Documentation updates

doc/conf.py

@@ -14,6 +14,7 @@
 
 import os
 import sys
+import subprocess
 
 # 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
@@ -32,18 +33,20 @@
     'sphinx.ext.autodoc',
     # generate autodoc summaries
     'sphinx.ext.autosummary',
-    # use mathjax for latex formulas
-    'sphinx.ext.mathjax',
-    # link to code
-    'sphinx.ext.viewcode',
+    # test snippets in the documentation
+    'sphinx.ext.doctest',
+    # link to external urls
+    'sphinx.ext.extlinks',
     # link to other projects' docs
     'sphinx.ext.intersphinx',
+    # use mathjax for latex formulas
+    'sphinx.ext.mathjax',
     # support numpy and google style docstrings
     'sphinx.ext.napoleon',
     # support todo items
     'sphinx.ext.todo',
-    # test snippets in the documentation
-    'sphinx.ext.doctest',
+    # link to code
+    'sphinx.ext.viewcode',
     # source parser for jupyter notebook files
     'nbsphinx',
     # code highlighting in jupyter cells
@@ -52,6 +55,11 @@
     'sphinxcontrib.jquery',
 ]
 
+autodoc_mock_imports = [
+    "PEtab",
+    "BasiCO"
+]
+
 # default autodoc options
 # list for special-members seems not to be possible before 1.8
 autodoc_default_options = {
@@ -68,7 +76,7 @@
     'numpy': ('https://numpy.org/devdocs/', None),
     'scipy': ('https://docs.scipy.org/doc/scipy/', None),
     'pandas': ('https://pandas.pydata.org/pandas-docs/dev', None),
-    'petab': ('https://petab.readthedocs.io/en/stable/', None),
+    'petab': ('https://petab.readthedocs.io/en/latest/', None),
     'amici': ('https://amici.readthedocs.io/en/latest/', None),
     'sklearn': ('https://scikit-learn.org/stable/', None),
 }
@@ -99,6 +107,27 @@
 #
 # The short X.Y version.
 
+# Resolve the current branch name
+def get_branch():
+    # Read the Docs sets this automatically ("latest", "stable", branch name...)
+    rtd_version = os.environ.get("READTHEDOCS_VERSION")
+    if rtd_version and rtd_version not in ("latest", "stable"):
+        return rtd_version
+    try:
+        return subprocess.check_output(
+            ["git", "rev-parse", "--abbrev-ref", "HEAD"],
+            text=True
+        ).strip()
+    except Exception:
+        return "main"
+    return "main"
+
+# Set up links that resolve to the branch of the documentation
+branch = get_branch()
+extlinks = {
+    "repository": (f"https://github.com/ICB-DCM/pyABC/blob/{branch}/%s", "%s",),
+}
+
 import pyabc  # noqa: E402
 
 version = pyabc.__version__

doc/installation.rst

@@ -77,20 +77,11 @@ home directory with
 
 .. _anacondaCluster:
 
-Installing Anaconda on a Cluster environment
---------------------------------------------
-
-To install `Anaconda <https://anaconda.com/products/distribution>`_, run::
-
-   wget https://repo.anaconda.com/archive/Anaconda3-2021.11-Linux-x86_64.sh
-   bash Anaconda3-2021.11-Linux-x86_64.sh
-
-and follow the installation guide.
-Replace the "2021.11" by the most recent version of Anaconda, see
-https://repo.anaconda.com/archive.
+Installing Miniconda on a Cluster environment
+---------------------------------------------
 
 `Miniconda <https://docs.conda.io/en/latest/miniconda.html>`_
-provides an alternative, minimal installer for conda, including
+provides a minimal installer for conda, including
 only conda, Python, and some core and useful packages. Install the latest
 version via::
 
@@ -102,7 +93,7 @@ version via::
 Optional dependencies
 ---------------------
 
-pyABC has various optional dependencies, see `setup.cfg`.
+pyABC has various optional dependencies, see :repository:`pyproject.toml`.
 
 In particular, pyABC has optional interfaces to the :ref:`R <api_external_r>`
 and :ref:`Julia <api_external_julia>` languages, see the API documentation