Remove non-package-related files, update links (#41)

Remove everything that is not related to the petab Python package. Closes #39 Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com>
PEtab-dev · Mar 19, 2021 · fd34613 · fd34613
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diff --git a/.github/ISSUE_TEMPLATE/petab-specification-changes.md b/.github/ISSUE_TEMPLATE/petab-specification-changes.md
diff --git a/.github/workflows/ci_tests.yml b/.github/workflows/ci_tests.yml
@@ -8,7 +8,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.8]
+        python-version: [3.7, 3.8, 3.9]
 
     steps:
     - name: Check out repository

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -1,25 +1,7 @@
-# PEtab contribution guide
+# 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:
@@ -38,7 +20,7 @@ To contribute to this repository:
 
   *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).*
+  [https://github.com/PEtab-dev/libpetab-python/blob/master/LICENSE](https://github.com/PEtab-dev/libpetab-python/blob/master/LICENSE).*
 
 * Assign a reviewer, or let us know otherwise, that your pull request is ready
   for review.

diff --git a/LICENSE b/LICENSE
@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2018 Data-driven Computational Modelling
+Copyright (c) 2018 petab package developers
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/README.md b/README.md
@@ -1,156 +1,33 @@
-![CI tests](https://github.com/PEtab-dev/PEtab/workflows/CI%20tests/badge.svg)
-[![Codacy Badge](https://api.codacy.com/project/badge/Grade/fd7dd5cee68e449983be5c43f230c7f3)](https://www.codacy.com/gh/PEtab-dev/PEtab?utm_source=github.com&amp;utm_medium=referral&amp;utm_content=PEtab-dev/PEtab&amp;utm_campaign=Badge_Grade)
-[![codecov](https://codecov.io/gh/PEtab-dev/PEtab/branch/master/graph/badge.svg)](https://codecov.io/gh/PEtab-dev/PEtab)
+![CI tests](https://github.com/PEtab-dev/libpetab-python/workflows/CI%20tests/badge.svg)
+[![Codacy Badge](https://api.codacy.com/project/badge/Grade/fd7dd5cee68e449983be5c43f230c7f3)](https://www.codacy.com/gh/PEtab-dev/libpetab-python)
+[![codecov](https://codecov.io/gh/PEtab-dev/libpetab-python/branch/master/graph/badge.svg)](https://codecov.io/gh/PEtab-dev/libpetab-python)
 [![PyPI version](https://badge.fury.io/py/petab.svg)](https://badge.fury.io/py/petab)
 
-# PEtab -- a data format for specifying parameter estimation problems in systems biology
+# petab - a Python package for handling PEtab files
 
-![Logo](doc/logo/PEtab.png)
-
-*PEtab* is a data format for specifying parameter estimation problems in systems biology.
-This repository provides extensive documentation and a Python library for easy
-access and validation of *PEtab* files.
-
-## About PEtab
-
-PEtab is built around [SBML](http://sbml.org/) and based on tab-separated values 
-(TSV) files. It is meant as a standardized way to provide information for 
-parameter estimation, which is out of the current scope of SBML. This includes
-for example:
-
-  - Specifying and linking measurements to models
-
-    - Defining model outputs
-
-    - Specifying noise models
-
-  - Specifying parameter bounds for optimization
-
-  - Specifying multiple simulation condition with potentially shared parameters
-
-![PEtab files](doc/gfx/petab_files.png)
+[PEtab](https://petab.readthedocs.io/) is a data format for specifying
+parameter estimation problems in systems biology. This repository provides
+the `petab` Python package for reading, writing and validating PEtab files.
 
 ## Documentation
 
-Documentation of the PEtab data format and Python library is available at
+Documentation of the `petab` Python package is available at
+[https://libpetab-python.readthedocs.io/en/latest/](https://libpetab-python.readthedocs.io/en/latest/).
+Documentation of the PEtab format in general is available at
 [https://petab.readthedocs.io/en/latest/](https://petab.readthedocs.io/en/latest/).
 
-## Examples
-
-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).
-
-
-## PEtab support in systems biology tools
-
-Where PEtab is supported (in alphabetical order):
-
-
-  - [AMICI](https://github.com/ICB-DCM/AMICI/)
-    ([Example](https://github.com/ICB-DCM/AMICI/blob/master/python/examples/example_petab/petab.ipynb))
-
-  - 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/)
-    ([HOWTO](https://github.com/dkaschek/dMod/wiki/Support-for-PEtab))
-
-  - [MEIGO](https://github.com/gingproc-IIM-CSIC/MEIGO64)
-    ([HOWTO](https://github.com/gingproc-IIM-CSIC/MEIGO64/tree/master/MEIGO/PEtabMEIGO))
-
-  - [parPE](https://github.com/ICB-DCM/parPE/)
+## Installation
 
-  - [pyABC](https://github.com/ICB-DCM/pyABC/) ([Example](https://pyabc.readthedocs.io/en/latest/examples/petab.html))
-
-  - [pyPESTO](https://github.com/ICB-DCM/pyPESTO/)
-    ([Example](https://pypesto.readthedocs.io/en/latest/example/petab_import.html))
-
-  - [SBML2Julia](https://github.com/paulflang/SBML2Julia)
-    ([Tutorial](https://sbml2julia.readthedocs.io/en/latest/python_api.html))
-
-If your project or tool is using PEtab, and you would like to have it listed
-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>`>=0.10.20` | Copasi | D2D | dMod | MEIGO | parPE<br>`develop`  | pyABC<br>`>=0.10.1` | pyPESTO<br>`>=0.0.11` | SBML2Julia |
-|----|----------------------------------------------------------------|----------------------|--------|-----|------|-------|-----------------------|-------|------------------------|------------|
-| 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
-
-If you would like to use PEtab yourself, please have a look at:
-
-* [a PEtab tutorial](https://petab.readthedocs.io/en/latest/tutorial.html)
-  going through the individual steps of setting up a parameter estimation
-  problem in PEtab, independently of any specific software
-* [the PEtab format reference](https://petab.readthedocs.io/en/stable/documentation_data_format.html)
-* the example models provided in the
-  [benchmark collection](https://github.com/Benchmarking-Initiative/Benchmark-Models-PEtab).
-* the tutorials provided with each of the softwares supporting PEtab
-
-To convert your existing parameter estimation problem to the PEtab format, you 
-will have to:
-
-1. Specify your model in SBML.
-
-1. Create a condition table.
-
-1. Create a table of observables.
-
-1. Create a table of measurements.
-
-1. Create a parameter table.
-
-If you are using Python, some handy functions of the
-[PEtab library](https://petab.readthedocs.io/en/latest/modules.html) can help
-you with that. This include also a PEtab validator called `petablint` which
-you can use to check if your files adhere to the PEtab standard. If you have 
-further questions regarding PEtab, feel free to post an 
-[issue](https://github.com/PEtab-dev/PEtab/issues) at our github repository.
-
-## PEtab Python library
-
-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
+The PEtab library is available on [pypi](https://pypi.org/project/petab/)
+and the easiest way to install it is running
 
     pip3 install petab
 
 It will require Python>=3.7.1 to run.
 
 Development versions of the PEtab library can be installed using
 
-    pip3 install https://github.com/PEtab-dev/PEtab/archive/develop.zip
+    pip3 install https://github.com/PEtab-dev/libpetab-python/archive/develop.zip
 
 (replace `develop` by the branch or commit you would like to install).
 
@@ -168,20 +45,20 @@ be:
   - `petab.create_combine_archive` to create a
     [COMBINE Archive](https://combinearchive.org/index/) from PEtab files
 
-### Library examples
+## 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)
+* [Validation](https://github.com/PEtab-dev/libpetab-python/blob/master/doc/example/example_petablint.ipynb)
+* [Visualization](https://github.com/PEtab-dev/libpetab-python/blob/master/doc/example/example_visualization.ipynb)
 
 
 ## Getting help
 
-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/).
+If you have any question or problems with this package, feel free to post them
+at our GitHub [issue tracker](https://github.com/PEtab-dev/libpetab-python/issues/).
 
-## Contributing to PEtab
+## Contributing
 
-Contributions and feedback to PEtab are very welcome, see our
+Contributions and feedback to this package are very welcome, see our
 [contribution guide](CONTRIBUTING.md).
diff --git a/doc/compile_doc.sh b/doc/compile_doc.sh
diff --git a/doc/compile_tutorial.sh b/doc/compile_tutorial.sh
diff --git a/doc/conf.py b/doc/conf.py
@@ -17,8 +17,8 @@
 # -- Project information -----------------------------------------------------
 
 project = 'PEtab'
-copyright = '2019, Daniel Weindl, Yannik Schälte, Dantong Wang, Carolin Loos, Jan Hasenauer, Paul Stapor, Elba Raimúndez Álvarez, Erika Dudkin, Charles Tapley Hoyt, Fabian Fröhlich'
-author = 'Daniel Weindl, Yannik Schälte, Dantong Wang, Carolin Loos, Jan Hasenauer, Paul Stapor, Elba Raimúndez Álvarez, Erika Dudkin, Charles Tapley Hoyt, Fabian Fröhlich'
+copyright = '2018-2021, the PEtab developers'
+author = 'PEtab developers'
 
 # The full version, including alpha/beta/rc tags
 release = 'latest'
@@ -87,8 +87,8 @@ def setup(app):
 
 html_context = {
     "display_github": True,
-    "github_user": "ICB-DCM",
-    "github_repo": "petab",
+    "github_user": "petab-dev",
+    "github_repo": "libpetab-python",
     "github_version": "develop",
     "conf_py_path": "/doc",
 }