doc: fix paths, formatting, typos (#2674)

Author: dweindl

README.md

@@ -128,23 +128,25 @@ There is a list of [publications using AMICI](https://amici.readthedocs.io/en/la
 If you used AMICI in your work, we are happy to include
 your project, please let us know via a GitHub issue.
 
-When using AMICI in your project, please cite
+When using AMICI in your project, please cite:
+
 * Fröhlich, F., Weindl, D., Schälte, Y., Pathirana, D., Paszkowski, Ł., Lines, G.T., Stapor, P. and Hasenauer, J., 2021.
   AMICI: High-Performance Sensitivity Analysis for Large Ordinary Differential Equation Models. Bioinformatics, btab227,
   [DOI:10.1093/bioinformatics/btab227](https://doi.org/10.1093/bioinformatics/btab227).
-```
-@article{frohlich2020amici,
-  title={AMICI: High-Performance Sensitivity Analysis for Large Ordinary Differential Equation Models},
-  author={Fr{\"o}hlich, Fabian and Weindl, Daniel and Sch{\"a}lte, Yannik and Pathirana, Dilan and Paszkowski, {\L}ukasz and Lines, Glenn Terje and Stapor, Paul and Hasenauer, Jan},
-  journal = {Bioinformatics},
-  year = {2021},
-  month = {04},
-  issn = {1367-4803},
-  doi = {10.1093/bioinformatics/btab227},
-  note = {btab227},
-  eprint = {https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btab227/36866220/btab227.pdf},
-}
-```
+
+  ```bibtex
+  @article{frohlich2020amici,
+    title={AMICI: High-Performance Sensitivity Analysis for Large Ordinary Differential Equation Models},
+    author={Fr{\"o}hlich, Fabian and Weindl, Daniel and Sch{\"a}lte, Yannik and Pathirana, Dilan and Paszkowski, {\L}ukasz and Lines, Glenn Terje and Stapor, Paul and Hasenauer, Jan},
+    journal = {Bioinformatics},
+    year = {2021},
+    month = {04},
+    issn = {1367-4803},
+    doi = {10.1093/bioinformatics/btab227},
+    note = {btab227},
+    eprint = {https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btab227/36866220/btab227.pdf},
+  }
+  ```
 
 When presenting work that employs AMICI, feel free to use one of the icons in
 [doc/gfx/](https://github.com/AMICI-dev/AMICI/tree/master/doc/gfx),

doc/background.rst

@@ -52,13 +52,13 @@ publications:
 .. note::
 
    Implementation details of the latest AMICI versions may differ from the ones
-   given in the references manuscripts.
+   given in the referenced manuscripts.
 
 
 Third-Party numerical algorithms used by AMICI
 ----------------------------------------------
 
-AMICI uses the following packages from SUNDIALS:
+AMICI uses the following packages from `SUNDIALS <https://computing.llnl.gov/projects/sundials>`__:
 
 * CVODES:
 
@@ -70,7 +70,7 @@ AMICI uses the following packages from SUNDIALS:
 
 * IDAS
 
-AMICI uses the following packages from SuiteSparse:
+AMICI uses the following packages from `SuiteSparse <https://github.com/DrTimothyAldenDavis/SuiteSparse>`__:
 
 * Algorithm 907: **KLU** A Direct Sparse Solver for Circuit Simulation
   Problems. Timothy A. Davis, Ekanathan Palamadai Natarajan,

doc/how_to_cite.rst

@@ -32,12 +32,12 @@ When using AMICI in your project, please cite
      }
 
 When presenting work that employs AMICI, feel free to use one of the icons in
-`documentation/gfx/ <https://github.com/AMICI-dev/AMICI/tree/master/documentation/gfx>`_,
+`documentation/gfx/ <https://github.com/AMICI-dev/AMICI/tree/master/doc/gfx>`_,
 which are available under a
-`CC0 <https://github.com/AMICI-dev/AMICI/tree/master/documentation/gfx/LICENSE.md>`_
+`CC0 <https://github.com/AMICI-dev/AMICI/tree/master/doc/gfx/LICENSE.md>`_
 license:
 
-.. image:: https://raw.githubusercontent.com/AMICI-dev/AMICI/master/documentation/gfx/logo_text.png
-   :target: https://raw.githubusercontent.com/AMICI-dev/AMICI/master/documentation/gfx/logo_text.png
+.. image:: https://raw.githubusercontent.com/AMICI-dev/AMICI/master/doc/gfx/logo_text.png
+   :target: https://raw.githubusercontent.com/AMICI-dev/AMICI/master/doc/gfx/logo_text.png
    :height: 75
    :alt: AMICI LOGO