Bugfix broken links reported by check-docs (#56)

* Remove broken link to SRSchur MATLAB code.

* Replace link to Jan Brandts publication by link to preprint.

* Remove Brandts link in references.rst.

Author: msmdev

README.rst

@@ -139,7 +139,7 @@ for the longstanding and productive collaboration in the field of Markov modelin
 M. Weber, together with Susanna Röblitz and K. Fackeldey, had the original idea to employ Schur
 vectors instead of eigenvectors in the coarse-graining of non-reversible transition matrices. |br|
 Further, we would like to thank `Fabian Paul`_ for valuable discussions regarding the sorting of Schur vectors and his
-effort to translate the original sorting routine for real Schur forms, `SRSchur`_ published by `Jan Brandts`_,
+effort to translate the original sorting routine for real Schur forms, SRSchur published by `Jan Brandts`_,
 from MATLAB into `Python code`_,
 M. Weber and `Alexander Sikorski`_ for pointing us to `SLEPc`_ for sorted partial Schur decompositions,
 and A. Sikorski for supplying us with an `code example`_ and guidance how to interface SLEPc in Python.
@@ -152,8 +152,7 @@ Further, utility functions found in `pygpcca/utils/_utils.py`_ originate from MS
 .. _`CMD`: https://www.zib.de/numeric/cmd
 .. _`ZIB`: https://www.zib.de/
 .. _`Fabian Paul`: https://github.com/fabian-paul
-.. _`SRSchur`: http://m2matlabdb.ma.tum.de/SRSchur.m?MP_ID=119
-.. _`Jan Brandts`: https://doi.org/10.1002/nla.274
+.. _`Jan Brandts`: https://www.math.uu.nl/publications/preprints/1180.pdf
 .. _`Python code`: https://gist.github.com/fabian-paul/14679b43ed27aa25fdb8a2e8f021bad5
 .. _`Alexander Sikorski`: https://www.zib.de/members/sikorski
 .. _`SLEPc`: https://slepc.upv.es/

docs/source/acknowledgments.rst

@@ -5,7 +5,7 @@ for the longstanding and productive collaboration in the field of Markov modelin
 M. Weber, together with Susanna Röblitz and K. Fackeldey, had the original idea to employ Schur
 vectors instead of eigenvectors in the coarse-graining of non-reversible transition matrices.
 Further, we would like to thank `Fabian Paul`_ for valuable discussions regarding the sorting of Schur vectors and his
-effort to translate the original sorting routine for real Schur forms, `SRSchur`_ published by `Jan Brandts`_,
+effort to translate the original sorting routine for real Schur forms, SRSchur published by `Jan Brandts`_,
 from MATLAB into `Python code`_,
 M. Weber and `Alexander Sikorski`_ for pointing us to `SLEPc`_ for sorted partial Schur decompositions,
 and A. Sikorski for supplying us with an `code example`_ and guidance how to interface SLEPc in Python.
@@ -18,8 +18,7 @@ Further, utility functions found in `pygpcca/utils/_utils.py`_ originate from MS
 .. _`CMD`: https://www.zib.de/numeric/cmd
 .. _`ZIB`: https://www.zib.de/
 .. _`Fabian Paul`: https://github.com/fabian-paul
-.. _`SRSchur`: http://m2matlabdb.ma.tum.de/SRSchur.m?MP_ID=119
-.. _`Jan Brandts`: https://doi.org/10.1002/nla.274
+.. _`Jan Brandts`: https://www.math.uu.nl/publications/preprints/1180.pdf
 .. _`Python code`: https://gist.github.com/fabian-paul/14679b43ed27aa25fdb8a2e8f021bad5
 .. _`Alexander Sikorski`: https://www.zib.de/members/sikorski
 .. _`SLEPc`: https://slepc.upv.es/

docs/source/installation.rst

@@ -15,7 +15,7 @@ Conda
 This is the recommended way of installing, since this package also includes `PETSc`_/`SLEPc`_ libraries.
 We use `PETSc`_/`SLEPc`_ internally to speed up the computation of the leading Schur vectors. These are optional
 dependencies - if they're not present, we compute a full Schur decomposition instead and sort it using the method
-introduced by `Brandts (2002)`_. Note that this scales cubically in sample number, making it essential to use
+introduced by `Brandts (2001)`_. Note that this scales cubically in sample number, making it essential to use
 `PETSc`_/`SLEPc`_ for large sample numbers. `PETSc`_/`SLEPc`_ implement iterative methods to only compute
 the leading Schur vectors, which is computationally much less expensive.
 
@@ -86,7 +86,7 @@ The installation steps can be roughly outlined as::
     # install slepc4py
     pip install --user petsc4py
 
-.. _`Brandts (2002)`: https://doi.org/10.1002/nla.274
+.. _`Brandts (2001)`: https://www.math.uu.nl/publications/preprints/1180.pdf
 .. _`PETSc`: https://www.mcs.anl.gov/petsc/
 .. _`SLEPc`: https://slepc.upv.es/
 .. _`PETSc installation guide`: https://www.mcs.anl.gov/petsc/documentation/installation.html

docs/source/references.rst

@@ -19,9 +19,8 @@ References
 
 .. [Brandts02]
     Jan H. Brandts, |br|
-    *Matlab code for sorting real Schur forms*, |br|
+    *Matlab ode for sorting real Schur forms*, |br|
     Numerical Linear Algebra with Applications, 9(3):249-261, 2002.
-    `doi:10.1002/nla.274 <https://doi.org/10.1002/nla.274>`__.
 
 .. [Roeblitz13]
     Susanna Röblitz and Marcus Weber, |br|