Release 0.1.11

.github/workflows/ci.yml

@@ -3,12 +3,14 @@ name: CI
 # trigger
 on:
   push:
-    branches:
-    - main
   pull_request:
+    branches:
+      - main
   schedule:
     # run Tuesday and Friday at 02:00 UTC
     - cron: '00 2 * * TUE,FRI'
+  workflow_dispatch:
+  merge_group:
 
 jobs:
   base:

.pre-commit-config.yaml

@@ -5,12 +5,12 @@
 
 repos:
 - repo: https://github.com/psf/black
-  rev: 22.6.0
+  rev: 23.10.0
   hooks:
   - id: black
     description: The uncompromising code formatter
 - repo: https://github.com/pycqa/isort
-  rev: 5.10.1
+  rev: 5.12.0
   hooks:
   - id: isort
     name: isort (python)
@@ -21,14 +21,14 @@ repos:
     name: isort (pyi)
     types: [pyi]
 - repo: https://github.com/nbQA-dev/nbQA
-  rev: 1.3.1
+  rev: 1.7.0
   hooks:
     - id: nbqa-black
     - id: nbqa-pyupgrade
       args: [--py36-plus]
     - id: nbqa-isort
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.3.0
+  rev: v4.5.0
   hooks:
   - id: check-yaml
     description: Check yaml files for parseable syntax

.readthedocs.yaml

@@ -0,0 +1,27 @@
+# .readthedocs.yml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  builder: html
+  configuration: doc/conf.py
+  fail_on_warning: True
+
+python:
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - doc
+
+build:
+  os: "ubuntu-22.04"
+  apt_packages:
+    - libatlas-base-dev
+    - swig
+  tools:
+    python: "3.11"

changes.md

@@ -1,5 +1,15 @@
 # Changes
 
+## 0.1.11
+- fixed bug in stepwise moves when working with multiple subspaces (#65)
+- fixed bug in FAMoS switching (#68)
+- removed `BidirectionalCandidateSpace` and `ForwardAndBackwardCandidateSpace` (#68)
+- set estimated parameters as the nominal values in exported PEtab problems (#77)
+- many CI, doc, and code quality improvements by @dweindl (#57, #58, #59, #60, #61, #63, #69, #70, #71, #72, #74)
+- fixed bug in model hash reproducibility (#78)
+- refactored `governing_method` out of `CandidateSpace` (#73)
+- fixed bug related to attempted calibration of virtual models (#75)
+
 ## 0.1.10
 - added `Model.set_estimated_parameters`
   - now expected that `Model.estimated_parameters` has untransformed values

doc/.gitignore

@@ -0,0 +1,2 @@
+_build
+generated

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/api.rst

@@ -0,0 +1,20 @@
+petab-select Python API
+=======================
+
+.. rubric:: Modules
+
+.. autosummary::
+   :toctree: generated
+
+   petab_select
+   petab_select.candidate_space
+   petab_select.constants
+   petab_select.criteria
+   petab_select.handlers
+   petab_select.misc
+   petab_select.model
+   petab_select.model_space
+   petab_select.model_subspace
+   petab_select.petab
+   petab_select.problem
+   petab_select.ui

doc/conf.py

@@ -0,0 +1,76 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+import inspect
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+project = 'petab-select'
+copyright = '2023, The PEtab Select developers'
+author = 'The PEtab Select developers'
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = [
+    "readthedocs_ext.readthedocs",
+    "sphinx.ext.napoleon",
+    "sphinx.ext.autodoc",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.viewcode",
+    "sphinx.ext.mathjax",
+    "nbsphinx",
+    "IPython.sphinxext.ipython_console_highlighting",
+    "recommonmark",
+    "sphinx_autodoc_typehints",
+]
+
+templates_path = ['_templates']
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+
+intersphinx_mapping = {
+    "petab": (
+        "https://petab.readthedocs.io/projects/libpetab-python/en/latest/",
+        None,
+    ),
+    "pandas": ("https://pandas.pydata.org/docs/", None),
+    "numpy": ("https://numpy.org/devdocs/", None),
+    "python": ("https://docs.python.org/3", None),
+}
+
+autosummary_generate = True
+autodoc_default_options = {
+    "special-members": "__init__",
+    "inherited-members": True,
+}
+
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = 'sphinx_rtd_theme'
+# html_static_path = ['_static']
+
+
+def autodoc_skip_member(app, what, name, obj, skip, options):
+    """Exclude some objects from the documentation."""
+    if inspect.isbuiltin(obj):
+        return True
+
+    # Skip inherited members from builtins
+    #  (skips, for example, all the int/str-derived methods of enums
+    if (
+        objclass := getattr(obj, "__objclass__", None)
+    ) and objclass.__module__ == "builtins":
+        return True
+
+    return None
+
+
+def setup(app: "sphinx.application.Sphinx"):
+    app.connect("autodoc-skip-member", autodoc_skip_member, priority=0)

doc/examples.rst

@@ -0,0 +1,11 @@
+Examples
+========
+
+Various example notebooks.
+
+.. toctree::
+   :maxdepth: 1
+
+   examples/example_cli_famos.ipynb
+   examples/workflow_cli.ipynb
+   examples/workflow_python.ipynb

doc/examples/example_cli_famos_helpers.py

@@ -1,5 +1,5 @@
 from pathlib import Path
-from typing import Tuple
+from typing import List, Tuple
 
 import pandas as pd
 
@@ -47,7 +47,9 @@ def calibrate(
     )
 
 
-def parse_summary_to_progress_list(summary_tsv: str) -> Tuple[Method, set]:
+def parse_summary_to_progress_list(
+    summary_tsv: str,
+) -> List[Tuple[Method, set]]:
     """Get progress information from the summary file."""
     df_raw = pd.read_csv(summary_tsv, sep='\t')
     df = df_raw.loc[~pd.isnull(df_raw["predecessor change"])]

doc/index.rst

@@ -0,0 +1,22 @@
+.. petab-select documentation master file, created by
+   sphinx-quickstart on Mon Oct 23 09:01:31 2023.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to petab-select's documentation!
+========================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   examples
+   api
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

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
+
+%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.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

petab_select/__init__.py

@@ -1,5 +1,7 @@
 """Model selection extension for PEtab."""
 
+import sys
+
 from .candidate_space import *
 from .constants import *
 from .criteria import *
@@ -9,3 +11,9 @@
 from .model_subspace import *
 from .problem import *
 from .ui import *
+
+__all__ = [
+    x
+    for x in dir(sys.modules[__name__])
+    if not x.startswith('_') and x != 'sys'
+]