diff --git a/docs/source/api/developer.rst b/docs/source/api/developer.rst
index 2d14753a3..8b013ec55 100644
--- a/docs/source/api/developer.rst
+++ b/docs/source/api/developer.rst
@@ -10,7 +10,6 @@ OTT Backend
moscot.backends.ott.SinkhornSolver
moscot.backends.ott.GWSolver
- moscot.backends.ott.FGWSolver
moscot.backends.ott.OTTOutput
moscot.backends.ott.OTTCost
diff --git a/docs/source/api/user.rst b/docs/source/api/user.rst
index c7e674cf4..8924defcc 100644
--- a/docs/source/api/user.rst
+++ b/docs/source/api/user.rst
@@ -28,4 +28,3 @@ Generic Problems
SinkhornProblem
GWProblem
- FGWProblem
diff --git a/docs/source/conf.py b/docs/source/conf.py
index c3b329f5e..085c221be 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -49,6 +49,7 @@
"sphinx.ext.autodoc",
"sphinx.ext.napoleon",
"sphinx.ext.viewcode",
+ "sphinx.ext.mathjax",
"sphinx_autodoc_typehints",
"sphinx.ext.intersphinx",
"sphinx.ext.autosummary",
diff --git a/docs/source/extensions/typed_returns.py b/docs/source/extensions/typed_returns.py
index a18e9933f..d5126910f 100644
--- a/docs/source/extensions/typed_returns.py
+++ b/docs/source/extensions/typed_returns.py
@@ -10,7 +10,10 @@ def process_return(lines: Iterable[str]) -> Iterator[str]:
m = re.fullmatch(r"(?P\w+)\s+:\s+(?P[\w.]+)", line)
if m:
# Once this is in scanpydoc, we can use the fancy hover stuff
- yield f'**{m["param"]}** : :class:`~{m["type"]}`'
+ if m["param"]:
+ yield f'**{m["param"]}** : :class:`~{m["type"]}`'
+ else:
+ yield f':class:`~{m["type"]}`'
else:
yield line
diff --git a/src/moscot/_docs/_docs.py b/src/moscot/_docs/_docs.py
index 29727d604..a4ffa25e5 100644
--- a/src/moscot/_docs/_docs.py
+++ b/src/moscot/_docs/_docs.py
@@ -85,7 +85,7 @@
data
- If `data` is a :class:`str` this should correspond to a column in :attr:`anndata.AnnData.obs`.
The transport map is applied to the subset corresponding to the source distribution
- (if `forward` is `True`) or target distribution (if `forward` is `False`) of that column.
+ (if `forward` is `True`) or target distribution (if `forward` is :obj:`False`) of that column.
- If `data` is a :class:npt.ArrayLike the transport map is applied to `data`.
- If `data` is a :class:`dict` then the keys should correspond to the tuple defining a single optimal
transport map and the value should be one of the two cases described above.
@@ -94,18 +94,20 @@
subset
Subset of :attr:`anndata.AnnData.obs` ``['{key}']`` values of which the policy is to be applied to.
"""
-_marginal_kwargs = """\
+_marginal_kwargs = r"""
marginal_kwargs
- keyword arguments for :meth:`moscot.problems.BirthDeathProblem._estimate_marginals`, i.e.
- for modeling the birth-death process. The keyword arguments
- are either used for :func:`moscot.problems.time._utils.beta`, i.e. one of:
+ Keyword arguments for :meth:`~moscot.problems.BirthDeathProblem._estimate_marginals`. If ``'scaling'``
+ is in ``marginal_kwargs``, the left marginals are computed as
+ :math:`\exp(\frac{(\textit{proliferation} - \textit{apoptosis}) \cdot (t_2 - t_1)}{\textit{scaling}})`.
+ Otherwise, the left marginals are computed using a birth-death process. The keyword arguments
+ are either used for :func:`~moscot.problems.time._utils.beta`, i.e. one of:
- beta_max: float
- beta_min: float
- beta_center: float
- beta_width: float
- or for :func:`moscot.problems.time._utils.beta`, i.e. one of:
+ or for :func:`~moscot.problems.time._utils.delta`, i.e. one of:
- delta_max: float
- delta_min: float
@@ -127,13 +129,35 @@
_a = """\
a
Specifies the left marginals. If of type :class:`str` the left marginals are taken from
- :attr:`anndata.AnnData.obs` ``['{a}']``. If `a` is `None` uniform marginals are used.
+ :attr:`anndata.AnnData.obs` ``['{a}']``. If ``a`` is `None` uniform marginals are used.
"""
_b = """\
b
Specifies the right marginals. If of type :class:`str` the right marginals are taken from
:attr:`anndata.AnnData.obs` ``['{b}']``. If `b` is `None` uniform marginals are used.
"""
+_a_temporal = r"""
+a
+ Specifies the left marginals. If
+ - ``a`` is :class:`str` - the left marginals are taken from :attr:`anndata.AnnData.obs`,
+ - if :meth:`~moscot.problems.base._birth_death.BirthDeathMixin.score_genes_for_marginals` was run and
+ if ``a`` is `None`, marginals are computed based on a birth-death process as suggested in
+ :cite:`schiebinger:19`,
+ - if :meth:`~moscot.problems.base._birth_death.BirthDeathMixin.score_genes_for_marginals` was run and
+ if ``a`` is `None`, and additionally ``'scaling'`` is provided in ``marginal_kwargs``,
+ the marginals are computed as
+ :math:`\exp(\frac{(\textit{proliferation} - \textit{apoptosis}) \cdot (t_2 - t_1)}{\textit{scaling}})`
+ rather than using a birth-death process,
+ - otherwise or if ``a`` is :obj:`False`, uniform marginals are used.
+"""
+_b_temporal = """\
+b
+ Specifies the right marginals. If
+ - ``b`` is :class:`str` - the left marginals are taken from :attr:`anndata.AnnData.obs`,
+ - if :meth:`~moscot.problems.base._birth_death.BirthDeathMixin.score_genes_for_marginals` was run
+ uniform (mean of left marginals) right marginals are used,
+ - otherwise or if ``b`` is :obj:`False`, uniform marginals are used.
+"""
_time_key = """\
time_key
Time point key in :attr:`anndata.AnnData.obs`.
@@ -400,6 +424,8 @@
converged=_converged,
a=_a,
b=_b,
+ a_temporal=_a_temporal,
+ b_temporal=_b_temporal,
time_key=_time_key,
spatial_key=_spatial_key,
batch_key=_batch_key,
diff --git a/src/moscot/_docs/_docs_mixins.py b/src/moscot/_docs/_docs_mixins.py
index 3af941609..89e5b1f14 100644
--- a/src/moscot/_docs/_docs_mixins.py
+++ b/src/moscot/_docs/_docs_mixins.py
@@ -55,10 +55,7 @@
for the corresponding plotting functions are stored.
See TODO Notebook for how :mod:`moscot.plotting` works.
"""
-_return_cell_transition = """\
-retun_cell_transition
- Transition matrix of cells or groups of cells.
-"""
+_return_cell_transition = "Transition matrix of cells or groups of cells."
_notes_cell_transition = """\
To visualise the results, see :func:`moscot.pl.cell_transition`.
"""
diff --git a/src/moscot/problems/base/_birth_death.py b/src/moscot/problems/base/_birth_death.py
index cbec0471e..d42c8baf8 100644
--- a/src/moscot/problems/base/_birth_death.py
+++ b/src/moscot/problems/base/_birth_death.py
@@ -1,4 +1,5 @@
-from typing import Any, Union, Literal, Callable, Optional, Protocol, Sequence, TYPE_CHECKING
+from types import MappingProxyType
+from typing import Any, Union, Literal, Mapping, Callable, Optional, Protocol, Sequence, TYPE_CHECKING
import numpy as np
@@ -68,7 +69,7 @@ def score_genes_for_marginals(
to proliferation and/or apoptosis must be passed.
Alternatively, proliferation and apoptosis genes for humans and mice are saved in :mod:`moscot`.
- The gene scores will be used in :meth:`moscot.problems.TemporalProblem.prepare` to estimate the initial
+ The gene scores will be used in :meth:`~moscot.problems.CompoundBaseProblem.prepare` to estimate the initial
growth rates as suggested in :cite:`schiebinger:19`
Parameters
@@ -175,9 +176,10 @@ def _estimate_marginals(
source: bool,
proliferation_key: Optional[str] = None,
apoptosis_key: Optional[str] = None,
- **kwargs: Any,
+ marginal_kwargs: Mapping[str, Any] = MappingProxyType({}),
+ **_: Any,
) -> ArrayLike:
- def estimate(key: Optional[str], *, fn: Callable[..., ArrayLike]) -> ArrayLike:
+ def estimate(key: Optional[str], *, fn: Callable[..., ArrayLike], **kwargs: Any) -> ArrayLike:
if key is None:
return np.zeros(adata.n_obs, dtype=float)
try:
@@ -189,16 +191,22 @@ def estimate(key: Optional[str], *, fn: Callable[..., ArrayLike]) -> ArrayLike:
raise ValueError("Either `proliferation_key` or `apoptosis_key` must be specified.")
self.proliferation_key = proliferation_key
self.apoptosis_key = apoptosis_key
+ if "scaling" in marginal_kwargs:
+ beta_fn = delta_fn = lambda x, *args, **kwargs: x
+ scaling = marginal_kwargs["scaling"]
+ else:
+ beta_fn, delta_fn = beta, delta
+ scaling = 1
+ birth = estimate(proliferation_key, fn=beta_fn, **marginal_kwargs)
+ death = estimate(apoptosis_key, fn=delta_fn, **marginal_kwargs)
+
+ prior_growth = np.exp((birth - death) * self.delta / scaling)
- birth = estimate(proliferation_key, fn=beta)
- death = estimate(apoptosis_key, fn=delta)
- prior_growth = np.exp((birth - death) * self.delta)
scaling = np.sum(prior_growth)
normalized_growth = prior_growth / scaling
if source:
self._scaling = scaling
self._prior_growth = prior_growth
-
return normalized_growth if source else np.full(self.adata_tgt.n_obs, fill_value=np.mean(normalized_growth))
# TODO(michalk8): temporary fix to satisfy the mixin, consider removing the mixin
diff --git a/src/moscot/problems/base/_compound_problem.py b/src/moscot/problems/base/_compound_problem.py
index 5b11a53e6..3d24b1c62 100644
--- a/src/moscot/problems/base/_compound_problem.py
+++ b/src/moscot/problems/base/_compound_problem.py
@@ -351,7 +351,7 @@ def _(
return res if return_all else current_mass
@d.get_sections(base="BaseCompoundProblem_push", sections=["Parameters", "Raises"])
- @d.dedent
+ @d.dedent # TODO(@MUCDK) document private _apply
def push(self, *args: Any, **kwargs: Any) -> ApplyOutput_t[K]:
"""
Push mass from `start` to `end`.
@@ -371,7 +371,7 @@ def push(self, *args: Any, **kwargs: Any) -> ApplyOutput_t[K]:
%(scale_by_marginals)s
kwargs
- keyword arguments for :meth:`moscot.problems.CompoundProblem._apply`.
+ keyword arguments for policy-specific `_apply` method of :class:`moscot.problems.CompoundProblem`.
Returns
-------
@@ -382,7 +382,7 @@ def push(self, *args: Any, **kwargs: Any) -> ApplyOutput_t[K]:
return self._apply(*args, forward=True, **kwargs)
@d.get_sections(base="BaseCompoundProblem_pull", sections=["Parameters", "Raises"])
- @d.dedent
+ @d.dedent # TODO(@MUCDK) document private functions
def pull(self, *args: Any, **kwargs: Any) -> ApplyOutput_t[K]:
"""
Pull mass from `end` to `start`.
@@ -402,7 +402,7 @@ def pull(self, *args: Any, **kwargs: Any) -> ApplyOutput_t[K]:
%(scale_by_marginals)s
kwargs
- Keyword arguments for :meth:`moscot.problems.CompoundProblem._apply`.
+ keyword arguments for policy-specific `_apply` method of :class:`moscot.problems.CompoundProblem`.
Returns
-------
diff --git a/src/moscot/problems/time/_lineage.py b/src/moscot/problems/time/_lineage.py
index a75fba7fe..c0736eabb 100644
--- a/src/moscot/problems/time/_lineage.py
+++ b/src/moscot/problems/time/_lineage.py
@@ -48,6 +48,7 @@ def prepare(
cost: Literal["sq_euclidean", "cosine", "bures", "unbalanced_bures"] = "sq_euclidean",
a: Optional[str] = None,
b: Optional[str] = None,
+ marginal_kwargs: Mapping[str, Any] = MappingProxyType({}),
**kwargs: Any,
) -> "TemporalProblem":
"""
@@ -61,8 +62,9 @@ def prepare(
%(joint_attr)s
%(policy)s
%(cost_lin)s
- %(a)s
- %(b)s
+ %(a_temporal)s
+ %(b_temporal)s
+ %(marginal_kwargs)s
%(kwargs_prepare)s
@@ -84,7 +86,7 @@ def prepare(
xy, x, y = handle_cost(xy=xy, x=kwargs.pop("x", None), y=kwargs.pop("y", None), cost=cost)
# TODO(michalk8): needs to be modified
- marginal_kwargs = dict(kwargs.pop("marginal_kwargs", {}))
+ marginal_kwargs = dict(marginal_kwargs)
marginal_kwargs["proliferation_key"] = self.proliferation_key
marginal_kwargs["apoptosis_key"] = self.apoptosis_key
if a is None:
@@ -316,6 +318,7 @@ def prepare(
] = "sq_euclidean",
a: Optional[str] = None,
b: Optional[str] = None,
+ marginal_kwargs: Mapping[str, Any] = MappingProxyType({}),
**kwargs: Any,
) -> "LineageProblem":
"""
@@ -331,8 +334,9 @@ def prepare(
%(joint_attr)s
%(policy)s
%(cost)s
- %(a)s
- %(b)s
+ %(a_temporal)s
+ %(b_temporal)s
+ %(marginal_kwargs)s
%(kwargs_prepare)s
Returns
@@ -364,6 +368,7 @@ def prepare(
cost=cost,
a=a,
b=b,
+ marginal_kwargs=marginal_kwargs,
**kwargs,
)
diff --git a/src/moscot/problems/time/_mixins.py b/src/moscot/problems/time/_mixins.py
index 66f73c6b9..f4ac87d90 100644
--- a/src/moscot/problems/time/_mixins.py
+++ b/src/moscot/problems/time/_mixins.py
@@ -2,6 +2,7 @@
from pathlib import Path
import itertools
+from pandas.api.types import infer_dtype, is_numeric_dtype
import pandas as pd
import numpy as np
@@ -457,6 +458,7 @@ def _get_data(
target_data,
)
+ @d_mixins.dedent
def compute_interpolated_distance(
self: TemporalMixinProtocol[K, B],
source: K,
@@ -500,7 +502,7 @@ def compute_interpolated_distance(
%(use_posterior_marginals)s
%(seed_sampling)s
%(backend)s
- %(kwargs_divergence)
+ %(kwargs_divergence)s
Returns
-------
@@ -532,6 +534,7 @@ def compute_interpolated_distance(
point_cloud_1=intermediate_data, point_cloud_2=interpolation, backend=backend, **kwargs
)
+ @d_mixins.dedent
def compute_random_distance(
self: TemporalMixinProtocol[K, B],
source: K,
@@ -542,7 +545,7 @@ def compute_random_distance(
account_for_unbalancedness: bool = False,
posterior_marginals: bool = True,
seed: Optional[int] = None,
- backend: Literal["ott"] = "ott",
+ backend: Literal["ott"] = "ott", # TODO: not used
**kwargs: Any,
) -> Numeric_t:
"""
@@ -564,7 +567,7 @@ def compute_random_distance(
%(use_posterior_marginals)s
%(seed_interpolation)s
%(backend)s
- %(kwargs_divergence)
+ %(kwargs_divergence)s
Returns
-------
@@ -590,6 +593,7 @@ def compute_random_distance(
)
return self._compute_wasserstein_distance(intermediate_data, random_interpolation, **kwargs)
+ @d_mixins.dedent
def compute_time_point_distances(
self: TemporalMixinProtocol[K, B],
source: K,
@@ -768,4 +772,9 @@ def temporal_key(self) -> Optional[str]:
def temporal_key(self: TemporalMixinProtocol[K, B], key: Optional[str]) -> None:
if key is not None and key not in self.adata.obs:
raise KeyError(f"Unable to find temporal key in `adata.obs[{key!r}]`.")
+ if key is not None and not is_numeric_dtype(self.adata.obs[key]):
+ raise TypeError(
+ "Temporal key has to be of numeric type."
+ f"Found `adata.obs[{key!r}]` to be of type `{infer_dtype(self.adata.obs[key])}`."
+ )
self._temporal_key = key
diff --git a/src/moscot/problems/time/_utils.py b/src/moscot/problems/time/_utils.py
index 8e2679da9..44553023e 100644
--- a/src/moscot/problems/time/_utils.py
+++ b/src/moscot/problems/time/_utils.py
@@ -11,30 +11,30 @@ def logistic(x: ArrayLike, L: float, k: float, center: float = 0) -> ArrayLike:
return L / (1 + np.exp(-k * (x - center)))
-def gen_logistic(p: ArrayLike, beta_max: float, beta_min: float, center: float, width: float) -> ArrayLike:
+def gen_logistic(p: ArrayLike, sup: float, inf: float, center: float, width: float) -> ArrayLike:
"""Shifted logistic function."""
- return beta_min + logistic(p, L=beta_max - beta_min, k=4 / width, center=center)
+ return inf + logistic(p, L=sup - inf, k=4 / width, center=center)
def beta(
p: ArrayLike,
beta_max: float = 1.7,
beta_min: float = 0.3,
- center: float = 0.25,
- width: float = 0.5,
+ beta_center: float = 0.25,
+ beta_width: float = 0.5,
**_: Any,
) -> ArrayLike:
"""Birth process."""
- return gen_logistic(p, beta_max, beta_min, center, width)
+ return gen_logistic(p, beta_max, beta_min, beta_center, beta_width)
def delta(
a: ArrayLike,
delta_max: float = 1.7,
delta_min: float = 0.3,
- center: float = 0.1,
- width: float = 0.2,
- **kwargs: Any,
+ delta_center: float = 0.1,
+ delta_width: float = 0.2,
+ **_: Any,
) -> ArrayLike:
"""Death process."""
- return gen_logistic(a, delta_max, delta_min, center, width)
+ return gen_logistic(a, delta_max, delta_min, delta_center, delta_width)
diff --git a/tests/problems/time/test_mixins.py b/tests/problems/time/test_mixins.py
index 8418a9b52..b6b76a711 100644
--- a/tests/problems/time/test_mixins.py
+++ b/tests/problems/time/test_mixins.py
@@ -332,3 +332,16 @@ def test_cell_transition_regression_notparam(
res = result.sort_index().sort_index(1)
df_expected = adata_time_with_tmap.uns["cell_transition_gt"].sort_index().sort_index(1)
np.testing.assert_almost_equal(res.values, df_expected.values, decimal=8)
+
+ @pytest.mark.fast()
+ @pytest.mark.parametrize("temporal_key", ["celltype", "time", "missing"])
+ def test_temporal_key_numeric(self, adata_time: AnnData, temporal_key: str):
+ problem = TemporalProblem(adata_time)
+ if temporal_key == "missing":
+ with pytest.raises(KeyError, match="Unable to find temporal key"):
+ problem = problem.prepare(temporal_key)
+ elif temporal_key == "celltype":
+ with pytest.raises(TypeError, match="Temporal key has to be of numeric type"):
+ problem = problem.prepare(temporal_key)
+ elif temporal_key == "time":
+ problem = problem.prepare(temporal_key)
diff --git a/tests/problems/time/test_temporal_base_problem.py b/tests/problems/time/test_temporal_base_problem.py
index 47270f8ad..38b876005 100644
--- a/tests/problems/time/test_temporal_base_problem.py
+++ b/tests/problems/time/test_temporal_base_problem.py
@@ -1,4 +1,4 @@
-from typing import List, Optional
+from typing import Any, List, Mapping, Optional
import pytest
@@ -95,3 +95,38 @@ def test_posterior_growth_rates(self, adata_time_marginal_estimations: AnnData):
gr = prob.posterior_growth_rates
assert isinstance(gr, np.ndarray)
+
+ @pytest.mark.fast()
+ @pytest.mark.parametrize(
+ "marginal_kwargs", [{}, {"delta_width": 0.9}, {"delta_center": 0.9}, {"beta_width": 0.9}, {"beta_center": 0.9}]
+ )
+ def test_marginal_kwargs(self, adata_time_marginal_estimations: AnnData, marginal_kwargs: Mapping[str, Any]):
+ t1, t2 = 0, 1
+ adata_x = adata_time_marginal_estimations[adata_time_marginal_estimations.obs["time"] == t1]
+ adata_y = adata_time_marginal_estimations[adata_time_marginal_estimations.obs["time"] == t2]
+
+ prob = BirthDeathProblem(adata_x, adata_y, src_key=t1, tgt_key=t2)
+ prob = prob.prepare(
+ x={"attr": "X"},
+ y={"attr": "X"},
+ a=True,
+ b=True,
+ proliferation_key="proliferation",
+ apoptosis_key="apoptosis",
+ )
+
+ gr1 = prob.prior_growth_rates
+ prob = prob.prepare(
+ x={"attr": "X"},
+ y={"attr": "X"},
+ a=True,
+ b=True,
+ proliferation_key="proliferation",
+ apoptosis_key="apoptosis",
+ marginal_kwargs=marginal_kwargs,
+ )
+ gr2 = prob.prior_growth_rates
+ if len(marginal_kwargs) > 0:
+ assert not np.allclose(gr1, gr2)
+ else:
+ assert np.allclose(gr1, gr2)
diff --git a/tests/problems/time/test_temporal_problem.py b/tests/problems/time/test_temporal_problem.py
index 82c9c5ab5..4d0aa22b5 100644
--- a/tests/problems/time/test_temporal_problem.py
+++ b/tests/problems/time/test_temporal_problem.py
@@ -7,6 +7,7 @@
from anndata import AnnData
+from tests._utils import ATOL, RTOL
from moscot.problems.time import TemporalProblem
from moscot.solvers._output import BaseSolverOutput
from tests.problems.conftest import (
@@ -135,6 +136,24 @@ def test_apoptosis_key_pipeline(self, adata_time: AnnData):
problem.apoptosis_key = "new_apoptosis"
assert problem.apoptosis_key == "new_apoptosis"
+ @pytest.mark.fast()
+ @pytest.mark.parametrize("scaling", [0.1, 1, 4])
+ def test_proliferation_key_c_pipeline(self, adata_time: AnnData, scaling: float):
+ keys = np.sort(np.unique(adata_time.obs["time"].values))
+ adata_time = adata_time[adata_time.obs["time"].isin([keys[0], keys[1]])]
+ delta = keys[1] - keys[0]
+ problem = TemporalProblem(adata_time)
+ assert problem.proliferation_key is None
+
+ problem.score_genes_for_marginals(gene_set_proliferation="human", gene_set_apoptosis="human")
+ assert problem.proliferation_key == "proliferation"
+
+ problem = problem.prepare(time_key="time", marginal_kwargs={"scaling": scaling})
+ prolif = adata_time[adata_time.obs["time"] == keys[0]].obs["proliferation"]
+ apopt = adata_time[adata_time.obs["time"] == keys[0]].obs["apoptosis"]
+ expected_marginals = np.exp((prolif - apopt) * delta / scaling)
+ np.testing.assert_allclose(problem[keys[0], keys[1]]._prior_growth, expected_marginals, rtol=RTOL, atol=ATOL)
+
def test_cell_costs_source_pipeline(self, adata_time: AnnData):
problem = TemporalProblem(adata=adata_time)
problem = problem.prepare("time")
diff --git a/tox.ini b/tox.ini
index fb8d61247..1040311e3 100644
--- a/tox.ini
+++ b/tox.ini
@@ -113,26 +113,23 @@ commands =
[testenv:lint]
description = Perform linting.
-basepython = python3.9
deps = pre-commit>=2.14.0
skip_install = true
commands = pre-commit run --all-files --show-diff-on-failure {posargs:}
[testenv:clean-docs]
description = Clean the documentation artifacts.
-basepython = python3.8
deps =
skip_install = true
changedir = {toxinidir}/docs
-whitelist_externals = make
+allowlist_externals = make
commands = make clean
[testenv:docs]
description = Build the documentation.
-basepython = python3.9
skip_install = false
extras = docs
-whitelist_externals = sphinx-build
+allowlist_externals = sphinx-build
commands =
- sphinx-build --color -b html {toxinidir}/docs/source {toxinidir}/docs/build/html
+ sphinx-build --color -b html {toxinidir}/docs/source {toxinidir}/docs/build/html {posargs}
python -c 'import pathlib; print(f"Documentation is available under:", pathlib.Path(f"{toxinidir}") / "docs" / "build" / "html" / "index.html")'