update tools

Dockerfile

@@ -133,9 +133,9 @@ RUN AUTO_UPDATE=1 conda install --no-update-deps  -y  \
 # Tier 2: tools with regular updates (2-4/year)
 RUN AUTO_UPDATE=1 conda install --no-update-deps -y \
         -c daemontus \
-        biodivine_aeon=1.2.0=py311h9bf148f_0 \
+        biodivine_aeon=1.2.3=py311h9bf148f_0 \
         maboss=2.6.0=he9e06a5_1 \
-        pyboolnet=3.0.14=py311_0 \
+        pyboolnet=3.0.16=py311_0 \
     && conda clean -y --all && rm -rf /opt/conda/pkgs
 
 # Tier 3: tools with frequent updates (>4/year) or lightweight with thin dependencies
@@ -144,12 +144,12 @@ RUN AUTO_UPDATE=1 conda install --no-update-deps -y \
         algorecell_types=1.0=py_0 \
         bns-python=0.2=py_0 \
         bonesis=0.6.7=py_0 \
-        boon=1.26=py_0 \
+        boon=1.28=py_0 \
         boolsim-python=0.5=py_0 \
         cabean-python=1.0=py_0 \
         caspo-control=1.0=py_0 \
         casq=1.3.3=pyhd8ed1ab_0 \
-        colomoto_jupyter=0.8.9=py_0 \
+        colomoto_jupyter=0.8.11=py_0 \
         ginsim-python=0.4.5=py_0 \
         mpbn=3.8=py_0 \
         nordic=2.5.0=py_0 \

docs/_toc.yml

@@ -76,6 +76,9 @@ parts:
   - file: tools/pyboolnet
     sections:
     - glob: tutorials/[pP][yY][bB][oO][oO][lL][nN][eE][tT]/*
+  - file: tools/pydruglogics
+    sections:
+    - glob: tutorials/[pP][yY][dD][rR][uU][gG][lL][oO][gG][iI][cC][sS]/*
   - file: tools/pystablemotifs
     sections:
     - glob: tutorials/[pP][yY][sS][tT][aA][bB][lL][eE][mM][oO][tT][iI][fF][sS]/*

hooks/release_changes.json

@@ -124,6 +124,11 @@
         "description": "Generation, modification and analysis of Boolean networks",
         "release_url": "https://github.com/hklarner/PyBoolNet/releases/tag/v{}"
     },
+    "pydruglogics": {
+        "name": "PyDrugLogics",
+        "description": "Construct, optimize Boolean Models and perform in-silico perturbations of the models",
+        "release_url": "https://github.com/druglogics/pydruglogics/releases/tag/v{}"
+    },
     "pymaboss": {
         "name": "PyMaBoSS",
         "description": "Python interface to MaBoSS",

tools/index.md

@@ -25,6 +25,7 @@ The CoLoMoTo Docker image provides access to the following softwares:
 | NuSMV | http://nusmv.fbk.eu | Symbolic model-checker | Python module [`nusmv`](https://github.com/colomoto/colomoto-jupyter) |
 | Pint | https://loicpauleve.name/pint | Static analyzer for dynamics of Automata Networks | Python module [`pypint`](https://github.com/pauleve/pypint) |
 | PyBoolNet | https://github.com/hklarner/PyBoolNet | Generation, modification and analysis of Boolean networks | Python module [`PyBoolNet`](https://github.com/hklarner/PyBoolNet) |
+| PyDrugLogics | https://druglogics.github.io/pydruglogics/ | Construct, optimize Boolean Models and perform in-silico perturbations of the models | Python module [`pydruglogics`](https://druglogics.github.io/pydruglogics/api.html) |
 | pyStableMotifs | https://github.com/jcrozum/pystablemotifs | Target-control of Boolean networks | Python module [`pystablemotifs`](https://github.com/jcrozum/pystablemotifs) |
 | R-BoolNet | https://cran.r-project.org/package=BoolNet | Analysis and reconstruction of Boolean networks dynamics | RPY2 python interface |
 | scBoolSeq | https://github.com/bnediction/scBoolSeq | scRNA-Seq data binarisation and synthetic generation from Boolean dynamics | Python module [`scboolseq`](https://github.com/bnediction/scBoolSeq) |