doc: Restructure sphinx doc (#638)

* Create separate top-level categories for PEtab v1 and PEtab v2
* Move tutorial to v1 to accommodate a v2 tutorial (#627)
* Fix license formatting
* Update links

Author: dweindl

README.md

@@ -50,17 +50,17 @@ A wide range of PEtab examples can be found in the systems biology parameter est
 ## PEtab support in systems biology tools
 
 For a list of tools supporting PEtab, see the
-[PEtab website](https://petab.readthedocs.io/en/latest/software_support.html).
+[software support page](https://petab.readthedocs.io/en/latest/v1/software_support.html).
 
 
 ## Using PEtab
 
 If you would like to use PEtab yourself, please have a look at:
 
-* [a PEtab tutorial](https://petab.readthedocs.io/en/latest/tutorial.html)
+* [a PEtab tutorial](https://petab.readthedocs.io/en/latest/v1/tutorial/tutorial.html)
   going through the individual steps of setting up a parameter estimation
   problem in PEtab, independently of any specific software
-* [the PEtab format reference](https://petab.readthedocs.io/en/latest/documentation_data_format.html)
+* [the PEtab format reference](https://petab.readthedocs.io/en/latest/v1/documentation_data_format.html)
 * the example models provided in the
   [benchmark collection](https://github.com/Benchmarking-Initiative/Benchmark-Models-PEtab).
 * the tutorials provided with each of the softwares supporting PEtab

doc/compile_tutorial.sh

@@ -2,8 +2,8 @@
 
 # Build a pdflatex document from the tutorial
 
-pandoc tutorial.rst \
-    -o tutorial.pdf \
+pandoc v1/tutorial/tutorial.rst \
+    -o tutorial_v1.pdf \
     -V geometry:margin=1.5in -V geometry:a4paper -V fontsize=10pt \
     -V urlcolor=cyan \
     --toc \

doc/index.rst

@@ -3,22 +3,28 @@
 
 .. toctree::
    :maxdepth: 3
-   :caption: Data format
+   :caption: PEtab v1
 
    PEtab v1 specs <v1/documentation_data_format.rst>
+   v1/tutorial/tutorial
+   v1/software_support
+
+
+.. toctree::
+   :maxdepth: 3
+   :caption: PEtab v2
+
    PEtab v2 draft <v2/documentation_data_format.rst>
-   tutorial
 
 .. toctree::
    :maxdepth: 2
    :caption: About
 
-   software_support
    Development <development>
    how_to_cite
    license
    editorial_board
-   logo/LICENSE.md
+   Logo <logo/LICENSE.md>
 
 
 Indices and tables

doc/license.rst

@@ -2,3 +2,4 @@ License
 =======
 
 .. literalinclude:: ../LICENSE
+   :language: text

doc/src/update_tables.py

@@ -16,7 +16,7 @@
         },
     },
     "Tool support": {
-        "target": doc_dir / "software_support.rst",
+        "target": doc_dir / "v1" / "software_support.rst",
         "options": {
             "header-rows": "1",
         },