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pygad's Issues
pip editable install broken
Installing via pip install -e .
is broken. When importing pygad installed in such a way it is an empty module:
In [1]: import pygad as pg
In [2]: dir(pg)
Out[2]:
['__doc__',
'__file__',
'__loader__',
'__name__',
'__package__',
'__path__',
'__spec__']
As suggested by pypa/setuptools#3548 (comment) we can install pygad as
pip install -e . --config-settings editable_mode=strict
and voila
In [1]: import pygad as pg
In [2]: dir(pg)
Out[2]:
['BallMask',
'BoxMask',
'C',
...
'units',
'utils',
'write']
Should this be included in the docs?
UnitError
There is some unit error when plotting the default gas map on newer matplotlib version.
Code to reproduce
import pygad as pg
s = s = pg.Snapshot('snaps/snap_M1196_4x_470', load_double_prec=True)
pg.plotting.image(s.gas)
---------------------------------------------------------------------------
UnitError Traceback (most recent call last)
Cell In[50], line 1
----> 1 pg.plotting.image(s.gas)
File [/workspaces/pygad/pygad/plotting/maps.py:542](https://vscode-remote+codespaces-002bmigelo-002dliterate-002drobot-002dv7vprrwqr5hwq95.vscode-resource.vscode-cdn.net/workspaces/pygad/pygad/plotting/maps.py:542), in image(s, qty, av, units, logscale, surface_dens, field, reduction, extent, Npx, xaxis, yaxis, vlim, cmap, normcmaplum, desat, colors, colors_av, cunits, clogscale, csurf_dens, clim, ax, showcbar, cbartitle, scaleind, scaleunits, fontcolor, fontsize, outline, im_alpha, interpolation, maps, zero_is_white, **kwargs)
539 cbartitle = r'$\log_{10}$(' + cbartitle + ')'
540 cbartitle = cbartitle.strip()
--> 542 return plot_map(im_lum, colors=im_col,
543 extent=extent, vlim=vlim, clim=clim,
544 logscale=logscale, clogscale=clogscale,
545 units=units, cunits=cunits,
546 surface_dens=surface_dens, csurf_dens=csurf_dens,
547 cmap=cmap, normcmaplum=normcmaplum, desat=desat,
548 ax=ax, showcbar=showcbar, cbartitle=cbartitle,
549 scaleind=scaleind, scaleunits=scaleunits,
550 fontcolor=fontcolor, fontsize=fontsize, outline=outline,
551 im_alpha=im_alpha, xaxis=xaxis, yaxis=yaxis, subs=s,
552 interpolation=interpolation, zero_is_white=zero_is_white)
File [/workspaces/pygad/pygad/plotting/maps.py:178](https://vscode-remote+codespaces-002bmigelo-002dliterate-002drobot-002dv7vprrwqr5hwq95.vscode-resource.vscode-cdn.net/workspaces/pygad/pygad/plotting/maps.py:178), in plot_map(m, colors, extent, vlim, clim, logscale, clogscale, units, cunits, surface_dens, csurf_dens, cmap, normcmaplum, desat, ax, showcbar, cbartitle, scaleind, scaleunits, fontcolor, fontsize, outline, im_alpha, xaxis, yaxis, subs, interpolation, maps, zero_is_white)
176 clim = clim.in_units_of(cunits)
177 if clim is None:
--> 178 clim = np.percentile(colors[np.isfinite(colors)], [0.1,99.99])
179 if clogscale:
180 colors = np.log10(colors)
File <__array_function__ internals>:180, in percentile(*args, **kwargs)
File [~/.local/lib/python3.10/site-packages/numpy/lib/function_base.py:4134](https://vscode-remote+codespaces-002bmigelo-002dliterate-002drobot-002dv7vprrwqr5hwq95.vscode-resource.vscode-cdn.net/workspaces/~/.local/lib/python3.10/site-packages/numpy/lib/function_base.py:4134), in percentile(a, q, axis, out, overwrite_input, method, keepdims, interpolation)
4132 if not _quantile_is_valid(q):
4133 raise ValueError("Percentiles must be in the range [0, 100]")
-> 4134 return _quantile_unchecked(
4135 a, q, axis, out, overwrite_input, method, keepdims)
File [~/.local/lib/python3.10/site-packages/numpy/lib/function_base.py:4383](https://vscode-remote+codespaces-002bmigelo-002dliterate-002drobot-002dv7vprrwqr5hwq95.vscode-resource.vscode-cdn.net/workspaces/~/.local/lib/python3.10/site-packages/numpy/lib/function_base.py:4383), in _quantile_unchecked(a, q, axis, out, overwrite_input, method, keepdims)
4375 def _quantile_unchecked(a,
4376 q,
4377 axis=None,
(...)
4380 method="linear",
4381 keepdims=False):
4382 """Assumes that q is in [0, 1], and is an ndarray"""
-> 4383 r, k = _ureduce(a,
4384 func=_quantile_ureduce_func,
4385 q=q,
4386 axis=axis,
4387 out=out,
4388 overwrite_input=overwrite_input,
4389 method=method)
4390 if keepdims:
4391 return r.reshape(q.shape + k)
File [~/.local/lib/python3.10/site-packages/numpy/lib/function_base.py:3702](https://vscode-remote+codespaces-002bmigelo-002dliterate-002drobot-002dv7vprrwqr5hwq95.vscode-resource.vscode-cdn.net/workspaces/~/.local/lib/python3.10/site-packages/numpy/lib/function_base.py:3702), in _ureduce(a, func, **kwargs)
3699 else:
3700 keepdim = (1,) * a.ndim
-> 3702 r = func(a, **kwargs)
3703 return r, keepdim
File [~/.local/lib/python3.10/site-packages/numpy/lib/function_base.py:4552](https://vscode-remote+codespaces-002bmigelo-002dliterate-002drobot-002dv7vprrwqr5hwq95.vscode-resource.vscode-cdn.net/workspaces/~/.local/lib/python3.10/site-packages/numpy/lib/function_base.py:4552), in _quantile_ureduce_func(a, q, axis, out, overwrite_input, method)
4550 else:
4551 arr = a.copy()
-> 4552 result = _quantile(arr,
4553 quantiles=q,
4554 axis=axis,
4555 method=method,
4556 out=out)
4557 return result
File [~/.local/lib/python3.10/site-packages/numpy/lib/function_base.py:4669](https://vscode-remote+codespaces-002bmigelo-002dliterate-002drobot-002dv7vprrwqr5hwq95.vscode-resource.vscode-cdn.net/workspaces/~/.local/lib/python3.10/site-packages/numpy/lib/function_base.py:4669), in _quantile(arr, quantiles, axis, method, out)
4667 result_shape = virtual_indexes.shape + (1,) * (arr.ndim - 1)
4668 gamma = gamma.reshape(result_shape)
-> 4669 result = _lerp(previous,
4670 next,
4671 gamma,
4672 out=out)
4673 if np.any(slices_having_nans):
4674 if result.ndim == 0 and out is None:
4675 # can't write to a scalar
File [~/.local/lib/python3.10/site-packages/numpy/lib/function_base.py:4488](https://vscode-remote+codespaces-002bmigelo-002dliterate-002drobot-002dv7vprrwqr5hwq95.vscode-resource.vscode-cdn.net/workspaces/~/.local/lib/python3.10/site-packages/numpy/lib/function_base.py:4488), in _lerp(a, b, t, out)
4486 diff_b_a = subtract(b, a)
4487 # asanyarray is a stop-gap until gh-13105
-> 4488 lerp_interpolation = asanyarray(add(a, diff_b_a * t, out=out))
4489 subtract(b, diff_b_a * (1 - t), out=lerp_interpolation, where=t >= 0.5)
4490 if lerp_interpolation.ndim == 0 and out is None:
File [/workspaces/pygad/pygad/binning/core.py:300](https://vscode-remote+codespaces-002bmigelo-002dliterate-002drobot-002dv7vprrwqr5hwq95.vscode-resource.vscode-cdn.net/workspaces/pygad/pygad/binning/core.py:300), in Map.__array_wrap__(self, array, context)
299 def __array_wrap__(self, array, context=None):
--> 300 return UnitArr.__array_wrap__(self, array, context)
File [/workspaces/pygad/pygad/units/unit_arr.py:325](https://vscode-remote+codespaces-002bmigelo-002dliterate-002drobot-002dv7vprrwqr5hwq95.vscode-resource.vscode-cdn.net/workspaces/pygad/pygad/units/unit_arr.py:325), in UnitArr.__array_wrap__(self, array, context)
323 try:
324 ufunc = context[0]
--> 325 units = UnitArr._ufunc_registry[ufunc](*context[1])
326 if units is not None:
327 units = units.gather()
File [/workspaces/pygad/pygad/units/unit_arr.py:784](https://vscode-remote+codespaces-002bmigelo-002dliterate-002drobot-002dv7vprrwqr5hwq95.vscode-resource.vscode-cdn.net/workspaces/pygad/pygad/units/unit_arr.py:784), in _same_units_binary(a, b)
782 else:
783 a_units.in_units_of(b_units)
--> 784 raise units.UnitError('Units are not the same but they are ' +
785 'convertable. Use operator instead of ' +
786 'function or convert manually.')
787 else:
788 return a_units if a_units is not None else b_units
UnitError: 'Units are not the same but they are convertable. Use operator instead of function or convert manually.'
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Detected dependencies
docker-compose
docker-compose.yml
dockerfile
Dockerfile
python 3.11-slim-buster
github-actions
.github/workflows/workflow.yml
actions/checkout v4
actions/setup-python v5
pep621
pyproject.toml
setup-cfg
setup.cfg
numpy <1.25
matplotlib !=3.7.2,<3.9.0
astropy <=6.0.0
scipy <=1.12.0
h5py <=3.10.0
Pillow <=10.2.0
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