Dev (#153)

* Changing to JSON schema draft/2020-12

* Docs

* Supporting Snakefile 9

Author: felixleopoldo

README.md

@@ -42,6 +42,7 @@ You may also have a look at [this Medium story](https://medium.com/@felixleopold
     pages = {1--43},
     doi = {10.18637/jss.v114.i12}
 }
+
 ```
 
 ## Contact

docs/render_alg_docs.py

@@ -162,7 +162,7 @@ def info_to_small_table():
                 tab += str2link(info["data_types"][i]) +", "
             tab = tab[:-2]
         else:
-            tab += "\-"        
+            tab += r"\-"
         tab += "\n"
 
         # MCMC:

docs/source/_static/IMG_784FC721EEEE-1.png

@@ -44,7 +44,8 @@
     'sphinx_last_updated_by_git',
     'versionwarning.extension',
     "sphinxext.opengraph",
-    "sphinxcontrib.googleanalytics"
+    "sphinxcontrib.googleanalytics",
+    "sphinxcontrib.youtube"
 ]
 googleanalytics_id = "G-CDYR88PWR3"
 

docs/source/conf.py

@@ -1,14 +1,27 @@
 Authors
 ################
 
+.. image:: _static/IMG_784FC721EEEE-1.png
+   :width: 250
+
 | `Felix Rios <https://felixleopoldo.github.io>`_
 | `Department of Paediatrics, Division of Biomedical Data Science <https://medicine.nus.edu.sg/sites/bids/people.html>`_
 | NUS Singapore
 
+
+
+.. image:: https://avatar.unibas.ch/image/236B4DEB-A2B0-47C4-BDA0-D9D46334F7E9
+   :width: 250
+
+
 | `Giusi Moffa <https://dmi.unibas.ch/en/persons/moffa-giusi/>`_
 | `Department of Mathematics and Computer Science <https://dmi.unibas.ch/en/>`_
 | University of Basel, Switzerland
 
+.. image:: https://bsse.ethz.ch/cbg/group/people/person-detail.person_image.jpeg?persid=MjA3Mjc0
+   :width: 250
+
+
 | `Jack Kuipers <https://bsse.ethz.ch/cbg/group/people/person-detail.MjA3Mjc0.TGlzdC81MTYsOTQ0ODM3Mzc2.html>`_
 | `Department of Biosystems Science and Eng. <https://bsse.ethz.ch/>`_
 | ETH Zürich, Switzerland
@@ -57,14 +70,16 @@ BibTeX entry for citing Benchpress:
 
 .. code:: bibtex
 
-  @misc{rios2021benchpress,
-      title={Benchpress: a scalable and versatile workflow for benchmarking structure learning algorithms for graphical models}, 
-      author={Felix L. Rios and Giusi Moffa and Jack Kuipers},
-      year={2021},
-      eprint={2107.03863},
-      archivePrefix={arXiv (to appear in the Journal of Statistical Software)},
-      primaryClass={stat.ML}
-  }
+    @Article{rios2025benchpress,
+        author = {Felix L. Rios and Giusi Moffa and Jack Kuipers},
+        title = {{Benchpress}: A Versatile Platform for Structure Learning in Causal and Probabilistic Graphical Models},
+        journal = {Journal of Statistical Software},
+        year = {2025},
+        volume = {114},
+        number = {12},
+        pages = {1--43},
+        doi = {10.18637/jss.v114.i12}
+    }
 
 .. footbibliography::
 

docs/source/dev_guide.rst

@@ -83,11 +83,17 @@ generated datasets, the workflow also includes a number of standard datasets and
 
 .. rubric:: See also
 
-* The paper :footcite:t:`rios2021benchpress` (to appear in the `Journal of Statistical Software <https://www.jstatsoft.org/index>`_)
+* The paper :footcite:t:`rios2025benchpress` (to appear in the `Journal of Statistical Software <https://www.jstatsoft.org/index>`_)
 * The `GitHub <https://github.com/felixleopoldo/benchpress>`_ repository
 * This `Medium story <https://medium.com/@felixleopoldorios/structure-learning-using-benchpress-826847db0aa8>`_
 * This video tutorial `UAI 2023 Tutorial: Structure Learning Using Benchpress - YouTube <https://www.youtube.com/watch?v=tx3hIH3b9Hg>`_
-* The `Discord <https://discord.gg/9zzPwMDW>`_ chat for any kind of discussions etc.
+
+.. * The `Discord <https://discord.gg/9zzPwMDW>`_ chat for any kind of discussions etc.
+
+
+..  youtube:: tx3hIH3b9Hg
+   :width: 640
+   :height: 480
 
 .. .. note::
 
@@ -96,6 +102,7 @@ generated datasets, the workflow also includes a number of standard datasets and
 
 .. rubric:: News
 
+* 2025-09-10: Benchpress 2.13.0. This version supports `Snakemake 9 <https://snakemake.readthedocs.io/en/stable/>`_.
 * 2024-12-26: Benchpress 2.12.0. This version introduces the :ref:`pyagrum` module, providing access to the `pyAgrum <https://agrum.gitlab.io/>`_ library's structure learning capabilities for discrete valued Bayesian networks. 
 * 2024-12-16: Benchpress 2.11.0. This version introduces the :ref:`bips_tpc` module, based on the temporal PC (`tPC <https://github.com/bips-hb/tpc>`_) and the `micd <https://github.com/bips-hb/micd>`_ package. It enables causal discovery through the PC algorithm allowing for :ref:`edge_constraints`, mixed data, and missing data handling. Thanks `Leibniz-Institut für Präventionsforschung und Epidemiologie – (BIPS GmbH)  <https://github.com/bips-hb>`_. 
 * 2024-11-30: Benchpress 2.10.0. This version includes algorithms from the `missing value PC (MVPC) <https://github.com/TURuibo/MVPC>`_ package for sampling data with missing values (:ref:`mvpc_gen_data`) and causal discovery (:ref:`mvpc`) in the presence of missing values.

docs/source/index.rst

@@ -116,7 +116,7 @@ Start an interactive `Docker <https://www.docker.com/>`_ container (based on the
 
 .. prompt:: bash
 
-    docker run -it -w /mnt --privileged -v /absolute/path/to/benchpress:/mnt bpimages/snakemake:v8.11.6
+    docker run -it -w /mnt --privileged -v /absolute/path/to/benchpress:/mnt bpimages/snakemake:9.7.1
 
 Depending on your system, you may have to prepend the above command by *sudo*. 
 On Windows, you may have to escape spaces in the benchpress path using ^ or \`.

docs/source/installation.rst

@@ -18,7 +18,7 @@ bin_bn
    * - Docs
      - 
    * - Paper
-     - :footcite:t:`rios2021benchpress`
+     - :footcite:t:`rios2025benchpress`
    * - Graph type
      - `DAG <https://en.wikipedia.org/wiki/Directed_acyclic_graph>`__
    * - Docker 

docs/source/parameters/bin_bn.rst

@@ -18,7 +18,7 @@ sem_params
    * - Docs
      - 
    * - Paper
-     - :footcite:t:`rios2021benchpress`
+     - :footcite:t:`rios2025benchpress`
    * - Graph type
      - `DAG <https://en.wikipedia.org/wiki/Directed_acyclic_graph>`__
    * - Docker 

docs/source/parameters/sem_params.rst

@@ -10,4 +10,5 @@ requests
 sphinx-version-warning
 sphinx-last-updated-by-git
 sphinxcontrib-googleanalytics==0.4
-sphinxext-opengraph
+sphinxext-opengraph
+sphinxcontrib-youtube