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Merged
dweindl merged 2 commits into from
Mar 13, 2025
Merged

doc: intersphinx, tox env #358

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doc: intersphinx, tox env
dweindl Mar 12, 2025
357e3fc
Merge branch 'develop' into intersphinx
dweindl Mar 13, 2025
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2 changes: 2 additions & 0 deletions doc/conf.py
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Original file line number Diff line number Diff line change
Expand Up @@ -47,6 +47,7 @@
]

intersphinx_mapping = {
"petab": ("https://petab.readthedocs.io/en/latest/", None),
"pandas": ("https://pandas.pydata.org/docs/", None),
"numpy": ("https://numpy.org/devdocs/", None),
"sympy": ("https://docs.sympy.org/latest/", None),
Expand All @@ -62,6 +63,7 @@
exclude_patterns = [
"build/doctrees",
"build/html",
"build/jupyter_execute",
"**.ipynb_checkpoints",
"logo/LICENSE.md",
]
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8 changes: 6 additions & 2 deletions petab/v1/problem.py
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Expand Up @@ -42,7 +42,9 @@

class Problem:
"""
PEtab parameter estimation problem as defined by
PEtab parameter estimation problem.
A PEtab problem as defined by:
- model
- condition table
Expand All @@ -51,7 +53,9 @@ class Problem:
- observables table
- mapping table
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@dilpath dilpath Mar 12, 2025

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No mapping in v1? Fine for this PR

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@dweindl dweindl Mar 12, 2025

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No mapping in v1 in principle, but it was added there long ago for initial v2 support before we decided to have a separate v2.Problem. We should keep it there until petab.v2 has converged.

Optionally it may contain visualization tables.
Optionally, it may contain visualization tables.
See also :doc:`petab:v1/documentation_data_format`.
Parameters:
condition_df: PEtab condition table
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8 changes: 6 additions & 2 deletions petab/v2/problem.py
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Expand Up @@ -40,7 +40,9 @@

class Problem:
"""
PEtab parameter estimation problem as defined by
PEtab parameter estimation problem
A PEtab parameter estimation problem as defined by
- model
- condition table
Expand All @@ -50,7 +52,9 @@ class Problem:
- observables table
- mapping table
Optionally it may contain visualization tables.
Optionally, it may contain visualization tables.
See also :doc:`petab:v2/documentation_data_format`.
Parameters:
condition_df: PEtab condition table
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15 changes: 14 additions & 1 deletion tox.ini
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@@ -1,5 +1,5 @@
[tox]
envlist = quality,unit
envlist = quality,unit,doc
isolated_build = True

[testenv]
Expand All @@ -23,3 +23,16 @@ commands =
tests
description =
Basic tests

[testenv:doc]
description = Build the documentation
extras = doc,vis
deps=
# workaround for m2r2 issue with py3.13: No module named 'pkg_resources'
# see also: https://github.com/CrossNox/m2r2/issues/72
setuptools
allowlist_externals = rm
commands =
rm -rf {tox_root}/doc/build
sphinx-build -W -b html . build/html
changedir = {tox_root}/doc