Improve GPCCA.optimize(): Change complex conjugate splitting handling etc (#13)

* Skip instead of raise in GPCCA.optimize when splitting eigenvalues, if more then one cluster number was supplied.

* Add missing properties. Improve property names, add missing attributes, sort attributes/properties alphabetically, fix docstrings of GPCCA.

* Warn/raise indicating splitting of complex conjugated eigenvalues instead of only conjugated eigenvalues.

* Add example notebook adapted to changed properties and complex conjugate splitting handling.

* get_sectionsf -> get_sections in _checks.

* Improve grammar and fix typos/formulas in utils/_docs.py.

* Set 'fail_on_warning: false' in .readthedocs.yml.

* Replace metastable by macrostate.

* Always show UserWarning.

* Change data type of p from np.complex64 to np.complex128.

* Add reference values for tests checking skipping because of eigenvalue splitting.

* Don't raise, if m=n, but exclude from search for optimal cluster number.

* Add and modify tests to check for correct splitting behavior and related warnings.

* Fix linting

* Ensure float64

* Add dtype tests

* Fix .pre-commit-config.yml

* Remove from example_matrix_mu=0 in tests

* [ci skip] Add environment.yml for binder

Co-authored-by: Michal Klein <michal.klein@protonmail.com>

Author: msmdev

.pre-commit-config.yaml

@@ -72,9 +72,8 @@ repos:
     -   id: script-must-have-extension
         name: Check executable files use .sh extension
         types: [shell, executable]
-    -   id: shellcheck
 -   repo: https://github.com/myint/rstcheck
-    rev: master
+    rev: 3f92957478422df87bd730abde66f089cc1ee19b
     hooks:
     -   id: rstcheck
 -   repo: https://github.com/asottile/blacken-docs

docs/source/acknowledgements.rst docs/source/acknowledgments.rstdocs/source/acknowledgements.rst renamed to docs/source/acknowledgments.rst

@@ -1,5 +1,5 @@
-Acknowledgements
-================
+Acknowledgments
+===============
 We thank `Marcus Weber`_ and the Computational Molecular Design (`CMD`_) group at the Zuse Institute Berlin (`ZIB`_)
 for the longstanding and productive collaboration in the field of Markov modeling of non-reversible molecular dynamics.
 M. Weber, together with K. Fackeldey, had the original idea to employ Schur vectors instead of eigenvectors in the

docs/source/binder/requirements.txt

@@ -11,7 +11,7 @@
     installation
     api
     example
-    acknowledgements
+    acknowledgments
     references
 
 .. |br| raw:: html

docs/source/example.ipynb

@@ -1,4 +1,5 @@
 scipy
+docstring
 conda
 pygpcca
 pyGPCCA
@@ -22,3 +23,5 @@ Universitaet
 macOS
 Fackeldey
 Röblitz
+Sikorski
+Zuse

docs/source/index.rst

@@ -0,0 +1,6 @@
+name: pygpcca
+
+dependencies:
+-   matplotlib
+-   pip:
+    -   git+https://github.com/msmdev/pygpcca