skypybot: Hello @Lucia-Fonseca! Thanks for opening this PR. We checked the lines you've touched for [PEP 8](https://www.python.org/dev/peps/pep-0008) issues, and found:



* In the file [`skypy/power_spectrum/tests/test_halofit.py`](https://github.com/skypyproject/skypy/blob/274646a78a6cc78772c15434b70565d7fdda7485/skypy/power_spectrum/tests/test_halofit.py):

> [Line 18:11](https://github.com/skypyproject/skypy/blob/274646a78a6cc78772c15434b70565d7fdda7485/skypy/power_spectrum/tests/test_halofit.py#L18): [E127](https://duckduckgo.com/?q=pep8%20E127) continuation line over-indented for visual indent
> [Line 28:23](https://github.com/skypyproject/skypy/blob/274646a78a6cc78772c15434b70565d7fdda7485/skypy/power_spectrum/tests/test_halofit.py#L28): [E203](https://duckduckgo.com/?q=pep8%20E203) whitespace before ','
> [Line 28:54](https://github.com/skypyproject/skypy/blob/274646a78a6cc78772c15434b70565d7fdda7485/skypy/power_spectrum/tests/test_halofit.py#L28): [E203](https://duckduckgo.com/?q=pep8%20E203) whitespace before ','
> [Line 30:54](https://github.com/skypyproject/skypy/blob/274646a78a6cc78772c15434b70565d7fdda7485/skypy/power_spectrum/tests/test_halofit.py#L30): [E203](https://duckduckgo.com/?q=pep8%20E203) whitespace before ','
> [Line 54:30](https://github.com/skypyproject/skypy/blob/274646a78a6cc78772c15434b70565d7fdda7485/skypy/power_spectrum/tests/test_halofit.py#L54): [E231](https://duckduckgo.com/?q=pep8%20E231) missing whitespace after ','
> [Line 54:43](https://github.com/skypyproject/skypy/blob/274646a78a6cc78772c15434b70565d7fdda7485/skypy/power_spectrum/tests/test_halofit.py#L54): [E231](https://duckduckgo.com/?q=pep8%20E231) missing whitespace after ','
> [Line 55:42](https://github.com/skypyproject/skypy/blob/274646a78a6cc78772c15434b70565d7fdda7485/skypy/power_spectrum/tests/test_halofit.py#L55): [E231](https://duckduckgo.com/?q=pep8%20E231) missing whitespace after ','
> [Line 55:55](https://github.com/skypyproject/skypy/blob/274646a78a6cc78772c15434b70565d7fdda7485/skypy/power_spectrum/tests/test_halofit.py#L55): [E231](https://duckduckgo.com/?q=pep8%20E231) missing whitespace after ','


Lucia-Fonseca: @rrjbca could you help me understand why this is not passing all the checks? Thanks

Lucia-Fonseca: `test_camb` seems to fail here when I run `tox -e test-scipy14`:
`>       assert pkz.shape == (len(redshift), len(wavenumber))
E       assert (2, 2) == (2, 200)
E         At index 1 diff: 2 != 200`
However, if I run the same code in a Jupyter notebook, there is no such error and `pkz.shape` is actually `(2,200)`.
Any idea why this happens?
Lucia-Fonseca: Merge conflict resolved and all required checks passed.
rrjbca: Things like changing how `Mpc` renders, adding references and similar documentation changes have nothing to do with this PR. I am going to revert the Mpc changes that are not working and open a new issue. I will merge the other changes this time but please try to keep your pull requests focused.
diff --git a/skypy/power_spectrum/_camb.py b/skypy/power_spectrum/_camb.py
index 2d5752e..4f9c445 100644
--- a/skypy/power_spectrum/_camb.py
+++ b/skypy/power_spectrum/_camb.py
@@ -8,8 +8,9 @@ __all__ = [
 
 
 def camb(wavenumber, redshift, cosmology, A_s, n_s):
-    """ Return the CAMB computation of the linear matter power spectrum, on a
-    two dimensional grid of wavenumber and redshift
+    r'''CAMB linear matter power spectrum.
+    Compute the linear matter power spectrum on a two dimensional grid of
+    redshift and wavenumber using CAMB [1]_.
 
     Parameters
     ----------
@@ -31,11 +32,11 @@ def camb(wavenumber, redshift, cosmology, A_s, n_s):
 
     Returns
     -------
-    power_spectrum : (nk, nz) array_like
+    power_spectrum : (nz, nk) array_like
         Array of values for the linear matter power spectrum in  [Mpc^3]
         evaluated at the input wavenumbers for the given primordial power
         spectrum parameters, cosmology. For nz redshifts and nk wavenumbers
-        the returned array will have shape (nk, nz).
+        the returned array will have shape (nz, nk).
 
     Examples
     --------
@@ -46,23 +47,21 @@ def camb(wavenumber, redshift, cosmology, A_s, n_s):
     >>> wavenumber = np.array([1.e-2, 1.e-1, 1e0])
     >>> A_s = 2.e-9
     >>> n_s = 0.965
-    >>> camb(wavenumber, redshift, cosmology, A_s, n_s)  # doctest: +SKIP
-    array([[2.34758952e+04, 8.70837957e+03],
-           [3.03660813e+03, 1.12836115e+03],
-           [2.53124880e+01, 9.40802814e+00]])
+    >>> power_spectrum = camb(wavenumber, redshift, cosmology, A_s, n_s) # doctest: +SKIP
 
     References
     ----------
-    doi : 10.1086/309179
-    arXiv: astro-ph/9911177
+    .. [1] Lewis, A. and Challinor, A. and Lasenby, A. (2000),
+        doi : 10.1086/309179.
 
-    """
+    '''
 
     try:
         from camb import CAMBparams, get_results, model
     except ImportError:
-        raise Exception("camb is required to use skypy.linear.camb")
+        raise Exception("camb is required to use skypy.power_spectrum.camb")
 
+    return_shape = (*np.shape(redshift), *np.shape(wavenumber))
     redshift = np.atleast_1d(redshift)
 
     h2 = cosmology.h * cosmology.h
@@ -98,4 +97,4 @@ def camb(wavenumber, redshift, cosmology, A_s, n_s):
                                                    maxkh=np.max(k_h.value),
                                                    npoints=len(k_h.value))
 
-    return pzk[redshift_order[::-1]].T
+    return pzk[redshift_order[::-1]].reshape(return_shape)
diff --git a/skypy/power_spectrum/_halofit.py b/skypy/power_spectrum/_halofit.py
index a9942d1..fc7c76f 100644
--- a/skypy/power_spectrum/_halofit.py
+++ b/skypy/power_spectrum/_halofit.py
@@ -72,7 +72,7 @@ def halofit(wavenumber, redshift, linear_power_spectrum,
         Input wavenumbers in units of :math:`1/Mpc`.
     z : (nz,) array_like
         Input redshifts
-    P : (nk, nz) array_like
+    P : (nz, nk) array_like
         Linear power spectrum for given wavenumbers
         and redshifts :math:`Mpc^3`.
     cosmology : astropy.cosmology.Cosmology
@@ -83,7 +83,7 @@ def halofit(wavenumber, redshift, linear_power_spectrum,
 
     Returns
     -------
-    pknl : (nk, nz) array_like
+    pknl : (nz, nk) array_like
            Non-linear halo power spectrum in units of :math:`Mpc^3`.
 
     References
@@ -112,7 +112,7 @@ def halofit(wavenumber, redshift, linear_power_spectrum,
     return_shape = np.shape(linear_power_spectrum)
     redshift = np.atleast_1d(redshift)
     if np.ndim(linear_power_spectrum) == 1:
-        linear_power_spectrum = linear_power_spectrum[:, np.newaxis]
+        linear_power_spectrum = linear_power_spectrum[np.newaxis, :]
 
     # Declaration of variables
     if isiterable(redshift):
@@ -141,7 +141,7 @@ def halofit(wavenumber, redshift, linear_power_spectrum,
     lnk = np.log(wavenumber)
     k2 = np.square(wavenumber)
     k3 = np.power(wavenumber, 3)
-    dl2kz = (linear_power_spectrum.T * k3) / (2 * np.pi * np.pi)
+    dl2kz = (linear_power_spectrum * k3) / (2 * np.pi * np.pi)
 
     # Integrals required to evaluate Smith et al. 2003 equations C5, C7 & C8
     def integral_kn(lnR, n):
@@ -209,7 +209,7 @@ def halofit(wavenumber, redshift, linear_power_spectrum,
     # Halofit non-linear power spectrum, Smith et al. 2003 equation C1
     pknl = 2 * np.pi * np.pi * (dq2 + dh2) / k3
 
-    return pknl.T.reshape(return_shape)
+    return pknl.reshape(return_shape)
 
 
 halofit_smith = partial(halofit, parameters=_smith_parameters)

transpose power spectra
The power spectra are currently output which axes order `(nk, nz)`. This is the worse choice because it is always `P(k)` for a given `z` that is needed in computations, so the `P(k)` values for given `z` should always be contiguous in memory for the usual reasons. Which is also why every other power spectrum code returns `(nz, nk)`.

We had a vote and decided to change the order, which needs to happen before any code actually uses the power spectra.
diff --git a/skypy/power_spectrum/tests/data/camb_result.txt b/skypy/power_spectrum/tests/data/camb_result.txt
index fb4bd4b..1b33627 100644
--- a/skypy/power_spectrum/tests/data/camb_result.txt
+++ b/skypy/power_spectrum/tests/data/camb_result.txt
@@ -1,200 +1,2 @@
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-6.32085099e+02, 2.34046706e+02
-6.63141705e+02, 2.45547555e+02
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\ No newline at end of file
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diff --git a/skypy/power_spectrum/tests/data/linear_power.txt b/skypy/power_spectrum/tests/data/linear_power.txt
index d3a3dda..cad6763 100644
--- a/skypy/power_spectrum/tests/data/linear_power.txt
+++ b/skypy/power_spectrum/tests/data/linear_power.txt
@@ -1,100 +1,5 @@
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diff --git a/skypy/power_spectrum/tests/data/truth_bird.txt b/skypy/power_spectrum/tests/data/truth_bird.txt
index c0199e5..f471a79 100644
--- a/skypy/power_spectrum/tests/data/truth_bird.txt
+++ b/skypy/power_spectrum/tests/data/truth_bird.txt
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diff --git a/skypy/power_spectrum/tests/data/truth_smith.txt b/skypy/power_spectrum/tests/data/truth_smith.txt
index 8396b9e..7eb1ada 100644
--- a/skypy/power_spectrum/tests/data/truth_smith.txt
+++ b/skypy/power_spectrum/tests/data/truth_smith.txt
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diff --git a/skypy/power_spectrum/tests/data/truth_takahashi.txt b/skypy/power_spectrum/tests/data/truth_takahashi.txt
index 3821b05..7ccdde9 100644
--- a/skypy/power_spectrum/tests/data/truth_takahashi.txt
+++ b/skypy/power_spectrum/tests/data/truth_takahashi.txt
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diff --git a/skypy/power_spectrum/tests/test_camb.py b/skypy/power_spectrum/tests/test_camb.py
index 5c59e70..f99fde9 100644
--- a/skypy/power_spectrum/tests/test_camb.py
+++ b/skypy/power_spectrum/tests/test_camb.py
@@ -24,14 +24,15 @@ def test_camb():
     '''
     from skypy.power_spectrum import camb
 
+    # test shape and compare with the mocked power spectrum
     redshift = [0.0, 1.0]
     wavenumber = np.logspace(-4.0, np.log10(2.0), 200)
     pkz = camb(wavenumber, redshift, Planck15, 2.e-9, 0.965)
-    assert pkz.shape == (len(wavenumber), len(redshift))
+    assert pkz.shape == (len(redshift), len(wavenumber))
     assert allclose(pkz, test_pkz, rtol=1.e-4)
 
     # also check redshifts are ordered correctly
     redshift = [1.0, 0.0]
     pkz = camb(wavenumber, redshift, Planck15, 2.e-9, 0.965)
-    assert pkz.shape == (len(wavenumber), len(redshift))
-    assert allclose(pkz, test_pkz[:, np.argsort(redshift)], rtol=1.e-4)
+    assert pkz.shape == (len(redshift), len(wavenumber))
+    assert allclose(pkz, test_pkz[np.argsort(redshift), :], rtol=1.e-4)
diff --git a/skypy/power_spectrum/tests/test_halofit.py b/skypy/power_spectrum/tests/test_halofit.py
index c81f417..5dfc2db 100644
--- a/skypy/power_spectrum/tests/test_halofit.py
+++ b/skypy/power_spectrum/tests/test_halofit.py
@@ -43,15 +43,15 @@ def test_halofit():
 
     # Test when redshift is a scalar
     z_scalar = z[0]
-    power_1d = linear_power[:, 0]
-    truth_scalar_redshift = truth_smith[:, 0]
+    power_1d = linear_power[0, :]
+    truth_scalar_redshift = truth_smith[0, :]
     smith_scalar_redshift = halofit_smith(k, z_scalar, power_1d, Planck15)
     assert allclose(smith_scalar_redshift, truth_scalar_redshift)
     assert np.shape(smith_scalar_redshift) == np.shape(power_1d)
 
     # Test for failure when wavenumber is a scalar
     k_scalar = k[0]
-    power_1d = linear_power[0, :]
+    power_1d = linear_power[:, 0]
     with pytest.raises(TypeError):
         halofit_smith(k_scalar, z, power_1d, Planck15)
 

pip install -e .[test]
parse_log_pytest
pytest
pytest pytest-cov pytest-xdist pytest-mock pytest-asyncio
apt-get update apt-get install -y gcc
3.7
pytest --no-header -rA --tb=line --color=no -p no:cacheprovider -W ignore::DeprecationWarning
astropy==4.3.1
attrs @ file:///croot/attrs_1668696182826/work
certifi @ file:///croot/certifi_1671487769961/work/certifi
coverage==7.2.7
exceptiongroup==1.2.2
execnet==2.0.2
flit_core @ file:///opt/conda/conda-bld/flit-core_1644941570762/work/source/flit_core
hypothesis==6.79.4
importlib-metadata @ file:///tmp/build/80754af9/importlib-metadata_1648562407465/work
iniconfig @ file:///home/linux1/recipes/ci/iniconfig_1610983019677/work
networkx==2.6.3
numpy==1.21.6
packaging @ file:///croot/packaging_1671697413597/work
pluggy @ file:///tmp/build/80754af9/pluggy_1648042572264/work
py @ file:///opt/conda/conda-bld/py_1644396412707/work
pyerfa==2.0.0.3
pytest==7.1.2
pytest-arraydiff==0.6.1
pytest-astropy==0.11.0
pytest-astropy-header==0.2.2
pytest-asyncio==0.21.2
pytest-cov==4.1.0
pytest-doctestplus==1.0.0
pytest-filter-subpackage==0.1.2
pytest-mock==3.11.1
pytest-remotedata==0.4.1
pytest-xdist==3.5.0
PyYAML==6.0.1
scipy==1.7.3
-e git+https://github.com/skypyproject/skypy.git@f069858a6c9882a02c09131967070ec3e864e8ae#egg=skypy
sortedcontainers==2.4.0
tomli @ file:///opt/conda/conda-bld/tomli_1657175507142/work
typing_extensions @ file:///croot/typing_extensions_1669924550328/work
zipp @ file:///croot/zipp_1672387121353/work

name: skypy
channels:
  - defaults
  - https://repo.anaconda.com/pkgs/main
  - https://repo.anaconda.com/pkgs/r
  - conda-forge
dependencies:
  - _libgcc_mutex=0.1=main
  - _openmp_mutex=5.1=1_gnu
  - attrs=22.1.0=py37h06a4308_0
  - ca-certificates=2025.2.25=h06a4308_0
  - certifi=2022.12.7=py37h06a4308_0
  - flit-core=3.6.0=pyhd3eb1b0_0
  - importlib-metadata=4.11.3=py37h06a4308_0
  - importlib_metadata=4.11.3=hd3eb1b0_0
  - iniconfig=1.1.1=pyhd3eb1b0_0
  - ld_impl_linux-64=2.40=h12ee557_0
  - libffi=3.4.4=h6a678d5_1
  - libgcc-ng=11.2.0=h1234567_1
  - libgomp=11.2.0=h1234567_1
  - libstdcxx-ng=11.2.0=h1234567_1
  - ncurses=6.4=h6a678d5_0
  - openssl=1.1.1w=h7f8727e_0
  - packaging=22.0=py37h06a4308_0
  - pip=22.3.1=py37h06a4308_0
  - pluggy=1.0.0=py37h06a4308_1
  - py=1.11.0=pyhd3eb1b0_0
  - pytest=7.1.2=py37h06a4308_0
  - python=3.7.16=h7a1cb2a_0
  - readline=8.2=h5eee18b_0
  - setuptools=65.6.3=py37h06a4308_0
  - sqlite=3.45.3=h5eee18b_0
  - tk=8.6.14=h39e8969_0
  - tomli=2.0.1=py37h06a4308_0
  - typing_extensions=4.4.0=py37h06a4308_0
  - wheel=0.38.4=py37h06a4308_0
  - xz=5.6.4=h5eee18b_1
  - zipp=3.11.0=py37h06a4308_0
  - zlib=1.2.13=h5eee18b_1
  - pip:
      - astropy==4.3.1
      - coverage==7.2.7
      - exceptiongroup==1.2.2
      - execnet==2.0.2
      - hypothesis==6.79.4
      - networkx==2.6.3
      - numpy==1.21.6
      - pyerfa==2.0.0.3
      - pytest-arraydiff==0.6.1
      - pytest-astropy==0.11.0
      - pytest-astropy-header==0.2.2
      - pytest-asyncio==0.21.2
      - pytest-cov==4.1.0
      - pytest-doctestplus==1.0.0
      - pytest-filter-subpackage==0.1.2
      - pytest-mock==3.11.1
      - pytest-remotedata==0.4.1
      - pytest-xdist==3.5.0
      - pyyaml==6.0.1
      - scipy==1.7.3
      - skypy==0.3.dev6+gf069858
      - sortedcontainers==2.4.0
prefix: /opt/conda/envs/skypy

skypy/power_spectrum/tests/test_halofit.py::test_halofit
skypy/power_spectrum/_halofit.py skypy/power_spectrum/_camb.py
skypy/power_spectrum/_halofit.py skypy/power_spectrum/_camb.py