Version 0.2.2 #122

jvanhoefer · 2021-03-19T15:12:33Z

No description provided.

* add missing release notes * minor changes

* add logo license; fixes #108 * add pypi badge * invert python versions for readability

* .gitignore build folders * test macos * test windows * fix cache * fix typo * add all output files to .gitignore

* fix notebooks * add tests if SBML parts were created succesfully * change to libsbml.LIBSBML_OPERATION_SUCCESS * fix yanniks remarks * try fixing hdf5 * try without hdf5 * try ubuntu 18.04 * try ubuntu-latest again * simplify build * test cache * make build windows-compatible Co-authored-by: dilpath <dilan.private+github@outlook.com> Co-authored-by: yannikschaelte <yannik.schaelte@gmail.com>

* update swig * add pydocstyle, min versions of flake8 * fix pydocstyle

* unfix AMICI * fix notebooks Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com>

* add missing release notes (#111) (#112) * add missing release notes * minor changes * version ++1 * minor typos in docs * add release notes * Update doc/release_notes.rst Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * add commit numbers to release notes Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com>

codecov-io · 2021-03-19T15:14:18Z

Codecov Report

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…into develop

jvanhoefer · 2021-03-19T16:00:22Z

The problem with codacy seemed to be, that it didn't analyze the main branch due to renaming. The code quality is fine ("grade A").

yannikschaelte · 2021-03-19T16:01:34Z

The problem with codacy seemed to be, that it didn't analyze the main branch due to renaming. The code quality is fine ("grade A").

ah, thanks for pointing out. we may need to fix this also in other repositories.

dilpath

👍

dilpath · 2021-03-19T17:18:05Z

.github/workflows/deploy.yml

@@ -6,7 +6,7 @@ on:

 jobs:
  deploy:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-18.04


@yannikschaelte Do you know if ubuntu-latest is now possible?

yes, that should work (I thought I had changed it to latest everywhere)

dilpath · 2021-03-19T17:20:41Z

doc/format_specification.rst

@@ -67,7 +67,7 @@ odes

 Define **ODEs** (and states). An ODE consists of a `stateId` (string), a `rightHandSide` (string, encoding a mathematical expression), and an `initial value`. Initial values can be either numerical values or parameter Ids.

-For a more detailed description of the parsing of mathematical expressions ( for  `rightHandSide`) we refer to the [corresponding section](#parsing-of-mathematical-equations) of this documentation.
+For a more detailed description of the parsing of mathematical expressions ( for  `rightHandSide`) we refer to the :ref:`corresponding section<Parsing of mathematical equations>` of this documentation.


Suggested change

For a more detailed description of the parsing of mathematical expressions ( for `rightHandSide`) we refer to the :ref:`corresponding section<Parsing of mathematical equations>` of this documentation.

For a more detailed description of the parsing of mathematical expressions (for `rightHandSide`) we refer to the :ref:`corresponding section<Parsing of mathematical equations>` of this documentation.

dilpath · 2021-03-19T17:28:18Z

doc/release_notes.rst

+0.2.2 (2021-03-19)
+------------------
+
+* Add checks in SBML conversion, e.g. to catch invalid identifiers and equations (# 118).


Suggested change

* Add checks in SBML conversion, e.g. to catch invalid identifiers and equations (# 118).

* Add checks in SBML conversion, e.g. to catch invalid identifiers and equations (#118).

Not familiar but it looks like it's possible to make these links to the corresponding PRs (and issues) if desired.
Above is a typo fix, below is the typo fix + what should be a working link.

Suggested change

* Add checks in SBML conversion, e.g. to catch invalid identifiers and equations (# 118).

* Add checks in SBML conversion, e.g. to catch invalid identifiers and equations ([#118][p118]).

Might be that the PR numbers in the current format will be automatically linked on the GitHub releases page anyway, so the second suggestion here would be redundant

on github, they will be linked already. on rtd in either case not, but that's ok I think.

dilpath · 2021-03-19T17:29:15Z

tests/test_yaml2sbml/ode_input_invalid_SBML_identifier.yaml

+time:
+    variable: t
+
+parametersR:


Suggested change

parametersR:

parameters:

Did this typo come from yaml2sbml or manually? Might be worth checking

That is a very good point! Thank you! I am a bit surprised, since apparently this file is never used for testing and also was (looking also at the name) never intended to test these errors. This is a copy-paste error, that I will quickly fix in another PR before we do the new release :)

Did this typo come from yaml2sbml or manually? Might be worth checking

And no, fortunately copy paste error from another test case testing exactly these issues :)

dilpath · 2021-03-19T17:29:32Z

tests/test_yaml2sbml/ode_input_invalid_SBML_identifier.yaml

+      noiseDistribution: normal
+
+
+conditions2:


Suggested change

conditions2:

conditions:

As above, might be worth checking the source of this typo.

dilpath · 2021-03-19T17:33:34Z

yaml2sbml/yaml2sbml.py

+    if math is not None:
+        f.setMath(math)
+    else:
+        raise RuntimeError(f'Unable to generate assignment for funtion '
+                           f'{function_id}, libsbml can not parse the given '
+                           f'function expression, given by '
+                           f'lambda({arguments} , {formula}).')


Suggested change

if math is not None:

f.setMath(math)

else:

raise RuntimeError(f'Unable to generate assignment for funtion '

f'{function_id}, libsbml can not parse the given '

f'function expression, given by '

f'lambda({arguments} , {formula}).')

if math is not None:

f.setMath(math)

else:

raise RuntimeError(f'Unable to generate assignment for function '

f'{function_id}, libsbml can not parse the given '

f'function expression, given by '

f'lambda({arguments} , {formula}).')

* fix tests * Update tests/test_yaml2sbml.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Update tests/test_yaml2sbml.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com>

jvanhoefer and others added 9 commits February 22, 2021 16:41

add missing release notes (#111)

c4bbf43

* add missing release notes * minor changes

Add logo license; fixes #108 (#116)

0157684

* add logo license; fixes #108 * add pypi badge * invert python versions for readability

Add MacOS+Windows tests; clean up .gitignore (#115)

fa62bc2

* .gitignore build folders * test macos * test windows * fix cache * fix typo * add all output files to .gitignore

fix notebooks (#117)

1c1d234

Fix pydocstyle was not called; update swig (#120)

9923197

* update swig * add pydocstyle, min versions of flake8 * fix pydocstyle

Unfix AMICI version, fix notebooks (#113)

2e8c5b4

* unfix AMICI * fix notebooks Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com>

Merge branch 'main' into develop

3c268ee

jvanhoefer requested review from martamatos, yannikschaelte and dilpath March 19, 2021 15:12

Merge branch 'develop' of https://github.com/yaml2sbml-dev/yaml2sbml …

8f594a8

…into develop

yannikschaelte approved these changes Mar 19, 2021

View reviewed changes

dilpath approved these changes Mar 19, 2021

View reviewed changes

fix ubuntu latest

7a9cba2

jvanhoefer mentioned this pull request Mar 19, 2021

Fix tests #123

Merged

jvanhoefer merged commit 6f42ee5 into main Mar 21, 2021

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Version 0.2.2 #122

Version 0.2.2 #122

jvanhoefer commented Mar 19, 2021

codecov-io commented Mar 19, 2021 •

edited

jvanhoefer commented Mar 19, 2021

yannikschaelte commented Mar 19, 2021

dilpath left a comment

dilpath Mar 19, 2021

yannikschaelte Mar 19, 2021

dilpath Mar 19, 2021

dilpath Mar 19, 2021

dilpath Mar 19, 2021

yannikschaelte Mar 20, 2021

dilpath Mar 19, 2021

jvanhoefer Mar 19, 2021

jvanhoefer Mar 19, 2021

dilpath Mar 19, 2021

dilpath Mar 19, 2021

	For a more detailed description of the parsing of mathematical expressions ( for `rightHandSide`) we refer to the :ref:`corresponding section<Parsing of mathematical equations>` of this documentation.
	For a more detailed description of the parsing of mathematical expressions (for `rightHandSide`) we refer to the :ref:`corresponding section<Parsing of mathematical equations>` of this documentation.

	* Add checks in SBML conversion, e.g. to catch invalid identifiers and equations (# 118).
	* Add checks in SBML conversion, e.g. to catch invalid identifiers and equations (#118).

Version 0.2.2 #122

Version 0.2.2 #122

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jvanhoefer commented Mar 19, 2021

codecov-io commented Mar 19, 2021 • edited

Codecov Report

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codecov-io commented Mar 19, 2021 •

edited