change the structure to support install via setup.py

Author: tcezard

.gitignore

@@ -1,3 +1,7 @@
 *.pyc
 .idea
 .cache
+__pycache__
+build/
+*.egg-info/
+dist/

.travis.yml

@@ -3,7 +3,9 @@ python:
   - "3.4"
 
 # command to install dependencies
-install: "pip install -r requirements.txt"
+install:
+  - "pip install -r requirements.txt"
+  - "python setup.py install"
 script: PYTHONPATH=. py.test
 
 notifications:

CHANGELOG.md

@@ -0,0 +1,9 @@
+Changelog for EGCG-Core
+===========================
+
+0.2 (unreleased)
+------------------
+ - Support for installing via setup.py
+
+0.1.1
+------

EPPs/__init__.py

@@ -0,0 +1,3 @@
+import pkg_resources
+
+__version__ = pkg_resources.get_distribution("clarity_scripts").version

EPPs/assign_to_workflow_stage.py bin/assign_to_workflow_stage.py

@@ -1,3 +1,4 @@
+#!/usr/bin/env python
 import csv
 from os import remove
 from os.path import join, dirname, abspath

EPPs/convert_and_dispatch_genotypes.py bin/convert_and_dispatch_genotypes.py

@@ -1,3 +1,4 @@
+#!/usr/bin/env python
 import os
 import sys
 import time

EPPs/create_reagents_for_run.py bin/create_reagents_for_run.py

@@ -1,3 +1,4 @@
+#!/usr/bin/env python
 import sys
 from logging import FileHandler
 from egcg_core.app_logging import logging_default as log_cfg

EPPs/prepare_discard_plate.py bin/prepare_discard_plate.py

@@ -1,2 +1 @@
-git+https://github.com/EdinburghGenomics/EGCG-Core.git@v0.4.3
-genologics==0.3.8.post0
+EGCG-Core==0.6.7

requirements.txt

@@ -0,0 +1,35 @@
+#!/usr/bin/env python
+import glob
+import subprocess
+from setuptools import setup, find_packages
+from os.path import join, abspath, dirname
+import pip
+
+# Fetch version from git tags.
+#version = subprocess.Popen(["git", "describe", "--abbrev=0"],stdout=subprocess.PIPE, universal_newlines=True).communicate()[0].rstrip()
+#version = version.decode("utf-8")
+
+requirements_txt = join(abspath(dirname(__file__)), 'requirements.txt')
+# reqs is a list of requirement
+# e.g. ['django==1.5.1', 'mezzanine==1.4.6']
+requirements = [l.strip() for l in open(requirements_txt) if l and not l.startswith('#')]
+
+
+version = '0.1.1'
+
+
+setup(
+    name='clarity_scripts',
+    version=version,
+    packages=find_packages(exclude=('tests',)),
+    url='https://github.com/EdinburghGenomics/clarity_scripts',
+    license='MIT',
+    description='Clarity EPPs used in Edinburgh Genomics',
+    long_description='Set of scripts used at Edinburgh Genomics to automate steps of in Clarity LIMS',
+    install_requires=requirements,  # actual module requirements
+    scripts=glob.glob("bin/*.py"),
+    zip_safe=False,
+    author='Timothee Cezard',
+    author_email='timothee.cezard@ed.ac.uk'
+
+)

setup.py

@@ -1,6 +1,6 @@
 from tests.test_common import fake_all_inputs, TestEPP
 from unittest.mock import Mock, patch
-from EPPs import assign_to_workflow_stage
+from bin import assign_to_workflow_stage
 
 
 class TestAsignWorkflowStage(TestEPP):
@@ -31,14 +31,14 @@ def setUp(self):
         self.epp2._lims = Mock()
 
     def test_assign(self):
-        with patch('EPPs.assign_to_workflow_stage.get_workflow_stage', return_value=Mock(uri='a_uri')) as p:
+        with patch('bin.assign_to_workflow_stage.get_workflow_stage', return_value=Mock(uri='a_uri')) as p:
             self.epp._run()
             p.assert_called_with(self.epp.lims, self.epp.workflow_name, 'a_stage_name')
             exp_artifacts = ['a1', 'a2']
             assert sorted([a.id for a in self.epp.lims.route_artifacts.call_args[0][0]]) == exp_artifacts
             assert self.epp.lims.route_artifacts.call_args[1] == {'stage_uri': 'a_uri'}
 
-        with patch('EPPs.assign_to_workflow_stage.get_workflow_stage', return_value=Mock(uri='a_uri')) as p:
+        with patch('bin.assign_to_workflow_stage.get_workflow_stage', return_value=Mock(uri='a_uri')) as p:
             self.epp2._run()
             p.assert_called_with(self.epp2.lims, self.epp2.workflow_name, 'a_stage_name')
             print(self.epp2.lims.route_artifacts.call_count)

tests/test_assign_to_workflow_stage.py

@@ -1,5 +1,6 @@
 from os.path import join, dirname, abspath
 from unittest.case import TestCase
+
 from EPPs.common import EPP
 from unittest.mock import Mock
 
@@ -45,5 +46,6 @@ def setUp(self):
         self.epp._process = Mock()
         self.epp._lims = Mock()
 
+
     def test_init(self):
         assert self.epp.baseuri == 'http://server:8080'

tests/test_common.py

@@ -2,7 +2,7 @@
 from os.path import join
 from tests.test_common import TestCommon, TestEPP, FakeEntity
 from unittest.mock import Mock, patch
-from EPPs.convert_and_dispatch_genotypes import GenotypeConversion, UploadVcfToSamples
+from bin.convert_and_dispatch_genotypes import GenotypeConversion, UploadVcfToSamples
 
 
 class TestGenotypeConversion(TestCommon):
@@ -113,9 +113,9 @@ def setUp(self):
         self.epp._process = Mock(all_inputs=fake_all_inputs)
 
     def test_upload(self):
-        patched_log = patch('EPPs.convert_and_dispatch_genotypes.UploadVcfToSamples.info')
-        patched_generate_vcf = patch('EPPs.convert_and_dispatch_genotypes.GenotypeConversion.generate_vcf')
-        patched_remove = patch('EPPs.convert_and_dispatch_genotypes.remove')
+        patched_log = patch('bin.convert_and_dispatch_genotypes.UploadVcfToSamples.info')
+        patched_generate_vcf = patch('bin.convert_and_dispatch_genotypes.GenotypeConversion.generate_vcf')
+        patched_remove = patch('bin.convert_and_dispatch_genotypes.remove')
 
         exp_log_msgs = (
             ('Matching against %s artifacts', 1),

tests/test_convert_and_dispatch_genotypes.py

@@ -1,6 +1,6 @@
 from tests.test_common import fake_all_inputs, TestEPP, FakeEntity
 from unittest.mock import Mock, patch
-from EPPs import prepare_discard_plate
+from bin import prepare_discard_plate
 
 
 class FakeContainer(FakeEntity):
@@ -33,8 +33,8 @@ def setUp(self):
         self.epp._process = Mock(all_inputs=fake_all_inputs)
 
     def test_discard(self):
-        patched_stage = patch('EPPs.prepare_discard_plate.get_workflow_stage', return_value=Mock(uri='a_uri'))
-        patched_log = patch('EPPs.prepare_discard_plate.FindPlateToRoute.info')
+        patched_stage = patch('bin.prepare_discard_plate.get_workflow_stage', return_value=Mock(uri='a_uri'))
+        patched_log = patch('bin.prepare_discard_plate.FindPlateToRoute.info')
 
         exp_log_messages = (
             ('Found Stage %s uri: %s', 'Discard Plates EG 1.0', 'a_uri'),