Update Python package

.github/workflows/ci_python.yml

@@ -2,9 +2,9 @@ name: Test Python
 
 on:
   push:
-    branches: [ master, development ]
+    branches: [ master, development, experimental, test* ]
   pull_request:
-    branches: [ master, development ]
+    branches: [ master, development, experimental, test* ]
 
 jobs:
   build:
@@ -13,13 +13,13 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
 
     steps:
 
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v6
     - name: Set up Python  ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v6
       with:
         python-version:  ${{ matrix.python-version }}
 
@@ -31,6 +31,16 @@ jobs:
     - name: Install Python package
       run: |
         cd src/Python
-        python setup.py install
+        pip install .
+
+    - name: Run tests
+      run: |
+        cd src/Python/tests
+        python tests.py 
+        python diagnostic_test.py ../../../tests/minimax.wcon 
+
+    - name: Final version info
+      run: |
+        pip list
 
 

.gitignore

@@ -1,5 +1,6 @@
 # Random editor stuff
 *~
+*.swp
 
 # Python byte-compiled / optimized / DLL files
 *.pyc
@@ -9,9 +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/examples/view_wcon.py

@@ -4,5 +4,5 @@
 sys.path.append('..')
 from wcon import WCONWorms, MeasurementUnit
 
-file_name = 'asic-1 (ok415) on food L_2010_07_08__11_46_40___7___5.wcon'
+file_name = '../../../tests/minimax.wcon'
 w = WCONWorms.load_from_file(file_name)

src/Python/pyproject.toml

@@ -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/requirements.txt

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

src/Python/setup.py

@@ -12,6 +12,7 @@
 from codecs import open
 from os import path
 import os
+import shutil
 exec(open('wcon/version.py').read())
 
 here = path.abspath(path.dirname(__file__))
@@ -24,7 +25,13 @@
     with open(readme_path, encoding='utf-8') as f:
         long_description += f.read()
 
-print(os.listdir('.'))  # DEBUG
+# The canonical wcon_schema.json lives at the repository root so it can be
+# shared by every language implementation. setuptools cannot package files
+# from outside the package directory, so copy it into wcon/ at build time.
+repo_schema = path.join(here, '..', '..', 'wcon_schema.json')
+pkg_schema = path.join(here, 'wcon', 'wcon_schema.json')
+if path.exists(repo_schema):
+    shutil.copyfile(repo_schema, pkg_schema)
 
 setup(
     name='wcon',
@@ -51,8 +58,9 @@
     ],
     keywords='C. elegans worm tracking',
     packages=['wcon'],
-    package_data={'': ['../../wcon_schema.json']},
-    install_requires=['jsonschema', 'six', 'numpy', 'scipy<=0.17.1']
+    package_data={'wcon': ['wcon_schema.json']},
+    include_package_data=True,
+    install_requires=['jsonschema', 'six', 'scipy', 'pandas', 'psutil'],
     # Actually also requires numpy, scipy and numpy but I don't want to force
     # pip to install these since pip is bad at that for those packages.
 )

src/Python/tests/diagnostic_test.py

@@ -18,8 +18,10 @@
 idx = pd.IndexSlice
 import numpy as np
 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
 
@@ -51,6 +53,12 @@ def timing_function():
                                           validate_against_schema=False)
             print("Time to load w1: " + str(timing_function() - start_time))
 
+            print(" ------- W1 has " + str(len(w1.data)) + " rows and " +
+                  str(len(w1.data.columns)) + " columns")
+
+            print(pp.pformat(w1.data_as_odict))
+            print (' -------- ')
+
             # Save these worm tracks to a file, then load that file
             test_path = 'test.wcon'
             start_time = timing_function()
@@ -62,6 +70,12 @@ def timing_function():
                                           validate_against_schema=False)
             print("Time to load w2: " + str(timing_function() - start_time))
 
+            print(" ------- W2 has " + str(len(w2.data)) + " rows and " +
+                  str(len(w2.data.columns)) + " columns")
+
+            print(pp.pformat(w2.data_as_odict))
+            print (' -------- ')
+
             # x1 = w1.data.loc[:, idx[0, 'x', 0]].fillna(0)
             # x2 = w2.data.loc[:, idx[0, 'x', 0]].fillna(0)
             # cmm = np.flatnonzero(x1 != x2)
@@ -76,6 +90,14 @@ def timing_function():
             # "id" first in a data segment, etc.)
             w3 = WCONWorms.load_from_file(test_path,
                                           validate_against_schema=False)
+
+
+            print(" ------- W3 has " + str(len(w3.data)) + " rows and " +
+                  str(len(w3.data.columns)) + " columns")
+
+            print(pp.pformat(w3.data_as_odict))
+            print (' -------- ')
+
             assert(w2 == w3)
             assert(w1 == w2)
             assert(w1 == w3)

src/Python/tests/tests.py

@@ -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):
@@ -41,7 +41,7 @@ def flatten(list_of_lists):
     for element in list_of_lists:
         # If it's iterable but not a string or bytes, then recurse, otherwise
         # we are at a "leaf" node of our traversal
-        if(isinstance(element, collections.Iterable) and
+        if(isinstance(element, collections.abc.Iterable) and
            not isinstance(element, (str, bytes))):
             for sub_element in flatten(element):
                 yield sub_element
@@ -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/wcon/measurement_unit.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):
     """
@@ -637,12 +645,15 @@ def _create_from_atomic(cls, unit_string):
     @classmethod
     def _create_from_node(cls, node):
         """
-        node: is ast.Num or ast.BinOp or ast.UnaryOp or ast.Str or ast.Name
+        node: is ast.Constant (numeric) or ast.BinOp or ast.UnaryOp or ast.Name
             The expression to be transformed into a MeasurementUnit
 
         """
-        if isinstance(node, ast.Num):  # <number>
-            n = node.n
+        # ast.Num was deprecated in Python 3.8 and removed in 3.14;
+        # ast.Constant now represents all literal values.
+        if isinstance(node, ast.Constant) and isinstance(
+                node.value, (int, float)):  # <number>
+            n = node.value
             assert(n != 0)  # A unit cannot have zero in the expression
 
             u = cls()

src/Python/wcon/version.py

@@ -6,4 +6,4 @@
 # 2) we can import it in setup.py for the same reason
 # 3) we can import it into your module module
 # (from http://stackoverflow.com/questions/458550/)
-__version__ = '1.1.0'
+__version__ = '1.2.1'