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Merge pull request #387 from ICB-DCM/develop
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Release 0.1.0
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yannikschaelte authored Jun 17, 2020
2 parents f74b4d0 + 939d289 commit 6b34642
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4 changes: 4 additions & 0 deletions .gitignore
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Expand Up @@ -83,6 +83,10 @@ coverage_py.xml
doc/example/tmp
doc/example/amici_models/*

# storage
*.hdf5
*.csv

# general
data/.snakemake
data/.spyderproject
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8 changes: 5 additions & 3 deletions .rtd_pip_reqs.txt
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@@ -1,3 +1,5 @@
ipython
nbsphinx
sphinx_rtd_theme
ipython>=7.14.0
nbsphinx>=0.6.0
recommonmark>=0.6.0
sphinx_rtd_theme>=0.4.3
sphinx>=3.0.4
53 changes: 35 additions & 18 deletions .travis.yml
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@@ -1,11 +1,11 @@
language: python
python:
- "3.6"
- "3.8"

os:
- linux
dist:
- xenial
- bionic
compiler:
- gcc

Expand All @@ -15,39 +15,56 @@ addons:
apt:
update: true
packages:
- libhdf5-serial-dev
- zlib1g-dev
- libatlas-base-dev
- build-essential
- coinor-libipopt1v5
- coinor-libipopt-dev
- gfortran
- lcov
- swig3.0
- libatlas-base-dev
- libhdf5-serial-dev
- pandoc
- pkg-config
- python-dev
- swig3.0
- zlib1g-dev

install:
- mkdir -p ~/bin/ && ln -s /usr/bin/swig3.0 ~/bin/swig && export PATH=~/bin/:$PATH
- pip3 install --upgrade -r ./.travis_pip_reqs.txt
- pip3 install .
- pip3 install -r ./.travis_pip_reqs.txt
- pip3 install .[ipopt,dlib,pyswarm,pymc3]
- pip3 install https://github.com/petab-dev/petab/archive/develop.zip
- pip3 install -e
git+https://github.com/icb-dcm/amici.git@develop#egg=amici\&subdirectory=python/sdist
- git clone --depth 1
https://github.com/petab-dev/petab_test_suite tmp/petab_test_suite
- pip3 install -e tmp/petab_test_suite
- if [ "$TRAVIS_PULL_REQUEST" = "false" ]; then
git clone --depth 1
https://github.com/petab-dev/petab_test_suite tmp/petab_test_suite;
pip3 install -e tmp/petab_test_suite;
fi
- if [ "$TRAVIS_PULL_REQUEST" != "false" ]; then
pip install -r .rtd_pip_reqs.txt;
fi

# run tests
script:
- python3 -m flake8
--exclude=build,doc,example,tmp,amici_models
--per-file-ignores='*/__init__.py:F401'
- travis_wait 20 python3 -m pytest --cov=pypesto ./test/test_*
- travis_wait 20 xvfb-run -a python3 -m pytest
--cov=pypesto --cov-append ./test/visualize/test_*
- if [ "$TRAVIS_PULL_REQUEST" = "false" ]; then
./run_flake8.sh;
fi
- if [ "$TRAVIS_PULL_REQUEST" = "false" ]; then
travis_wait 20 python3 -m pytest --cov=pypesto ./test/test_*;
fi
- if [ "$TRAVIS_PULL_REQUEST" = "false" ]; then
travis_wait 20 xvfb-run -a python3 -m pytest
--cov=pypesto --cov-append ./test/visualize/test_*;
fi
- if [ "$TRAVIS_PULL_REQUEST" != "false" ]; then
sphinx-build -W -b html -d doc/_build/html doc/ doc/_build/html;
fi
- if [ "$TRAVIS_PULL_REQUEST" != "false" ]; then
test/run_notebook.sh doc/example/;
fi
- coverage xml
- if [ "$TRAVIS_PULL_REQUEST" = "false" ]; then
coverage xml;
fi

after_success:
- bash <(curl -s https://codecov.io/bash)
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7 changes: 5 additions & 2 deletions .travis_pip_reqs.txt
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Expand Up @@ -6,9 +6,12 @@ pytest
pytest-cov
coverage
flake8
dlib
pyswarm
flake8-bugbear
flake8-bandit
flake8-print
flake8-comprehensions
gitpython
sphinx
nbsphinx
sphinx_rtd_theme
cython
4 changes: 2 additions & 2 deletions doc/README.md
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@@ -1,6 +1,6 @@
# pyPESTO Documentation
# Documentation

This folder contains files for building the documentation of this package.
The `doc/` folder contains the files for building the pyPESTO documentation.


## Requirements
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4 changes: 0 additions & 4 deletions doc/api_engine.rst
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@@ -1,5 +1 @@
.. automodule:: pypesto.engine
:members:
:inherited-members:
:special-members:
:imported-members:
4 changes: 0 additions & 4 deletions doc/api_logging.rst
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@@ -1,5 +1 @@
.. automodule:: pypesto.logging
:members:
:inherited-members:
:special-members:
:imported-members:
4 changes: 0 additions & 4 deletions doc/api_objective.rst
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@@ -1,5 +1 @@
.. automodule:: pypesto.objective
:members:
:inherited-members:
:special-members:
:imported-members:
4 changes: 0 additions & 4 deletions doc/api_optimize.rst
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@@ -1,5 +1 @@
.. automodule:: pypesto.optimize
:members:
:inherited-members:
:special-members:
:imported-members:
4 changes: 0 additions & 4 deletions doc/api_petab.rst
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@@ -1,5 +1 @@
.. automodule:: pypesto.petab
:members:
:inherited-members:
:special-members:
:imported-members:
4 changes: 0 additions & 4 deletions doc/api_problem.rst
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@@ -1,5 +1 @@
.. automodule:: pypesto.problem
:members:
:inherited-members:
:special-members:
:imported-members:
4 changes: 0 additions & 4 deletions doc/api_profile.rst
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@@ -1,5 +1 @@
.. automodule:: pypesto.profile
:members:
:inherited-members:
:special-members:
:imported-members:
4 changes: 0 additions & 4 deletions doc/api_result.rst
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@@ -1,5 +1 @@
.. automodule:: pypesto.result
:members:
:inherited-members:
:special-members:
:imported-members:
4 changes: 0 additions & 4 deletions doc/api_sampling.rst
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@@ -1,5 +1 @@
.. automodule:: pypesto.sampling
:members:
:inherited-members:
:special-members:
:imported-members:
4 changes: 0 additions & 4 deletions doc/api_startpoint.rst
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@@ -1,5 +1 @@
.. automodule:: pypesto.startpoint
:members:
:inherited-members:
:special-members:
:imported-members:
4 changes: 0 additions & 4 deletions doc/api_storage.rst
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@@ -1,5 +1 @@
.. automodule:: pypesto.storage
:members:
:inherited-members:
:special-members:
:imported-members:
4 changes: 0 additions & 4 deletions doc/api_visualize.rst
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@@ -1,5 +1 @@
.. automodule:: pypesto.visualize
:members:
:inherited-members:
:special-members:
:imported-members:
17 changes: 10 additions & 7 deletions doc/conf.py
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Expand Up @@ -25,23 +25,26 @@
# -- General configuration ------------------------------------------------

# If your documentation needs a minimal Sphinx version, state it here.
#
# needs_sphinx = '1.0'
needs_sphinx = '3.0.4'

# Add any Sphinx extension module names here, as strings. They can be
# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
# ones.
extensions = ['sphinx.ext.autodoc',
'sphinx.ext.napoleon',
'IPython.sphinxext.ipython_console_highlighting',
'nbsphinx']
'nbsphinx',
'recommonmark']

# default autodoc options
# list for special-members seems not to be possible before 1.8
autodoc_default_flags = ['members',
'undoc-members',
'show-inheritance',
'imported-members']
autodoc_default_options = {
'members': True,
'undoc-members': True,
'special-members': '__init__, __call__',
'imported-members': True,
'show-inheritance': True,
}

# Add any paths that contain templates here, relative to this directory.
templates_path = ['_templates']
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6 changes: 4 additions & 2 deletions doc/examples.rst → doc/example.rst
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Expand Up @@ -11,8 +11,9 @@ The following examples cover typical use cases and should help get a better idea
example/fixed_parameters.ipynb
example/boehm_JProteomeRes2014.ipynb
example/petab_import.ipynb
example/hdf5_storage_result.ipynb
example/storage.ipynb
example/sampler_study.ipynb
example/sampling_diagnostics.ipynb

Download the examples as notebooks
----------------------------------
Expand All @@ -22,8 +23,9 @@ Download the examples as notebooks
* :download:`Fixed parameters <example/fixed_parameters.ipynb>`
* :download:`Boehm model <example/boehm_JProteomeRes2014.ipynb>`
* :download:`Petab import <example/petab_import.ipynb>`
* :download:`HDF5 storage <example/hdf5_storage_result.ipynb>`
* :download:`Storage <example/storage.ipynb>`
* :download:`Sampler study <example/sampler_study.ipynb>`
* :download:`Sampling diagnostics <example/sampling_diagnostics.ipynb>`

.. Note::
Some of the notebooks have extra dependencies.
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