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Merge pull request #391 from PEtab-dev/release_0.1.5
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Release 0.1.5

Library:

* New create empty observable function (issue 386) (#387)
* Deprecate petab.sbml.globalize_parameters (#381)
* Fix computing log10 likelihood (#380)
* Documentation update and typehints for visualization  (#372)
* Ordered result of `petab.get_output_parameters`
* Fix missing argument to parameters.create_parameter_df

Documentation:
* Add overview of supported PEtab feature in toolboxes
* Add contribution guide
* Fix optional values in documentation (#378)
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@dweindl
dweindl authored Mar 18, 2020
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17 changes: 17 additions & 0 deletions CHANGELOG.md
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## 0.1 series

### 0.1.5

Library:

* New create empty observable function (issue 386) (#387)
* Deprecate petab.sbml.globalize_parameters (#381)
* Fix computing log10 likelihood (#380)
* Documentation update and typehints for visualization (#372)
* Ordered result of `petab.get_output_parameters`
* Fix missing argument to parameters.create_parameter_df

Documentation:
* Add overview of supported PEtab feature in toolboxes
* Add contribution guide
* Fix optional values in documentation (#378)


### 0.1.4

Library:
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47 changes: 47 additions & 0 deletions CONTRIBUTING.md
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# PEtab contribution guide

We are happy about contributions to PEtab of any form.

This includes, but is not limited to:

* Extending / improving
[documentation and examples](https://petab.readthedocs.io/en/latest/)
* New library functionality
* Additional
[PEtab application examples](https://github.com/Benchmarking-Initiative/Benchmark-Models-PEtab)
* Additional minimal
[PEtab test cases](https://github.com/PEtab-dev/petab_test_suite)


## Extending PEtab

We are aware of the fact that PEtab may not serve everybody's needs. If you
have a suggestion of how to extend PEtab, feel free to post an
[issue](https://github.com/PEtab-dev/PEtab/issues) at our GitHub repository.


## Contributions to this repository

General:

* For code contributions, please adhere to the
[PEP8 style guide](https://www.python.org/dev/peps/pep-0008/)
* All new functionality should be covered by unit tests
* Please use Python type hints
* Please document all modules, functions, classes, attributes, arguments,
return values, ... in a style consistent with the rest of the library
* Use descriptive commit messages

To contribute to this repository:

* Create a pull request

*By creating a pull request you agree with your contribution being made
available under the license terms specified in
[https://github.com/PEtab-dev/PEtab/blob/master/LICENSE](https://github.com/PEtab-dev/PEtab/blob/master/LICENSE).*

* Assign a reviewer, or let us know otherwise, that your pull request is ready
for review.

* Wait for feedback (and feel free so send a gentle reminder if you did not
get any feedback within a week)
92 changes: 73 additions & 19 deletions README.md
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Documentation of the PEtab data format and Python library is available at
[https://petab.readthedocs.io/en/latest/](https://petab.readthedocs.io/en/latest/).

## References
## Examples

Where PEtab is used / supported:
A wide range of PEtab examples can be found in the systems biology parameter estimation
[benchmark problem collection](https://github.com/Benchmarking-Initiative/Benchmark-Models-PEtab).

- Within the systems biology optimization
[benchmark problem collection](https://github.com/Benchmarking-Initiative/Benchmark-Models-PEtab)

## PEtab support in systems biology tools

Where PEtab is supported (in alphabetical order):


- [AMICI](https://github.com/ICB-DCM/AMICI/)

- A PEtab -> [COPASI](http://copasi.org/)
[converter](https://github.com/copasi/python-petab-importer)

- [d2d](https://github.com/Data2Dynamics/d2d/)
([HOWTO](https://github.com/Data2Dynamics/d2d/wiki/Support-for-PEtab))

- [dmod](https://github.com/dkaschek/dMod/)
- [dMod](https://github.com/dkaschek/dMod/)

- [meigo](http://gingproc.iim.csic.es/meigo.html)
- [MEIGO](http://gingproc.iim.csic.es/meigo.html)

- [AMICI](https://github.com/ICB-DCM/AMICI/)
- [parPE](https://github.com/ICB-DCM/parPE/)

- [pyPESTO](https://github.com/ICB-DCM/pyPESTO/)
- [pyABC](https://github.com/ICB-DCM/pyABC/) ([Example](https://pyabc.readthedocs.io/en/latest/examples/petab.html))

- [pyABC](https://github.com/ICB-DCM/pyABC/)
- [pyPESTO](https://github.com/ICB-DCM/pyPESTO/)
([Example](https://pypesto.readthedocs.io/en/latest/example/petab_import.html))

If your project or tool is using PEtab, and you would like to have it listed
here, please let us know.
here, please [let us know](https://github.com/PEtab-dev/PEtab/issues).

### PEtab features supported in different tools

The following list provides an overview of supported PEtab features in
different tools, based on passed test cases of the
[PEtab test suite](https://github.com/PEtab-dev/petab_test_suite):

| ID | Test | AMICI<br>*`develop`* | Copasi | D2D | dMod | MEIGO | parPE<br>*`develop`* | pyABC | pyPESTO<br>*`develop`* |
|----|----------------------------------------------------------------|----------------------|--------|-----|------|-------|-----------------------|-------|------------------------|
| 1 | Basic simulation | +++ | | +++ | | +++ | --+ | +++ | +++ |
| 2 | Multiple simulation conditions | +++ | | +++ | | +++ | --+ | +++ | +++ |
| 3 | Numeric observable parameter overrides in measurement table | +++ | | +++ | | +++ | --+ | +++ | +++ |
| 4 | Parametric observable parameter overrides in measurement table | +++ | | +++ | | +++ | --+ | +++ | +++ |
| 5 | Parametric overrides in condition table | +++ | | +++ | | +++ | --+ | +++ | +++ |
| 6 | Time-point specific overrides in the measurement table | --- | | +++ | | --- | --- | --- | --- |
| 7 | Observable transformations to log10 scale | +-+ | | +++ | | ++- | --+ | +-+ | +-+ |
| 8 | Replicate measurements | +++ | | +++ | | --- | --+ | +++ | +++ |
| 9 | Pre-equilibration | +++ | | +++ | | --- | --+ | +++ | +++ |
| 10 | Partial pre-equilibration | +++ | | +++ | | --- | --+ | +++ | +++ |
| 11 | Numeric initial concentration in condition table | +++ | | +++ | | --- | --+ | +++ | +++ |
| 12 | Numeric initial compartment sizes in condition table | --- | | +++ | | --- | --- | --- | --- |
| 13 | Parametric initial concentrations in condition table | +++ | | +++ | | --- | --+ | +++ | +++ |
| 14 | Numeric noise parameter overrides in measurement table | +++ | | +++ | | +++ | --+ | +++ | +++ |
| 15 | Parametric noise parameter overrides in measurement table | +++ | | +++ | | +++ | --+ | +++ | +++ |
| 16 | Observable transformations to log scale | +-+ | | +++ | | ++- | --+ | +-+ | +-+ |

Legend:
* First character indicates whether computing simulated data is supported and simulations are correct (+) or not (-)
* Second character indicates whether computing chi2 values of residuals are supported and correct (+) or not (-)
* Third character indicates whether computing likelihoods is supported and correct (+) or not (-)

## Using PEtab

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1. Create a condition table, if appropriate

1. Create a table of observables

1. Create a table of measurements

1. Create a parameter table
Expand All @@ -88,8 +128,9 @@ further questions regarding PEtab, feel free to post an

## PEtab Python library

PEtab comes with a Python package for creating, checking, and working with
PEtab files. This library is available on pypi and the easiest way to install
PEtab comes with a Python package for creating, checking, visualizing and
working with PEtab files. This library is available on
[pypi](https://pypi.org/project/petab/) and the easiest way to install
it is running

pip3 install petab
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`petablint`

- `petab.create_parameter_df` to create the parameter table, once you
have set up the model, condition table and measurement table
have set up the model, condition table, observable table and measurement
table

- `petab.create_combine_archive` to create a
[COMBINE Archive](https://combinearchive.org/index/) from PEtab files

### Library examples

Examples for PEtab Python library usage:

* [Validation](https://github.com/PEtab-dev/PEtab/blob/master/doc/example/example_petablint.ipynb)
* [Visualization](https://github.com/PEtab-dev/PEtab/blob/master/doc/example/example_visualization.ipynb)


## Getting help

- Functions in `petab.migrations` for updating PEtab files from earlier
versions
If you have any question or problems with PEtab, feel free to post them at
our GitHub [issue tracker](https://github.com/PEtab-dev/PEtab/issues/).

## Extending PEtab
## Contributing to PEtab

We are aware of the fact that PEtab may not serve everybody's needs. If you
have a suggestion of how to extend PEtab, feel free to post an issue at our
github repository.
Contributions and feedback to PEtab are very welcome, see our
[contribution guide](CONTRIBUTING.md).
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