Updating docs and various READMEs; Various cleanup

CHANGELOG

@@ -1,7 +1,8 @@
 --- CHANGELOG ---
---- Assimulo-3.4.4 ---
+--- Assimulo-3.5.0 ---
     * Changed "numpy.float" to equivalent "numpy.float64" due to DeprecationWarnings in numpy >= 1.20.
     * Improved examples with sparse jacobians by omitting the zeros in the jacobians.
+    * Upgraded to Cython >= 3.
 
 --- Assimulo-3.4.3 ---
     * Improved compliance with newer scipy version by instead using corresponding numpy calls when more suitable.

INSTALL

@@ -6,10 +6,10 @@ INSTALL
 =======
 
 *REQUIREMENTS
-	- Python-2.7/3.* (with headers)
+	- Python-3 (with headers)
 	- Numpy, Scipy, Pylab
 	- Sundials-2.5/2.6/3.1/4.1
-	- Cython >= 0.18
+	- Cython >= 3
     - C-compiler
     - Fortran-compiler
     - BLAS

doc/sphinx/source/changelog.rst

@@ -3,6 +3,23 @@
 Changelog
 ==========
 
+--- Assimulo-3.5.0 ---
+    * Changed "numpy.float" to equivalent "numpy.float64" due to DeprecationWarnings in numpy >= 1.20.
+    * Improved examples with sparse jacobians by omitting the zeros in the jacobians.
+    * Upgraded to Cython >= 3.
+
+--- Assimulo-3.4.3 ---
+    * Improved compliance with newer scipy version by instead using corresponding numpy calls when more suitable.
+
+--- Assimulo-3.4.2 ---
+    * Updated an import statement in one of the examples to resolve compliance issues with scipy 1.10.1.
+
+--- Assimulo-3.4.1 ---
+    * Restored functionality of CVode with 'external_event_detection' = True, which broke with 3.4.0.
+    * CVode now allows rtol = 0.
+    * Added support for CVode (without sensitivities) with non-negative relative tolerance vector.
+      Requires a SUNDIALS installation supporting this, see README.
+
 --- Assimulo-3.4.0 ---
     * Removed Radau5ODE Fortran implementation. 
       This change should be seamless since the C implementation is numerically equivalent.

doc/sphinx/source/installation.rst

@@ -6,16 +6,16 @@ Installation
 
 Dependencies:
 
-- `Python-2.7 / 3.* <http://www.python.org/>`_
-- `Numpy <http://www.scipy.org/Download/>`_ (>1.6.1 for the solver DASP3)
+- `Python-3 <http://www.python.org/>`_
+- `Numpy <http://www.scipy.org/Download/>`_
 - `Scipy <http://www.scipy.org/Download/>`_
 - `Pylab <http://matplotlib.sourceforge.net/>`_
 
 Additional dependencies for compiling from source:
 
-- `Python-2.7 / 3.* <http://www.python.org/>`_ with headers (python-dev package for Ubuntu)
+- `Python-3 <http://www.python.org/>`_ with headers (python-dev package for Ubuntu)
 - `Sundials-2.6/2.7/3.1/4.1 <http://computation.llnl.gov/casc/sundials/main.html>`_ (for 64bits machines, install Sundials using -fPIC)
-- `Cython 0.18 <http://www.cython.org/>`_
+- `Cython 3.0.7 <http://www.cython.org/>`_
 - C compiler
 - Fortran compiler
 - BLAS (only needed for the solver GLIMDA)

setup.cfg

@@ -1,13 +1,13 @@
 [options]
 setup_requires =
     setuptools
-    numpy >= 1.17
+    numpy >= 1.26.3
     cython >= 3.0.7
 
 install_requires =
     python >= 3.11
-    numpy >= 1.17
-    scipy >= 1.3
+    numpy >= 1.26.3
+    scipy >= 1.11.4
     cython >= 3.0.7
     nose >= 1.3.7
     matplotlib > 3

setup.py

@@ -77,18 +77,18 @@ def remove_prefix(name, prefix):
 import numpy.distutils as nd
 
 try:
-    # from Cython.Distutils import build_ext ## TODO: obsolete?
+    from Cython.Distutils import build_ext
     from Cython.Build import cythonize
 except ImportError:
-    msg="Please upgrade to a newer Cython version, >= 0.18."
+    msg="Please upgrade to a newer Cython version, >= 3"
     logging.error(msg)
     raise Exception(msg)
 
 #Verify Cython version
 import Cython
 cython_version = Cython.__version__.split(".")
-if not (cython_version[0] > '0' or (cython_version[0] == '0' and cython_version[1] >= '18')):
-    msg="Please upgrade to a newer Cython version, >= 0.18."
+if not cython_version[0] >= '3':
+    msg="Please upgrade to a newer Cython version, >= 3"
     logging.error(msg)
     raise Exception(msg)
 
@@ -661,14 +661,6 @@ def fortran_extensionlists(self):
     change_dir = False
 
 ext_list = prepare.cython_extensionlists()
-
-#MAJOR HACK DUE TO NUMPY CHANGE IN VERSION 1.6.2 THAT DOES NOT SEEM TO
-#HANDLE EXTENSIONS OF BOTH TYPE (DISTUTILS AND NUMPY DISTUTILS) AT THE
-#SAME TIME.
-for e in ext_list:
-    e.extra_f77_compile_args = []
-    e.extra_f90_compile_args = []
-
 ext_list += prepare.fortran_extensionlists()
 
 # distutils part
@@ -677,7 +669,7 @@ def fortran_extensionlists(self):
 NAME = "Assimulo"
 AUTHOR = u"C. Winther (Andersson), C. Führer, J. Åkesson, M. Gäfvert"
 AUTHOR_EMAIL = "[email protected]"
-VERSION = "trunk" if version_number_arg == "Default" else version_number_arg
+VERSION = "3.5.0" if version_number_arg == "Default" else version_number_arg
 LICENSE = "LGPL"
 URL = "http://www.jmodelica.org/assimulo"
 DOWNLOAD_URL = "http://www.jmodelica.org/assimulo"
@@ -709,7 +701,7 @@ def fortran_extensionlists(self):
 http://www.jmodelica.org/assimulo . 
 
 The package requires Numpy, Scipy and Matplotlib and additionally for 
-compiling from source, Cython 0.18, Sundials 2.6/2.7/3.1/4.1, BLAS and LAPACK 
+compiling from source, Cython >=3, Sundials 2.6/2.7/3.1/4.1, BLAS and LAPACK 
 together with a C-compiler and a FORTRAN-compiler.
 """
 

src/lib/sundials_includes.pxd

@@ -24,8 +24,6 @@ see also Jon Olav Vik:
 http://codespeak.net/pipermail/cython-dev/2009-June/005947.html
 
 """
-#import numpy as N
-#cimport numpy as N
 
 from numpy cimport NPY_DOUBLE, npy_intp, NPY_INT
 
@@ -393,8 +391,8 @@ cdef extern from "cvodes/cvodes.h":
 
 
     #Statistics
-    int CVodeGetEstLocalErrors(void *cvode_mem, N_Vector ele)               #Estimated local errors
-    int CVodeGetErrWeights(void *cvode_mem, N_Vector eweight)               #Estimated local errors
+    int CVodeGetEstLocalErrors(void *cvode_mem, N_Vector ele) #Estimated local errors
+    int CVodeGetErrWeights(void *cvode_mem, N_Vector eweight) #Estimated local errors
     int CVodeGetSensNumRhsEvals(void *cvode_mem, long int *nfSevals)
     int CVodeGetNumRhsEvalsSens(void *cvode_mem, long int *nfevalsS)
     int CVodeGetSensNumErrTestFails(void *cvode_mem, long int *nSetfails)

src/solvers/radar5.py

@@ -736,9 +736,6 @@ def _get_rtol(self):
     rtol=property(_get_rtol,_set_rtol)
 
     def _get_grid(self):
-        """
-        TODO
-        """
         return self._grid
     def _set_grid(self, grid):
         self._grid