Merge pull request #582 from ICB-DCM/develop

Release 0.12.6
ICB-DCM · Aug 30, 2022 · b44299e · b44299e
2 parents b077f5a + 82fa78d
commit b44299e
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diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -8,6 +8,17 @@ Release Notes
 ...........
 
 
+0.12.6 (2022-08-30)
+-------------------
+
+Minor:
+
+* Add JOSS paper of version 0.12.5
+* Update Julia reference DiffEqJump -> JumpProcesses (name change)
+* Unfix jinja2
+* Update flake8 dependencies after new issues
+
+
 0.12.5 (2022-06-21)
 -------------------
 

diff --git a/doc/conf.py b/doc/conf.py
@@ -29,19 +29,26 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
+    # include documentation from docstrings
     'sphinx.ext.autodoc',
+    # generate autodoc summaries
+    'sphinx.ext.autosummary',
+    # use mathjax for latex formulas
     'sphinx.ext.mathjax',
     # link to code
     'sphinx.ext.viewcode',
     # link to other projects' docs
     'sphinx.ext.intersphinx',
+    # support numpy and google style docstrings
     'sphinx.ext.napoleon',
+    # support todo items
     'sphinx.ext.todo',
+    # test snippets in the documentation
     'sphinx.ext.doctest',
+    # source parser for jupyter notebook files
     'nbsphinx',
     # code highlighting in jupyter cells
     'IPython.sphinxext.ipython_console_highlighting',
-    'sphinx.ext.autosummary',
 ]
 
 # default autodoc options

diff --git a/doc/examples/model_julia/SIR.jl b/doc/examples/model_julia/SIR.jl
@@ -5,7 +5,7 @@ module SIR
 # Install dependencies
 using Pkg
 Pkg.add("Catalyst")
-Pkg.add("DiffEqJump")
+Pkg.add("JumpProcesses")
 
 # Define reaction network
 using Catalyst
@@ -24,7 +24,7 @@ tspan = (0.0, 250.0)
 prob  = DiscreteProblem(sir_model, u0, tspan, p)
 
 # formulate as Markov jump process
-using DiffEqJump
+using JumpProcesses
 jump_prob = JumpProblem(
     sir_model, prob, Direct(), save_positions=(false, false),
 )

diff --git a/doc/examples/using_julia.ipynb b/doc/examples/using_julia.ipynb
@@ -65,8 +65,8 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "CPU times: user 1min 28s, sys: 3.97 s, total: 1min 32s\n",
-      "Wall time: 1min 34s\n"
+      "CPU times: user 33.7 s, sys: 1.46 s, total: 35.1 s\n",
+      "Wall time: 34.9 s\n"
      ]
     }
    ],
@@ -501,7 +501,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.7"
+   "version": "3.10.4"
   }
  },
  "nbformat": 4,

diff --git a/doc/joss_0_12/concept.pdf b/doc/joss_0_12/concept.pdf