Merge pull request #173 from ICB-DCM/release_0.0.0a17

Release 0.0.0a17

.rtd_pip_reqs.txt

@@ -0,0 +1,5 @@
+sphinx
+sphinxcontrib-napoleon
+sphinx-markdown-tables
+sphinx-rtd-theme
+recommonmark

.travis.yml

@@ -2,14 +2,18 @@ language: python
 
 python:
 - '3.6'
+
 install:
-- pip install -U pytest pytest-cov codecov flake8
-- pip install -e .
+- pip install -U -r ./.travis_pip_reqs.txt
+- pip install -e .[reports]
+
 script:
 - pytest --cov
 - python3 -m flake8 --exclude=build,doc,example,tmp
+
 after_success:
 - codecov
+
 deploy:
   provider: pypi
   username: yannik.schaelte

.travis_pip_reqs.txt

@@ -0,0 +1,9 @@
+pytest
+pytest-cov
+codecov
+flake8
+sphinx
+sphinxcontrib-napoleon
+sphinx-markdown-tables
+sphinx-rtd-theme
+recommonmark

CHANGELOG.md

@@ -0,0 +1,28 @@
+# PEtab changelog
+
+### 0.0.0a17
+
+Data format: *No changes*
+
+Library:
+* Extended visualization support
+* Add helper function and test case to deal with timepoint-specific parameters
+  flatten_timepoint_specific_output_overrides (#128) (Closes #125)
+* Fix get_noise_distributions: so far we got 'normal' everywhere due to 
+  wrong grouping (#147)
+* Fix create_parameter_df: Exclude rule targets (#149)
+* Verify condition table column names occur as model parameters
+  (Closes #150) (#151)
+* More informative error messages in case of wrongly set observable and
+  noise parameters (Closes #118) (#155)
+* Update doc for copasi import and github installation (#158) 
+* Extend validator to check if all required parameters are present in
+  parameter table (Closes #43) (#159)
+* Setup documentation for RTD (#161)
+* Handle None in petab.core.split_parameter_replacement_list (Closes #121) 
+* Fix(lint) correct handling of optional columns. Check before access.
+* Remove obsolete generate_experiment_id.py (Closes #111) #166 
+
+### 0.0.0a16 and earlier
+
+See git history

README.md

@@ -36,7 +36,10 @@ for example:
 Where PEtab is used / supported:
 
   - Within the systems biology optimization 
-    [benchmark problem collection](https://github.com/LoosC/Benchmark-Models)
+    [benchmark problem collection](https://github.com/LeonardSchmiester/Benchmark-Models)
+
+  - A PEtab -> [COPASI](http://copasi.org/)
+    [converter](https://github.com/copasi/python-petab-importer)
 
   - [pyPESTO](https://github.com/ICB-DCM/pyPESTO/)
 
@@ -85,15 +88,24 @@ it is running
 
 It will require Python3.6 to run.
 
+Development versions of the PEtab library can be installed using
+
+    pip3 install https://github.com/ICB-DCM/PEtab/archive/develop.zip
+
+(replace `develop` by the branch or commit you would like to install).
+
 When setting up a new parameter estimation problem, the most useful tools will
 be:
 
-  - The PEtab validator, which is now automatically installed using Python entrypoints to 
-    be available as a shell command from anywhere called `petablint`
+  - The **PEtab validator**, which is now automatically installed using Python
+    entrypoints to be available as a shell command from anywhere called
+    `petablint`
 
   - `petab.core.create_parameter_df` to create the parameter table, once you
     have set up the model, condition table and measurement table
 
+  - Functions in `petab.sbml` to define observables and error model parameters
+    in the SBML model
 
 ## Extending PEtab
 

doc/CHANGELOG.md

@@ -0,0 +1 @@
+../CHANGELOG.md

doc/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

doc/conf.py

@@ -0,0 +1,78 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+import os
+import sys
+sys.path.insert(0, os.path.abspath('..'))
+
+# -- 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'
+
+# The full version, including alpha/beta/rc tags
+release = 'latest'
+
+
+# -- General configuration ---------------------------------------------------
+
+# 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.napoleon',
+    'sphinx.ext.autodoc',
+    'recommonmark',
+    'sphinx.ext.autosummary',
+    'sphinx_markdown_tables',
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = []
+
+master_doc = 'index'
+
+autosummary_generate = True
+
+autodoc_default_options = {
+    "members": None,
+    "imported-members": None,
+    "inherited-members": None,
+    "private-members": None,
+    "show-inheritance": None,
+}
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = 'sphinx_rtd_theme'
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']
+
+html_context = {
+    "display_github": True,
+    "github_user": "ICB-DCM",
+    "github_repo": "petab",
+    "github_version": "develop",
+    "conf_py_path": "/doc",
+}

doc/documentation_data_format.md

@@ -1,4 +1,4 @@
-# Optimization problem data format specification
+# PEtab data format specification
 
 This document explains the PEtab data format.
 

doc/index.rst

@@ -0,0 +1,29 @@
+Welcome to PEtab's documentation!
+=================================
+
+.. toctree::
+   :maxdepth: 3
+   :caption: Data format
+
+   Data format <documentation_data_format.md>
+
+.. toctree::
+   :maxdepth: 3
+   :caption: Python package
+
+   modules
+
+.. toctree::
+   :maxdepth: 2
+   :caption: About
+
+   Changelog <CHANGELOG.md>
+   license
+   logo/LICENSE.md
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

doc/license.rst

@@ -0,0 +1,4 @@
+License
+=======
+
+.. literalinclude:: ../LICENSE

doc/logo/LICENSE.md

@@ -1,3 +1,6 @@
-# PEtab logo licence
+# PEtab logo license
 
-The PEtab logo is free for use under the [CC0](https://creativecommons.org/share-your-work/public-domain/cc0) license.
+The PEtab logo is free for use under the
+[CC0](https://creativecommons.org/share-your-work/public-domain/cc0) license.
+
+![Logo](PEtab.png)

doc/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=.
+set BUILDDIR=build
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.http://sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

doc/modules.rst

@@ -0,0 +1,12 @@
+API Reference
+=============
+
+.. autosummary::
+   :toctree: build/_autosummary
+
+   petab
+   petab.core
+   petab.lint
+   petab.parameter_mapping
+   petab.petablint
+   petab.sbml

petab/__init__.py

@@ -1,6 +1,7 @@
+"""PEtab exports"""
+
 from .core import *  # noqa: F403, F401
 from .lint import *  # noqa: F403, F401
 from .sbml import *  # noqa: F403, F401
 from .parameter_mapping import *  # noqa: F403, F401
-from .generate_experiment_id import generate_experiment_id  # noqa: F403, F401
 from .version import __version__  # noqa: F401