contain
+  all pathways from all species. However, you can add the argument "species" and type the name of a particular one to
+  get only those pathways (e.g., "--species='Homo sapiens'""). Since Reactome has a hierarchy pathway structure, you can
+  get only the major pathways with the optional parameter "--top-hierarchy".

setup.py

@@ -1,5 +1,7 @@
 # -*- coding: utf-8 -*-
 
+"""Setup.py for Bio2BEL Reactome."""
+
 import codecs
 import os
 import re
@@ -8,32 +10,54 @@
 
 BIO2BEL_MODULE = 'reactome'
 PACKAGES = setuptools.find_packages(where='src')
-META_PATH = os.path.join('src', 'bio2bel_{}'.format(BIO2BEL_MODULE), '__init__.py')
+META_PATH = os.path.join('src', f'bio2bel_{BIO2BEL_MODULE}', '__init__.py')
+KEYWORDS = ['Biological Expression Language', 'BEL', 'Reactome', 'Systems Biology', 'Networks Biology']
+CLASSIFIERS = [
+    'Development Status :: 4 - Beta',
+    'Environment :: Console',
+    'Intended Audience :: Developers',
+    'Intended Audience :: Science/Research',
+    'License :: OSI Approved :: MIT License',
+    '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',
+]
 INSTALL_REQUIRES = [
     'click',
-    'bio2bel>=0.1.0',
+    'bio2bel>=0.2.0,<0.3.0',
     'compath_utils>=0.1.0',
     'bio2bel_hgnc>=0.1.0',
     'bio2bel_chebi>=0.1.0',
-    'pybel>=0.11.2',
+    'pybel>=0.12.0,<0.13.0',
     'sqlalchemy',
     'pandas',
     'tqdm',
     'flask',
     'flask_admin',
 ]
 EXTRAS_REQUIRE = {
-    'web': ['flask', 'flask_admin'],
+    'web': [
+        'flask',
+        'flask_admin',
+    ],
+    'docs': [
+        'sphinx',
+        'sphinx-rtd-theme',
+        'sphinx-click',
+    ],
 }
 ENTRY_POINTS = {
     'bio2bel': [
-        '{mname} = bio2bel_{mname}'.format(mname=BIO2BEL_MODULE),
+        f'{BIO2BEL_MODULE} = bio2bel_{BIO2BEL_MODULE}',
     ],
     'compath': [
-        '{mname} = bio2bel_{mname}'.format(mname=BIO2BEL_MODULE)
+        f'{BIO2BEL_MODULE} = bio2bel_{BIO2BEL_MODULE}',
     ],
     'console_scripts': [
-        'bio2bel_{mname} = bio2bel_{mname}.cli:main'.format(mname=BIO2BEL_MODULE),
+        f'bio2bel_{BIO2BEL_MODULE} = bio2bel_{BIO2BEL_MODULE}.cli:main',
     ]
 }
 
@@ -50,7 +74,7 @@ def read(*parts):
 
 
 def find_meta(meta):
-    """Extract __*meta*__ from META_FILE"""
+    """Extract __*meta*__ from META_FILE."""
     meta_match = re.search(
         r'^__{meta}__ = ["\']([^"\']*)["\']'.format(meta=meta),
         META_FILE, re.M
@@ -80,8 +104,11 @@ def get_long_description():
         maintainer_email=find_meta('email'),
         license=find_meta('license'),
         packages=PACKAGES,
+        classifiers=CLASSIFIERS,
+        keywords=KEYWORDS,
         package_dir={'': 'src'},
         install_requires=INSTALL_REQUIRES,
         extras_require=EXTRAS_REQUIRE,
         entry_points=ENTRY_POINTS,
+        zip_safe=False,
     )

src/bio2bel_reactome/constants.py

@@ -16,7 +16,7 @@
 
 # Namespace constants
 
-REACTOME = 'REACTOME'
-HGNC = 'HGNC'
-UNIPROT = 'UNIPROT'
-CHEBI = 'CHEBI'
+REACTOME = 'reactome'
+HGNC = 'hgnc'
+UNIPROT = 'uniprot'
+CHEBI = 'chebi'

src/bio2bel_reactome/manager.py

@@ -2,29 +2,30 @@
 
 """This module populates the tables of bio2bel_reactome."""
 
-import itertools as itt
 import logging
 from collections import Counter
+from typing import Mapping, Optional
+
+import itertools as itt
+from sqlalchemy import and_
+from tqdm import tqdm
 
 import bio2bel_chebi
 import bio2bel_hgnc
 from bio2bel.manager.bel_manager import BELManagerMixin
 from bio2bel.manager.flask_manager import FlaskMixin
 from bio2bel.manager.namespace_manager import BELNamespaceManagerMixin
-from pybel.manager.models import NamespaceEntry
-from pybel import BELGraph
-from sqlalchemy import and_
-from tqdm import tqdm
-
 from compath_utils import CompathManager
+from pybel import BELGraph
+from pybel.manager.models import NamespaceEntry
 from .constants import MODULE_NAME
 from .models import Base, Chemical, Pathway, Protein, Species
 from .parsers import *
 
 log = logging.getLogger(__name__)
 
 __all__ = [
-    'Manager'
+    'Manager',
 ]
 
 
@@ -49,44 +50,29 @@ def __init__(self, *args, **kwargs):
     def _base(self):
         return Base
 
-    def summarize(self):
-        """Summarize the database.
-
-        :rtype: dict[str,int]
-        """
+    def summarize(self) -> Mapping[str, int]:
+        """Summarize the database."""
         return dict(
             pathways=self._count_model(Pathway),
             proteins=self._count_model(Protein),
             chemicals=self.count_chemicals(),
             species=self.count_species()
         )
 
-    def count_pathways(self):
-        """Count the pathways in the database.
-
-        :rtype: int
-        """
+    def count_pathways(self) -> int:
+        """Count the pathways in the database."""
         return self.session.query(Pathway).count()
 
-    def count_chemicals(self):
-        """Count the chemicals in the database.
-
-        :rtype: int
-        """
+    def count_chemicals(self) -> int:
+        """Count the chemicals in the database."""
         return self.session.query(Chemical).count()
 
-    def count_proteins(self):
-        """Count the proteins in the database.
-
-        :rtype: int
-        """
+    def count_proteins(self) -> int:
+        """Count the proteins in the database."""
         return self.session.query(Protein).count()
 
-    def count_species(self):
-        """Count the species in the database.
-
-        :rtype: int
-        """
+    def count_species(self) -> int:
+        """Count the species in the database."""
         return self.session.query(Species).count()
 
     """Custom query methods"""
@@ -472,10 +458,10 @@ def to_bel(self) -> BELGraph:
 
     """Custom Methods to Populate the DB"""
 
-    def _populate_pathways(self, url=None):
-        """ Populate pathway table
+    def _populate_pathways(self, url: Optional[str] = None):
+        """Populate the pathway table.
 
-        :param url: Optional[str] url: url from pathway table file
+        :param url: url from pathway table file
         """
 
         df = get_pathway_names_df(url=url)