Summer 2022 Patch Release v1.0.1 (#581)

* added CD GitHub action * fixed bug in RunLog class (#548) * 800deg2 (#544) * added config files for matching 800deg2 survey * Added Xavier as contributor; match external catalogue fix * match 800 * match_ext: output distance * match_ext output_dist def value * Tutorial documentation (#543) * updating job script and tutorial * tutorial; fix config file * tutorial finished * no change * psfex update (minor bug) * psfex running * updated MCCD config files * comment in config file * config file fix for MCCD * config file fix for MCCD * removed unused option in usage str * Update docs/source/pipeline_tutorial.md Co-authored-by: Samuel Farrens <[email protected]> * improved tutorial according to PR review * Update docs/source/pipeline_tutorial.md Co-authored-by: Samuel Farrens <[email protected]> * tutorial clean-up * post_proc cleaned up; tutorial added output dir names * changes to tutorial, post-proc and mccd plot doc * get_images error msg testing * Update docs/source/pipeline_tutorial.md Co-authored-by: Samuel Farrens <[email protected]> * Update docs/source/pipeline_tutorial.md Co-authored-by: Samuel Farrens <[email protected]> * Update docs/source/pipeline_tutorial.md Co-authored-by: Samuel Farrens <[email protected]> * Update docs/source/pipeline_tutorial.md Co-authored-by: Samuel Farrens <[email protected]> * removed prompt from bash example * Update docs/source/post_processing.md Co-authored-by: Samuel Farrens <[email protected]> * PR review changes to doc * PR review changes to doc * Update docs/source/post_processing.md Co-authored-by: Samuel Farrens <[email protected]> Co-authored-by: Samuel Farrens <[email protected]> * added contribution guidelines (#550) * added contribution guidelines * Update CODE_OF_CONDUCT.md * tutorial bugfixes (#552) Co-authored-by: Lucie Baumont <[email protected]> * removed pep8 error exceptions (#554) * Understanding the API docs (#553) * added md for understanding the api docs * updates following reviwer comments * Update package versions (#539) * updated doc-tests * updated package versions * pin documentation packages * updated ShapePipe version and cleaned up * Config file clean up (#556) * Removed unused config files in example/cfis * Removed obsolete config dirs tutorial and ps3pi_cfis * removed old unions config files * Update docs/source/configuration.md Co-authored-by: Martin Kilbinger <[email protected]> * final clean up * removed obsolete distance-based overlap region flagging * removed errornous mccd_interp_runner call * Added Tobias' MCCD plot config file to validate joint cat * Added Tobias' MCCD plot config file to validate joint cat * removed duplicate config file * Random catalogue improvements (#570) * merge_final script: added option for additional tile ID path to select tiles; clean-up * typo in doc string * Updated docs and references (#579) * updated docs and references * Update docs/source/module_develop.md Co-authored-by: Martin Kilbinger <[email protected]> Co-authored-by: Martin Kilbinger <[email protected]> * Random runner updates (#573) * merge_final script: added option for additional tile ID path to select tiles; clean-up * typo in doc string * started to implement healpix mask output * healpix options for random/mask * Update shapepipe/modules/random_cat_package/random_cat.py Co-authored-by: Samuel Farrens <[email protected]> * Update shapepipe/modules/random_cat_package/random_cat.py Co-authored-by: Samuel Farrens <[email protected]> * Update shapepipe/modules/random_cat_package/random_cat.py Co-authored-by: Samuel Farrens <[email protected]> * Update shapepipe/modules/random_cat_package/random_cat.py Co-authored-by: Samuel Farrens <[email protected]> * Modifications for PR review * comments from PR review Co-authored-by: Samuel Farrens <[email protected]> * added masking for NGC objects (#575) * added masking for NGC objects * debugging ngc np binary file * Fixed bugs in new mask handling (input FITS files) * debug info to log file for checking existing images * mask: combined dso masks into dictionary * PR edits * Update shapepipe/modules/mask_package/mask.py Co-authored-by: Samuel Farrens <[email protected]> * Update shapepipe/modules/mask_package/mask.py Co-authored-by: Samuel Farrens <[email protected]> * Update shapepipe/modules/mask_package/mask.py Co-authored-by: Samuel Farrens <[email protected]> * Update shapepipe/modules/mask_package/mask.py Co-authored-by: Samuel Farrens <[email protected]> * added symlink * Update shapepipe/pipeline/file_io.py Co-authored-by: Samuel Farrens <[email protected]> * Update shapepipe/modules/mask_package/mask.py Co-authored-by: Samuel Farrens <[email protected]> * Update shapepipe/pipeline/file_io.py Co-authored-by: Samuel Farrens <[email protected]> * Update shapepipe/pipeline/file_io.py Co-authored-by: Samuel Farrens <[email protected]> * Update shapepipe/pipeline/file_io.py Co-authored-by: Samuel Farrens <[email protected]> * Update shapepipe/pipeline/file_io.py Co-authored-by: Samuel Farrens <[email protected]> * Update shapepipe/modules/mask_package/mask.py Co-authored-by: Samuel Farrens <[email protected]> * Update shapepipe/modules/mask_package/mask.py Co-authored-by: Samuel Farrens <[email protected]> * Update shapepipe/modules/mask_package/mask.py Co-authored-by: Samuel Farrens <[email protected]> * Update shapepipe/pipeline/file_io.py Co-authored-by: Samuel Farrens <[email protected]> * PR suggestions Co-authored-by: Samuel Farrens <[email protected]> * update patch version Co-authored-by: Martin Kilbinger <[email protected]> Co-authored-by: Lucie Baumont <[email protected]> Co-authored-by: Lucie Baumont <[email protected]> Co-authored-by: Tobias Liaudat <[email protected]>
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diff --git a/docs/source/about.md b/docs/source/about.md
@@ -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`.
diff --git a/docs/source/basic_execution.md b/docs/source/basic_execution.md
@@ -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).
 

diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -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'
diff --git a/docs/source/contributors.md b/docs/source/contributors.md
@@ -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

diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -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/
diff --git a/docs/source/installation.md b/docs/source/installation.md
@@ -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 [email protected]: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 .
 ```

diff --git a/docs/source/module_develop.md b/docs/source/module_develop.md
@@ -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:
 

diff --git a/docs/source/refs.bib b/docs/source/refs.bib
@@ -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",

diff --git a/docs/source/understanding_api.md b/docs/source/understanding_api.md
@@ -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