cleanups, fixes in references, etc

examples/PyMPDATA_examples/Arabas_and_Farhat_2020/__init__.py

@@ -1,10 +1,8 @@
 """
-This module contains an implementation of a paper on pricing European and
-American options using the PyMPDATA library.
-The paper is available at: [Arabas and Farhat 2020](https://doi.org/10.1016/j.cam.2019.05.023).
+This example implements simulations presented in the [Arabas and Farhat 2020](https://doi.org/10.1016/j.cam.2019.05.023)
+  study on pricing of European and American options using MPDATA.
 
 Each notebook in this directory corresponds to a figure or a table in the paper.
-I.e. the notebook `fig_1.ipynb` corresponds to Figure 1 in the paper.
 """
 
 from .simulation import Simulation

examples/PyMPDATA_examples/Bartman_et_al_2022/__init__.py

@@ -1,4 +1,4 @@
 """
 This example is based on the paper:
-[Bartman et al. 2022](https://joss.theoj.org/papers/10e7361e43785dbb1b3d659c5b01757a).
+[Bartman et al. 2022](https://doi.org/10.21105/joss.03896).
 """

examples/PyMPDATA_examples/DPDC/__init__.py

@@ -1,6 +1,3 @@
-# https://github.com/pdoc3/pdoc/issues/199
-# https://github.com/python/cpython/pull/20809
 """
 This example demonstrates the use of the Double-Pass Donor-Cell option in `PyMPDATA.options`.
 """
-pass

examples/PyMPDATA_examples/Jarecka_et_al_2015/__init__.py

@@ -1,6 +1,7 @@
 """
-This module showcases the PyMPDATA implementation of the shallow water equations
-as presented in the paper [Jarecka_et_al_2015](https://doi.org/10.1016/j.jcp.2015.02.003).
+This module showcases the PyMPDATA implementation of an MPDATA-based shallow-water equations
+solver discussed and bencharked against analytical solutions in
+[Jarecka_et_al_2015](https://doi.org/10.1016/j.jcp.2015.02.003).
 """
 
 from .plot_output import plot_output

examples/PyMPDATA_examples/Molenkamp_test_as_in_Jaruga_et_al_2015_Fig_12/__init__.py

@@ -1,5 +1,5 @@
 """
 This is an example based on the solid-body rotation test from
-[Molenkap 1968](http://dx.doi.org/10.1175/1520-0450(1968)007%3C0160:AOFDMA%3E2.0.CO;2)
+[Molenkap 1968](http://doi.org/10.1175/1520-0450(1968)007%3C0160:AOFDMA%3E2.0.CO;2)
 (as in Fig. 12 in [Jaruga et al. 2015](https://doi.org/10.5194/gmd-8-1005-2015)).
 """

examples/PyMPDATA_examples/Olesik_et_al_2022/__init__.py

@@ -1,5 +1,5 @@
 """
 This is a PyMPDATA implementation of 1D particle population condensational growth
 problem with coordinate transformations, as presented in
-[Olesik et al. 2020](https://arxiv.org/abs/2011.14726).
+[Olesik et al. 2022](https://doi.org/10.5194/gmd-15-3879-2022).
 """

examples/PyMPDATA_examples/Shipway_and_Hill_2012/__init__.py

@@ -1,7 +1,7 @@
 """
-This is an example of 2D spectral-spatial problem of droplet
+This is an example of 2D droplet size-spectral/spatial problem of
 condensational growth in a column of air,
-as described in [Shipway and Hill, 2012](https://doi.org/10.1002/qj.1913).
+as described in [Shipway and Hill 2012](https://doi.org/10.1002/qj.1913).
 """
 
 from .arakawa_c import arakawa_c

examples/PyMPDATA_examples/Williamson_and_Rasch_1989_as_in_Jaruga_et_al_2015_Fig_14/__init__.py

@@ -1,9 +1,6 @@
-# https://github.com/pdoc3/pdoc/issues/199
-# https://github.com/python/cpython/pull/20809
 """
 This example is based on
 [Williamson and Rasch 1989](https://doi.org/10.1175/1520-0493(1989)117%3C0102:TDSLTW%3E2.0.CO;2).
 It demonstrates the use of `PyMPDATA.solver.g_factor`
 to transform the advection problem onto a sphere.
 """
-pass

examples/PyMPDATA_examples/advection_diffusion_1d/__init__.py

@@ -1,7 +1,4 @@
-# https://github.com/pdoc3/pdoc/issues/199
-# https://github.com/python/cpython/pull/20809
 """
-PyMPDATA advection-diffusion 1D example with error analysis
+PyMPDATA 1D advection-diffusion example with error analysis
 for different initial parameters.
 """
-pass