Properly configure setup.py; Clean up main directory

iandanforth · Jul 2, 2018 · 9d03dda · 9d03dda
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Showing 29 changed files with 57 additions and 11 deletions.
diff --git a/MANIFEST.in b/MANIFEST.in
@@ -0,0 +1 @@
+include README.md LICENSE
diff --git a/...in_Fuglevand_2017_Muscle_Fatigue_Model.py → ...in_Fuglevand_2017_Muscle_Fatigue_Model.py b/...in_Fuglevand_2017_Muscle_Fatigue_Model.py → ...in_Fuglevand_2017_Muscle_Fatigue_Model.py
diff --git a/asynctest.py → notes/asynctest.py b/asynctest.py → notes/asynctest.py
diff --git a/default_config.yaml → notes/default_config.yaml b/default_config.yaml → notes/default_config.yaml
diff --git a/notes/gen_debug_charts.py b/notes/gen_debug_charts.py
@@ -24,7 +24,7 @@
 )
 
 # Motor Neuron Pool Charts
-if True:
+if False:
 
     # Recruitment Thresholds
     if True:
@@ -161,7 +161,7 @@
     plot(fig, filename='nominal-fatigabilities')
 
 # Force Charts
-if False:
+if True:
     xs = np.arange(0.0, 70.0, 0.1)
     forces = []
     all_forces_by_excitation = []

diff --git a/model_runs/limited/limited_run_config.yaml → ...odel_runs/limited/limited_run_config.yaml b/model_runs/limited/limited_run_config.yaml → ...odel_runs/limited/limited_run_config.yaml
diff --git a/run_muscle_fatigue_model.py → notes/run_muscle_fatigue_model.py b/run_muscle_fatigue_model.py → notes/run_muscle_fatigue_model.py
diff --git a/notes/target_force_sims.py b/notes/target_force_sims.py
@@ -0,0 +1,40 @@
+import sys
+import os
+import numpy as np
+import plotly.graph_objs as go
+from plotly.offline import plot
+
+sys.path.insert(0, os.path.abspath('..'))
+from pymuscle import PotvinMuscleFibers
+from pymuscle import PotvinMotorNeuronPool
+
+motor_unit_count = 120
+motor_unit_indices = np.arange(1, motor_unit_count + 1)
+
+# Motor Neuron Pool
+pool = PotvinMotorNeuronPool(motor_unit_count)
+
+# Fibers
+fibers = PotvinMuscleFibers(motor_unit_count)
+
+# Target Force - 20% MVC
+max_force = 2234.0
+target_percent = 40
+target_force = max_force * (target_percent / 100)
+excitations = np.full(motor_unit_count, 1.0)
+e_inc = 0.01
+total_force = 0
+sim_time = 0.0
+sim_duration = 200.0
+time_inc = 0.1
+while sim_time < sim_duration:
+    while total_force < target_force:
+        firing_rates = pool.step(excitations)
+        normalized_firing_rates = fibers._normalize_firing_rates(firing_rates)
+        normalized_forcFaImes = fibers._calc_normalized_forces(normalized_firing_rates)
+        inst_forces = fibers._calc_inst_forces(normalized_forces)
+        total_force = fibers._calc_total_inst_force(inst_forces)
+        excitations += e_inc
+    sim_time += time_inc
+
+print(excitations[0])
diff --git a/tests/artifacts/full/README.md → notes/tests/artifacts/full/README.md b/tests/artifacts/full/README.md → notes/tests/artifacts/full/README.md
diff --git a/...o adapt) - Force - Strength (w adapt).csv → ...o adapt) - Force - Strength (w adapt).csv b/...o adapt) - Force - Strength (w adapt).csv → ...o adapt) - Force - Strength (w adapt).csv
diff --git a/...acts/full/matlab/0.50 B - Firing Rate.csv → ...acts/full/matlab/0.50 B - Firing Rate.csv b/...acts/full/matlab/0.50 B - Firing Rate.csv → ...acts/full/matlab/0.50 B - Firing Rate.csv
diff --git a/... C - Individual MU Force Time-History.csv → ... C - Individual MU Force Time-History.csv b/... C - Individual MU Force Time-History.csv → ... C - Individual MU Force Time-History.csv
diff --git a/...atlab/0.50 D - MU Capacity - relative.csv → ...atlab/0.50 D - MU Capacity - relative.csv b/...atlab/0.50 D - MU Capacity - relative.csv → ...atlab/0.50 D - MU Capacity - relative.csv
diff --git a/...o adapt) - Force - Strength (w adapt).csv → ...o adapt) - Force - Strength (w adapt).csv b/...o adapt) - Force - Strength (w adapt).csv → ...o adapt) - Force - Strength (w adapt).csv
diff --git a/.../python/python - 0.50 B - Firing Rate.csv → .../python/python - 0.50 B - Firing Rate.csv b/.../python/python - 0.50 B - Firing Rate.csv → .../python/python - 0.50 B - Firing Rate.csv
diff --git a/... C - Individual MU Force Time-History.csv → ... C - Individual MU Force Time-History.csv b/... C - Individual MU Force Time-History.csv → ... C - Individual MU Force Time-History.csv
diff --git a/...hon - 0.50 D - MU Capacity - relative.csv → ...hon - 0.50 D - MU Capacity - relative.csv b/...hon - 0.50 D - MU Capacity - relative.csv → ...hon - 0.50 D - MU Capacity - relative.csv
diff --git a/tests/artifacts/limited/README.md → notes/tests/artifacts/limited/README.md b/tests/artifacts/limited/README.md → notes/tests/artifacts/limited/README.md
diff --git a/...o adapt) - Force - Strength (w adapt).csv → ...o adapt) - Force - Strength (w adapt).csv b/...o adapt) - Force - Strength (w adapt).csv → ...o adapt) - Force - Strength (w adapt).csv
diff --git a/...s/limited/matlab/0.50 B - Firing Rate.csv → ...s/limited/matlab/0.50 B - Firing Rate.csv b/...s/limited/matlab/0.50 B - Firing Rate.csv → ...s/limited/matlab/0.50 B - Firing Rate.csv
diff --git a/... C - Individual MU Force Time-History.csv → ... C - Individual MU Force Time-History.csv b/... C - Individual MU Force Time-History.csv → ... C - Individual MU Force Time-History.csv
diff --git a/...atlab/0.50 D - MU Capacity - relative.csv → ...atlab/0.50 D - MU Capacity - relative.csv b/...atlab/0.50 D - MU Capacity - relative.csv → ...atlab/0.50 D - MU Capacity - relative.csv
diff --git a/...o adapt) - Force - Strength (w adapt).csv → ...o adapt) - Force - Strength (w adapt).csv b/...o adapt) - Force - Strength (w adapt).csv → ...o adapt) - Force - Strength (w adapt).csv
diff --git a/.../python/python - 0.50 B - Firing Rate.csv → .../python/python - 0.50 B - Firing Rate.csv b/.../python/python - 0.50 B - Firing Rate.csv → .../python/python - 0.50 B - Firing Rate.csv
diff --git a/... C - Individual MU Force Time-History.csv → ... C - Individual MU Force Time-History.csv b/... C - Individual MU Force Time-History.csv → ... C - Individual MU Force Time-History.csv
diff --git a/...hon - 0.50 D - MU Capacity - relative.csv → ...hon - 0.50 D - MU Capacity - relative.csv b/...hon - 0.50 D - MU Capacity - relative.csv → ...hon - 0.50 D - MU Capacity - relative.csv
diff --git a/tests/compare_artifacts.py → notes/tests/compare_artifacts.py b/tests/compare_artifacts.py → notes/tests/compare_artifacts.py
diff --git a/pymuscle/__version__.py b/pymuscle/__version__.py
@@ -0,0 +1,5 @@
+# pymuscle
+
+VERSION = (0, 0, 1)
+
+__version__ = '.'.join(map(str, VERSION))
diff --git a/setup.py b/setup.py
@@ -1,6 +1,5 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
-# Written by Kenneth Reitz: https://github.com/kennethreitz/setup.py
 
 # Note: To use the 'upload' functionality of this file, you must:
 #   $ pip install twine
@@ -14,16 +13,16 @@
 
 # Package meta-data.
 NAME = 'pymuscle'
-DESCRIPTION = 'Simulated muscles for virtual agents'
+DESCRIPTION = 'A motor unit based model of skeletal muscle and fatigue'
 URL = 'https://github.com/iandanforth/pymuscle'
 EMAIL = '[email protected]'
 AUTHOR = 'Ian Danforth'
 REQUIRES_PYTHON = '>=3.6.0'
-VERSION = '0.0.1'
+VERSION = None
 
 # What packages are required for this module to be executed?
 REQUIRED = [
-    # 'requests', 'maya', 'records',
+    'numpy',
 ]
 
 # The rest you shouldn't have to touch too much :)
@@ -77,10 +76,10 @@ def run(self):
         self.status('Uploading the package to PyPi via Twine…')
         os.system('twine upload dist/*')
 
-        self.status('Pushing git tags…')
-        os.system('git tag v{0}'.format(about['__version__']))
-        os.system('git push --tags')
-        
+        # self.status('Pushing git tags…')
+        # os.system('git tag v{0}'.format(about['__version__']))
+        # os.system('git push --tags')
+
         sys.exit()
 
 
@@ -96,6 +95,7 @@ def run(self):
     python_requires=REQUIRES_PYTHON,
     url=URL,
     # packages=find_packages(exclude=('tests',)),
+    # If your package is a single module, use this instead of 'packages':
     py_modules=[NAME],
 
     # entry_points={
@@ -118,4 +118,4 @@ def run(self):
     cmdclass={
         'upload': UploadCommand,
     },
-)
+)