Merge pull request #737 from theislab/fix/linting_attr

Fixing Linting and Plotting Error

.gitignore

@@ -154,3 +154,4 @@ packages.dot
 
 # plotting tests
 tests/plotting/actual_figures/
+tests/plotting/figures/

docs/conf.py

@@ -119,7 +119,7 @@
 tippy_enable_mathjax = True
 # no need because of sphinxcontrib-bibtex
 tippy_enable_doitips = False
-
+linkcheck_report_timeouts_as_broken = True
 linkcheck_ignore = [
  # 403 Client Error
  r"https://doi.org/10.1126/science.aad0501",

src/moscot/problems/space/_mapping.py

@@ -174,8 +174,8 @@ def prepare(
  - :attr:`spatial_key` - key in :attr:`~anndata.AnnData.obsm` where the spatial coordinates are stored.
  - :attr:`batch_key` - key in :attr:`~anndata.AnnData.obs` where batches are stored.
  - :attr:`stage` - set to ``'prepared'``.
- - :attr:`problem_kind` - set to ``'quadratic'`` (if both ``spatial_key`` and ``sc_attr`` are passed)
- or ``'linear'`` (if both ``spatial_key`` and ``sc_attr`` are `None`).
+ - :attr:`problem_kind` - set to ``'quadratic'`` (if both `spatial_key` and `sc_attr` are passed)
+ or ``'linear'`` (if both `spatial_key` and `sc_attr` are `None`).
  """
  if sc_attr:
  x = {"attr": "obsm", "key": spatial_key} if isinstance(spatial_key, str) else spatial_key
@@ -292,15 +292,15 @@ def solve(
  Whether to :func:`~jax.jit` the underlying :mod:`ott` solver.
  min_iterations
  Minimum number of :term:`(fused) GW <Gromov-Wasserstein>` or :term:`Sinkhorn` iterations,
- depending on :attr:`alpha`.
+ depending on `alpha`.
  max_iterations
  Maximum number of :term:`(fused) GW <Gromov-Wasserstein>` or :term:`Sinkhorn` iterations,
- depending on :attr:`alpha`.
+ depending on `alpha`.
  threshold
  Convergence threshold of the :term:`GW <Gromov-Wasserstein>` or the :term:`Sinkhorn` algorithm,
- depending on :attr:`alpha`.
+ depending on `alpha`.
  linear_solver_kwargs
- Keyword arguments for the inner :term:`linear problem` solver. Only used when :attr:`alpha` > 0.
+ Keyword arguments for the inner :term:`linear problem` solver. Only used when `alpha` > 0.
  device
  Transfer the solution to a different device, see :meth:`~moscot.base.output.BaseSolverOutput.to`.
  If :obj:`None`, keep the output on the original device.

src/moscot/problems/space/_mixins.py

@@ -412,20 +412,20 @@ def correlate( # type: ignore[misc]
  corr_method
  Correlation method. Valid options are:
 
- - ``'pearson'`` - `Pearson correlation <https://en.wikipedia.org/wiki/Pearson_correlation_coefficient>`_.
- - ``'spearman'`` - `Spearman's rank correlation
- <https://en.wikipedia.org/wiki/Spearman%27s_rank_correlation_coefficient>`_.
+  - ``'pearson'`` - `Pearson correlation <https://en.wikipedia.org/wiki/Pearson_correlation_coefficient>`_.
+  - ``'spearman'`` - `Spearman rank correlation <https://en.wikipedia.org/wiki/Spearman%27s_rank_correlation_coefficient>`_.
+
  device
  Device where to transfer the solutions, see :meth:`~moscot.base.output.BaseSolverOutput.to`.
  groupby
  Optional key in :attr:`~anndata.AnnData.obs`, containing categorical annotations for grouping.
- batch_size:
+ batch_size
  Number of features to process at once. If :obj:`None`, process all features at once.
  Larger values will require more memory.
 
  Returns
  -------
- Correlation for each solution in :attr:`solutions`.
+ Correlation for each solution in `solutions`.
  """
  var_sc = self._filter_vars(var_names)
  if var_sc is None or not len(var_sc):