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**COCOS**
(!!!)
Ignore this [Bug report withdrawn]
...
What is broken
- nothing, ignore this :)
io.compass - Use last revision by default
Function pleque.io.compass.cdb() uses revision=1 as a default parameter value. I would propose a change to revision=-1, i.e. the most recent revision.
Arguments:
- On the one hand, the original behaviour enforces some degree of reproducibility of the returned value on subsequent calls. On the other hand, there are cases where the
revision=1data in CDB are broken (cause exception when you attempt to load them) but a fixed version of the data are available inrevision=2. As a result, the original behaviour ensures that that particular discharge will always throw error, possibly misleading the user into thinking that no "fixed data" exist. - A second argument for the change is the fact that the
pyCDBclient loads the most recent revision by default. A user then might logically expect the same behaviour fromplequeas well, since this feels as the defining property/philosophy of the CDB database itself (i.e. "last revision is always/eventually the best revision which everyone should use").
Equilibrium.psi_n function not returning correct values
Equilibrium._psi_lcfs wrongly identified in Equilibrium.find_extremes
I discovered this issue by using Equilibrium.psi_n function which returns wrong values.
**Export support**
- gfile
- HDC
- CPO
- IMAS via OMAS
Nine or zero?
I suppose there should be 9 instead of 0
attrs_pos = [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 15, 17]instead of
attrs_pos = [0, 1, 2, 3, 4, 5, 6, 7, 8, 0, 10, 11, 13, 15, 17]pleque/pleque/io/readgeqdsk.py
Line 78 in 4cb78cc
Correct formula for effective poloidal heat flux expansion coefficient
There is a typo in the last part of the formula, it should be f_{pol,heat}
pleque.utils.flux_expansions.effective_poloidal_heat_flux_exp_coef
https://pleque.readthedocs.io/en/latest/flux_expansion.html?highlight=flux%20expansion
Correct text entry
https://pleque.readthedocs.io/en/latest/flux_expansion.html?highlight=flux%20expansion
is inclination angle of poloidal magnetic field and the target plane.
Replace and by between (everywhere)
Set ".shot" attribute of Equilibrium when loading using io.compass.cdb()
Currently, Equilibrium object loaded via pleque.io.compass.cdb() has .shot=0. This then causes further minor inconveniences such as the loss of this metadata when writing the equilibrium into a file, e.g. to_geqdsk(). While I usually depend on the filename to store this metadata (shot number and time) I feel like it would be nice to have this additional backup given that this is already a feature of the eqdsk format.
Proposal for fix:
Probaly just add something like
# Accessing `sig_ref` instead of parameter `shot` should handle cases when user uses `shot=None`
eq.shot = sig_ref.record_number
added just below
Line 40 in a414deb
Proposal for further investigation:
- Might be worth to look into the other
iooptions (such ascudb) and how they handle theshotattribute, potentially fix them as well
**Prepare documentation**
To transpose, or not to transpose, that is the question (OMAS)
I had to remove the transposition to load the OMAS file in OMFIT properly. What is the correct convention?
Lines 101 to 103 in db69eef
copy object to itself
@smartass101 @coobas
Is it possible to simply satisfy something like this:
class A:
def __init__(self, name):
if isinstance(name, str):
self.name = name
elif isinstance(name, A):
self = name
a = A('foo')
b = A(a)Where I intend to a and b be the same objects/or copies of one object.
Thanks
**Field line tracing**
Support only Python 3?
Vote (thumbs up) for not supporting Python 2. (Or have you decided already? :)
FluxSurface class
- implement into
class Equilibriumas
def flux_surface(*coordinates, psi_n=None, coord_type=('psi_n'), resolution = 100, **coords):
"""
:param resolution: number of points used for generation of FluxSurface
:return FluxSurface or list of FluSurfaces generated on given coordinates.
"""
grid = False
...- add test file to test all implemented functions
- FluxSurface should accept instance of
Coordinateson input - implement (r, theta) coordinates into
Coordinates class - implement
as_arrayintoCoordinates - all functions returning some set of points should return instance of
Coordinates
create naming convention
Local variable might be referenced before assignment
Are you sure that this will not happen?
Line 279 in a7d00f9
PyCharm gives me:
Warning:(288, 32) Local variable 'tmp2' might be referenced before assignment
**Prepare basics of coordinates class**
**Import support**
- gfile
- CDB
- HDC
- CPO
- IMAS via OMAS
The magnetic_axis.R and magnetic_axis.Z does not return R, Z coordinates
Line 506 in a1f203f
Pleque Structure
While preparing export of FluxFunction objects to omas I realised this is one way how to get equilibrium data from a coordinate object is for example this:
coords._eq.tor_flux(coords)
I am not sure if the possibility or need to do this is a good Idea. I am also afraid it could lead to growing ambiguity, cyclic referencing and confusion in the module and it's using as it grows.
Please correct me if I'm wrong.
Equilibriumclass functions work with coordinates objects, e.g.:
The equilibrium object has to be passed to the coordinates upon creation and is saved as a property :
code
Isn't this kind of a cycle which could in future fire back? Another disadvantage is (as I've already mentioned) is that the user has to be either keeping both equilibrium and coordinates objects to get
some equilibrium value for the coordinates (although the equilibrium is saved in coordinates), e.g.:
equi = Equilibrium(...)
coords = equi.coordinates(...)
equi.tor_flux(coords)
`
or keep using this:
equi = Equilibrium(...)
coords = equi.coordinates(...)
coords._equi.tor_flux(coords)
`
I might be wrong disliking this and maybe this way is the correct way. But I think the structure of the whole module should be changed to avoid this. One possibility to solve this could could be by using inheritance by making the coordinates class child class of the equilibrium. What do you think?
Test failures on master
Hello, I just cloned master and ran:
python3 -m venv testvenv
source testvenv/bin/activate
pip install -U pip
pip install -e .
pip install pytest
pytestand got the following test failures/errors:
===================================================================================================================================================== warnings summary ======================================================================================================================================================
pleque/core/equilibrium.py:215: 5 tests with warnings
tests/compu_test.py: 1 test with warning
tests/test_2Dinterpolation.py: 6 tests with warnings
tests/test_cocos.py: 48 tests with warnings
tests/test_coordinates.py: 6 tests with warnings
tests/test_equilibria.py: 12 tests with warnings
tests/test_gfile.py: 12 tests with warnings
tests/test_io.py: 6 tests with warnings
tests/test_surface_param.py: 1 test with warning
/home/peter/Codes/pleque/pleque/core/equilibrium.py:215: DeprecationWarning: np.asscalar(a) is deprecated since NumPy v1.16, use a.item() instead
pleque/core/coordinates.py:463
/home/peter/Codes/pleque/pleque/core/coordinates.py:463: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated since Python 3.3,and in 3.9 it will stop working
pleque/io/metis.py:37
/home/peter/Codes/pleque/pleque/io/metis.py:37: PendingDeprecationWarning: dropping variables using `drop` will be deprecated; using drop_vars is encouraged.
testvenv/lib64/python3.7/site-packages/numpy/lib/type_check.py:277
/home/peter/Codes/pleque/testvenv/lib64/python3.7/site-packages/numpy/lib/type_check.py:277: FutureWarning: elementwise == comparison failed and returning scalar instead; this will raise an error or perform elementwise comparison in the future.
testvenv/lib64/python3.7/site-packages/omas/omas_setup.py:16
/home/peter/Codes/pleque/testvenv/lib64/python3.7/site-packages/omas/omas_setup.py:16: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated since Python 3.3,and in 3.9 it will stop working
testvenv/lib64/python3.7/site-packages/omas/omas_hdc.py:9
/home/peter/Codes/pleque/testvenv/lib64/python3.7/site-packages/omas/omas_hdc.py:9: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated since Python 3.3,and in 3.9 it will stop working
-- Docs: https://docs.pytest.org/en/latest/warnings.html
================================================================================================================================================== short test summary info ==================================================================================================================================================
FAILED tests/compu_test.py::test_compu - ValueError: all the input array dimensions for the concatenation axis must match exactly, but along dimension 1, the array at index 0 has size 0 and the array at index 1 has size 2
FAILED tests/surfaces_test.py::test_surfs - assert array([], shape=(1, 0), dtype=float64) is None
FAILED tests/test_cocos.py::test_directions[5-1] - ValueError: all the input array dimensions for the concatenation axis must match exactly, but along dimension 1, the array at index 0 has size 0 and the array at index 1 has size 2
FAILED tests/test_cocos.py::test_directions[5-2] - ValueError: all the input array dimensions for the concatenation axis must match exactly, but along dimension 1, the array at index 0 has size 0 and the array at index 1 has size 2
FAILED tests/test_cocos.py::test_directions[5-3] - ValueError: all the input array dimensions for the concatenation axis must match exactly, but along dimension 1, the array at index 0 has size 0 and the array at index 1 has size 2
FAILED tests/test_cocos.py::test_directions[5-4] - ValueError: all the input array dimensions for the concatenation axis must match exactly, but along dimension 1, the array at index 0 has size 0 and the array at index 1 has size 2
FAILED tests/test_cocos.py::test_coordinates_transforms[5-1] - ValueError: all the input array dimensions for the concatenation axis must match exactly, but along dimension 1, the array at index 0 has size 0 and the array at index 1 has size 2
FAILED tests/test_cocos.py::test_coordinates_transforms[5-2] - ValueError: all the input array dimensions for the concatenation axis must match exactly, but along dimension 1, the array at index 0 has size 0 and the array at index 1 has size 2
FAILED tests/test_cocos.py::test_coordinates_transforms[5-3] - ValueError: all the input array dimensions for the concatenation axis must match exactly, but along dimension 1, the array at index 0 has size 0 and the array at index 1 has size 2
FAILED tests/test_cocos.py::test_coordinates_transforms[5-4] - ValueError: all the input array dimensions for the concatenation axis must match exactly, but along dimension 1, the array at index 0 has size 0 and the array at index 1 has size 2
FAILED tests/test_cocos.py::test_coordinates_transforms[5-5] - ValueError: all the input array dimensions for the concatenation axis must match exactly, but along dimension 1, the array at index 0 has size 0 and the array at index 1 has size 2
FAILED tests/test_cocos.py::test_coordinates_transforms[5-6] - ValueError: all the input array dimensions for the concatenation axis must match exactly, but along dimension 1, the array at index 0 has size 0 and the array at index 1 has size 2
FAILED tests/test_cocos.py::test_coordinates_transforms[5-7] - ValueError: all the input array dimensions for the concatenation axis must match exactly, but along dimension 1, the array at index 0 has size 0 and the array at index 1 has size 2
FAILED tests/test_cocos.py::test_coordinates_transforms[5-8] - ValueError: all the input array dimensions for the concatenation axis must match exactly, but along dimension 1, the array at index 0 has size 0 and the array at index 1 has size 2
FAILED tests/test_cocos.py::test_cocos_consistency[5-1] - ValueError: all the input array dimensions for the concatenation axis must match exactly, but along dimension 1, the array at index 0 has size 0 and the array at index 1 has size 2
FAILED tests/test_cocos.py::test_cocos_consistency[5-2] - ValueError: all the input array dimensions for the concatenation axis must match exactly, but along dimension 1, the array at index 0 has size 0 and the array at index 1 has size 2
FAILED tests/test_cocos.py::test_cocos_consistency[5-3] - ValueError: all the input array dimensions for the concatenation axis must match exactly, but along dimension 1, the array at index 0 has size 0 and the array at index 1 has size 2
FAILED tests/test_cocos.py::test_cocos_consistency[5-4] - ValueError: all the input array dimensions for the concatenation axis must match exactly, but along dimension 1, the array at index 0 has size 0 and the array at index 1 has size 2
FAILED tests/test_cocos.py::test_cocos_consistency[5-5] - ValueError: all the input array dimensions for the concatenation axis must match exactly, but along dimension 1, the array at index 0 has size 0 and the array at index 1 has size 2
FAILED tests/test_cocos.py::test_cocos_consistency[5-6] - ValueError: all the input array dimensions for the concatenation axis must match exactly, but along dimension 1, the array at index 0 has size 0 and the array at index 1 has size 2
FAILED tests/test_cocos.py::test_cocos_consistency[5-7] - ValueError: all the input array dimensions for the concatenation axis must match exactly, but along dimension 1, the array at index 0 has size 0 and the array at index 1 has size 2
FAILED tests/test_cocos.py::test_cocos_consistency[5-8] - ValueError: all the input array dimensions for the concatenation axis must match exactly, but along dimension 1, the array at index 0 has size 0 and the array at index 1 has size 2
FAILED tests/test_equilibria.py::test_equilibria[4] - ValueError: all the input array dimensions for the concatenation axis must match exactly, but along dimension 1, the array at index 0 has size 0 and the array at index 2 has size 2
FAILED tests/test_equilibria.py::test_equilibria[5] - ValueError: all the input array dimensions for the concatenation axis must match exactly, but along dimension 1, the array at index 0 has size 0 and the array at index 1 has size 2
FAILED tests/test_gfile.py::test_calculated_profiles[5] - ValueError: all the input array dimensions for the concatenation axis must match exactly, but along dimension 1, the array at index 0 has size 0 and the array at index 1 has size 2
FAILED tests/test_surface_param.py::test_q_profiles - ValueError: all the input array dimensions for the concatenation axis must match exactly, but along dimension 1, the array at index 0 has size 0 and the array at index 1 has size 2
ERROR tests/test_2Dinterpolation.py::test_surfacefunction[4-data0-coord10-coord20-3-1] - ValueError: all the input array dimensions for the concatenation axis must match exactly, but along dimension 1, the array at index 0 has size 0 and the array at index 2 has size 2
ERROR tests/test_2Dinterpolation.py::test_surfacefunction[4-data1-coord11-coord21-3-0] - ValueError: all the input array dimensions for the concatenation axis must match exactly, but along dimension 1, the array at index 0 has size 0 and the array at index 2 has size 2
ERROR tests/test_2Dinterpolation.py::test_surfacefunction[5-data0-coord10-coord20-3-1] - ValueError: all the input array dimensions for the concatenation axis must match exactly, but along dimension 1, the array at index 0 has size 0 and the array at index 1 has size 2
ERROR tests/test_2Dinterpolation.py::test_surfacefunction[5-data1-coord11-coord21-3-0] - ValueError: all the input array dimensions for the concatenation axis must match exactly, but along dimension 1, the array at index 0 has size 0 and the array at index 1 has size 2
ERROR tests/test_coordinates.py::test_coordinates[4] - ValueError: all the input array dimensions for the concatenation axis must match exactly, but along dimension 1, the array at index 0 has size 0 and the array at index 2 has size 2
ERROR tests/test_coordinates.py::test_coordinates[5] - ValueError: all the input array dimensions for the concatenation axis must match exactly, but along dimension 1, the array at index 0 has size 0 and the array at index 1 has size 2
ERROR tests/test_equilibria.py::test_critical[4] - ValueError: all the input array dimensions for the concatenation axis must match exactly, but along dimension 1, the array at index 0 has size 0 and the array at index 2 has size 2
ERROR tests/test_equilibria.py::test_eq_properties[4] - ValueError: all the input array dimensions for the concatenation axis must match exactly, but along dimension 1, the array at index 0 has size 0 and the array at index 2 has size 2
ERROR tests/test_equilibria.py::test_critical[5] - ValueError: all the input array dimensions for the concatenation axis must match exactly, but along dimension 1, the array at index 0 has size 0 and the array at index 1 has size 2
ERROR tests/test_equilibria.py::test_eq_properties[5] - ValueError: all the input array dimensions for the concatenation axis must match exactly, but along dimension 1, the array at index 0 has size 0 and the array at index 1 has size 2
ERROR tests/test_gfile.py::test_from_to_gfile[4] - ValueError: all the input array dimensions for the concatenation axis must match exactly, but along dimension 1, the array at index 0 has size 0 and the array at index 2 has size 2
ERROR tests/test_gfile.py::test_from_to_gfile[5] - ValueError: all the input array dimensions for the concatenation axis must match exactly, but along dimension 1, the array at index 0 has size 0 and the array at index 1 has size 2
ERROR tests/test_io.py::test_dict2xarray[4] - ValueError: all the input array dimensions for the concatenation axis must match exactly, but along dimension 1, the array at index 0 has size 0 and the array at index 2 has size 2
ERROR tests/test_io.py::test_dict2xarray[5] - ValueError: all the input array dimensions for the concatenation axis must match exactly, but along dimension 1, the array at index 0 has size 0 and the array at index 1 has size 2
======================================================================================================================= 26 failed, 56 passed, 1 skipped, 102 warnings, 14 errors in 226.26s (0:03:46) =======================================================================================================================
Happy to attach the full failure log if that would be helpful!
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