Release 0.1.18

.readthedocs.yaml

@@ -0,0 +1,17 @@
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+version: 2
+
+sphinx:
+   configuration: doc/conf.py
+   fail_on_warning: true
+
+
+python:
+   version: 3.8
+   install:
+   - method: pip
+     path: .
+     extra_requirements:
+        - doc

CHANGELOG.md

@@ -2,6 +2,12 @@
 
 ## 0.1 series
 
+### 0.1.18
+
+* Fixed various documentation issues
+* Parameter mapping: Added option to ignore time-point specific
+  noiseParameters (#51)
+
 ### 0.1.17
 
 * Updated package URL

README.md

@@ -1,4 +1,4 @@
-![CI tests](https://github.com/PEtab-dev/libpetab-python/workflows/CI%20tests/badge.svg)
+[![CI](https://github.com/PEtab-dev/libpetab-python/actions/workflows/ci_tests.yml/badge.svg?branch=master)](https://github.com/PEtab-dev/libpetab-python/actions/workflows/ci_tests.yml)
 [![Codacy Badge](https://api.codacy.com/project/badge/Grade/fd7dd5cee68e449983be5c43f230c7f3)](https://www.codacy.com/gh/PEtab-dev/libpetab-python)
 [![codecov](https://codecov.io/gh/PEtab-dev/libpetab-python/branch/master/graph/badge.svg)](https://codecov.io/gh/PEtab-dev/libpetab-python)
 [![PyPI version](https://badge.fury.io/py/petab.svg)](https://badge.fury.io/py/petab)
@@ -34,16 +34,18 @@ Development versions of the PEtab library can be installed using
 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
+  - The [PEtab validator](https://petab.readthedocs.io/projects/libpetab-python/en/latest/example/example_petablint.html),
+    which is automatically installed using Python
+    entrypoints to be available as a shell command from anywhere, called
     `petablint`
 
-  - `petab.create_parameter_df` to create the parameter table, once you
-    have set up the model, condition table, observable table and measurement
-    table
+  - [`petab.create_parameter_df`](https://petab.readthedocs.io/projects/libpetab-python/en/latest/build/_autosummary/petab.parameters.html#petab.parameters.create_parameter_df)
+    to create the parameter table, once you have set up the model, 
+    condition table, observable table and measurement table
 
-  - `petab.create_combine_archive` to create a
-    [COMBINE Archive](https://combinearchive.org/index/) from PEtab files
+  - [`petab.create_combine_archive`](https://petab.readthedocs.io/projects/libpetab-python/en/latest/build/_autosummary/petab.core.html#petab.core.create_combine_archive)
+    to create a [COMBINE Archive](https://combinearchive.org/index/) from PEtab
+    files
 
 ## Examples
 

doc/conf.py

@@ -4,28 +4,30 @@
 # list see the documentation:
 # https://www.sphinx-doc.org/en/master/usage/configuration.html
 
+import os
+import subprocess
+import sys
+import warnings
+
 # -- 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 = '2018-2021, the PEtab developers'
+project = 'libpetab-python'
+copyright = '2018, the PEtab developers'
 author = 'PEtab developers'
 
 # The full version, including alpha/beta/rc tags
 release = 'latest'
 
 # -- Custom pre-build --------------------------------------------------------
 
-import subprocess
 
 subprocess.run(['python', 'md2rst.py'])
 
@@ -37,19 +39,33 @@
 extensions = [
     'sphinx.ext.napoleon',
     'sphinx.ext.autodoc',
-    'recommonmark',
     'sphinx.ext.autosummary',
+    'sphinx.ext.intersphinx',
+    'sphinx.ext.viewcode',
+    'recommonmark',
     'sphinx_markdown_tables',
     'nbsphinx',
 ]
 
+intersphinx_mapping = {
+    'pandas': ('https://pandas.pydata.org/docs/', None),
+    'numpy': ('https://numpy.org/devdocs/', None),
+    'sympy': ('https://docs.sympy.org/latest/', None),
+    'python': ('https://docs.python.org/3', None),
+}
+
 # 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 = ['build/doctrees', 'build/html']
+exclude_patterns = [
+    'build/doctrees',
+    'build/html',
+    '**.ipynb_checkpoints',
+    'logo/LICENSE.md',
+]
 
 master_doc = 'index'
 
@@ -72,14 +88,21 @@
     '.md': 'markdown',
 }
 
+# ignore numpy warnings
+warnings.filterwarnings("ignore", message="numpy.dtype size changed")
+warnings.filterwarnings("ignore", message="numpy.ufunc size changed")
+# ignore recommonmark warnings
+#  https://github.com/readthedocs/recommonmark/issues/177
+warnings.filterwarnings("ignore",
+                        message="Container node skipped: type=document")
+
 # -- 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'
-def setup(app):
-    app.add_stylesheet('custom.css')
+
 # 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".
@@ -94,3 +117,14 @@ def setup(app):
 }
 
 html_logo = 'logo/PEtab.png'
+
+
+def skip_some_objects(app, what, name, obj, skip, options):
+    """Exclude some objects from the documentation"""
+    if getattr(obj, '__module__', None) == 'collections':
+        return True
+
+
+def setup(app):
+    """Sphinx setup"""
+    app.connect('autodoc-skip-member', skip_some_objects)