remove tl.snf as it fails with numpy >=2; we don't have a usecase for…

… this function yet

tools/muon/cluster_analyze_embed_muon.xml

@@ -67,18 +67,6 @@ mu.tl.mofa(
     copy=False
 )
 
-#else if $method.method == 'tl.snf'
-mu.tl.snf(
-    mdata,
-    n_neighbors=$method.n_neighbors,
-    @CMD_neighbor_keys@
-    key_added='$method.key_added',
-    n_iterations=$method.n_iterations,
-    sigma=$method.sigma,
-    eps=$method.eps,
-    copy=False
-)
-
 #else if $method.method == 'tl.umap'
 mu.tl.umap(
     mdata,
@@ -110,7 +98,6 @@ mu.tl.umap(
                 <option value="tl.leiden">Cluster: Cluster cells using the Leiden algorithm, using 'muon.tl.leiden'</option>
                 <option value="tl.louvain">Cluster: Cluster cells using the Louvain algorithm, using 'muon.tl.louvain'</option>
                 <option value="tl.mofa">Analyze: Run Multi Omics Factor Analysis, using 'muon.tl.mofa'</option>
-                <option value="tl.snf">Analyze: Similarity Network Fusion, using 'muon.tl.snf'</option>
                 <option value="tl.umap">Embed: Embed the multimodal neighborhood graph using UMAP, using 'muon.tl.umap'</option>
             </param>
             <when value="tl.leiden">
@@ -173,14 +160,6 @@ mu.tl.umap(
                 <param argument="smooth_warping" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Learn the alignment of covariates (e.g. time points) from different groups?"/>
                 <param argument="seed" type="integer" value="1" label="Random seed"/>
             </when>
-            <when value="tl.snf">
-                <param argument="n_neighbors" type="integer" value="20" label="Number of neighbours to be used in the K-nearest neighbours step"/>
-                <expand macro="param_neighbor_keys"/>
-                <expand macro="param_key_added_common"/>
-                <param argument="n_iterations" type="integer" value="20" label="Number of iterations for the diffusion process"/>
-                <param argument="sigma" type="float" value="0.5" label="Variance for the local model when calculating affinity matrices"/>
-                <expand macro="param_eps" eps_value="2.220446049250313e-16"/>
-            </when>
             <when value="tl.umap">
                 <param argument="min_dist" type="float" min="0" value="0.5" label="The effective minimum distance between embedded points"
                     help="Smaller values will result in a more clustered/clumped embedding where nearby points on the manifold are drawn closer together, while larger values will result on a more even dispersal of points."/>
@@ -383,42 +362,7 @@ mu.tl.umap(
             </output>
         </test>
         <test expect_num_outputs="2">
-            <!-- test5: tl.snf -->
-            <param name="mdata" location="https://zenodo.org/records/12570984/files/pbmc3k_chr21_processed.h5mu"/>
-            <param name="method" value="tl.snf"/>
-            <param name="n_neighbors" value="5"/>
-            <param name="key_added" value="neighbors"/>
-            <param name="n_iterations" value="10"/>
-            <param name="sigma" value="0.5"/>
-            <section name="advanced_common">
-                <param name="show_log" value="true" />
-            </section>
-            <output name="hidden_output">
-                <assert_contents>
-                    <has_text_matching expression="mu.tl.snf"/>
-                    <has_text_matching expression="n_neighbors=5"/>
-                    <has_text_matching expression="key_added='neighbors'"/>
-                    <has_text_matching expression="n_iterations=10"/>
-                    <has_text_matching expression="sigma=0.5"/>
-                </assert_contents>
-            </output>
-            <assert_stdout>
-                <has_text_matching expression="179 × 490"/>
-                <has_text_matching expression="179 x 178"/>
-                <has_text_matching expression="179 x 312"/>
-            </assert_stdout>
-            <output name="mudata_out" ftype="h5ad">
-                <assert_contents>
-                    <has_h5_keys keys="mod/rna"/>
-                    <has_h5_keys keys="mod/atac"/>
-                    <has_h5_keys keys="uns/neighbors"/>
-                    <has_h5_keys keys="obsp/neighbors_connectivities"/>
-                    <has_h5_keys keys="obsp/neighbors_distances"/>
-                </assert_contents>
-            </output>
-        </test>
-        <test expect_num_outputs="2">
-            <!-- test6: tl.umap -->
+            <!-- test5: tl.umap -->
             <param name="mdata" location="https://zenodo.org/records/12570984/files/pp.neighbors.h5mu"/>
             <param name="method" value="tl.umap"/>
             <param name="min_dist" value="0.5"/>