Merge pull request #179 from kant2002/kant/update-packaging

Test on experimental branch

Author: pgleeson

.gitignore

@@ -1,5 +1,6 @@
 # Random editor stuff
 *~
+*.swp
 
 # Python byte-compiled / optimized / DLL files
 *.pyc
@@ -9,11 +10,14 @@ src/Python/dist/*
 src/Python/tests/test_chunk*
 src/Python/wcon.egg*
 .pypirc
+openworm/
 
 #Matlab
 *.asv
 
 # Scala
 src/scala/target/*
+src/scala/**/target/*
+
 /src/Python/example_saved_file.WCON
 /src/Python/wcon/wcon_schema.json

src/Python/Pipfile

@@ -0,0 +1,17 @@
+[[source]]
+url = "https://pypi.org/simple"
+verify_ssl = true
+name = "pypi"
+
+[packages]
+pandas = "*"
+six = "*"
+numpy = "*"
+psutil = "*"
+jsonschema = "*"
+scipy = "*"
+
+[dev-packages]
+
+[requires]
+python_version = "3.9"

src/Python/Pipfile.lock

@@ -0,0 +1,21 @@
+[project]
+name = "wcon"
+version = "1.1.0"
+authors = [
+  { name="Kerr, R; Brown, A; Currie, M; OpenWorm", email="ichoran@gmail.com" },
+]
+description = "Worm tracker Commons Object Notation"
+readme = "README.md"
+requires-python = ">=3.9"
+classifiers = [
+    'Development Status :: 4 - Beta',
+    'Intended Audience :: Science/Research',
+    'Topic :: Scientific/Engineering :: Bio-Informatics',
+    "Programming Language :: Python :: 3",
+    "Operating System :: OS Independent",
+]
+license = "MIT"
+
+[project.urls]
+Homepage = "https://github.com/openworm/tracker-commons"
+Issues = "https://github.com/openworm/tracker-commons/issues"

src/Python/pyproject.toml

@@ -0,0 +1,6 @@
+six
+jsonschema
+numpy
+pandas
+psutil
+scipy

src/Python/requirements.txt

@@ -20,7 +20,8 @@
 import time
 import pprint as pp
 
-sys.path.append('..')
+dir_path = os.path.dirname(os.path.realpath(__file__))
+sys.path.append(os.path.join(dir_path, '..'))
 from wcon import WCONWorms, MeasurementUnit
 from wcon.measurement_unit import MeasurementUnitAtom
 

src/Python/tests/.bbb.wcon.swp

@@ -16,20 +16,20 @@
 import shutil
 from scipy.constants import pi
 
-sys.path.append('..')
+dir_path = os.path.dirname(os.path.realpath(__file__))
+sys.path.append(os.path.join(dir_path, '..'))
 from wcon import WCONWorms, MeasurementUnit
 from wcon.measurement_unit import MeasurementUnitAtom
 
-
 def setUpModule():
     # If the wcon module is installed via pip, wcon_schema.json is included
     # in the proper place.  In the git repo it is not, however, so to test
-    # we must copy it over temporarily, then remove it once tests are done.
-    shutil.copyfile('../../../wcon_schema.json', '../wcon/wcon_schema.json')
+    # we must copy it over temporarily, then remove it once tests are done.    
+    shutil.copyfile(os.path.join(dir_path, '..', '..', '..', 'wcon_schema.json'), os.path.join(dir_path, '..', 'wcon', 'wcon_schema.json'))
 
 
 def tearDownModule():
-    os.remove('../wcon/wcon_schema.json')
+    os.remove(os.path.join(dir_path, '..', 'wcon', 'wcon_schema.json'))
 
 
 def flatten(list_of_lists):
@@ -192,7 +192,9 @@ def _validate_from_schema(self, wcon_string):
         except AttributeError:
             # Only load _wcon_schema if this method gets called.  Once
             # it's loaded, though, persist it in memory and don't lose it
-            with open("../../../wcon_schema.json", "r") as wcon_schema_file:
+            wcon_schema_path = os.path.abspath(os.path.join(os.path.dirname(__file__),
+                                                '..', '..', '..', 'wcon_schema.json'))
+            with open(wcon_schema_path, "r") as wcon_schema_file:
                 self._wcon_schema = json.loads(wcon_schema_file.read())
 
             # Now that the schema has been loaded, we can try again
@@ -204,7 +206,8 @@ def test_schema(self):
         self._validate_from_schema(basic_wcon)
 
     def test_equality_operator(self):
-        JSON_path = '../../../tests/minimax.wcon'
+        JSON_path = os.path.abspath(os.path.join(os.path.dirname(__file__),
+                                                '..', '..', '..', 'tests', 'minimax.wcon'))
         w2 = WCONWorms.load_from_file(JSON_path)
         w2.units['y'] = MeasurementUnit.create('m')
         w2data = w2.data.copy()

src/Python/tests/diagnostic_test.py

@@ -23,6 +23,14 @@
 import operator as op
 from scipy.constants import convert_temperature, pi
 
+def F2C(val):
+    return convert_temperature(val, 'F', 'C')
+def C2F(val):
+    return convert_temperature(val, 'C', 'F')
+def K2C(val):
+    return convert_temperature(val, 'K', 'C')
+def C2K(val):
+    return convert_temperature(val, 'C', 'K')
 
 def C2C(x):
     """

src/Python/tests/tests.py

@@ -116,8 +116,8 @@ def df_upsert(src, dest):
                         src.columns.isin(dest.columns)]
 
             # Sort our slices so they will be lined up for comparison
-            dest_sliced.sort_index(inplace=True)
-            src_sliced.sort_index(inplace=True)
+            dest_sliced.sort_index(axis=1, inplace=True)
+            src_sliced.sort_index(axis=1, inplace=True)
 
             # Align src_sliced's row/column labels to dest_sliced. The two
             # were built with independent .isin() masks so column order may
@@ -231,7 +231,10 @@ def convert_origin(df):
 
                 # Now reset our 'ox' values to zero.
                 if offset in cur_worm.columns.get_level_values(0):
-                    df.loc[:, (worm_id, offset)] = np.zeros(ox_column.shape)
+                    df.loc[:, (worm_id, offset)] = np.zeros(ox_column.shape, dtype=pd.Int64Dtype)
+            else:
+                all_x_columns = cur_worm.loc[:, (coord)].fillna(0).astype('float64')
+                df.loc[:, (worm_id, coord)] = all_x_columns.values
 
     # Drop the offset columns entirely from the dataframe.
     # This is so DataFrames with and without offsets