Merge pull request #304 from sbmlteam/docs

Docs

CMakeLists.txt

@@ -1060,10 +1060,10 @@ libSBML version ${PACKAGE_VERSION}
 ----------------------------------------------------------------------
 
    More information and the latest version are available online at
-   http://sbml.org/Software/libSBML
+   https://sbml.org/software/libsbml/
 
    Please report problems using the issue tracker at
-   http://sbml.org/Software/libsbml/issue-tracker
+   https://github.com/sbmlteam/libsbml/issues
 
    To contact the developers directly, email libsbml-team@googlegroups.com
 

NEWS.txt

@@ -1,20 +1,29 @@
            libSBML NEWS -- History of user-visible changes
 
 ====================================================================
-5.19.1 (Current development branch)
+5.20.0
 ====================================================================
-STABLE RELEASE
+
+Given the length of time since our last release the list of changes
+and acknowledgements of contributions is incomplete. We apologise and
+offer thanks to anyone who has been involved and those people who have
+contributed their spare time to continuing maintenance and development.
+
+* Addition of support for the SBML Spatial package
+
+  - Now that the first official version of the specification for the
+    SBML Level 3 Spatial package is available, the libSBML API for
+    'spatial' is now included in the stable release of libSBML. 
+    Thus a CMake build using '-WITH_STABLE_PACKAGES' will now include
+    the spatial package code.
 
 * New features
-
-  - 'comp' package-specific updates:
-  - 'distrib' package-specific updates:
-  - 'fbc' package-specific updates:
-  - 'groups' package-specific updates:
-  - 'layout' package-specific updates:
-  - 'multi' package-specific updates:
-  - 'qual' package-specific updates:
-  - 'render' package-specific updates:
+
+  - There is a new converter SBMLRateRuleConverter which will take 
+    a model with RateRules and infer the corresponding reaction network.
+    This is still considered under development and we would really
+    appreciate any feedback.
+
 
 * Bug fixes
 
@@ -28,39 +37,16 @@ STABLE RELEASE
     updated for Python 3.10 changes. Thanks to
     Zbigniew Jędrzejewski-Szmek for submitting the changes.
 
-  - 'comp' package-specific bug fixes:
-  - 'distrib' package-specific bug fixes:
-  - 'fbc' package-specific bug fixes:
-  - 'groups' package-specific bug fixes:
-  - 'layout' package-specific bug fixes:
-  - 'multi' package-specific bug fixes:
-  - 'qual' package-specific bug fixes:
-  - 'render' package-specific bug fixes:
-
 * Configuration/build system changes
 
   - Extensive continuous integration testing has been added to 
     the GitHub repository.
 
-
 * Miscellaneous
 
+  - Note there is now a Julia interface to libSBML available
+    at https://lcsb-biocore.github.io/SBML.jl/stable/
 
-EXPERIMENTAL PACKAGES
-
-* New features
-
-  - 'arrays' package-specific updates:
-  - 'dyn' package-specific updates:
-  - 'req' package-specific updates:
-  - 'spatial' package-specific updates:
-
- * Bug fixes
-
-  - 'arrays' package-specific bug fixes:
-  - 'dyn' package-specific bug fixes:
-  - 'req' package-specific bug fixes:
-  - 'spatial' package-specific bug fixes:
 
 ====================================================================
 5.19.0 (2020-11-27)

configure

@@ -28837,7 +28837,7 @@ echo "More information and the latest version are available online at"
 echo "http://sbml.org/Software/libSBML"
 echo ""
 echo "Please report problems using the issue tracker at"
-echo "http://sbml.org/software/libsbml/issue-tracker"
+echo "https://github.com/sbmlteam/libsbml/issues"
 echo ""
 echo "To contact the developers directly, email libsbml-team@googlegroups.com"
 echo ""

configure.ac

@@ -822,7 +822,7 @@ echo "More information and the latest version are available online at"
 echo "http://sbml.org/Software/libSBML"
 echo ""
 echo "Please report problems using the issue tracker at"
-echo "http://sbml.org/software/libsbml/issue-tracker"
+echo "https://github.com/sbmlteam/libsbml/issues"
 echo ""
 echo "To contact the developers directly, email libsbml-team@googlegroups.com"
 echo ""

dev/misc-files/readmes-for-downloads-new-dir-struct/stable/linux/32-bit/README.md.in

@@ -54,7 +54,7 @@ If you need to use a different XML parser library, it will be necessary to build
 
 For additional information about this version of libSBML, please see the documentation or [visit the libSBML website](http://sbml.org/Software/libSBML).
 
-Please report problems using our tracker: [http://sbml.org/Software/libSBML/issue-tracker](http://sbml.org/Software/libSBML/issue-tracker)
+Please report problems using our tracker: [https://github.com/sbmlteam/libsbml/issues](https://github.com/sbmlteam/libsbml/issues)
 
 Thank you for your interest in libSBML!
 

dev/misc-files/readmes-for-downloads-new-dir-struct/stable/linux/32-bit/R_interface/README.md.in

@@ -10,7 +10,7 @@ The binary installation will provide a faster installation but will only work if
 
 For additional information about this version of libSBML, please see the documentation or [visit the libSBML website](http://sbml.org/Software/libSBML).
 
-Please report problems using our tracker: [http://sbml.org/Software/libSBML/issue-tracker](http://sbml.org/Software/libSBML/issue-tracker)
+Please report problems using our tracker: [https://github.com/sbmlteam/libsbml/issues](https://github.com/sbmlteam/libsbml/issues)
 
 Thank you for your interest in libSBML!
 

dev/misc-files/readmes-for-downloads-new-dir-struct/stable/linux/32-bit/R_interface/binary-package/README.md.in

@@ -17,7 +17,7 @@ Once you have installed the R libSBML library, follow the instructions for [how
 
 For additional information about this version of libSBML, please see the documentation or [visit the libSBML website](http://sbml.org/Software/libSBML).
 
-Please report problems using our tracker: [http://sbml.org/Software/libSBML/issue-tracker](http://sbml.org/Software/libSBML/issue-tracker)
+Please report problems using our tracker: [https://github.com/sbmlteam/libsbml/issues](https://github.com/sbmlteam/libsbml/issues)
 
 Thank you for your interest in libSBML!
 

dev/misc-files/readmes-for-downloads-new-dir-struct/stable/linux/32-bit/R_interface/source-package/README.md.in

@@ -17,7 +17,7 @@ Once you have installed the R libSBML library, follow the instructions for [how
 
 For additional information about this version of libSBML, please see the documentation or [visit the libSBML website](http://sbml.org/Software/libSBML).
 
-Please report problems using our tracker: [http://sbml.org/Software/libSBML/issue-tracker](http://sbml.org/Software/libSBML/issue-tracker)
+Please report problems using our tracker: [https://github.com/sbmlteam/libsbml/issues](https://github.com/sbmlteam/libsbml/issues)
 
 Thank you for your interest in libSBML!
 

dev/misc-files/readmes-for-downloads-new-dir-struct/stable/linux/64-bit/README.md.in

@@ -54,7 +54,7 @@ If you need to use a different XML parser library, it will be necessary to build
 
 For additional information about this version of libSBML, please see the documentation or [visit the libSBML website](http://sbml.org/Software/libSBML).
 
-Please report problems using our tracker: [http://sbml.org/Software/libSBML/issue-tracker](http://sbml.org/Software/libSBML/issue-tracker)
+Please report problems using our tracker: [https://github.com/sbmlteam/libsbml/issues](https://github.com/sbmlteam/libsbml/issues)
 
 Thank you for your interest in libSBML!
 

dev/misc-files/readmes-for-downloads-new-dir-struct/stable/linux/64-bit/R_interface/README.md.in

@@ -10,7 +10,7 @@ The binary installation will provide a faster installation but will only work if
 
 For additional information about this version of libSBML, please see the documentation or [visit the libSBML website](http://sbml.org/Software/libSBML).
 
-Please report problems using our tracker: [http://sbml.org/Software/libSBML/issue-tracker](http://sbml.org/Software/libSBML/issue-tracker)
+Please report problems using our tracker: [https://github.com/sbmlteam/libsbml/issues](https://github.com/sbmlteam/libsbml/issues)
 
 Thank you for your interest in libSBML!
 

dev/misc-files/readmes-for-downloads-new-dir-struct/stable/linux/64-bit/R_interface/binary-package/README.md.in

@@ -17,7 +17,7 @@ Once you have installed the R libSBML library, follow the instructions for [how
 
 For additional information about this version of libSBML, please see the documentation or [visit the libSBML website](http://sbml.org/Software/libSBML).
 
-Please report problems using our tracker: [http://sbml.org/Software/libSBML/issue-tracker](http://sbml.org/Software/libSBML/issue-tracker)
+Please report problems using our tracker: [https://github.com/sbmlteam/libsbml/issues](https://github.com/sbmlteam/libsbml/issues)
 
 Thank you for your interest in libSBML!
 

dev/misc-files/readmes-for-downloads-new-dir-struct/stable/linux/64-bit/R_interface/source-package/README.md.in

@@ -17,7 +17,7 @@ Once you have installed the R libSBML library, follow the instructions for [how
 
 For additional information about this version of libSBML, please see the documentation or [visit the libSBML website](http://sbml.org/Software/libSBML).
 
-Please report problems using our tracker: [http://sbml.org/Software/libSBML/issue-tracker](http://sbml.org/Software/libSBML/issue-tracker)
+Please report problems using our tracker: [https://github.com/sbmlteam/libsbml/issues](https://github.com/sbmlteam/libsbml/issues)
 
 Thank you for your interest in libSBML!
 

dev/misc-files/readmes-for-downloads-new-dir-struct/stable/linux/README.md.in

@@ -4,7 +4,7 @@ Please navigate to either the [32-bit](32-bit) or [64-bit](64-bit) folders, to m
 
 For additional information about this version of libSBML, please see the documentation or [visit the libSBML website](http://sbml.org/Software/libSBML).
 
-Please report problems using our tracker: [http://sbml.org/Software/libSBML/issue-tracker](http://sbml.org/Software/libSBML/issue-tracker)
+Please report problems using our tracker: [https://github.com/sbmlteam/libsbml/issues](https://github.com/sbmlteam/libsbml/issues)
 
 Thank you for your interest in libSBML!
 

dev/misc-files/readmes-for-downloads-new-dir-struct/stable/macos/README.md.in

@@ -57,7 +57,7 @@ If you need to use a different XML parser library, it will be necessary to build
 
 For additional information about this version of libSBML, please see the documentation or [visit the libSBML website](http://sbml.org/Software/libSBML).
 
-Please report problems using our tracker: [http://sbml.org/Software/libSBML/issue-tracker](http://sbml.org/Software/libSBML/issue-tracker)
+Please report problems using our tracker: [https://github.com/sbmlteam/libsbml/issues](https://github.com/sbmlteam/libsbml/issues)
 
 Thank you for your interest in libSBML!
 

dev/misc-files/readmes-for-downloads-new-dir-struct/stable/macos/R_interface/README.md.in

@@ -10,7 +10,7 @@ The binary installation will provide a faster installation but will only work if
 
 For additional information about this version of libSBML, please see the documentation or [visit the libSBML website](http://sbml.org/Software/libSBML).
 
-Please report problems using our tracker: [http://sbml.org/Software/libSBML/issue-tracker](http://sbml.org/Software/libSBML/issue-tracker)
+Please report problems using our tracker: [https://github.com/sbmlteam/libsbml/issues](https://github.com/sbmlteam/libsbml/issues)
 
 Thank you for your interest in libSBML!
 

dev/misc-files/readmes-for-downloads-new-dir-struct/stable/macos/R_interface/binary-package/README.md.in

@@ -17,7 +17,7 @@ Once you have installed the R libSBML library, follow the instructions for [how
 
 For additional information about this version of libSBML, please see the documentation or [visit the libSBML website](http://sbml.org/Software/libSBML).
 
-Please report problems using our tracker: [http://sbml.org/Software/libSBML/issue-tracker](http://sbml.org/Software/libSBML/issue-tracker)
+Please report problems using our tracker: [https://github.com/sbmlteam/libsbml/issues](https://github.com/sbmlteam/libsbml/issues)
 
 Thank you for your interest in libSBML!
 

dev/misc-files/readmes-for-downloads-new-dir-struct/stable/macos/R_interface/source-package/README.md.in

@@ -17,7 +17,7 @@ Once you have installed the R libSBML library, follow the instructions for [how
 
 For additional information about this version of libSBML, please see the documentation or [visit the libSBML website](http://sbml.org/Software/libSBML).
 
-Please report problems using our tracker: [http://sbml.org/Software/libSBML/issue-tracker](http://sbml.org/Software/libSBML/issue-tracker)
+Please report problems using our tracker: [https://github.com/sbmlteam/libsbml/issues](https://github.com/sbmlteam/libsbml/issues)
 
 Thank you for your interest in libSBML!
 

dev/misc-files/readmes-for-downloads-new-dir-struct/stable/windows/32-bit/README.md.in

@@ -42,7 +42,7 @@ If you need to use a different XML parser library, it will be necessary to build
 
 For additional information about this version of libSBML, please see the documentation or [visit the libSBML website](http://sbml.org/Software/libSBML).
 
-Please report problems using our tracker: [http://sbml.org/Software/libSBML/issue-tracker](http://sbml.org/Software/libSBML/issue-tracker)
+Please report problems using our tracker: [https://github.com/sbmlteam/libsbml/issues](https://github.com/sbmlteam/libsbml/issues)
 
 Thank you for your interest in libSBML!
 

dev/misc-files/readmes-for-downloads-new-dir-struct/stable/windows/32-bit/R_interface/README.md.in

@@ -19,7 +19,7 @@ Once you have installed the R libSBML library, follow the instructions for [how
 
 For additional information about this version of libSBML, please see the documentation or [visit the libSBML website](http://sbml.org/Software/libSBML).
 
-Please report problems using our tracker: [http://sbml.org/Software/libSBML/issue-tracker](http://sbml.org/Software/libSBML/issue-tracker)
+Please report problems using our tracker: [https://github.com/sbmlteam/libsbml/issues](https://github.com/sbmlteam/libsbml/issues)
 
 Thank you for your interest in libSBML!
 

dev/misc-files/readmes-for-downloads-new-dir-struct/stable/windows/32-bit/python/README.md.in

@@ -22,7 +22,7 @@ If that fails, please check the instructions for [how to access libSBML](http://
 
 For additional information about this version of libSBML, please see the documentation or [visit the libSBML website](http://sbml.org/Software/libSBML).
 
-Please report problems using our tracker: [http://sbml.org/Software/libSBML/issue-tracker](http://sbml.org/Software/libSBML/issue-tracker)
+Please report problems using our tracker: [https://github.com/sbmlteam/libsbml/issues](https://github.com/sbmlteam/libsbml/issues)
 
 Thank you for your interest in libSBML!
 

dev/misc-files/readmes-for-downloads-new-dir-struct/stable/windows/64-bit/README.md.in

@@ -42,7 +42,7 @@ If you need to use a different XML parser library, it will be necessary to build
 
 For additional information about this version of libSBML, please see the documentation or [visit the libSBML website](http://sbml.org/Software/libSBML).
 
-Please report problems using our tracker: [http://sbml.org/Software/libSBML/issue-tracker](http://sbml.org/Software/libSBML/issue-tracker)
+Please report problems using our tracker: [https://github.com/sbmlteam/libsbml/issues](https://github.com/sbmlteam/libsbml/issues)
 
 Thank you for your interest in libSBML!
 

dev/misc-files/readmes-for-downloads-new-dir-struct/stable/windows/64-bit/R_interface/README.md.in

@@ -19,7 +19,7 @@ Once you have installed the R libSBML library, follow the instructions for [how
 
 For additional information about this version of libSBML, please see the documentation or [visit the libSBML website](http://sbml.org/Software/libSBML).
 
-Please report problems using our tracker: [http://sbml.org/Software/libSBML/issue-tracker](http://sbml.org/Software/libSBML/issue-tracker)
+Please report problems using our tracker: [https://github.com/sbmlteam/libsbml/issues](https://github.com/sbmlteam/libsbml/issues)
 
 Thank you for your interest in libSBML!
 

dev/misc-files/readmes-for-downloads-new-dir-struct/stable/windows/64-bit/python/README.md.in

@@ -22,7 +22,7 @@ If that fails, please check the instructions for [how to access libSBML](http://
 
 For additional information about this version of libSBML, please see the documentation or [visit the libSBML website](http://sbml.org/Software/libSBML).
 
-Please report problems using our tracker: [http://sbml.org/Software/libSBML/issue-tracker](http://sbml.org/Software/libSBML/issue-tracker)
+Please report problems using our tracker: [https://github.com/sbmlteam/libsbml/issues](https://github.com/sbmlteam/libsbml/issues)
 
 Thank you for your interest in libSBML!
 

dev/misc-files/readmes-for-downloads-new-dir-struct/stable/windows/README.md.in

@@ -4,7 +4,7 @@ Please navigate to either the [32-bit](32-bit) or [64-bit](64-bit) folders, to m
 
 For additional information about this version of libSBML, please see the documentation or [visit the libSBML website](http://sbml.org/Software/libSBML).
 
-Please report problems using our tracker: [http://sbml.org/Software/libSBML/issue-tracker](http://sbml.org/Software/libSBML/issue-tracker)
+Please report problems using our tracker: [https://github.com/sbmlteam/libsbml/issues](https://github.com/sbmlteam/libsbml/issues)
 
 Thank you for your interest in libSBML!
 

dev/misc-files/readmes-for-downloads/linux/32-bit/README.md.in

@@ -40,7 +40,7 @@ the libSBML website at
 
 Please report problems with libSBML using the tracker at
 
-[http://sbml.org/Software/libSBML/issue-tracker](http://sbml.org/Software/libSBML/issue-tracker)
+[https://github.com/sbmlteam/libsbml/issues](https://github.com/sbmlteam/libsbml/issues)
 
 Thank you for your interest in libSBML!
 

dev/misc-files/readmes-for-downloads/linux/64-bit/README.md.in

@@ -40,7 +40,7 @@ the libSBML website at
 
 Please report problems with libSBML using the tracker at
 
-[http://sbml.org/Software/libSBML/issue-tracker](http://sbml.org/Software/libSBML/issue-tracker)
+[https://github.com/sbmlteam/libsbml/issues](https://github.com/sbmlteam/libsbml/issues)
 
 Thank you for your interest in libSBML!
 

dev/misc-files/readmes-for-downloads/linux/README.md.in

@@ -28,7 +28,7 @@ the documentation or visit the libSBML website at
 
 Please report problems with libSBML using the tracker at
 
-[http://sbml.org/Software/libSBML/issue-tracker](http://sbml.org/Software/libSBML/issue-tracker)
+[https://github.com/sbmlteam/libsbml/issues](https://github.com/sbmlteam/libsbml/issues)
 
 Thank you for your interest in libSBML!
 

dev/misc-files/readmes-for-downloads/macos/README.md.in

@@ -45,7 +45,7 @@ libSBML website at
 
 Please report problems with libSBML using the tracker at
 
-[http://sbml.org/Software/libSBML/issue-tracker](http://sbml.org/Software/libSBML/issue-tracker)
+[https://github.com/sbmlteam/libsbml/issues](https://github.com/sbmlteam/libsbml/issues)
 
 Thank you for your interest in libSBML!
 

dev/misc-files/readmes-for-downloads/windows/32-bit/README.md.in

@@ -49,7 +49,7 @@ Detailed information about libSBML can be found at
 
 Please report problems with libSBML using the tracker at
 
-[http://sbml.org/Software/libSBML/issue-tracker](http://sbml.org/Software/libSBML/issue-tracker)
+[https://github.com/sbmlteam/libsbml/issues](https://github.com/sbmlteam/libsbml/issues)
 
 Thank you for your interest in libSBML!
 

dev/misc-files/readmes-for-downloads/windows/32-bit/python/README.md.in

@@ -24,7 +24,7 @@ is available for viewing online at
 
 Please report any problems with libSBML using the tracker at
 
-[http://sbml.org/Software/libSBML/issue-tracker](http://sbml.org/Software/libSBML/issue-tracker)
+[https://github.com/sbmlteam/libsbml/issues](https://github.com/sbmlteam/libsbml/issues)
 
 Thank you for your interest in libSBML!
 

dev/misc-files/readmes-for-downloads/windows/64-bit/README.md.in

@@ -51,7 +51,7 @@ Detailed information about libSBML can be found at
 
 Please report problems with libSBML using the tracker at
 
-[http://sbml.org/Software/libSBML/issue-tracker](http://sbml.org/Software/libSBML/issue-tracker)
+[https://github.com/sbmlteam/libsbml/issues](https://github.com/sbmlteam/libsbml/issues)
 
 Thank you for your interest in libSBML!
 

dev/misc-files/readmes-for-downloads/windows/64-bit/python/README.md.in

@@ -24,7 +24,7 @@ is available for viewing online at
 
 Please report any problems with libSBML using the tracker at
 
-[http://sbml.org/Software/libSBML/issue-tracker](http://sbml.org/Software/libSBML/issue-tracker)
+[https://github.com/sbmlteam/libsbml/issues](https://github.com/sbmlteam/libsbml/issues)
 
 Thank you for your interest in libSBML!
 

dev/misc-files/readmes-for-downloads/windows/README.md.in

@@ -12,7 +12,7 @@ For more information about libSBML, please visit the libSBML website at
 
 Please report any problems with libSBML using the tracker at
 
-[http://sbml.org/Software/libSBML/issue-tracker](http://sbml.org/Software/libSBML/issue-tracker)
+[https://github.com/sbmlteam/libsbml/issues](https://github.com/sbmlteam/libsbml/issues)
 
 Thank you for your interest in libSBML!
 

docs/historical/README_OLD.txt

@@ -15,7 +15,7 @@
                    http://sbml.org/Software/libSBML
 
        Please report problems with libSBML using the tracker at
-            http://sbml.org/Software/libSBML/issue-tracker
+            https://github.com/sbmlteam/libsbml/issues
 
   Mailing lists and online web forums for discussing libSBML are at
                         http://sbml.org/Forums
@@ -279,7 +279,7 @@ We invite you to report bugs and other problems using the issue
 tracker for libSBML on SourceForge.  The following URL will take you
 there directly:
 
-  http://sbml.org/Software/libSBML/issue-tracker
+  https://github.com/sbmlteam/libsbml/issues
 
 You can also ask questions on the 'sbml-interoperability' mailing
 list, either over email or using the web forum interface (see below).