Merge pull request #17 from simleo/rename_package

Rename package to biotracks

README.rst

@@ -11,7 +11,7 @@ Steps to follow to use the package:
 
    python setup.py install
 
-+ **step 2** - create a ``cell_track_dpkg.ini`` configuration file and place it in the same directory as your tracking file. The file must be structured as follows:
++ **step 2** - create a ``biotracks.ini`` configuration file and place it in the same directory as your tracking file. The file must be structured as follows:
 
 .. code-block::
 

dpkg/createdp.py → biotracks/createdp.py

@@ -4,7 +4,7 @@
 
 import datapackage as dp
 from jsontableschema import infer
-import dpkg.names as names
+from .names import OBJECTS_TABLE_NAME, LINKS_TABLE_NAME
 
 
 def create_dpkg(top_level_dict, dict_, directory, joint_id):
@@ -34,7 +34,7 @@ def create_dpkg(top_level_dict, dict_, directory, joint_id):
                        primary_key=joint_id)
 
     myDP.descriptor['resources'].append(
-        {"name": names.OBJECTS_TABLE_NAME,
+        {"name": OBJECTS_TABLE_NAME,
          "path": path,
          "schema": schema,
          }
@@ -51,13 +51,13 @@ def create_dpkg(top_level_dict, dict_, directory, joint_id):
             "fields": joint_id,
             "reference": {
                 "datapackage": "",
-                "resource": names.OBJECTS_TABLE_NAME,
+                "resource": OBJECTS_TABLE_NAME,
                 "fields": joint_id
             }
         }]
 
     myDP.descriptor['resources'].append(
-        {"name": names.LINKS_TABLE_NAME,
+        {"name": LINKS_TABLE_NAME,
          "path": path,
          "schema": schema,
          }

dpkg/pushtopandas.py → biotracks/pushtopandas.py

@@ -6,7 +6,7 @@
     from datapackage.pushpull import _convert_path as convert_path
 import pandas as pd
 
-import dpkg.names as names
+from .names import OBJECTS_TABLE_NAME, LINKS_TABLE_NAME
 
 
 def push_to_pandas(directory, object_id_cmso):
@@ -20,8 +20,8 @@ def push_to_pandas(directory, object_id_cmso):
     storage = dp.push_datapackage(descriptor=descr, backend='pandas')
     print(storage.buckets)
 
-    objects = storage[convert_path("objects.csv", names.OBJECTS_TABLE_NAME)]
-    links = storage[convert_path("links.csv", names.LINKS_TABLE_NAME)]
+    objects = storage[convert_path("objects.csv", OBJECTS_TABLE_NAME)]
+    links = storage[convert_path("links.csv", LINKS_TABLE_NAME)]
 
     objects.reset_index(inplace=True)
     print(objects.head()), print(links.head())

dpkg/readfile.py → biotracks/readfile.py

@@ -7,7 +7,9 @@
 import xlrd
 from xlrd import XLRDError
 
-import dpkg.names as names
+from .names import (
+    X_COORD_NAME, Y_COORD_NAME, FRAME_NAME, OBJECT_NAME, LINK_NAME
+)
 
 
 def xls_to_csv(xls_file):
@@ -250,10 +252,10 @@ def read_cellprofiler(cp_file, track_dict):
     cp_df = pd.read_csv(cp_file)
     # dictionary for the objects
     objects_dict = {}
-    x = track_dict.get(names.X_COORD_NAME)
-    y = track_dict.get(names.Y_COORD_NAME)
-    frame = track_dict.get(names.FRAME_NAME)
-    obj_id = track_dict.get(names.OBJECT_NAME)
+    x = track_dict.get(X_COORD_NAME)
+    y = track_dict.get(Y_COORD_NAME)
+    frame = track_dict.get(FRAME_NAME)
+    obj_id = track_dict.get(OBJECT_NAME)
     # parse the digits used for the tracking settings (e.g. 15)
     digits = x.split('_')[2]
     # sort the dataframe by [track_id, frame]
@@ -310,7 +312,7 @@ def read_cellprofiler(cp_file, track_dict):
     for key, value in links_dict.items():
         for object_ in value:
             links_df = links_df.append([[key, object_]])
-    links_df.columns = [track_dict.get(names.LINK_NAME), obj_id]
+    links_df.columns = [track_dict.get(LINK_NAME), obj_id]
 
     return (objects_df, links_df)
 

docs/index.rst

@@ -1,16 +1,13 @@
-.. sample documentation master file, created by
-   sphinx-quickstart.
+Data package representation for cell migration tracking data.
 
-Welcome to dpkg's documentation!
-==================================
 
-Contents:
+Contents
+========
 
 .. toctree::
    :maxdepth: 2
 
 
-
 Indices and tables
 ==================
 

scripts/create_dpkg.py

@@ -7,12 +7,12 @@
 import numpy as np
 import pandas as pd
 
-import dpkg.createdp as createdp
-import dpkg.plot as plot
-import dpkg.pushtopandas as pushtopandas
-import dpkg.readfile as readfile
-import dpkg.names as names
-from dpkg.configuration import readConfigFile
+import biotracks.createdp as createdp
+import biotracks.plot as plot
+import biotracks.pushtopandas as pushtopandas
+import biotracks.readfile as readfile
+import biotracks.names as names
+from biotracks.configuration import readConfigFile
 
 # global variable - file name from the command line
 f = sys.argv[1]

setup.py

@@ -6,7 +6,7 @@
 from distutils.dep_util import newer
 
 VERSION_FILE = "VERSION"
-PY_VERSION_FILE = "dpkg/version.py"
+PY_VERSION_FILE = "biotracks/version.py"
 
 
 def get_version_string():
@@ -36,13 +36,13 @@ def run(self):
 
 
 setup(
-    name='cell_track_dpkg',
+    name='biotracks',
     version=get_version_string(),
     description='Data package representation for cell migration tracking data',
     long_description=readme,
     author='paola masuzzo',
     author_email='[email protected]',
-    url='https://github.com/pcmasuzzo/cell_track_dpkg',
+    url='https://github.com/CellMigStandOrg/biotracks',
     license="BSD",
     cmdclass={"build_py": BuildPy},
     classifiers=[

tests/context.py

@@ -4,4 +4,4 @@
 import os
 sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), '..')))
 
-import dpkg
+import biotracks

tests/test_config.py

@@ -1,4 +1,4 @@
-from dpkg.configuration import readConfigFile
+from biotracks.configuration import readConfigFile
 from pytest import fixture
 import os
 
@@ -7,7 +7,7 @@
 def ini_file():
     directory = os.path.dirname(__file__)
     return os.path.join(
-        directory, "test_files", "cell_track_dpkg.ini")
+        directory, "test_files", "biotracks.ini")
 
 
 class TestReadConfigFile(object):

tests/test_readfile.py

@@ -2,9 +2,9 @@
 import os
 import sys
 # needed if using pytest (not needed for py.test)
-sys.path.append(os.path.dirname(os.path.realpath(__file__)) + "/../dpkg")
+sys.path.append(os.path.dirname(os.path.realpath(__file__)) + "/../biotracks")
 
-from dpkg import readfile
+from biotracks import readfile
 from pytest import fixture
 import pandas as pd