CosmoStat
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diff --git a/‎docs/source/module_develop.md‎
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diff --git a/‎docs/source/refs.bib‎
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diff --git a/‎docs/source/understanding_api.md‎
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@@ -10,10 +10,18 @@ function (PSF) modelling technique. The code has been designed to facilitate
 the inclusion of new or improved processing steps to adapt to advances made
 in the coming years.
 
+```{figure} https://www.skysurvey.cc/wp-content/uploads/2022/04/UNIONS-Logo-TextBlack-1K-300x82.png
+---
+figclass: margin
+alt: UNIONS logo
+target: https://www.skysurvey.cc/
+---
+```
+
 The primary application of ShapePipe so far has been to the Ultraviolet
-Near-Infrared Optical Northern Survey (UNIONS) data (see {cite:t}`guinot:21`
+Near-Infrared Optical Northern Survey (UNIONS) data (see {cite:t}`guinot:22`
 and Kilbinger et al., in prep).
 
 We plan to add features and find new applications for ShapePipe and will update
 this documentation accordingly. For more details on the first public release
-of ShapePipe please see Farrens et al. (in prep).
+of ShapePipe please see {cite:t}`farrens:22b`.
@@ -5,14 +5,14 @@ ShapePipe pipelines are launched and managed via the `shapepipe_run` script.
 A list of command line arguments can be displayed using the `--help`
 option:
 
+```{seealso}
+:class: margin
+The `shapepipe` environment will need to be built and activated in order to run this script (see [Installation](installation.md)).
+```
 ```bash
 shapepipe_run --help
 ```
 
-```{warning}
-The `shapepipe` environment will need to be built and activated in order to run this script (see [Installation](installation.md)).
-```
-
 The options for defining a pipeline are managed via a
 [configuration file](configuration.md).
 
 
@@ -25,7 +25,7 @@
 # The short X.Y version
 version = '1.0'
 # The full version, including alpha/beta/rc tags
-release = '1.0.0'
+release = '1.0.1'
 
 
 # -- General configuration ---------------------------------------------------
@@ -113,7 +113,12 @@
     'use_issues_button': True,
     'use_download_button': False,
     'use_fullscreen_button': False,
+    'use_edit_page_button': True,
+    'path_to_docs': 'docs/source',
+    'extra_navbar': "<p></p>",
 }
+html_collapsible_definitions = True
+html_awesome_headerlinks = True
 
 # The name for this set of Sphinx documents.  If None, it defaults to
 # "<project> v<release> documentation".
@@ -153,4 +158,5 @@
 # -- BibTeX Setting  ----------------------------------------------
 
 bibtex_bibfiles = ['refs.bib']
-bibtex_default_style = 'alpha'
+bibtex_default_style = 'unsrt'
+bibtex_reference_style = 'author_year'
@@ -7,6 +7,34 @@ possible applications of the package.
 Below will list the individuals who have contributed to the development of
 ShapePipe so far.
 
+```{figure} https://avatars.githubusercontent.com/u/6851839?v=4
+---
+figclass: margin
+alt: Samuel Farrens
+width: 25%
+target: https://github.com/sfarrens
+---
+Samuel Farrens
+```
+```{figure} https://avatars.githubusercontent.com/u/39480528?v=4
+---
+figclass: margin
+alt: Axel Guinot
+width: 25%
+target: https://github.com/aguinot
+---
+Axel Guinot
+```
+```{figure} https://avatars.githubusercontent.com/u/4549196?v=4
+---
+figclass: margin
+alt: Martin Kilbinger
+width: 25%
+target: https://github.com/martinkilbinger
+---
+Martin Kilbinger
+```
+
 ## Maintainers
 
 - [Samuel Farrens](https://github.com/sfarrens) : Development lead, core package developer, performance and debugging
 
@@ -4,6 +4,12 @@ ShapePipe
 .. Include table of contents
 .. include:: toc.rst
 
+.. figure:: img/cosmostat_logo.jpg
+  :figclass: margin
+  :width: 100%
+  :alt: CosmoStat Logo
+  :target: http://www.cosmostat.org/
+
 ShapePipe is a galaxy shape measurement pipeline developed within the
 |link-to-cosmostat| lab at CEA Paris-Saclay.
 
@@ -13,9 +19,7 @@ we invite you to |link-to-issues| on the GitHub repository an we will do our
 best to help you.
 
 We kindly request that if you use ShapePipe for your academic work that you
-cite :cite:`guinot:21` and Farrens et al. (in prep).
-
-|CS_LOGO|
+cite :cite:t:`guinot:22` and :cite:t:`farrens:22b`.
 
 .. |link-to-cosmostat| raw:: html
 
@@ -25,8 +29,3 @@ cite :cite:`guinot:21` and Farrens et al. (in prep).
 
   <a href="https://github.com/CosmoStat/shapepipe/issues/new/choose"
   target="_blank">open an issue</a>
-
-.. |CS_LOGO| image:: img/cosmostat_logo.jpg
-  :width: 45%
-  :alt: CosmoStat Logo
-  :target: http://www.cosmostat.org/
@@ -1,26 +1,31 @@
 # Installation
 
-```{important}
+```{attention}
 ShapePipe was not designed to be a stand-alone Python library. Instead users
 are expected to install the full ShapePipe environment on the system(s) where
 data should be processed.
 ```
 
 ## Standard Installation
 
-The standard installation of ShapePipe manages [dependencies](dependencies.md)
-and scripts using a [Conda](https://docs.conda.io/en/latest/) environment.
-Therefore, to follow the standard installation Conda must be available on the
-system.
-
 ```{tip}
+:class: margin
 Check out [Miniconda](https://docs.conda.io/en/latest/miniconda.html) for a
 light weight and easy installation of Conda.
 ```
 
+The standard installation of ShapePipe manages [dependencies](dependencies.md)
+and scripts using a [Conda](https://docs.conda.io/en/latest/) environment.
+Therefore, to follow the standard installation Conda must be available on the
+system.
+
 The ShapePipe package should first be cloned (or downloaded) from the
 [GitHub repository](https://github.com/CosmoStat/shapepipe).
 
+```{note}
+:class: margin
+Developers should simply clone the repository as usual.
+```
 ```bash
 git clone -b <VERSION> --depth 1 git@github.com:CosmoStat/shapepipe.git
 cd shapepipe
@@ -32,10 +37,6 @@ where `<VERSION>` is a
 [latest release](https://github.com/CosmoStat/shapepipe/releases/latest)
 unless you want to reproduce an older set of results.
 
-```{note}
-Developers should simply clone the repository as usual.
-```
-
 Then, the entire ShapePipe environment, including dependencies, can be built
 using the `install_shapepipe` script as follows.
 
@@ -93,15 +94,15 @@ entire ShapePipe environment.
 
 ## Installing the ShapePipe Library Only
 
-```{warning}
-Note, this method will not include any system executables or examples.
-```
-
 The ShapePipe library, i.e. the core package not including module
 dependencies, can be installed in the following ways.
 
 After cloning the repository.
 
+```{warning}
+:class: margin
+Note, this method will not include any system executables or examples.
+```
 ```bash
 pip install .
 ```
 
@@ -67,6 +67,12 @@ def example_module(*args):
 In the specific case of a module that executes an executable available on the
 system, the module runner should also import the `execute` function.
 
+```{note}
+:class: margin
+If no `stdout` or `stderr` are provided by the given module, the module
+runner should simply return `None, None`.
+```
+
 ```python
 from shapepipe.modules.module_decorator import module_runner
 from shapepipe.modules.module_name_package.module_name import ...
@@ -84,10 +90,7 @@ def example_module(*args):
     return stdout, stderr
 ```
 
-```{note}
-If no `stdout` or `stderr` are provided by the given module, the the module
-runner should simply return `None, None`.
-```
+
 
 The module runner decorator takes the following keyword arguments:
 
 
@@ -318,11 +318,36 @@ @ARTICLE{farrens:22
       adsnote = {Provided by the SAO/NASA Astrophysics Data System}
 }
 
-@article{guinot:21,
-        author = {{Guinot}, A. and {Kilbinger}, M. and {Farrens}, S. and others},
+@ARTICLE{farrens:22b,
+       author = {{Farrens}, S. and {Guinot}, A. and {Kilbinger}, M. and {Liaudat}, T. and {Baumont}, L. and {Jimenez}, X. and {Peel}, A. and {Pujol}, A. and {Schmitz}, M. and {Starck}, J. -L. and {Vitorelli}, A.~Z.},
+        title = "{ShapePipe: A modular weak-lensing processing and analysis pipeline}",
+      journal = {arXiv e-prints},
+     keywords = {Astrophysics - Instrumentation and Methods for Astrophysics, Astrophysics - Cosmology and Nongalactic Astrophysics},
+         year = 2022,
+        month = jun,
+          eid = {arXiv:2206.14689},
+        pages = {arXiv:2206.14689},
+archivePrefix = {arXiv},
+       eprint = {2206.14689},
+ primaryClass = {astro-ph.IM},
+       adsurl = {https://ui.adsabs.harvard.edu/abs/2022arXiv220614689F},
+      adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+@ARTICLE{guinot:22,
+       author = {{Guinot}, Axel and {Kilbinger}, Martin and {Farrens}, Samuel and {Peel}, Austin and {Pujol}, Arnau and {Schmitz}, Morgan and {Starck}, Jean-Luc and {Erben}, Thomas and {Gavazzi}, Raphael and {Gwyn}, Stephen and {Hudson}, Michael J. and {Hiledebrandt}, Hendrik and {Liaudat}, Tobias and {Miller}, Lance and {Spitzer}, Isaac and {Van Waerbeke}, Ludovic and {Cuillandre}, Jean-Charles and {Fabbro}, S{\'e}bastien and {McConnachie}, Alan},
         title = "{ShapePipe: a new shape measurement pipeline and weak-lensing application to UNIONS/CFIS data}",
-        journal = {Submitted to \aap},
-        year = 2021,
+      journal = {arXiv e-prints},
+     keywords = {Astrophysics - Cosmology and Nongalactic Astrophysics},
+         year = 2022,
+        month = apr,
+          eid = {arXiv:2204.04798},
+        pages = {arXiv:2204.04798},
+archivePrefix = {arXiv},
+       eprint = {2204.04798},
+ primaryClass = {astro-ph.CO},
+       adsurl = {https://ui.adsabs.harvard.edu/abs/2022arXiv220404798G},
+      adsnote = {Provided by the SAO/NASA Astrophysics Data System}
 }
 
 @ARTICLE{harnois:15,
@@ -437,33 +462,33 @@ @ARTICLE{jarvis:04
       adsnote = {Provided by the SAO/NASA Astrophysics Data System}
 }
 
-@ARTICLE{jarvis:16, 
-   author = {{Jarvis}, M. and {Sheldon}, E. and {Zuntz}, J. and {Kacprzak}, T. and 
+@ARTICLE{jarvis:16,
+   author = {{Jarvis}, M. and {Sheldon}, E. and {Zuntz}, J. and {Kacprzak}, T. and
         {Bridle}, S.~L. and {Amara}, A. and {Armstrong}, R. and {Becker}, M.~R. and
         {Bernstein}, G.~M. and {Bonnett}, C. and {Chang}, C. and {Das}, R. and
-        {Dietrich}, J.~P. and {Drlica-Wagner}, A. and {Eifler}, T.~F. and 
+        {Dietrich}, J.~P. and {Drlica-Wagner}, A. and {Eifler}, T.~F. and
         {Gangkofner}, C. and {Gruen}, D. and {Hirsch}, M. and {Huff}, E.~M. and
-        {Jain}, B. and {Kent}, S. and {Kirk}, D. and {MacCrann}, N. and 
+        {Jain}, B. and {Kent}, S. and {Kirk}, D. and {MacCrann}, N. and
         {Melchior}, P. and {Plazas}, A.~A. and {Refregier}, A. and {Rowe}, B. and
-        {Rykoff}, E.~S. and {Samuroff}, S. and {S{\'a}nchez}, C. and 
-        {Suchyta}, E. and {Troxel}, M.~A. and {Vikram}, V. and {Abbott}, T. and 
+        {Rykoff}, E.~S. and {Samuroff}, S. and {S{\'a}nchez}, C. and
+        {Suchyta}, E. and {Troxel}, M.~A. and {Vikram}, V. and {Abbott}, T. and
         {Abdalla}, F.~B. and {Allam}, S. and {Annis}, J. and {Benoit-L{\'e}vy}, A. and
         {Bertin}, E. and {Brooks}, D. and {Buckley-Geer}, E. and {Burke}, D.~L. and
         {Capozzi}, D. and {Carnero Rosell}, A. and {Carrasco Kind}, M. and
-        {Carretero}, J. and {Castander}, F.~J. and {Clampitt}, J. and 
+        {Carretero}, J. and {Castander}, F.~J. and {Clampitt}, J. and
         {Crocce}, M. and {Cunha}, C.~E. and {D'Andrea}, C.~B. and {da Costa}, L.~N. and
-        {DePoy}, D.~L. and {Desai}, S. and {Diehl}, H.~T. and {Doel}, P. and  
+        {DePoy}, D.~L. and {Desai}, S. and {Diehl}, H.~T. and {Doel}, P. and
         {Fausti Neto}, A. and {Flaugher}, B. and {Fosalba}, P. and {Frieman}, J. and
-        {Gaztanaga}, E. and {Gerdes}, D.~W. and {Gruendl}, R.~A. and 
+        {Gaztanaga}, E. and {Gerdes}, D.~W. and {Gruendl}, R.~A. and
         {Gutierrez}, G. and {Honscheid}, K. and {James}, D.~J. and {Kuehn}, K. and
-        {Kuropatkin}, N. and {Lahav}, O. and {Li}, T.~S. and {Lima}, M. and 
+        {Kuropatkin}, N. and {Lahav}, O. and {Li}, T.~S. and {Lima}, M. and
         {March}, M. and {Martini}, P. and {Miquel}, R. and {Mohr}, J.~J. and
-        {Neilsen}, E. and {Nord}, B. and {Ogando}, R. and {Reil}, K. and  
+        {Neilsen}, E. and {Nord}, B. and {Ogando}, R. and {Reil}, K. and
         {Romer}, A.~K. and {Roodman}, A. and {Sako}, M. and {Sanchez}, E. and
         {Scarpine}, V. and {Schubnell}, M. and {Sevilla-Noarbe}, I. and
-        {Smith}, R.~C. and {Soares-Santos}, M. and {Sobreira}, F. and 
+        {Smith}, R.~C. and {Soares-Santos}, M. and {Sobreira}, F. and
         {Swanson}, M.~E.~C. and {Tarle}, G. and {Thaler}, J. and {Thomas}, D. and
-        {Walker}, A.~R. and {Wechsler}, R.~H.}, 
+        {Walker}, A.~R. and {Wechsler}, R.~H.},
     title = "{The DES Science Verification weak lensing shear catalogues}",
   journal = {\mnras},
 archivePrefix = "arXiv",
 
@@ -1,13 +1,14 @@
 # Understanding the API Documentation
 
-This page aims to help ShapePipe users and developers understand the
-Application Programming Interface (API) documentation.
-
 ```{note}
+:class: margin
 If you are already familiar with this type of documentation you can skip this
 page.
 ```
 
+This page aims to help ShapePipe users and developers understand the
+Application Programming Interface (API) documentation.
+
 ## What Are API Docs?
 
 The API documentation is designed to communicate in clear way what each class
@@ -18,19 +19,20 @@ with three double quotes `"""`) written in the code.
 
 ## Standard API Docs
 
+```{note}
+:class: margin
+If an optional argument does not explicitly specify the default parameter value
+then the user should expect that this means the default will be `None`, `''`,
+`[]`, etc. depending on the input data type.
+```
+
 All the classes/functions include a short description of what they do. This is
 followed by a `Parameters` section containing a bullet point list of the
 expected input arguments. For each parameter you will see in brackets the
 expected input type (e.g. `int`, `float`, `list`, etc.) followed by a brief
 description of what the argument is for. Parameters listed as *optional* in the
 brackets do not need to be provided and will default to some predefined value.
 
-```{note}
-If an optional argument does not explicitly specify the default parameter value
-then the user should expect that this means the default will be `None`, `''`,
-`[]`, etc. depending on the input data type.
-```
-
 For functions that return objects a `Returns` section will follow the
 `Parameters` section. This will provide a brief description of what is provided
 by this function. Following `Returns` you will always find `Return type`, which