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

@@ -1,7 +1,6 @@
-# Optimization problem data format specification
-
-This document explains the data format used for the benchmark collection.
+# PEtab data format specification
 
+This document explains the PEtab data format.
 
 ## Purpose
 
@@ -12,10 +11,11 @@ systems biology, especially for the case of Ordinary Differential Equation
 
 ## Overview
 
-This data format specifies a parameter estimation problems using a number of
-text-based files ([Systems Biology Markup Language (SBML)](http://sbml.org)
-and [Tab-Separated Values
-(TSV)](https://www.iana.org/assignments/media-types/text/tab-separated-values)), i.e.
+The PEtab data format specifies a parameter estimation problem using a number
+of text-based files ([Systems Biology Markup Language (SBML)](http://sbml.org)
+and
+[Tab-Separated Values (TSV)](https://www.iana.org/assignments/media-types/text/tab-separated-values)),
+i.e.
 
 - An SBML model [SBML]
 
@@ -33,6 +33,8 @@ and [Tab-Separated Values
 - (optional) A visualization file, which contains specifications how the data
   and/or simulations should be plotted by the visualization routines [TSV]
 
+![Files constituting a PEtab problem](gfx/petab_files.png)
+
 The following sections will describe the minimum requirements of those
 components in the core standard, which should provide all information for
 defining the parameter estimation problem.