Doc execute tuto_simul_cbox.md

snek5000 · Oct 21, 2022 · 2f72afb · 2f72afb
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diff --git a/docs/conf.py b/docs/conf.py
@@ -112,6 +112,7 @@ def root(module):
     ".rst": "restructuredtext",
     ".ipynb": "myst-nb",
     ".myst": "myst-nb",
+    ".md": "myst-nb",
 }
 
 # Execute Doxygen
@@ -189,7 +190,12 @@ def root(module):
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path.
-exclude_patterns = ["_build", "Thumbs.db", ".DS_Store", "examples/snek5000-*/README.md"]
+exclude_patterns = [
+    "_build",
+    "Thumbs.db",
+    ".DS_Store",
+    "examples/snek5000-*/README.md",
+]
 
 # -- Options for HTML output -------------------------------------------------
 
@@ -282,3 +288,20 @@ def autodoc_skip_member(app, what, name, obj, skip, options):
 
 def setup(app):
     app.connect("autodoc-skip-member", autodoc_skip_member)
+
+
+myst_enable_extensions = [
+    "amsmath",
+    "colon_fence",
+    "deflist",
+    "dollarmath",
+    "fieldlist",
+    "html_admonition",
+    "html_image",
+    "linkify",
+    "replacements",
+    "smartquotes",
+    "strikethrough",
+    "substitution",
+    "tasklist",
+]
diff --git a/docs/examples/snek5000-canonical/src/snek5000_canonical/__init__.py b/docs/examples/snek5000-canonical/src/snek5000_canonical/__init__.py
@@ -1,4 +1,3 @@
-
 from .solver import Simul
 from .output import Output
 

diff --git a/docs/examples/snek5000-canonical/src/snek5000_canonical/solver.py b/docs/examples/snek5000-canonical/src/snek5000_canonical/solver.py
@@ -1,5 +1,6 @@
 from snek5000.info import InfoSolverMake
 from snek5000.solvers.base import SimulNek
+
 # To use KTH Framework import SimulKTH instead
 # from snek5000.solvers.kth import SimulKTH
 

diff --git a/docs/examples/snek5000-tgv/src/snek5000_tgv/__init__.py b/docs/examples/snek5000-tgv/src/snek5000_tgv/__init__.py
@@ -1,4 +1,3 @@
-
 from .solver import Simul
 from .output import Output
 

diff --git a/docs/examples/snek5000-tgv/src/snek5000_tgv/output.py b/docs/examples/snek5000-tgv/src/snek5000_tgv/output.py
@@ -22,4 +22,5 @@ def post_init(self):
             self.write_size(size)
             self.write_makefile_usr(makefile_usr)
 
+
 Output = OutputTGV
diff --git a/docs/tuto_simul_cbox.md b/docs/tuto_simul_cbox.md
@@ -1,15 +1,10 @@
 ---
-jupyter:
-  jupytext:
-    text_representation:
-      extension: .md
-      format_name: markdown
-      format_version: '1.3'
-      jupytext_version: 1.14.1
-  kernelspec:
-    display_name: Python 3.9.13 ('env-snek')
-    language: python
-    name: python3
+jupytext:
+  text_representation:
+    format_name: myst
+kernelspec:
+  display_name: Python 3
+  name: python3
 ---
 
 <!-- #region tags=[] -->
@@ -19,10 +14,9 @@ jupyter:
 
 ## Initialize and setup simulation parameters
 
+This example is based on [this study](https://www.cambridge.org/core/journals/journal-of-fluid-mechanics/article/abs/from-onset-of-unsteadiness-to-chaos-in-a-differentially-heated-square-cavity/617F4CB2C23DD74C3D0CB872AE7C0045). The configuration is a square cavity. The control parameters are Prandtl $= 0.71$ and Rayleigh $= 1.86 \times 10^{8}$. The mesh size is $64 \times 64$. We want to have $25$ probes (history points) to record the variable signals. We will use these probe signals in monitoring and postprocessing of the simulation. See [this example](https://github.com/snek5000/snek5000-cbox/blob/gh-actions/doc/examples/run_side_short.py) for the implementation. The simulation was executed as follows:
 
-This example is based on [this study](https://www.cambridge.org/core/journals/journal-of-fluid-mechanics/article/abs/from-onset-of-unsteadiness-to-chaos-in-a-differentially-heated-square-cavity/617F4CB2C23DD74C3D0CB872AE7C0045). The configuration is a square cavity. The contol parameters are Prandtl $= 0.71$ and Rayleigh $= 1.86 \times 10^{8}$. The mesh size is $64 \times 64$. We want to have $25$ probes (history points) to record the variable signals. We will use these probe signals in monitoring and postprocessing of the simulation. See [this example](https://github.com/snek5000/snek5000-cbox/blob/gh-actions/doc/examples/run_side_short.py) for the implementation. The simulation was executed as follows:
-
-```py
+```{code-cell}
 import numpy as np
 
 from snek5000_cbox.solver import Simul

diff --git a/docs/tutorials.rst b/docs/tutorials.rst
@@ -22,6 +22,6 @@ Tutorials
     ipynb/executed/tuto_load_print_stdout
 
 .. toctree::
-    :caption: Packaging
+    :caption: Create your own Snek5000 solver
 
-    packaging 
+    packaging
diff --git a/setup.cfg b/setup.cfg
@@ -58,6 +58,7 @@ docs =
     nbdime
     # https://github.com/sphinx-doc/sphinx/issues/8198
     pygments >= 2.4.1
+    linkify-it-py
 
 tests =
     pytest
Original file line number	Diff line number	Diff line change
		@@ -1,4 +1,3 @@

		from .solver import Simul
		from .output import Output

Expand Down
Original file line number	Diff line number	Diff line change
Expand Up		@@ -22,4 +22,5 @@ def post_init(self):
		self.write_size(size)
		self.write_makefile_usr(makefile_usr)


		Output = OutputTGV
-Original file line number
+Diff line change
@@ Expand Up / @@ -58,6 +58,7 @@ docs = @@
         nbdime
         # https://github.com/sphinx-doc/sphinx/issues/8198
         pygments >= 2.4.1
+        linkify-it-py
     tests =
         pytest
@@ Expand Down @@