Merge pull request #387 from ICB-DCM/develop

Release 0.1.0
ICB-DCM · Jun 17, 2020 · 6b34642 · 6b34642
2 parents f74b4d0 + 939d289
commit 6b34642
Show file tree

Hide file tree

Showing 93 changed files with 6,397 additions and 3,646 deletions.
diff --git a/.gitignore b/.gitignore
@@ -83,6 +83,10 @@ coverage_py.xml
 doc/example/tmp
 doc/example/amici_models/*
 
+# storage
+*.hdf5
+*.csv
+
 # general
 data/.snakemake
 data/.spyderproject

diff --git a/.rtd_pip_reqs.txt b/.rtd_pip_reqs.txt
@@ -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
diff --git a/.travis.yml b/.travis.yml
@@ -1,11 +1,11 @@
 language: python
 python:
-  - "3.6"
+  - "3.8"
 
 os:
   - linux
 dist:
-  - xenial
+  - bionic
 compiler:
   - gcc
 
@@ -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)

diff --git a/.travis_pip_reqs.txt b/.travis_pip_reqs.txt
@@ -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
diff --git a/doc/README.md b/doc/README.md
@@ -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

diff --git a/doc/api_engine.rst b/doc/api_engine.rst
@@ -1,5 +1 @@
 .. automodule:: pypesto.engine
-   :members:
-   :inherited-members:
-   :special-members:
-   :imported-members:
diff --git a/doc/api_logging.rst b/doc/api_logging.rst
@@ -1,5 +1 @@
 .. automodule:: pypesto.logging
-   :members:
-   :inherited-members:
-   :special-members:
-   :imported-members:
diff --git a/doc/api_objective.rst b/doc/api_objective.rst
@@ -1,5 +1 @@
 .. automodule:: pypesto.objective
-   :members:
-   :inherited-members:
-   :special-members:
-   :imported-members:
diff --git a/doc/api_optimize.rst b/doc/api_optimize.rst
@@ -1,5 +1 @@
 .. automodule:: pypesto.optimize
-   :members:
-   :inherited-members:
-   :special-members:
-   :imported-members:
diff --git a/doc/api_petab.rst b/doc/api_petab.rst
@@ -1,5 +1 @@
 .. automodule:: pypesto.petab
-   :members:
-   :inherited-members:
-   :special-members:
-   :imported-members:
diff --git a/doc/api_problem.rst b/doc/api_problem.rst
@@ -1,5 +1 @@
 .. automodule:: pypesto.problem
-   :members:
-   :inherited-members:
-   :special-members:
-   :imported-members:
diff --git a/doc/api_profile.rst b/doc/api_profile.rst
@@ -1,5 +1 @@
 .. automodule:: pypesto.profile
-   :members:
-   :inherited-members:
-   :special-members:
-   :imported-members:
diff --git a/doc/api_result.rst b/doc/api_result.rst
@@ -1,5 +1 @@
 .. automodule:: pypesto.result
-   :members:
-   :inherited-members:
-   :special-members:
-   :imported-members:
diff --git a/doc/api_sampling.rst b/doc/api_sampling.rst
@@ -1,5 +1 @@
 .. automodule:: pypesto.sampling
-   :members:
-   :inherited-members:
-   :special-members:
-   :imported-members:
diff --git a/doc/api_startpoint.rst b/doc/api_startpoint.rst
@@ -1,5 +1 @@
 .. automodule:: pypesto.startpoint
-   :members:
-   :inherited-members:
-   :special-members:
-   :imported-members:
diff --git a/doc/api_storage.rst b/doc/api_storage.rst
@@ -1,5 +1 @@
 .. automodule:: pypesto.storage
-   :members:
-   :inherited-members:
-   :special-members:
-   :imported-members:
diff --git a/doc/api_visualize.rst b/doc/api_visualize.rst
@@ -1,5 +1 @@
 .. automodule:: pypesto.visualize
-   :members:
-   :inherited-members:
-   :special-members:
-   :imported-members:
diff --git a/doc/conf.py b/doc/conf.py
@@ -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']

diff --git a/doc/examples.rst → doc/example.rst b/doc/examples.rst → doc/example.rst
@@ -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
 ----------------------------------
@@ -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.