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Docs #304

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merged 36 commits into from
Apr 3, 2023
Merged

Docs #304

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6c71fb0
Adding docs from specification
skeating Mar 13, 2023
ff7cc9a
Adding docs from specification
skeating Mar 13, 2023
bf4967f
more docs
skeating Mar 15, 2023
9bc6086
docs
skeating Mar 16, 2023
e26bd3a
docs
skeating Mar 16, 2023
df44a34
docs
skeating Mar 16, 2023
973c007
- add distrib to docs
fbergmann Mar 16, 2023
82f5a42
- fix nav-items going to negative
fbergmann Mar 16, 2023
a254328
docs for distrib classes
skeating Mar 17, 2023
66bac28
Update information for spatial and distrib.
luciansmith Mar 20, 2023
4c87c5d
Merge branch 'docs' of https://github.com/sbmlteam/libsbml into docs
luciansmith Mar 20, 2023
489123d
started docs of new ast funcs
skeating Mar 22, 2023
2a68557
- bump version to 5.20.0
fbergmann Mar 23, 2023
552a1c1
- mark spatial as stable package
fbergmann Mar 23, 2023
9bd98bc
start on xml node from file
skeating Mar 24, 2023
aa1ad60
sorting xmlns for math element
skeating Mar 24, 2023
27463ac
more ast docs
skeating Mar 24, 2023
97d3cf7
test multi ns on math
skeating Mar 25, 2023
34905b8
adding tests
skeating Mar 25, 2023
8e5d5b2
checked in bad version
skeating Mar 25, 2023
c715430
Merge branch 'xml-from-file' into docs
skeating Mar 25, 2023
efcb975
Merge branch 'xmlns-in-math' into docs
skeating Mar 25, 2023
57360d9
Merge remote-tracking branch 'origin/update-version' into docs
skeating Mar 25, 2023
08ec020
finishing AST documentation
skeating Mar 29, 2023
b55959a
remove broken link
skeating Mar 29, 2023
07662f5
adding a description of the raterule converter
skeating Mar 29, 2023
6f6b38e
removing broken links
skeating Mar 29, 2023
7d1228d
- update issue tracker link
fbergmann Mar 30, 2023
dbac341
Merge branch 'development' into docs
fbergmann Mar 30, 2023
327ba63
- update links
fbergmann Mar 30, 2023
84ea563
- update supported to lv3v2r2
fbergmann Mar 30, 2023
112bb05
- more sf -> github
fbergmann Mar 30, 2023
d9457d5
- missed one reference
fbergmann Mar 30, 2023
41798e6
- fix astnode (broken by merge)
fbergmann Mar 30, 2023
f32a1e6
- fix erata links
fbergmann Mar 31, 2023
e54f13b
add some NEWS
skeating Apr 2, 2023
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4 changes: 2 additions & 2 deletions CMakeLists.txt
Original file line number Diff line number Diff line change
Expand Up @@ -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

Expand Down
58 changes: 22 additions & 36 deletions NEWS.txt
Original file line number Diff line number Diff line change
@@ -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

Expand All @@ -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)
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2 changes: 1 addition & 1 deletion configure
Original file line number Diff line number Diff line change
Expand Up @@ -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 ""
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2 changes: 1 addition & 1 deletion configure.ac
Original file line number Diff line number Diff line change
Expand Up @@ -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 ""
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Original file line number Diff line number Diff line change
Expand Up @@ -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!

Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -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!

Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -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!

Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -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!

Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -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!

Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -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!

Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -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!

Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -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!

Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -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!

Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -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!

Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -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!

Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -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!

Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -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!

Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -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!

Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -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!

Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -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!

Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -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!

Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -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!

Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -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!

Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -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!

Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -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!

Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -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!

Expand Down
2 changes: 1 addition & 1 deletion dev/misc-files/readmes-for-downloads/linux/README.md.in
Original file line number Diff line number Diff line change
Expand Up @@ -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!

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2 changes: 1 addition & 1 deletion dev/misc-files/readmes-for-downloads/macos/README.md.in
Original file line number Diff line number Diff line change
Expand Up @@ -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!

Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -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!

Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -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!

Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -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!

Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -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!

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2 changes: 1 addition & 1 deletion dev/misc-files/readmes-for-downloads/windows/README.md.in
Original file line number Diff line number Diff line change
Expand Up @@ -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!

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4 changes: 2 additions & 2 deletions docs/historical/README_OLD.txt
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -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).
Expand Down
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