Merge pull request #197 from AguaClara/v0.0.24

v0.0.24: Changes to floc_model, tube_sizing, and Sphinx documentation

.travis.yml

@@ -34,7 +34,7 @@ deploy:
   skip-cleanup: true
   github-token: "$GITHUB_TOKEN"
   keep-history: true
-  local-dir: docs/build
+  local-dir: docs/build/html
   target-branch: gh-pages
   on:
     tags: true

aguaclara/core/constants.py

@@ -3,25 +3,36 @@
 
 from aguaclara.core.units import unit_registry as u
 
+# NOTE: "#: <optional_description>"  required for Sphinx autodocumentation
+
+#: Gravitational constant
 GRAVITY = 9.80665 * u.m / u.s ** 2
 
+#: Density of water
 WATER_DENSITY = 1000 * u.kg / u.m ** 3
+#: Kinematic viscosity of water
 WATER_NU = 1 * 10 ** -6 * u.m ** 2 / u.s
 
+#: Atmospheric pressure
 ATM_P = 1 * u.atm
+#: Average kinematic viscosity of air
 AIR_NU = 12 * u.mm ** 2 / u.s
-AIR_DENSITY = 1.204 * u.kg / u.mm ** 3
 
-# The influence of viscosity on mixing in jet reactors
+#: The influence of viscosity on mixing in jet reactors
 JET_ROUND_RATIO = 0.08
-# Estimate for plane jets in the flocculator and sed tank jet reverser.
+#: An estimate for plane jet ratios in the flocculator and sed tank jet reverser
 JET_PLANE_RATIO = 0.0124
 
+#:
 LFP_FLOW_MAX = 16.1 * u.L / u.s
 
-FITTING_S_MIN = 5 * u.cm  # Between fittings and tank wall in a tank.
+#: Between fittings and tank wall in a tank.
+FITTING_S_MIN = 5 * u.cm
+#:
 CHANNEL_W_MIN = 15 * u.cm
 
+#:
 VC_ORIFICE_RATIO = 0.63
 
+#:
 K_KOZENY = 5

aguaclara/core/data/unit_definitions.txt

@@ -1,7 +1,7 @@
 """
 Created on Fri June 23 2017
 
-author: Sage Weber-Shirk
+Author: Sage Weber-Shirk
 
 Last modified: Mon Jun 26 2017
 By: Sage Weber-Shirk
@@ -12,3 +12,4 @@ NTU = 1.47 * (mg / L)
 dollar = [money] = USD
 lempira = dollar * 0.0427 = HNL
 equivalent = mole = eq
+rev = revolution

aguaclara/core/materials.py

@@ -5,11 +5,17 @@
 """
 from aguaclara.core.units import unit_registry as u
 
+#:
 PVC_PIPE_ROUGH = 0.12 * u.mm
 
+#:
 CONCRETE_PIPE_ROUGH = 2 * u.mm
+#:
 CONCRETE_DENSITY = 2400 * (u.kg / u.m ** 3)
+#:
 CONCRETE_THICKNESS_MIN = 5 * u.cm
 
+#:
 REBAR_D = 0.5 * u.inch
+#:
 ACRYLIC_T = 1 * u.cm

aguaclara/core/physchem.py

@@ -10,8 +10,7 @@
 import numpy as np
 from scipy import interpolate, integrate
 
-gravity = 9.80665 * u.m/u.s**2
-"""Define the gravitational constant, in m/s²."""
+gravity = con.GRAVITY
 
 ###################### Simple geometry ######################
 """A few equations for useful geometry.
@@ -31,8 +30,9 @@ def diam_circle(AreaCircle):
     return np.sqrt(4 * AreaCircle / np.pi)
 
 ######################### Hydraulics #########################
-RE_TRANSITION_PIPE = 2100
 
+RE_TRANSITION_PIPE = 2100
+""" """
 K_KOZENY = con.K_KOZENY
 
 WATER_DENSITY_TABLE = [(273.15, 278.15, 283.15, 293.15, 303.15, 313.15,
@@ -78,8 +78,6 @@ def viscosity_kinematic(temp):
 
     If given units, the function will automatically convert to Kelvin.
     If not given units, the function will assume Kelvin.
-
-    TODO: This should return meter ** 2 / second.
     """
     ut.check_range([temp, ">0", "Temperature in Kelvin"])
     return (viscosity_dynamic(temp).magnitude

aguaclara/core/pipeline.py

@@ -10,21 +10,27 @@
 import numpy
 
 @u.wraps(u.m**3/u.s, [u.m, u.m, None, u.m], False)
-def flow_pipeline(diameters: numpy.ndarray, lengths: numpy.ndarray, k_minors: numpy.ndarray, target_headloss: float,
+def flow_pipeline(diameters, lengths, k_minors, target_headloss,
                   nu=con.WATER_NU, pipe_rough=mats.PVC_PIPE_ROUGH):
     """
     This function takes a single pipeline with multiple sections, each potentially with different diameters,
     lengths and minor loss coefficients and determines the flow rate for a given headloss.
 
-    Args:
-        diameters: list of diameters, where the i_th diameter corresponds to the i_th pipe section
-        lengths: list of diameters, where the i_th diameter corresponds to the i_th pipe section
-        k_minors: list of diameters, where the i_th diameter corresponds to the i_th pipe section
-        target_headloss: a single headloss describing the total headloss through the system
-        nu: The fluid dynamic viscosity of the fluid. Defaults to water at room temperature (1 * 10**-6 * m**2/s)
-        pipe_rough:  The pipe roughness. Defaults to PVC roughness.
-    Returns:
-        flow: the total flow through the system
+    :param diameters: list of diameters, where the i_th diameter corresponds to the i_th pipe section
+    :type diameters: numpy.ndarray
+    :param lengths: list of diameters, where the i_th diameter corresponds to the i_th pipe section
+    :type lengths: numpy.ndarray
+    :param k_minors: list of diameters, where the i_th diameter corresponds to the i_th pipe section
+    :type k_minors: numpy.ndarray
+    :param target_headloss: a single headloss describing the total headloss through the system
+    :type target_headloss: float
+    :param nu: The fluid dynamic viscosity of the fluid. Defaults to water at room temperature (1 * 10**-6 * m**2/s)
+    :type nu: float
+    :param pipe_rough:  The pipe roughness. Defaults to PVC roughness.
+    :type pipe_rough: float
+
+    :return: the total flow through the system
+    :rtype: float
     """
 
     # Ensure all the arguments except total headloss are the same length

aguaclara/core/units.py

@@ -1,15 +1,30 @@
-"""Module containing global `pint` unit registry.
-
-The `pint` module supports arithmetic involving *physical quantities*
-each of which has a magnitude and units, for example 1 cm or 3 kg.
-The units of a quantity come from a `pint` *unit registry*, and it
-appears that `pint` supports arithmetic operations only on quantities
-whose units come from the same unit registry (an attempt to perform
-an operation on quantities whose units come from different unit
-registries raises an exception). This module contains a single global
-unit registry `unit_registry` that can be used by any number of other
-modules.
+"""Module containing global ``pint`` unit registry.
 
+The ``pint`` package supports arithmetic involving **physical quantities**
+each of which has a magnitude and units, for example 1 cm or 3 kg m/s^2.
+The units of a quantity come from ``pint``'s **unit registry**. This module
+contains a single global unit registry ``unit_registry`` that can be used by any
+number of other modules. The ``aguaclara`` has also defined and added some of
+its own units to the ``unit_registry``:
+
+  * NTU = 1.47 * (mg / L)
+  * dollar = [money] = USD
+  * lempira = dollar * 0.0427 = HNL
+  * equivalent = mole = eq
+  * rev = revolution
+
+:Examples:
+
+>>> from aguaclara.core.units import unit_registry as u
+>>> rpm = 10 * u.rev/u.min
+>>> rpm
+<Quantity(10.0, 'rev / minute')>
+>>> rpm.magnitude
+10.0
+>>> rpm.units
+<Unit('rev / minute')>
+>>> rpm.to(u.rad/u.s)
+<Quantity(1.0471975511965976, 'radian / second')>
 """
 
 import os
@@ -20,6 +35,7 @@
     system='mks',
     autoconvert_offset_to_baseunit=True
 )
+"""A global unit registry that can be used by any of other module."""
 
 # default formatting includes 4 significant digits.
 # This can be overridden on a per-print basis with
@@ -31,28 +47,27 @@
                                             "data", "unit_definitions.txt"))
 
 
-def set_sig_figs(n: int):
+def set_sig_figs(n):
     """Set the default number of significant figures used to print pint,
     pandas and numpy values quantities. Defaults to 4.
 
-    Args:
-        n: number of significant figures to display
-
-    Example:
-        import aguaclara
-        from aguaclara.units import unit_registry as u
-        h=2.5532532522352543*u.m
-        e = 25532532522352543*u.m
-        print('h before sigfig adjustment: ',h)
-        print('e before sigfig adjustment: ',e)
-        aguaclara.units.set_sig_figs(10)
-        print('h after sigfig adjustment: ',h)
-        print('e after sigfig adjustment: ',e)
-
-        h before sigfig adjustment:  2.553 meter
-        e before sigfig adjustment:  2.553e+16 meter
-        h after sigfig adjustment:  2.553253252 meter
-        e after sigfig adjustment:  2.553253252e+16 meter
+    :param n: number of significant figures to display
+    :type n: int
+
+    :Examples:
+
+    >>> from aguaclara.core.units import set_sig_figs, unit_registry as u
+    >>> h = 2.5532532522352543*u.m
+    >>> e = 25532532522352543*u.m
+    >>> print('h before sigfig adjustment:',h)
+    h before sigfig adjustment: 2.553 meter
+    >>> print('e before sigfig adjustment:',e)
+    e before sigfig adjustment: 2.553e+16 meter
+    >>> set_sig_figs(10)
+    >>> print('h after sigfig adjustment:',h)
+    h after sigfig adjustment: 2.553253252 meter
+    >>> print('e after sigfig adjustment:',e)
+    e after sigfig adjustment: 2.553253252e+16 meter
     """
     unit_registry.default_format = '.' + str(n) + 'g'
     pd.options.display.float_format = ('{:,.' + str(n) + '}').format

aguaclara/core/utility.py

@@ -10,13 +10,12 @@
 
 
 def round_sf(number, digits):
-    """Returns inputted value rounded to number
-    of significant figures desired.
+    """Returns inputted value rounded to number of significant figures desired.
 
-    Parameters:
-       number: Value to be rounded
-       digits: number of significant digits
-       to be rounded to.
+    :param number: Value to be rounded
+    :type number: float
+    :param digits: number of significant digits to be rounded to.
+    :type digits: int
     """
     units = None
     try:

aguaclara/play.py

@@ -34,8 +34,11 @@
 # from aguaclara.design.floc import Flocculator
 import aguaclara.design.human_access as ha
 
-import aguaclara.research.procoda_parser as pp
 import aguaclara.research.environmental_processes_analysis as epa
+import aguaclara.research.floc_model as fm
+import aguaclara.research.procoda_parser as procoda_parser
+import aguaclara.research.peristaltic_pump as peristaltic_pump
+import aguaclara.research.stock_qc as stock_qc
 
 def set_sig_figs(n=4):
     """Set the number of significant figures used to print Pint, Pandas, and

aguaclara/research/data/3_stop_tubing.txt

@@ -0,0 +1,27 @@
+Color	Diameter (mm)
+orange-black	0.13
+orange-red	0.19
+orange-blue	0.25
+orange-green	0.38
+green-yellow	0.44
+orange-yellow	0.51
+white-yellow	0.57
+orange-white	0.64
+black-black 0.76
+orange-orange	0.89
+white-black	0.95
+white-white	1.02
+white-red	1.09
+red-red	1.14
+red-grey	1.22
+grey-grey	1.3
+yellow-yellow	1.42
+yellow-blue	1.52
+blue-blue	1.65
+blue-green	1.75
+green-green	1.85
+purple-purple	2.06
+purple-black	2.29
+purple-orange	2.54
+purple-white	2.79
+black-white	3.17

aguaclara/research/data/LS_tubing.txt

@@ -0,0 +1,10 @@
+Number	Flow (mL/rev)
+13	.06
+14	.21
+15	1.6
+16	.8
+17	2.8
+18	3.8
+24	2.8
+35	3.8
+36	4.8