search

Benchmarking-Initiative / Benchmark-Models-PEtab

A collection of mathematical models with experimental data in the PEtab format as benchmark problems in order to evaluate new and existing methodologies for data-based modelling
BSD 3-Clause "New" or "Revised" License
26 stars 14 forks source link

Add python package #167

Closed yannikschaelte closed 2 years ago

yannikschaelte commented 2 years ago

OLD, UPDATED BELOW:

dweindl commented 2 years ago

  • [ ] Someone with admin rights would need to upload secrets for twine for auto-deploy

  • Upon model additions/edits, new releases would need to be created on pypi to ensure consistency. Possible to automate?

Do we really need it on pypi? Could just pip install it from github? Saves us from changing the version number in every commit.

yannikschaelte commented 2 years ago
  • [ ] Someone with admin rights would need to upload secrets for twine for auto-deploy
  • Upon model additions/edits, new releases would need to be created on pypi to ensure consistency. Possible to automate?

Do we really need it on pypi? Could just pip install it from github? Saves us from changing the version number in every commit.

@dweindl I removed the pypi deploy. However, while pip install git+... is possible, I'm not sure how an install from git with source would work?

dweindl commented 2 years ago

I'm not sure how an install from git with source would work?

Ah, right, won't work with that directory structure :(. Would have to move everything into the package directory. Wouldn't do that.

:thinking:

dweindl commented 2 years ago

I'm not sure how an install from git with source would work?

Ah, right, won't work with that directory structure :(. Would have to move everything into the package directory. Wouldn't do that.

thinking

Ah no, at least on Linux pip install git+https://github.com/Benchmarking-Initiative/Benchmark-Models-PEtab.git@fixes_ys#subdirectory=src/python works.

Could somebody tests this on Windows?

pip install git+https://github.com/Benchmarking-Initiative/Benchmark-Models-PEtab.git@fixes_ys#subdirectory=src/python
python -c "from benchmark_models_petab import get_problem; print(get_problem('Zheng_PNAS2012').get_x_ids())"

I guess it only works if symlinks are enabled?!

yannikschaelte commented 2 years ago

I'm not sure how an install from git with source would work?

Ah, right, won't work with that directory structure :(. Would have to move everything into the package directory. Wouldn't do that. thinking

Ah no, at least on Linux pip install git+https://github.com/Benchmarking-Initiative/Benchmark-Models-PEtab.git@fixes_ys#subdirectory=src/python works.

Could somebody tests this on Windows?

pip install git+https://github.com/Benchmarking-Initiative/Benchmark-Models-PEtab.git@fixes_ys#subdirectory=src/python
python -c "from benchmark_models_petab import get_problem; print(get_problem('Zheng_PNAS2012').get_x_ids())"

I guess it only works if symlinks are enabled?!

Windows testing would take some effort. Maybe just assume we'll be notified when this becomes a problem?