Improve doc (no graphviz) (and fix readthedocs build?)

.readthedocs.yml

@@ -8,7 +8,7 @@ build:
     - build-essential
     - gfortran
     - libopenmpi-dev
-    - graphviz
+    # - graphviz
   jobs:
     pre_install:
       - git clone --depth=1 https://github.com/snek5000/Nek5000.git /home/docs/Nek5000

docs/Makefile

@@ -44,4 +44,4 @@ cleanall: clean
 	@rm -rf _generated/*
 
 format:
-	mdformat --wrap 88 *.md
+	mdformat --wrap 88 .

docs/how-to/index.md

@@ -8,6 +8,7 @@ maxdepth: 1
 ---
 restart.md
 history_points.md
+snek-make.md
 ```
 
 ## For developer of Snek5000 solvers

docs/how-to/restart.md

@@ -27,8 +27,8 @@ Moreover, there are with Nek5000 two different methods to restart a simulation:
    toolbox).
 
 With Snek5000, restarting can be done with the command line `snek-restart` (recommanded)
-or with a Python function {func}`snek5000.load_for_restart`. In this page, with
-focus on the former method.
+or with a Python function {func}`snek5000.load_for_restart`. In this page, with focus on
+the former method.
 
 One can get the documentation of the command with
 

docs/how-to/snek-make.md

@@ -0,0 +1,34 @@
+---
+jupytext:
+  formats: ipynb,md:myst
+  text_representation:
+    extension: .md
+    format_name: myst
+    format_version: 0.13
+    jupytext_version: 1.14.1
+kernelspec:
+  display_name: Python 3 (ipykernel)
+  language: python
+  name: python3
+---
+
+# How to execute Snakemake commands from a directory
+
+Sometimes, it can be useful to execute the Snakemake targets without Python coding from
+the directory of a simulation. Calling directly Snakemake can be slightly difficult so
+there is a Snek5000 command, `snek-make`, for this task. The help of this function can
+be obtained with (the `!` is for calling a command in Jupyter):
+
+```{code-cell} ipython3
+!snek-make -h
+```
+
+From a simulation directory, `snek-make -l` lists the available targets. One can do for
+example:
+
+```bash
+snek-make cleanall
+snek-make compile
+snek-make show_config
+snek-make run_fg
+```