remove machine-specific paths

.gitignore

@@ -109,5 +109,6 @@ venv.bak/
 .idea/
 omero_py/omeroweb/
 omero_py/pipeline/
-*.ipynb
+**.ipynb
 data/
+notebooks/

MANIFEST.in

+include core/trap_templates/*.npy
\ No newline at end of file

core/segment.py

@@ -4,11 +4,12 @@ cell segmentation, nucleus segmentation."""
 from skimage import feature
 import numpy as np
 from scipy.spatial import distance
+from pathlib import Path
 
 from core.traps import identify_trap_locations
 
-trap_template = np.load('/Users/s1893247/PhD/pipeline-core/core/trap_templates'
-                        '/trap_bg_1.npy')
+trap_template_directory = Path(__file__).parent / 'trap_templates'
+trap_template = np.load(trap_template_directory / 'trap_bg_1.npy')
 
 
 def align_timelapse_images(raw_data, channel=0, reference_reset_time=80,

setup.py

@@ -10,6 +10,7 @@ setup(
     author_email='diane.adjavon@ed.ac.uk',
     description='Core utilities for microscopy pipeline',
     python_requires='>=3.6',
+    include_package_data=True,
     install_requires=[
         'numpy',
         'pandas',

test/test_local_expt.py

 import logging
 from logging.handlers import RotatingFileHandler
 import unittest
+from pathlib import Path
 
 from core.experiment import Experiment
 
@@ -27,8 +28,8 @@ logger.addHandler(file_handler)
 
 logger.debug('Set up the loggers as test.')
 
-
-root_directory = '/Users/s1893247/PhD/pipeline-core/data/glclvl_0.1_mig1_msn2_maf1_sfp1_dot6_03'
+data_directory = Path(__file__).parent.parent / 'data/'
+root_directory = data_directory / 'glclvl_0.1_mig1_msn2_maf1_sfp1_dot6_03'
 
 class TestCase(unittest.TestCase):
     def setUp(self):