Rename codebase to use hetnetpy from hetio

Merges #42
Closes #40

`pip install hetnetpy` now installs two packages: hetnetpy and hetio.
`import hetio` will trigger a warning. The source code uses a
symbolic link. Behavior on windows unknown.

.travis.yml

@@ -6,7 +6,7 @@ python:
   - "3.5"
   - "3.6"
 install:
-  - pip install .[test]
+  - pip install ".[test]"
   - python setup.py sdist bdist_wheel
 script:
   - py.test
@@ -16,18 +16,18 @@ deploy:
       secure: 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
     file_glob: true
     file:
-      - dist/hetio-*.tar.gz
-      - dist/hetio-*.whl
+      - dist/hetnetpy-*.tar.gz
+      - dist/hetnetpy-*.whl
     on:
       python: '3.6'
-      repo: hetio/hetio
+      repo: hetio/hetnetpy
       tags: true
   - provider: pypi
     user: dhimmel
     password:
       secure: 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
     on:
       python: '3.6'
-      repo: hetio/hetio
+      repo: hetio/hetnetpy
       tags: true
     distributions: sdist bdist_wheel

README.md

@@ -1,18 +1,25 @@
 # Hetnets in Python
 
 [![Latest DOI](https://zenodo.org/badge/14475/dhimmel/hetio.svg)](https://zenodo.org/badge/latestdoi/14475/dhimmel/hetio)
-[![GitHub issues](https://img.shields.io/github/issues/hetio/hetio.svg)](https://github.com/hetio/hetio/issues)
-[![Build Status](https://travis-ci.com/hetio/hetio.svg?branch=master)](https://travis-ci.com/hetio/hetio)
+[![GitHub issues](https://img.shields.io/github/issues/hetio/hetnetpy.svg)](https://github.com/hetio/hetnetpy/issues)
+[![Build Status](https://travis-ci.com/hetio/hetnetpy.svg?branch=master)](https://travis-ci.com/hetio/hetnetpy)
+
+## Overview
+
+Hetnetpy is a Python 3 package for creating, querying, and operating on hetnets.
+This software provides convenient data structures for hetnets, as well as algorithms for edge prediction.
+It is specifically tailored and streamlined for hetnets compared to other more generic network software.
+See https://het.io/software for additional software packages designed specifically for hetnets.
 
 ## Package relocation
 
-**Critical**:
-This is the final release before the package name [changes](https://github.com/hetio/hetio/issues/40) to `hetnetpy` from `hetio`.
-Future development will occur in the `hetio/hetnetpy` [repository](https://github.com/hetio/hetnetpy).
-PyPI releases will be available at <https://pypi.org/project/hetnetpy/>.
+Note that this package was previousely named `hetio`, available at the following repositories:
+
+- <https://github.com/hetio/hetnetpy> (current)
+- <https://github.com/hetio/hetio> (former)
+- <https://github.com/dhimmel/hetio> (former)
 
-Users of v0.2.11 will see a warning when importing `hetio`.
-These users should either switch to using `hetnetpy` or downgrade to `hetio<=0.2.10` to avoid the warning.
+In July 2019, the package was [renamed](https://github.com/hetio/hetnetpy/issues/40) to `hetnetpy` to more clearly represent its functionality and disambiguiate it from other products.
 
 ## Background
 
@@ -22,22 +29,22 @@ These users should either switch to using `hetnetpy` or downgrade to `hetio<=0.2
 
 **Impetus**: Development originated with a [study](https://doi.org/10.1371/journal.pcbi.1004259 "Heterogeneous Network Edge Prediction: A Data Integration Approach to Prioritize Disease-Associated Genes") to predict disease-associated genes and continues with a successive [study](https://doi.org/10.7554/eLife.26726 "Systematic integration of biomedical knowledge prioritizes drugs for repurposing") to repurpose drugs.
 
-**Caution**: Documentation is currently spotty, testing coverage is moderate, and the API is not fully stable. Contributions are welcome. Please use [GitHub Issues](https://github.com/hetio/hetio/issues) for feedback, questions, or troubleshooting.
+**Caution**: Documentation is currently spotty, testing coverage is moderate, and the API is not fully stable. Contributions are welcome. Please use [GitHub Issues](https://github.com/hetio/hetnetpy/issues) for feedback, questions, or troubleshooting.
 
 ## Installation
 
-[![PyPI](https://img.shields.io/pypi/v/hetio.svg)](https://pypi.org/project/hetio/)
+[![PyPI](https://img.shields.io/pypi/v/hetnetpy.svg)](https://pypi.org/project/hetnetpy/)
 
 Please use Python 3.4 or higher. To install the current PyPI version (recommended), run:
 
 ```sh
-pip install hetio
+pip install hetnetpy
 ```
 
 For the latest GitHub version, run:
 
 ```sh
-pip install git+https://github.com/hetio/hetio.git#egg=hetio
+pip install git+https://github.com/hetio/hetnetpy.git#egg=hetnetpy
 ```
 
 For development, clone or download-and-extract the repository. Then run `pip install --editable .` from the repository's root directory. The `--editable` flag specifies [editable](https://pythonhosted.org/setuptools/setuptools.html#development-mode) mode, so updating the source updates your installation.
@@ -56,10 +63,10 @@ A Graph object stores a heterogeneous network and relies on the following classe
 ## Release instructions
 
 This section is only relevant for project maintainers.
-Travis CI deployments are used to upload releases to [PyPI](https://pypi.org/project/hetio) and [GitHub releases](https://github.com/hetio/hetio/releases).
+Travis CI deployments are used to upload releases to [PyPI](https://pypi.org/project/hetnetpy) and [GitHub releases](https://github.com/hetio/hetnetpy/releases).
 To create a new release, do the following:
 
-1. Bump the version in [`__init__.py`](hetio/__init__.py).
+1. Bump the version in [`__init__.py`](hetnetpy/__init__.py).
 
 2. Add a release notes file in [`release-notes`](release-notes).
   Format as a commit message that will be used as the GitHub release description.
@@ -68,7 +75,7 @@ To create a new release, do the following:
 
   ```sh
   TAG=v`python setup.py --version`
-  git add hetio/__init__.py release-notes/$TAG.*
+  git add hetnetpy/__init__.py release-notes/$TAG.*
   git commit --message "Prepare $TAG release"
   git push
   git tag --annotate $TAG --file release-notes/$TAG.*

hetio

@@ -0,0 +1 @@
+hetnetpy

hetnetpy/__init__.py

@@ -0,0 +1,11 @@
+__version__ = "0.3.0"
+
+if __name__ == "hetio":
+    # https://github.com/hetio/hetnetpy/issues/40
+    import warnings
+    message = (
+        "The 'hetio' package has been renamed to 'hetnetpy'. "
+        "Future versions will remove the ability to 'import hetio'. "
+        "Switch to 'import hetnetpy'."
+    )
+    warnings.warn(message, FutureWarning)

hetio/abbreviation.py → hetnetpy/abbreviation.py

@@ -2,7 +2,7 @@
 
 import regex
 
-import hetio.hetnet
+import hetnetpy.hetnet
 
 
 def validate_abbreviations(metagraph):
@@ -113,12 +113,12 @@ def create_abbreviations(metagraph):
 def metaedges_from_metapath(abbreviation, standardize_by=None):
     """
     Get the abbreviated metaedges for an abbreviated metapath.
-    Pass a hetio.MetaGraph object to `standardize_by` to standardize metaedge
+    Pass a hetnetpy.MetaGraph object to `standardize_by` to standardize metaedge
     abbreviations based on the non-inverted orietatation. Pass `text` to
     standardize by alphabetical/forward-direction arrangment of the
     abbreviation. Default (`None`) does not standardize.
     """
-    if isinstance(standardize_by, hetio.hetnet.MetaGraph):
+    if isinstance(standardize_by, hetnetpy.hetnet.MetaGraph):
         metapath = standardize_by.metapath_from_abbrev(abbreviation)
         return [metaedge.get_standard_abbrev() for metaedge in metapath]
     # Note that this is a valid regex module pattern but will not work in the

hetio/hetnet.py → hetnetpy/hetnet.py

@@ -2,7 +2,7 @@
 import functools
 import re
 
-import hetio.abbreviation
+import hetnetpy.abbreviation
 
 direction_to_inverse = {
     'forward': 'backward',
@@ -255,7 +255,7 @@ def get_metaedge(self, metaedge):
             raise ValueError('Cannot interpret object of type {}'.format(type(metaedge).__name__))
         if metaedge in self.neo4j_to_metaedge:
             return self.neo4j_to_metaedge[metaedge]
-        metaedge_id = hetio.abbreviation.metaedge_id_from_abbreviation(self, metaedge)
+        metaedge_id = hetnetpy.abbreviation.metaedge_id_from_abbreviation(self, metaedge)
         return self.get_edge(metaedge_id)
 
     def get_metapath(self, metapath):
@@ -302,10 +302,10 @@ def from_edge_tuples(metaedge_tuples, kind_to_abbrev=None):
             metagraph.add_edge(edge_tuple)
 
         if kind_to_abbrev is None:
-            kind_to_abbrev = hetio.abbreviation.create_abbreviations(metagraph)
+            kind_to_abbrev = hetnetpy.abbreviation.create_abbreviations(metagraph)
         metagraph.set_abbreviations(kind_to_abbrev)
 
-        assert hetio.abbreviation.validate_abbreviations(metagraph)
+        assert hetnetpy.abbreviation.validate_abbreviations(metagraph)
 
         return metagraph
 
@@ -441,9 +441,9 @@ def get_metapath_from_edges(self, edges):
     def metapath_from_abbrev(self, abbrev):
         """Retrieve a metapath from its abbreviation"""
         metaedges = list()
-        metaedge_abbrevs = hetio.abbreviation.metaedges_from_metapath(abbrev)
+        metaedge_abbrevs = hetnetpy.abbreviation.metaedges_from_metapath(abbrev)
         for metaedge_abbrev in metaedge_abbrevs:
-            metaedge_id = hetio.abbreviation.metaedge_id_from_abbreviation(
+            metaedge_id = hetnetpy.abbreviation.metaedge_id_from_abbreviation(
                 self, metaedge_abbrev)
             metaedges.append(self.get_edge(metaedge_id))
         return self.get_metapath_from_edges(tuple(metaedges))
@@ -561,7 +561,7 @@ def __init__(self, metagraph, data=dict()):
 
         Parameters
         ----------
-        metagraph : hetio.hetnet.MetaGraph
+        metagraph : hetnetpy.hetnet.MetaGraph
             metagraph with the potential types of nodes and relationships
         """
         BaseGraph.__init__(self)
@@ -574,7 +574,7 @@ def add_node(self, kind, identifier, name=None, data={}):
 
         Parameters
         ----------
-        metagraph : hetio.hetnet.MetaGraph
+        metagraph : hetnetpy.hetnet.MetaGraph
             metagraph with the potential types of nodes and relationships
         kind : str
             metanode kind
@@ -601,9 +601,9 @@ def add_edge(self, source_id, target_id, kind, direction, data=dict()):
 
         Parameters
         ----------
-        source_id : hetio.hetnet.Node or tuple of (metanode, node) identifiers
+        source_id : hetnetpy.hetnet.Node or tuple of (metanode, node) identifiers
             the source node for the edge
-        target_id : hetio.hetnet.Node or tuple of (metanode, node) identifiers
+        target_id : hetnetpy.hetnet.Node or tuple of (metanode, node) identifiers
             the target node for the edge
         kind : str
             the metaedge kind

hetio/matrix.py → hetnetpy/matrix.py

@@ -40,8 +40,8 @@ def metaedge_to_adjacency_matrix(
 
     Parameters
     ==========
-    graph : hetio.hetnet.graph
-    metaedge : hetio.hetnet.MetaEdge or an alternative metaedge specification
+    graph : hetnetpy.hetnet.graph
+    metaedge : hetnetpy.hetnet.MetaEdge or an alternative metaedge specification
     dtype : type
     dense_threshold : float (0 ≤ dense_threshold ≤ 1)
         minimum proportion of nonzero values at which to output a dense matrix.

hetio/neo4j.py → hetnetpy/neo4j.py

@@ -2,7 +2,7 @@
 import itertools
 import textwrap
 
-import hetio.hetnet
+import hetnetpy.hetnet
 
 
 @functools.lru_cache()
@@ -119,7 +119,7 @@ def as_label(metanode):
     """
     import warnings
     warnings.warn(
-        "hetio.neo4j.as_label is deprecated. Use metanode.neo4j_label instead.",
+        "hetnetpy.neo4j.as_label is deprecated. Use metanode.neo4j_label instead.",
         DeprecationWarning,
     )
     return metanode.neo4j_label
@@ -131,10 +131,10 @@ def as_type(metaedge):
     """
     import warnings
     warnings.warn(
-        "hetio.neo4j.as_type is deprecated. Use metaedge.neo4j_rel_type instead.",
+        "hetnetpy.neo4j.as_type is deprecated. Use metaedge.neo4j_rel_type instead.",
         DeprecationWarning,
     )
-    assert isinstance(metaedge, hetio.hetnet.MetaEdge)
+    assert isinstance(metaedge, hetnetpy.hetnet.MetaEdge)
     return metaedge.neo4j_rel_type
 
 
@@ -168,7 +168,7 @@ def cypher_path(metarels):
     Format a metapath for cypher.
     """
     # Convert metapath to metarels
-    if isinstance(metarels, hetio.hetnet.MetaPath):
+    if isinstance(metarels, hetnetpy.hetnet.MetaPath):
         metarels = metapath_to_metarels(metarels)
 
     # Create cypher query
@@ -357,7 +357,7 @@ def construct_dwpc_query(metarels, property='name', join_hint='midpoint', index_
         which is the default, uses the `labeled` method.
     """
     # Convert metapath to metarels
-    if isinstance(metarels, hetio.hetnet.MetaPath):
+    if isinstance(metarels, hetnetpy.hetnet.MetaPath):
         metarels = metapath_to_metarels(metarels)
 
     # create cypher path query
@@ -435,7 +435,7 @@ def construct_pdp_query(metarels, dwpc=None, path_style='list', return_property=
         which is the default, uses the `labeled` method.
     """
     # Convert metapath to metarels
-    if isinstance(metarels, hetio.hetnet.MetaPath):
+    if isinstance(metarels, hetnetpy.hetnet.MetaPath):
         metarels = metapath_to_metarels(metarels)
 
     # create cypher path query

hetio/pathtools.py → hetnetpy/pathtools.py

@@ -2,7 +2,7 @@
 import functools
 import operator
 
-from hetio.hetnet import Node, Path
+from hetnetpy.hetnet import Node, Path
 
 
 def DWPC(paths, damping_exponent, exclude_edges=set(), exclude_masked=True):

hetio/permute.py → hetnetpy/permute.py

@@ -2,7 +2,7 @@
 import random
 import logging
 
-from hetio.hetnet import Graph
+from hetnetpy.hetnet import Graph
 
 
 def permute_graph(graph, multiplier=10, seed=0, metaedge_to_excluded=dict(), log=False):
@@ -19,7 +19,7 @@ def permute_graph(graph, multiplier=10, seed=0, metaedge_to_excluded=dict(), log
 
     Parameters
     ----------
-    graph : hetio.hetnet.Graph
+    graph : hetnetpy.hetnet.Graph
         Input hetnet to create a permuted derivative from
     multiplier : int or float
         This is multiplied by the number of edges for each metaedge to
@@ -36,7 +36,7 @@ def permute_graph(graph, multiplier=10, seed=0, metaedge_to_excluded=dict(), log
 
     Returns
     -------
-    permuted_graph : hetio.hetnet.Graph
+    permuted_graph : hetnetpy.hetnet.Graph
         A permuted hetnet derived from the input graph.
     stats : list of dicts
         A list where each item is a dictionary of permutation statistics at a

hetio/readwrite.py → hetnetpy/readwrite.py

@@ -16,7 +16,7 @@
 except ImportError:
     fspath = str
 
-from hetio.hetnet import Graph, MetaGraph
+from hetnetpy.hetnet import Graph, MetaGraph
 
 
 def read_graph(path, formatting=None):

release-notes/v0.3.0.txt

@@ -0,0 +1,6 @@
+hetio/hetnetpy v0.3.0
+=====================
+
+This release is the first with the new package name `hetnetpy`.
+Users should now use `pip install hetnetpy` and `import hetnetpy`.
+`import hetio` will still work but will trigger a FutureWarning.

setup.py

@@ -7,7 +7,7 @@
 directory = pathlib.Path(__file__).parent.absolute()
 
 # version
-init_path = directory.joinpath('hetio', '__init__.py')
+init_path = directory.joinpath('hetnetpy', '__init__.py')
 with init_path.open() as read_file:
     text = read_file.read()
 pattern = re.compile(r"^__version__ = ['\"]([^'\"]*)['\"]", re.MULTILINE)
@@ -30,9 +30,9 @@
 
 setuptools.setup(
     # Package details
-    name='hetio',
+    name='hetnetpy',
     version=version,
-    url='https://github.com/hetio/hetio',
+    url='https://github.com/hetio/hetnetpy',
     description='Hetnets in Python',
     long_description_content_type='text/markdown',
     long_description=long_description,
@@ -43,7 +43,7 @@
     author_email='[email protected]',
 
     # Package topics
-    keywords='hetnet graph heterogeneous network neo4j hetio',
+    keywords='hetnet graph heterogeneous network neo4j hetio hetnetpy',
     classifiers=[
         'Intended Audience :: Science/Research',
         'Topic :: Scientific/Engineering :: Bio-Informatics',
@@ -56,7 +56,7 @@
         'Programming Language :: Python :: 3.6',
     ],
 
-    packages=['hetio'],
+    packages=['hetnetpy', 'hetio'],
 
     # Specify python version
     python_requires='>=3.4',