fix merge conflict in authors

AUTHORS.rst

@@ -9,7 +9,7 @@ Current maintainers
 * Anowar Shajib `ajshajib <https://github.com/ajshajib/>`_
 * Daniel Gilman `dangilman <https://github.com/dangilman/>`_
 
-lenstronomy developer `mailing list <[email protected]>`_
+Contact the lenstronomy developers via `email <[email protected]>`_ if you have questions.
 
 
 
@@ -28,6 +28,7 @@ Contributors (alphabetic)
 * Aymeric Galan `aymgal <https://github.com/aymgal/>`_
 * Matthew R. Gomer `mattgomer <https://github.com/mattgomer>`_
 * Natalie B. Hogg `nataliehogg <https://github.com/nataliehogg>`_
+* Tyler Hughes
 * Daniel Johnson `DanJohnson98 <https://github.com/DanJohnson98>`_
 * Felix A. Kuhn
 * Felix Mayor
@@ -37,6 +38,7 @@ Contributors (alphabetic)
 * Brian Nord `bnord <https://github.com/bnord/>`_
 * Giulia Pagano
 * Ji Won Park `jiwoncpark <https://github.com/jiwoncpark/>`_
+* Jackson O'Donnell `jhod0 <https://github.com/jhod0/>`_
 * Thomas Schmidt `Thomas-01 <https://github.com/Thomas-01/>`_
 * Dominique Sluse
 * Luca Teodori `lucateo <https://github.com/lucateo/>`_
@@ -53,5 +55,12 @@ Contributors (alphabetic)
 Past development lead
 ---------------------
 
-The initial source code of lenstronomy was developed by Simon Birrer `sibirrer <https://github.com/sibirrer/>`_
-in 2014-2018 and made public in 2018. The lenstronomy developement moved to the project repository in 2022.
+The initial source code of lenstronomy was developed by Simon Birrer (`sibirrer <https://github.com/sibirrer/>`_)
+in 2014-2018 and made public in 2018. From 2018-2022 the development of lenstronomy was hosted on Simon Birrer's
+repository with increased contributions from many people.
+The lenstronomy development moved to the `project repository <https://github.com/lenstronomy/>`_ in 2022.
+
+
+Lenstronomy logo
+----------------
+The lenstronomy logo was designed by Zoe Alexander `zoe-blyss <https://github.com/zoe-blyss>`_.

PUBLISHED.rst

@@ -2,10 +2,10 @@
 Published work with lenstronomy
 ===============================
 
-In this section you can find the concept papers **lenstronomy** is based on the list of science publications that made
-use of **lenstronomy**. Please let the developers know when you publish a paper that made use of **lenstronomy**.
-We are happy to include your publication in this list.
-
+In this section you can find the concept papers **lenstronomy** is based on and a list of science publications that made
+use of **lenstronomy** before 09/2022.
+For a more complete and current list of publications using lenstronomy we refer to the `NASA/ADS query <https://ui.adsabs.harvard.edu/search/p_=0&q=citations(author%3A%22%5EBirrer%22%20title%3A%22lenstronomy%22)&sort=date%20desc%2C%20bibcode%20desc>`_
+(this incudes all publications citing lenstronomy papers, which is not the same as publications making active use of the software).
 
 
 Core lenstronomy methodology and software publications
@@ -44,6 +44,10 @@ Related software publications
 
 
 
+=====================================
+Scientific publication before 09/2022
+=====================================
+
 
 
 
@@ -235,6 +239,10 @@ Galaxy formation and evolution
 * Early results from GLASS-JWST. V: the first rest-frame optical size-luminosity relation of galaxies at  z>7; `Yang et al. 2022b <https://arxiv.org/abs/2207.13101>`_
     *galaxy size measurement from JWST data with Galight/lenstronomy*
 
+* A New Polar Ring Galaxy Discovered in the COSMOS Field; `Nishimura et al. 2022 <https://arxiv.org/abs/2208.12388>`_
+
+* Webb's PEARLS: dust attenuation and gravitational lensing in the backlit-galaxy system VV 191; `Keel et al. 2022 <https://arxiv.org/abs/2208.14475>`_
+
 
 
 Automatized Lens Modeling
@@ -347,7 +355,6 @@ Large scale structure
 
 
 
-
 Others
 ------
 

README.rst

@@ -1,7 +1,6 @@
-====================================================
-lenstronomy - gravitational lensing software package
-====================================================
 
+.. image:: https://raw.githubusercontent.com/lenstronomy/lenstronomy/main/docs/figures/logo_text.png
+    :target: https://raw.githubusercontent.com/lenstronomy/lenstronomy/main/docs/figures/logo_text.png
 
 .. image:: https://github.com/lenstronomy/lenstronomy/workflows/Tests/badge.svg
     :target: https://github.com/lenstronomy/lenstronomy/actions
@@ -26,8 +25,9 @@ lenstronomy - gravitational lensing software package
 .. image:: https://img.shields.io/badge/arXiv-1803.09746%20-yellowgreen.svg
     :target: https://arxiv.org/abs/1803.09746
 
-.. image:: https://raw.githubusercontent.com/lenstronomy/lenstronomy/main/docs/figures/readme_fig.png
-    :target: https://raw.githubusercontent.com/lenstronomy/lenstronomy/main/docs/figures/readme_fig.png
+..
+    .. image:: https://raw.githubusercontent.com/lenstronomy/lenstronomy/main/docs/figures/readme_fig.png
+        :target: https://raw.githubusercontent.com/lenstronomy/lenstronomy/main/docs/figures/readme_fig.png
 
 
 ``lenstronomy`` is a multi-purpose software package to model strong gravitational lenses.

docs/conf.py

@@ -31,7 +31,13 @@
 
 # Add any Sphinx extension module names here, as strings. They can be extensions
 # coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
-extensions = ['sphinx.ext.autodoc', 'sphinx.ext.coverage', 'sphinx.ext.mathjax', 'sphinx.ext.viewcode']
+extensions = ['sphinx.ext.autodoc', 'sphinx.ext.coverage', 'sphinx.ext.mathjax', 'sphinx.ext.viewcode']\
+#    , 'sphinx.ext.autosectionlabel']
+
+autodoc_default_options = {
+    'member-order': 'bysource',
+    'special-members': '__init__',
+}
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']

docs/index.rst

@@ -12,11 +12,11 @@ Contents:
    :maxdepth: 2
 
    installation
-   modules
    usage
    contributing
    mailinglist
    authors
    published
    affiliatedpackages
+   lenstronomy
    history

docs/lenstronomy.Data.rst

@@ -1,38 +1,53 @@
-lenstronomy\.Data package
-=========================
+lenstronomy.Data package
+========================
 
 Submodules
 ----------
 
-lenstronomy\.Data\.coord\_transforms module
--------------------------------------------
+lenstronomy.Data.coord\_transforms module
+-----------------------------------------
 
 .. automodule:: lenstronomy.Data.coord_transforms
-    :members:
-    :undoc-members:
-    :show-inheritance:
+   :members:
+   :undoc-members:
+   :show-inheritance:
 
-lenstronomy\.Data\.imaging\_data module
----------------------------------------
+lenstronomy.Data.image\_noise module
+------------------------------------
+
+.. automodule:: lenstronomy.Data.image_noise
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+lenstronomy.Data.imaging\_data module
+-------------------------------------
 
 .. automodule:: lenstronomy.Data.imaging_data
-    :members:
-    :undoc-members:
-    :show-inheritance:
+   :members:
+   :undoc-members:
+   :show-inheritance:
 
-lenstronomy\.Data\.psf module
------------------------------
+lenstronomy.Data.pixel\_grid module
+-----------------------------------
 
-.. automodule:: lenstronomy.Data.psf
-    :members:
-    :undoc-members:
-    :show-inheritance:
+.. automodule:: lenstronomy.Data.pixel_grid
+   :members:
+   :undoc-members:
+   :show-inheritance:
 
+lenstronomy.Data.psf module
+---------------------------
+
+.. automodule:: lenstronomy.Data.psf
+   :members:
+   :undoc-members:
+   :show-inheritance:
 
 Module contents
 ---------------
 
 .. automodule:: lenstronomy.Data
-    :members:
-    :undoc-members:
-    :show-inheritance:
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/lenstronomy.Sampling.rst

@@ -45,6 +45,14 @@ lenstronomy.Sampling.special\_param module
     :undoc-members:
     :show-inheritance:
 
+lenstronomy.Sampling.param\_group module
+------------------------------------------
+
+.. automodule:: lenstronomy.Sampling.param_group
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
 
 Module contents
 ---------------

docs/usage.rst

@@ -17,7 +17,7 @@ user to directly access a lot of tools and each module can also be used as stand
 Example notebooks
 -----------------
 
-We have made an extension module available at `https://github.com/lenstronomy/lenstronom-tutorials <https://github.com/lenstronomy/lenstronom-tutorials/>`_.
+We have made an extension module available at `https://github.com/lenstronomy/lenstronomy-tutorials <https://github.com/lenstronomy/lenstronomy-tutorials/>`_.
 You can find simple example notebooks for various cases. The latest versions of the notebooks should be compatible with the recent pip version of lenstronomy.
 
 

lenstronomy/Analysis/kinematics_api.py

@@ -51,7 +51,7 @@ def __init__(self, z_lens, z_source, kwargs_model, kwargs_aperture, kwargs_seein
         :param kwargs_mge_mass: keyword arguments that go into the MGE decomposition routine
         :param kwargs_mge_light: keyword arguments that go into the MGE decomposition routine
         :param sampling_number: int, number of spectral rendering to compute the light weighted integrated LOS
-        dispersion within the aperture. This keyword should be chosen high enough to result in converged results within the tolerance.
+         dispersion within the aperture. This keyword should be chosen high enough to result in converged results within the tolerance.
         :param num_kin_sampling: number of kinematic renderings on a total IFU
         :param num_psf_sampling: number of PSF displacements for each kinematic rendering on the IFU
         """

lenstronomy/Cosmo/background.py

@@ -17,7 +17,7 @@ def __init__(self, cosmo=None, interp=False, **kwargs_interp):
         :param cosmo: instance of astropy.cosmology
         :param interp: boolean, if True, uses interpolated cosmology to evaluate specific redshifts
         :param kwargs_interp: keyword arguments of CosmoInterp specifying the interpolation interval and maximum
-        redshift
+         redshift
         :return: Background class with instance of astropy.cosmology
         """
 
@@ -29,9 +29,11 @@ def __init__(self, cosmo=None, interp=False, **kwargs_interp):
         else:
             self.cosmo = cosmo
 
-    def a_z(self, z):
+    @staticmethod
+    def a_z(z):
         """
         returns scale factor (a_0 = 1) for given redshift
+
         :param z: redshift
         :return: scale factor
         """
@@ -72,6 +74,7 @@ def T_xy(self, z_observer, z_source):
     def rho_crit(self):
         """
         critical density
+
         :return: value in M_sol/Mpc^3
         """
         h = self.cosmo.H(0).value / 100.

lenstronomy/Cosmo/cosmo_solver.py

@@ -85,15 +85,20 @@ class InvertCosmo(object):
     """
     class to do an interpolation and call the inverse of this interpolation to get H_0 and omega_m
     """
-    def __init__(self, z_d, z_s, H0_range=np.linspace(10, 100, 90), omega_m_range=np.linspace(0.05, 1, 95)):
+    def __init__(self, z_d, z_s, H0_range=None, omega_m_range=None):
         self.z_d = z_d
         self.z_s = z_s
+        if H0_range is None:
+            H0_range = np.linspace(10, 100, 90)
+        if omega_m_range is None:
+            omega_m_range = np.linspace(0.05, 1, 95)
         self._H0_range = H0_range
         self._omega_m_range = omega_m_range
 
     def _make_interpolation(self):
         """
         creates an interpolation grid in H_0, omega_m and computes quantities in Dd and Ds_Dds
+
         :return:
         """
         grid2d = np.dstack(np.meshgrid(self._H0_range, self._omega_m_range)).reshape(-1, 2)
@@ -115,6 +120,7 @@ def _make_interpolation(self):
     def get_cosmo(self, Dd, Ds_Dds):
         """
         return the values of H0 and omega_m computed with an interpolation
+
         :param Dd: flat
         :param Ds_Dds: float
         :return:

lenstronomy/Cosmo/kde_likelihood.py

@@ -14,11 +14,11 @@ def __init__(self, D_d_sample, D_delta_t_sample, kde_type='scipy_gaussian', band
 
         :param D_d_sample: 1-d numpy array of angular diameter distances to the lens plane
         :param D_delta_t_sample: 1-d numpy array of time-delay distances
-        kde_type : string
-            The kernel to use.  Valid kernels are
-            'scipy_gaussian' or
-            ['gaussian'|'tophat'|'epanechnikov'|'exponential'|'linear'|'cosine']
-            Default is 'gaussian'.
+        :param kde_type: The kernel to use.  Valid kernels are
+         'scipy_gaussian' or
+         ['gaussian'|'tophat'|'epanechnikov'|'exponential'|'linear'|'cosine']
+         Default is 'gaussian'.
+        :type kde_type: string
         :param bandwidth: width of kernel (in same units as the angular diameter quantities)
         """
         values = np.vstack([D_d_sample, D_delta_t_sample])

lenstronomy/Cosmo/lcdm.py

@@ -40,6 +40,7 @@ def _get_cosom(self, H_0, Om0, Ode0=None):
     def D_d(self, H_0, Om0, Ode0=None):
         """
         angular diameter to deflector
+
         :param H_0: Hubble parameter [km/s/Mpc]
         :param Om0: normalized matter density at present time
         :return: float [Mpc]
@@ -50,6 +51,7 @@ def D_d(self, H_0, Om0, Ode0=None):
     def D_s(self, H_0, Om0, Ode0=None):
         """
         angular diameter to source
+
         :param H_0: Hubble parameter [km/s/Mpc]
         :param Om0: normalized matter density at present time
         :return: float [Mpc]
@@ -60,6 +62,7 @@ def D_s(self, H_0, Om0, Ode0=None):
     def D_ds(self, H_0, Om0, Ode0=None):
         """
         angular diameter from deflector to source
+
         :param H_0: Hubble parameter [km/s/Mpc]
         :param Om0: normalized matter density at present time
         :return: float [Mpc]
@@ -69,7 +72,8 @@ def D_ds(self, H_0, Om0, Ode0=None):
 
     def D_dt(self, H_0, Om0, Ode0=None):
         """
-        time delay distance
+        time-delay distance
+
         :param H_0: Hubble parameter [km/s/Mpc]
         :param Om0: normalized matter density at present time
         :return: float [Mpc]