Add Plasma Constants and Paramters #38

rocco8773 · 2019-05-07T19:00:47Z

Creating two new sub-modules:

bapsflib.plasma.constants
- module focuses on providing a number of physical constants
- all constants are provided as an astropy.constants.Constant
- current constants documentation
bapsflib.plasma.parameters
- module focuses on providing a number of plasma parameters
- functionality of parameters is designed to be useful with values and units typically acquired during experiments
- Units follow the NRL Plasma Formulary. All units are in Gaussian cgs except for temperature, which is expressed in eV.
- all parameters are returned as astropy.units.Quantity
- current parameters documentation

Tasks before merge:

bapsflib.plasma.constants
- Review and add all desired physical constants
- Agree on naming for all constants
- All constants must be astropy.constants.Constant
- Cover with tests
bapsflib.plasma.constants
- Review and add all desired plasma paramters
- Agree on naming for all parameters
- Parameter functionality is consistent and suit to how plasma values are measured/calculated in the lab environment
- All constants must be astropy.units.Quantity
- Units follow the NRL Plasma Formulary scheme
- Cover with tests

…nstants `e`, `e_gauss`, and `u` to BaPSFConstant to provided clearer metadata; update docstring constant table with a 'system' units column

…clotron frequency, electron-cyclotron frequency, ion-cyclotron frequency, and a generic plasma frequency

…'parameters' modules (also added to __all__)

…bapsflib.plasma.parameters modules

…lectron-plasma frequency (`ope`) and the ion-plasma frequency (`opi`)

…_hybrid_frequency` and [alias] `oLH`)

…equency` and [alias] `oUH`)

…ngth (`inertial_length`, `lpi`, and `lpe`)

…"Lengths"

…ency`

… up in the autosummary table

…cs`)

… auto-documentation

… bapsflib.plasma.parameters are built up

codecov · 2019-05-09T02:06:00Z

Codecov Report

Merging #38 into master will decrease coverage by 2.34%.
The diff coverage is 60.5%.

@@            Coverage Diff            @@
##           master     #38      +/-   ##
=========================================
- Coverage   96.85%   94.5%   -2.35%     
=========================================
  Files          49      52       +3     
  Lines        3113    3202      +89     
  Branches      566     595      +29     
=========================================
+ Hits         3015    3026      +11     
- Misses         97     175      +78     
  Partials        1       1

Impacted Files	Coverage Δ
bapsflib/_hdf/utils/hdfreaddata.py	`100% <ø> (ø)`	⬆️
bapsflib/utils/units/decorators.py	`100% <100%> (ø)`
bapsflib/__init__.py	`100% <100%> (ø)`	⬆️
bapsflib/plasma/constants.py	`100% <100%> (ø)`
bapsflib/utils/errors.py	`100% <100%> (ø)`	⬆️
bapsflib/plasma/__init__.py	`100% <100%> (ø)`	⬆️
bapsflib/utils/units/__init__.py	`100% <100%> (ø)`
bapsflib/utils/__init__.py	`100% <100%> (ø)`	⬆️
bapsflib/utils/decorators.py	`100% <100%> (ø)`	⬆️
bapsflib/utils/units/equivalencies.py	`22.72% <22.72%> (ø)`
... and 23 more

Continue to review full report at Codecov.

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…s; make `check_quantity` and `_check_quantity` enforce specified unit

…s.py)

…asmaPy does not support python 3.5)

…ython 3.5

…s package; move func temperature_and_energy to new equivalencies module; add equivalencies to bapsflib.utils imports

…y` and `check_relativistic` to new module; include in imports and __all__ for bapsflib.utils.units.__init__ and bapsflib.utils.__init__

…e an enfoce kwarg to foce unit conversion or just check equivalency

…gname` -> `val_name`; improve descriptive comments; improve conditioning for `equivalencies` kwarg; streamline process of function and increase readability of function

…ched

…Quantity

…e if the imaginary component is zero

…antity`

…of the `chec_quantity` decorator

# Conflicts: # bapsflib/__init__.py # bapsflib/plasma/__init__.py # bapsflib/plasma/core.py # bapsflib/utils/__init__.py # bapsflib/utils/decorators.py # docs/src/bapsflib.rst

pep8speaks · 2019-10-27T19:45:40Z

Hello @rocco8773! Thanks for updating your pull request.

In the file bapsflib/utils/__init__.py:

Line 18:1: E402 module level import not at top of file
Line 21:1: E402 module level import not at top of file
Line 22:1: E402 module level import not at top of file

In the file bapsflib/utils/units/decorators.py:

Line 35:62: W291 trailing whitespace
Line 36:63: W291 trailing whitespace
Line 37:58: W291 trailing whitespace
Line 62:80: E501 line too long (115 > 79 characters)
Line 72:80: E501 line too long (80 > 79 characters)
Line 100:67: W291 trailing whitespace
Line 112:69: W291 trailing whitespace
Line 118:66: W291 trailing whitespace
Line 119:67: W291 trailing whitespace

In the file bapsflib/utils/units/tests/test_decorators.py:

Line 366:1: E303 too many blank lines (5)

rocco8773 added 30 commits April 18, 2019 16:23

refactor class BaPSFConstant - > LaPDConstant

5e1e0a5

initial commit for bapsflib.plasma.constants

2cdbefd

add plasma py to requirements

7dbc693

define class BaPSFConstant for BaPSF constants

b1fe7dc

only import elementary charge constants e and e_gauss; convert co…

3ed2fbd

…nstants `e`, `e_gauss`, and `u` to BaPSFConstant to provided clearer metadata; update docstring constant table with a 'system' units column

initial commit

c4a737c

initial commit for bapsflib.plasma.parameters; added functions for cy…

550d4c1

…clotron frequency, electron-cyclotron frequency, ion-cyclotron frequency, and a generic plasma frequency

initial commit for bapsflib.plasma.parameters auto-documentation

48fe9e8

removed import of 'core' module and added imports of 'constants' and …

3a93a65

…'parameters' modules (also added to __all__)

updated to reflect the creation of the bapsflib.plasma.constants and …

c5da4c1

…bapsflib.plasma.parameters modules

added the bapsflib.plasma package to the auto-documentation

39345e3

refactor conts -> const; add plasma parameter functions for the e…

a976247

…lectron-plasma frequency (`ope`) and the ion-plasma frequency (`opi`)

updated auto-documentation

c65df60

add plasma parameter for the Lower-Hybrid Resonance Frequency (`lower…

cf273d9

…_hybrid_frequency` and [alias] `oLH`)

add lower_hybrid_frequency and oLH to auto-documentation

af1e6f4

add plasma parameter for the Upper-Hybrid frequency (`upper_hybrid_fr…

d8e93e3

…equency` and [alias] `oUH`)

add upper_hybrid_frequency and oUH to auto-documentation

21ea884

make docstrings case consistent; add plasma parameters of inertial le…

2dfa004

…ngth (`inertial_length`, `lpi`, and `lpe`)

add inertial length to auto-documentation; create a rubric title for …

639a25e

…"Lengths"

refactor plasma parameter plasma_frequency_generic -> `plasma_frequ…

8c14f5f

…ency`

rework docstrings for oLH and oUP such that the "alias" tag shows…

7ee412a

… up in the autosummary table

add plasma parameter Debye length (Debye_length and [alias] lD)

986813e

add Debye_length and lD to the auto-documentation

fd7a726

create Exception PhysicsError

04a13aa

add plasma parameter ion sound speed (ion_sound_speed and [alias] `…

93a40a1

…cs`)

create "Velocities" function table; add ion_sound_speed and cs to…

8e0b3e2

… auto-documentation

add __all__; improve arg and kwarg passthroughs

37ab77f

slowly removing core.py and elements as bapsflib.plasma.constants and…

d911da6

… bapsflib.plasma.parameters are built up

Merge branch 'master' into add_astropy_units_to_plasma

63b8a1d

ensure sphinx uses python3 to make documentation

6b71b0a

rocco8773 added 24 commits May 8, 2019 19:06

add an equivalencies kwarg to _check_quantity; fix some PEP 8 issue…

0535971

…s; make `check_quantity` and `_check_quantity` enforce specified unit

add temperature_and_energy() to __all__

20f86ce

move package decorators to their own module (bapsflib/utils/decorator…

612fe5c

…s.py)

move __all__ to top (PEP 8)

ec70e07

update to version 1.1.0.dev (dropping support for python 3.5 since Pl…

ea71397

…asmaPy does not support python 3.5)

update CI, README.md, and setup.py to reflected dropped support for p…

9520d83

…ython 3.5

setup sphinx extension intersphinx

662e999

create package bapsflib.utils.units; add equivalencies module to unit…

fbf49ac

…s package; move func temperature_and_energy to new equivalencies module; add equivalencies to bapsflib.utils imports

create decorators module in bapsflib.utils.units; move `check_quantit…

ace5e54

…y` and `check_relativistic` to new module; include in imports and __all__ for bapsflib.utils.units.__init__ and bapsflib.utils.__init__

remove excess lines (PEP 8)

32e4e4b

improve typing annotations; clarify wording of docstrings; incorporat…

4124c8f

…e an enfoce kwarg to foce unit conversion or just check equivalency

for func _check_quantity...refactor argument arg -> val and `ar…

8ccf787

…gname` -> `val_name`; improve descriptive comments; improve conditioning for `equivalencies` kwarg; streamline process of function and increase readability of function

add a pragma: no cover for an if-statement that should never be rea…

dd4dd63

…ched

add ValueError to the try-except for converting val to astropy.units.…

69958b2

…Quantity

replace np.iscomplex with np.iscomplexobj, iscomplex will return Fals…

07fa1fd

…e if the imaginary component is zero

improve type annotations

3ffecea

allow for equivalencies elements that are tuples of length 2

0b8b779

do not allow equivalencies are are not lists or None (raise ValueError)

41c4776

initial commit for test class TestCheckQuantity

10f1373

allow for pass-through of enforce from check_quantity to `_check_qu…

2692368

…antity`

remove unused imports

eb26574

define test method test_check_quantity_decorator to cover behavior …

bedcdb2

…of the `chec_quantity` decorator

move __all__ to top of imports (PEP 8)

ea340fa

Merge branch 'master' into add_astropy_units_to_plasma

dfac711

rocco8773 modified the milestones: v1.0.1, v1.1.0 May 24, 2019

rocco8773 added 2 commits June 6, 2019 15:39

Merge branch 'master' into add_astropy_units_to_plasma

86e054e

# Conflicts: # bapsflib/__init__.py # bapsflib/plasma/__init__.py # bapsflib/plasma/core.py # bapsflib/utils/__init__.py # bapsflib/utils/decorators.py # docs/src/bapsflib.rst

import check_quantity and check_relativistic

68e30f7

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Add Plasma Constants and Paramters #38

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