Merge pull request #25 from PathwayMerger/ppi-exporter

Ppi exporter

Author: ddomingof

.coveragerc

@@ -5,10 +5,8 @@
 #########################
 
 [flake8]
-ignore = 
-	E501
-	I100  # Import statements are in the wrong order
-	I101  # Imported names are in the wrong order
+ignore =
+    E501 # Line too long
 	F405 # Stars import
 	F403 # imports not used in init
 	F401 # imports not used in init
@@ -25,7 +23,10 @@ exclude =
     *.egg-info,
     .cache,
     .eggs
-max-complexity = 10
+max-complexity = 20
+max-line-length = 120
 import-order-style = pycharm
-application-import-names = pathme
+application-import-names =
+    pathme
+    tests
 format = ${cyan}%(path)s${reset}:${yellow_bold}%(row)d${reset}:${green_bold}%(col)d${reset}: ${red_bold}%(code)s${reset} %(text)s

.flake8

@@ -1,8 +1,6 @@
 # See: https://docs.readthedocs.io/en/latest/yaml-config.html
-build:
-    image: latest
 python:
-  version: 3.6
+  version: 3
   pip_install: true
   extra_requirements:
-  - docs
+    - docs

.readthedocs.yml

@@ -1,8 +1,9 @@
 sudo: false
 cache: pip
+
 language: python
 python:
-- 3.6
+  - 3.7
 stages:
   - lint
   - docs
@@ -13,9 +14,6 @@ jobs:
     - stage: lint
       env: TOXENV=manifest
     - env: TOXENV=flake8
-    - env: TOXENV=flake8-kegg
-    - env: TOXENV=xenon
-    - env: TOXENV=vulture
     - env: TOXENV=pyroma
     # docs stage
     - stage: docs
@@ -25,21 +23,11 @@ jobs:
     # test stage
     - stage: test
       env: TOXENV=py
-    - env: TOXENV=py PATHME_TESTS=tests/test_kegg/
-matrix:
-  allow_failures:
-      - env: TOXENV=flake8
-      - env: TOXENV=xenon
-      - env: TOXENV=vulture
 install:
-- pip install --upgrade pip
-- pip install tox
-- pip install codecov
-- pip install coverage
+  - sh -c 'if [ "$TOXENV" = "py" ]; then pip install tox codecov; else pip install tox; fi'
 script:
-- tox
+  - tox
 after_success:
-- tox -e coverage-report
-- codecov
+  - sh -c 'if [ "$TOXENV" = "py" ]; then tox -e coverage-report; codecov; fi'
 notifications:
   slack: pybel:n2KbWKBum3musnBg3L76gGwq

.travis.yml

@@ -186,7 +186,7 @@
       same "printed page" as the copyright notice for easier
       identification within third-party archives.
 
-   Copyright 2018-2019 Daniel Domingo-Fernandez
+   Copyright 2018-2020 Daniel Domingo-Fernández
 
    Licensed under the Apache License, Version 2.0 (the "License");
    you may not use this file except in compliance with the License.

LICENSE

@@ -18,8 +18,8 @@
 source_suffix = '.rst'
 master_doc = 'index'
 project = 'PathMe'
-copyright = '2018, Daniel Domingo-Fernández, Sarah Mubeen, and Josep Marin Llao'
-author = 'Daniel Domingo-Fernández, Sarah Mubeen, and Josep Marin Llao'
+copyright = '2020, Daniel Domingo-Fernández, Sarah Mubeen, Josep Marin Llao, and Charles Tapley Hoyt'
+author = 'Daniel Domingo-Fernández, Sarah Mubeen, Josep Marin Llao, and Charles Tapley Hoyt'
 
 release = '0.1.12-dev'
 
@@ -44,7 +44,7 @@
 latex_elements = {}
 latex_documents = [
     (master_doc, 'pathme.tex', 'PathMe Documentation',
-     'Sarah Mubeen, Josep Marin Llao, and Daniel Domingo-Fernández', 'manual'),
+     'Daniel Domingo-Fernández, Sarah Mubeen, Josep Marin Llao, and Charles Tapley Hoyt', 'manual'),
 ]
 man_pages = [
     (master_doc, 'pathme', 'PathMe Documentation', [author], 1)

doc8.ini

@@ -35,7 +35,6 @@ classifiers =
     Operating System :: OS Independent
     Programming Language :: Python
     Programming Language :: Python :: 3.7
-    Programming Language :: Python :: 3.6
     Programming Language :: Python :: 3 :: Only
     Topic :: Scientific/Engineering :: Bio-Informatics
 
@@ -65,7 +64,7 @@ install_requires =
 # Random options
 zip_safe = false
 include_package_data = True
-python_requires = >=3.6
+python_requires = >=3.7
 
 # Where is my code
 packages = find:
@@ -100,6 +99,16 @@ max-line-length = 120
 [coverage:run]
 branch = True
 source = pathme
+omit =
+    src/pathme/__main__.py
+    src/pathme/cli.py
+    tests/*
+    docs/*
+
+[coverage:paths]
+source =
+    src/pathme
+    .tox/*/lib/python*/site-packages/pathme
 
 [coverage:report]
 show_missing = True

docs/source/conf.py

@@ -15,8 +15,8 @@
 import pathme.kegg.cli
 import pathme.reactome.cli
 import pathme.wikipathways.cli
-from .constants import CX_DIR, KEGG_BEL, REACTOME_BEL, SPIA_DIR, UNIVERSE_DIR, WIKIPATHWAYS_BEL
-from .export_utils import get_universe_graph, iterate_universe_graphs, spia_export_helper
+from .constants import CX_DIR, KEGG_BEL, PPI_DIR, REACTOME_BEL, SPIA_DIR, UNIVERSE_DIR, WIKIPATHWAYS_BEL
+from .export_utils import export_helper, get_universe_graph, iterate_universe_graphs
 
 logger = logging.getLogger(__name__)
 
@@ -69,14 +69,31 @@ def export():
 def spia(kegg_path, reactome_path, wikipathways_path, output):
     """Export BEL Pickles to SPIA Excel."""
     click.echo(f'Results will be exported to {output}')
-    spia_export_helper(
+    export_helper(
         kegg_path=kegg_path,
         reactome_path=reactome_path,
         wikipathways_path=wikipathways_path,
         output=output,
     )
 
 
+@export.command()
+@kegg_path_option
+@reactome_path_option
+@wikipathways_path_option
+@click.option('-o', '--output', help='Output directory', default=PPI_DIR, show_default=True)
+def ppi(kegg_path, reactome_path, wikipathways_path, output):
+    """Export BEL Pickles to PPI-like tsv file."""
+    click.echo(f'Results will be exported to {output}')
+    export_helper(
+        kegg_path=kegg_path,
+        reactome_path=reactome_path,
+        wikipathways_path=wikipathways_path,
+        output=output,
+        format='ppi',
+    )
+
+
 @export.command()
 @kegg_path_option
 @reactome_path_option
@@ -94,11 +111,11 @@ def cx(kegg_path, reactome_path, wikipathways_path, output, no_flatten, no_norma
 
     click.echo(f'Results will be exported to {output}')
     for source, path, graph in iterate_universe_graphs(
-        kegg_path=kegg_path,
-        reactome_path=reactome_path,
-        wikipathways_path=wikipathways_path,
-        flatten=(not no_flatten),
-        normalize_names=(not no_normalize_names),
+            kegg_path=kegg_path,
+            reactome_path=reactome_path,
+            wikipathways_path=wikipathways_path,
+            flatten=(not no_flatten),
+            normalize_names=(not no_normalize_names),
     ):
         with open(os.path.join(output, f"{path.strip('.pickle')}.cx.json"), 'w') as file:
             to_cx_file(graph, file)

setup.cfg

@@ -39,16 +39,19 @@ def get_data_dir() -> str:
 
 SPIA_DIR = os.path.join(DATA_DIR, 'spia')
 CX_DIR = os.path.join(DATA_DIR, 'cx')
+PPI_DIR = os.path.join(DATA_DIR, 'ppi')
 UNIVERSE_DIR = os.path.join(DATA_DIR, 'universe')
 
 
-def ensure_pathme_folders():  # TODO why is this a function?
+def ensure_pathme_folders():
     """Ensure data folders are created."""
     os.makedirs(KEGG_DIR, exist_ok=True)
     os.makedirs(REACTOME_DIR, exist_ok=True)
     os.makedirs(WIKIPATHWAYS_DIR, exist_ok=True)
     os.makedirs(KEGG_CACHE, exist_ok=True)
     os.makedirs(SPIA_DIR, exist_ok=True)
+    os.makedirs(CX_DIR, exist_ok=True)
+    os.makedirs(PPI_DIR, exist_ok=True)
     os.makedirs(UNIVERSE_DIR, exist_ok=True)
 
     os.makedirs(KEGG_BEL, exist_ok=True)