[ci skip] Remove sphinx-paramlinks (#584)

cellrank/external/kernels/_statot_kernel.py

@@ -34,7 +34,7 @@ class OTKernel(OTKernel_, error=_error):
     %(adata)s
     terminal_states
         Categorical :class:`pandas.Series` where non-`NaN` values mark terminal states.
-        If `None`, terminal states are assumed to be already present in :paramref:`adata` ``['terminal_states']``.
+        If `None`, terminal states are assumed to be already present in :attr:`adata` ``['terminal_states']``.
     g
         Key in :attr:`anndata.AnnData.obs` containing relative growth rates for cells or the array itself.
     cluster_key
@@ -114,7 +114,7 @@ def compute_transition_matrix(
         Returns
         -------
         :class:`cellrank.external.kernels.OTKernel`
-            Makes :paramref:`transition_matrix` available.
+            Makes :attr:`transition_matrix` available.
         """
         if method not in ("ent", "quad", "unbal"):
             raise ValueError(f"Invalid method `{method!r}`.")

cellrank/pl/_gene_trend.py

@@ -97,7 +97,7 @@ def gene_trends(
         If ``same_plot=False``, show ``lineages`` in rows and ``genes`` in columns.
     %(model_callback)s
     conf_int
-        Whether to compute and show confidence interval. If the :paramref:`model` is :class:`cellrank.ul.models.GAMR`,
+        Whether to compute and show confidence interval. If the :attr:`model` is :class:`cellrank.ul.models.GAMR`,
         it can also specify the confidence level, the default is `0.95`.
     same_plot
         Whether to plot all lineages for each gene in the same plot.

cellrank/tl/estimators/_base_estimator.py

@@ -77,18 +77,18 @@ class BaseEstimator(LineageEstimatorMixin, Partitioner, ABC):
         Either a :class:`cellrank.tl.kernels.Kernel` object, an :class:`anndata.AnnData` object which
         stores the transition matrix in ``.obsp`` attribute or :mod:`numpy` or :mod:`scipy` array.
     inplace
-        Whether to modify :paramref:`adata` object inplace or make a copy.
+        Whether to modify :attr:`adata` object inplace or make a copy.
     read_from_adata
-        Whether to read available attributes in :paramref:`adata`, if present.
+        Whether to read available attributes in :attr:`adata`, if present.
     obsp_key
         Key in ``obj.obsp`` when ``obj`` is an :class:`anndata.AnnData` object.
     g2m_key
-        Key in :paramref:`adata` ``.obs``. Can be used to detect cell-cycle driven start- or endpoints.
+        Key in :attr:`adata` ``.obs``. Can be used to detect cell-cycle driven start- or endpoints.
     s_key
-        Key in :paramref:`adata` ``.obs``. Can be used to detect cell-cycle driven start- or endpoints.
+        Key in :attr:`adata` ``.obs``. Can be used to detect cell-cycle driven start- or endpoints.
     write_to_adata
-        Whether to write the transition matrix to :paramref:`adata` ``.obsp`` and the parameters to
-        :paramref:`adata` ``.uns``.
+        Whether to write the transition matrix to :attr:`adata` ``.obsp`` and the parameters to
+        :attr:`adata` ``.uns``.
     %(write_to_adata.parameters)s
         Only used when ``write_to_adata=True``.
     """
@@ -249,7 +249,7 @@ def set_terminal_states(
             belonging to a transient state or a :class:`dict`, where each key is the name of the recurrent class and
             values are list of cell names.
         cluster_key
-            If a key to cluster labels is given, :paramref:`{fs}` will be associated with these for naming and colors.
+            If a key to cluster labels is given, :attr:`{fs}` will be associated with these for naming and colors.
         %(en_cutoff_p_thresh)s
         add_to_existing
             Whether to add these categories to existing ones. Cells already belonging to recurrent classes will be
@@ -261,8 +261,8 @@ def set_terminal_states(
         None
             Nothing, but updates the following fields:
 
-                - :paramref:`{fsp}`
-                - :paramref:`{fs}`
+                - :attr:`{fsp}`
+                - :attr:`{fs}`
         """
 
         self._set_categorical_labels(
@@ -283,19 +283,19 @@ def rename_terminal_states(
         self, new_names: Mapping[str, str], update_adata: bool = True
     ) -> None:
         """
-        Rename the names of :paramref:`{ts}`.
+        Rename the names of :attr:`{ts}`.
 
         Parameters
         ----------
         new_names
             Mapping where keys are the old names and the values are the new names. New names must be unique.
         update_adata
-            Whether to update underlying :paramref:`adata` object as well or not.
+            Whether to update underlying :attr:`adata` object as well or not.
 
         Returns
         -------
         None
-            Nothing, just updates the names of :paramref:`{ts}`.
+            Nothing, just updates the names of :attr:`{ts}`.
         """
 
         term_states = self._get(P.TERM)
@@ -372,7 +372,7 @@ def compute_absorption_probabilities(
         Compute absorption probabilities of a Markov chain.
 
         For each cell, this computes the probability of it reaching any of the approximate recurrent classes defined
-        by :paramref:`{fs}`.
+        by :attr:`{fs}`.
 
         Parameters
         ----------
@@ -421,8 +421,8 @@ def compute_absorption_probabilities(
         None
             Nothing, but updates the following fields:
 
-                - :paramref:`{abs_prob}` - probabilities of being absorbed into the terminal states.
-                - :paramref:`{lat}` - mean times until absorption to subset absorbing states and optionally
+                - :attr:`{abs_prob}` - probabilities of being absorbed into the terminal states.
+                - :attr:`{lat}` - mean times until absorption to subset absorbing states and optionally
                   their variances saved as ``'{{lineage}} mean'`` and ``'{{lineage}} var'``, respectively,
                   for each subset of absorbing states specified in ``time_to_absorption``.
         """
@@ -675,7 +675,7 @@ def compute_lineage_drivers(
         Parameters
         ----------
         lineages
-            Either a set of lineage names from :paramref:`absorption_probabilities` `.names` or `None`,
+            Either a set of lineage names from :attr:`absorption_probabilities` `.names` or `None`,
             in which case all lineages are considered.
         method
             Mode to use when calculating p-values and confidence intervals. Can be one of:
@@ -684,13 +684,13 @@ def compute_lineage_drivers(
                 - {tm.PERM_TEST.s!r} - use permutation test.
 
         cluster_key
-            Key from :paramref:`adata` ``.obs`` to obtain cluster annotations. These are considered for ``clusters``.
+            Key from :attr:`adata` ``.obs`` to obtain cluster annotations. These are considered for ``clusters``.
         clusters
             Restrict the correlations to these clusters.
         layer
-            Key from :paramref:`adata` ``.layers``.
+            Key from :attr:`adata` ``.layers``.
         use_raw
-            Whether or not to use :paramref:`adata` ``.raw`` to correlate gene expression.
+            Whether or not to use :attr:`adata` ``.raw`` to correlate gene expression.
             If using a layer other than ``.X``, this must be set to `False`.
         confidence_level
             Confidence level for the confidence interval calculation. Must be in `[0, 1]`.
@@ -709,14 +709,14 @@ def compute_lineage_drivers(
             Only if ``return_drivers=True``.
 
         None
-            Updates :paramref:`adata` ``.var`` or :paramref:`adata` ``.raw.var``, depending ``use_raw`` with:
+            Updates :attr:`adata` ``.var`` or :attr:`adata` ``.raw.var``, depending ``use_raw`` with:
 
                 - ``'{{direction}} {{lineage}} corr'`` - the potential lineage drivers.
                 - ``'{{direction}} {{lineage}} qval'`` - the corrected p-values.
 
             Updates the following fields:
 
-                - :paramref:`{lin_drivers}` - same as the returned values.
+                - :attr:`{lin_drivers}` - same as the returned values.
 
         References
         ----------
@@ -858,7 +858,7 @@ def plot_lineage_drivers(
         ncols
             Number of columns.
         use_raw
-            Whether to look in :paramref:`adata` ``.raw.var`` or :paramref:`adata` ``.var``.
+            Whether to look in :attr:`adata` ``.raw.var`` or :attr:`adata` ``.var``.
         title_fmt
             Title format. Possible keywords include `{gene}`, `{qval}`, `{corr}` for gene name,
             q-value and correlation, respectively.
@@ -1122,10 +1122,10 @@ def fit(
         None
             Nothing, just makes available the following fields:
 
-                - :paramref:`{fsp}`
-                - :paramref:`{fs}`
-                - :paramref:`{ap}`
-                - :paramref:`{pd}`
+                - :attr:`{fsp}`
+                - :attr:`{fs}`
+                - :attr:`{ap}`
+                - :attr:`{pd}`
         """
         self._fit_terminal_states(**kwargs)
         if compute_absorption_probabilities:
@@ -1168,7 +1168,7 @@ def _set_or_debug(
             logg.debug(f"Unable to set attribute `.{attr}`, skipping")
 
     def copy(self) -> "BaseEstimator":
-        """Return a copy of self, including the underlying :paramref:`adata` object."""
+        """Return a copy of self, including the underlying :attr:`adata` object."""
         k = deepcopy(self.kernel)  # ensure we copy the adata object
         res = type(self)(k, read_from_adata=False)
         for k, v in self.__dict__.items():

cellrank/tl/estimators/_cflare.py

@@ -67,7 +67,7 @@ def compute_terminal_states(
         method
             Method to be used for clustering. Must be one of `'louvain'`, `'leiden'` or `'kmeans'`.
         cluster_key
-            If a key to cluster labels is given, :paramref:`{fs}` will get associated with these for naming and colors.
+            If a key to cluster labels is given, :attr:`{fs}` will get associated with these for naming and colors.
         n_clusters_kmeans
             If `None`, this is set to ``use + 1``.
         n_neighbors
@@ -94,8 +94,8 @@ def compute_terminal_states(
         None
             Nothing, but updates the following fields:
 
-                - :paramref:`{fsp}`
-                - :paramref:`{fs}`
+                - :attr:`{fsp}`
+                - :attr:`{fs}`
         """
 
         def _compute_macrostates_prob() -> Series:
@@ -301,10 +301,10 @@ def fit(
         None
             Nothing, just makes available the following fields:
 
-                - :paramref:`{fsp}`
-                - :paramref:`{fs}`
-                - :paramref:`{ap}`
-                - :paramref:`{pd}`
+                - :attr:`{fsp}`
+                - :attr:`{fs}`
+                - :attr:`{ap}`
+                - :attr:`{pd}`
         """
         super().fit(
             n_lineages=n_lineages,

cellrank/tl/estimators/_decomposition.py

@@ -80,7 +80,7 @@ def compute_eigendecomposition(
         None
             Nothing, but updates the following field:
 
-                - :paramref:`{prop}`
+                - :attr:`{prop}`
         """
 
         def get_top_k_evals():
@@ -431,9 +431,9 @@ def compute_schur(
         None
             Nothing, but updates the following fields:
 
-                - :paramref:`{schur_vectors}`
-                - :paramref:`{schur_matrix}`
-                - :paramref:`{eigendec}`
+                - :attr:`{schur_vectors}`
+                - :attr:`{schur_matrix}`
+                - :attr:`{eigendec}`
         """
         if n_components < 2:
             raise ValueError(

cellrank/tl/estimators/_gpcca.py

@@ -109,11 +109,11 @@ def compute_macrostates(
         None
             Nothing, but updates the following fields:
 
-                - :paramref:`{msp}`
-                - :paramref:`{ms}`
-                - :paramref:`{schur}`
-                - :paramref:`{coarse_T}`
-                - :paramref:`{coarse_stat}`
+                - :attr:`{msp}`
+                - :attr:`{ms}`
+                - :attr:`{schur}`
+                - :attr:`{coarse_T}`
+                - :attr:`{coarse_stat}`
         """
 
         was_from_eigengap = False
@@ -261,8 +261,8 @@ def set_terminal_states_from_macrostates(
         None
             Nothing, just updates the following fields:
 
-                - :paramref:`{fsp}`
-                - :paramref:`{fs}`
+                - :attr:`{fsp}`
+                - :attr:`{fs}`
         """
 
         if not isinstance(n_cells, int):
@@ -383,8 +383,8 @@ def compute_terminal_states(
         None
             Nothing, just updates the following fields:
 
-                - :paramref:`{fsp}`
-                - :paramref:`{fs}`
+                - :attr:`{fsp}`
+                - :attr:`{fs}`
         """
 
         if len(self._get(P.MACRO).cat.categories) == 1:
@@ -444,14 +444,14 @@ def compute_gdpt(
         n_components
             Number of real Schur vectors to consider.
         key_added
-            Key in :paramref:`adata` ``.obs`` where to save the pseudotime.
+            Key in :attr:`adata` ``.obs`` where to save the pseudotime.
         kwargs
             Keyword arguments for :meth:`cellrank.tl.GPCCA.compute_schur` if Schur decomposition is not found.
 
         Returns
         -------
         None
-            Nothing, just updates :paramref:`adata` ``.obs[key_added]`` with the computed pseudotime.
+            Nothing, just updates :attr:`adata` ``.obs[key_added]`` with the computed pseudotime.
         """
 
         def _get_dpt_row(e_vals: np.ndarray, e_vecs: np.ndarray, i: int):
@@ -870,13 +870,13 @@ def _set_macrostates(
             Fuzzy clustering.
         %(n_cells)s
         cluster_key
-            Key from :paramref:`adata` ``.obs`` to get reference cluster annotations.
+            Key from :attr:`adata` ``.obs`` to get reference cluster annotations.
         en_cutoff
             Threshold to decide when we we want to warn the user about an uncertain name mapping. This happens when
             one fuzzy state overlaps with several reference clusters, and the most likely cells are distributed almost
             evenly across the reference clusters.
         p_thresh
-            Only used to detect cell cycle stages. These have to be present in :paramref:`adata` ``.obs`` as
+            Only used to detect cell cycle stages. These have to be present in :attr:`adata` ``.obs`` as
             `'G2M_score'` and `'S_score'`.
         check_row_sums
             Check whether rows in `memberships` sum to `1`.
@@ -1071,12 +1071,12 @@ def fit(
         None
             Nothing, just makes available the following fields:
 
-                - :paramref:`{msp}`
-                - :paramref:`{ms}`
-                - :paramref:`{fsp}`
-                - :paramref:`{fs}`
-                - :paramref:`{ap}`
-                - :paramref:`{pd}`
+                - :attr:`{msp}`
+                - :attr:`{ms}`
+                - :attr:`{fsp}`
+                - :attr:`{fs}`
+                - :attr:`{ap}`
+                - :attr:`{pd}`
         """
 
         super().fit(
@@ -1157,7 +1157,7 @@ def _set_initial_states_from_macrostates(
         Returns
         -------
         None
-            Nothing, just writes to :paramref:`adata`:
+            Nothing, just writes to :attr:`adata`:
 
                 - ``.obs[{key!r}]`` - probability of being an initial state.
                 - ``.obs[{probs_key!r}]`` - top ``n_cells`` from each initial state.

cellrank/tl/estimators/_property.py

@@ -298,7 +298,7 @@ def _plot_vectors(
         abs_value
             Whether to take the absolute value before plotting.
         cluster_key
-            Key in :paramref:`adata` ``.obs`` for plotting categorical observations.
+            Key in :attr:`adata` ``.obs`` for plotting categorical observations.
         %(basis)s
         kwargs
             Keyword arguments for :func:`scvelo.pl.scatter`.
@@ -409,7 +409,7 @@ def _plot_discrete(
         lineages
             Plot only these lineages. If `None`, plot all lineages.
         cluster_key
-            Key from :paramref:`adata` ``.obs`` for plotting categorical observations.
+            Key from :attr:`adata` ``.obs`` for plotting categorical observations.
         same_plot
             Whether to plot the lineages on the same plot or separately.
         title
@@ -543,10 +543,10 @@ def _plot_continuous(
         lineages
             Plot only these lineages. If `None`, plot all lineages.
         cluster_key
-            Key from :paramref:`adata` ``.obs`` for plotting categorical observations.
+            Key from :attr:`adata` ``.obs`` for plotting categorical observations.
         %(time_mode)s
         time_key
-            Key from :paramref:`adata` ``.obs`` to use as a pseudotime ordering of the cells.
+            Key from :attr:`adata` ``.obs`` to use as a pseudotime ordering of the cells.
         title
             Either `None`, in which case titles are ``'{to,from} {terminal,initial} {state}'``,
             or an array of titles, one per lineage.
@@ -873,9 +873,9 @@ def compute_partition(self) -> None:
         None
             Nothing, but updates the following fields:
 
-                - :paramref:`recurrent_classes`
-                - :paramref:`transient_classes`
-                - :paramref:`is_irreducible`
+                - :attr:`recurrent_classes`
+                - :attr:`transient_classes`
+                - :attr:`is_irreducible`
         """
 
         start = logg.info("Computing communication classes")