pipy setup

.gitignore

@@ -7,6 +7,8 @@ __pycache__/
 *$py.class
 *.py_rm_me
 tmp*
+*.csv
+*.pdf
 
 # C extensions
 *.so

makefile

@@ -90,14 +90,30 @@ pylint:
 	chmod 755 tmp_pylint
 	tmp_pylint
 
+# --------------------------------------------------------------------------------
+dist_archive:
+	#python3 -m pip install --user --upgrade setuptools wheel
+	python3 setup.py sdist bdist_wheel
+	find dist
+
+clean_dist:
+	rm -rf dist build enrichmentanalysis.egg-info
+
+# --------------------------------------------------------------------------------
+upload_pypi_test:
+	python setup.py register -r pypitest
+	python setup.py sdist upload -r pypitest
+
+# ----------------------------------------------------------------------------------------
 clean:
+	rm -f *.csv
 	rm -f relationship_*.txt
 	rm -f tmp_pylint
 	make -f makefile clean_pyc
 
 clean_pyc:
 	find . -name \*.pyc | xargs rm -f
-	find . -name \*.stackdump | xargs rm -f
+	find . -name \*.st\*p | xargs rm -f
 
 clobber_materials:
 	rm goa_human.*; wget http://geneontology.org/gene-associations/goa_human.gaf.gz; gunzip goa_human.gaf.gz

setup.py

@@ -1,48 +1,56 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 # -*- coding: UTF-8 -*-
 """Setup for PyPI usage."""
 
-import os.path as op
-
 from glob import glob
 from setuptools import setup
-from setup_helper import SetupHelper
-
-
-NAME = "reactomeneo4j"
-CLASSIFIERS = [
-    'Development Status :: 4 - Beta',
-    'Intended Audience :: Science/Research',
-    'License :: OSI Approved :: BSD License',
-    'Programming Language :: Python :: 3',
-    'Topic :: Scientific/Engineering :: Bio-Informatics',
-    ]
 
-# Use the helper
-HLPR = SetupHelper(initfile="reactomeneo4j/__init__.py", readmefile="README.md")
+def get_long_description():
+    """Get the package's long description."""
+    with open("README.md", "r") as fh:
+        long_description = fh.read()
 
-SETUP_DIR = op.abspath(op.dirname(__file__))
+PACKAGES = [
+    'reactomeneo4j',
+    'reactomeneo4j/code',
+    'reactomeneo4j/code/cli',
+    'reactomeneo4j/code/enrich',
+    'reactomeneo4j/code/ex',
+    'reactomeneo4j/code/mkpy',
+    'reactomeneo4j/code/node',
+    'reactomeneo4j/code/query',
+    'reactomeneo4j/code/rest',
+    'reactomeneo4j/code/run',
+    'reactomeneo4j/code/schema',
+    'reactomeneo4j/code/subdag',
+    'reactomeneo4j/code/wrpy',
+    'reactomeneo4j/data',
+    'reactomeneo4j/data/all',
+    'reactomeneo4j/data/hsa',
+    'reactomeneo4j/data/hsa/pathways',
+    'reactomeneo4j/data/pwy',
+    'reactomeneo4j/work',
+]
 
 setup(
-    name=NAME,
-    version=0.1,
+    name='reactomeneo4j',
+    version='0.0.1',
     author='DV Klopfenstein',
     author_email='dvklopfenstein@gmail.com',
-    license=HLPR.license,
-    long_description=('Explore peer-reviewed biological pathways '
-                      'in Reactome using Python to run neo4j queries'),
-    packages=[
-        NAME,
-        NAME + ".code",
-        NAME + ".code.node",
-        NAME + ".code.node.query",
-        NAME + ".code.schema",
-        NAME + ".data",
-        NAME + ".work"],
-    include_package_data=True,
+    long_description=get_long_description(),
+    packages=PACKAGES,
+    package_dir={p:'src/{PKG}'format(PKG=p) for p in PACKAGES},
+    # include_package_data=True,
     # package_data={"reactomeneo4j.test_data.nbt_3102": ["*.*"]},
-    scripts=glob('scripts/*.py'),
-    classifiers=CLASSIFIERS,
+    scripts=glob('src/bin/*.py'),
+    classifiers=[
+        'Development Status :: 4 - Beta',
+        'Intended Audience :: Science/Research',
+        'License :: OSI Approved :: BSD License',
+        'Programming Language :: Python :: 3',
+        'Topic :: Scientific/Engineering :: Bio-Informatics',
+        'Operating System :: OS Independent',
+    ],
     url='http://github.com/dvklopfenstein/reactome_neo4j_py',
     description='Explore biological pathways in Reactome from the command-line',
     install_requires=['timeit', 'datetime', 'collections'],

src/reactomeneo4j/__init__.py

@@ -1 +1,2 @@
 # Python scripts for accessing biological processes in Reactome using neo4j queries.
+name = 'reactomeneo4j'