# HG changeset patch
# User iuc
# Date 1699807438 0
# Node ID 6f0d0c784f099db137b9ddfc5d424926e4a6f7dc
# Parent  ee98d611afc6e82e7642d8858c39d75d8da3e586
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 656ce7ff596a8870b77848469e85b406c7bd9344

diff -r ee98d611afc6 -r 6f0d0c784f09 inspect.xml
--- a/inspect.xml	Wed Jun 22 07:19:33 2022 +0000
+++ b/inspect.xml	Sun Nov 12 16:43:58 2023 +0000
@@ -16,7 +16,7 @@
 
 pd.options.display.precision = 15
 
-adata = ad.read('$input')
+adata = ad.read_h5ad('$input')
 
 #if $inspect.info == 'general'
 with open('$general', 'w', encoding="utf-8") as f:
@@ -42,8 +42,8 @@
 
 #else if $inspect.info == 'uns'
     #if $inspect.uns_info == 'neighbors'
-io.mmwrite('uns_neighbors_connectivities.mtx', adata.uns['neighbors']['connectivities'])
-io.mmwrite('uns_neighbors_distances.mtx', adata.uns['neighbors']['distances'])
+io.mmwrite('uns_neighbors_connectivities.mtx', adata.obsp['connectivities'])
+io.mmwrite('uns_neighbors_distances.mtx', adata.obsp['distances'])
     #else if $inspect.uns_info == 'paga'
 io.mmwrite('uns_paga_connectivities.mtx', adata.uns['paga']['connectivities'])
 io.mmwrite('uns_paga_connectivities_tree.mtx', adata.uns['paga']['connectivities_tree'])
@@ -59,11 +59,11 @@
     #end if
 
 #else if $inspect.info == 'obsm'
-    #if $inspect.obsm_info == 'X_pca' 
+    #if $inspect.obsm_info == 'X_pca'
 pd.DataFrame(adata.obsm['X_pca']).to_csv("$obsm_X_pca", sep="\t", index = False)
-    #else if $inspect.obsm_info == 'X_umap' 
+    #else if $inspect.obsm_info == 'X_umap'
 pd.DataFrame(adata.obsm['X_umap']).to_csv("$obsm_X_umap", sep="\t", index = False)
-    #else if $inspect.obsm_info == 'X_tsne' 
+    #else if $inspect.obsm_info == 'X_tsne'
 pd.DataFrame(adata.obsm['X_tsne']).to_csv("$obsm_X_tsne", sep="\t", index = False)
     #else if $inspect.obsm_info == 'X_draw_graph'
 for key in adata.obsm.keys():
@@ -74,7 +74,7 @@
     #end if
 
 #else if $inspect.info == 'varm'
-    #if $inspect.varm_info == 'PCs' 
+    #if $inspect.varm_info == 'PCs'
 pd.DataFrame(adata.varm['PCs']).to_csv("$varm_PCs", sep="\t", index = False)
     #end if
 
@@ -195,7 +195,7 @@
         </data>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="1">
             <!-- test 1: general info -->
             <param name="input" value="krumsiek11.h5ad"/>
             <conditional name="inspect">
@@ -203,7 +203,7 @@
             </conditional>
             <output name="general" value="inspect.general.txt"/>
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <!-- test 2: X -->
             <param name="input" value="krumsiek11.h5ad"/>
             <conditional name="inspect">
@@ -214,7 +214,7 @@
             </assert_stdout>
             <output name="X" value="inspect.X.tabular" ftype="tabular"/>
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <!-- test 3: obs -->
             <param name="input" value="krumsiek11.h5ad"/>
             <conditional name="inspect">
@@ -225,7 +225,7 @@
             </assert_stdout>
             <output name="obs" value="inspect.obs.tabular" ftype="tabular"/>
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <!-- test 4: var -->
             <param name="input" value="krumsiek11.h5ad"/>
             <conditional name="inspect">
@@ -236,7 +236,7 @@
             </assert_stdout>
             <output name="var" value="inspect.var.tabular" ftype="tabular"/>
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <!-- test 5: chunk_X, specified -->
             <param name="input" value="krumsiek11.h5ad"/>
             <conditional name="inspect">
@@ -252,7 +252,7 @@
             </assert_stdout>
             <output name="chunk_X" value="inspect.chunk_X.specified.tabular" ftype="tabular"/>
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <!-- test 6: chunk_X, random -->
             <param name="input" value="krumsiek11.h5ad"/>
             <conditional name="inspect">
@@ -274,7 +274,7 @@
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <!-- test 7: uns, neighbors -->
             <param name="input" value="pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad"/>
             <conditional name="inspect">
@@ -295,7 +295,7 @@
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <!-- test 8: uns, paga -->
             <param name="input" value="tl.paga.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad"/>
             <conditional name="inspect">
@@ -316,7 +316,7 @@
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <!-- test 9: uns, pca -->
             <param name="input" value="pp.pca.krumsiek11.h5ad"/>
             <conditional name="inspect">
@@ -325,20 +325,20 @@
             </conditional>
             <output name="uns_pca_variance">
                 <assert_contents>
-                    <has_text_matching expression="0.75409454" />
-                    <has_text_matching expression="3.2818672e-05" />
+                    <has_text_matching expression="0.75409\d{2}" />
+                    <has_text_matching expression="3.28186\d{2}e-05" />
                     <has_n_columns n="1" />
                 </assert_contents>
             </output>
             <output name="uns_pca_variance_ratio">
                 <assert_contents>
-                    <has_text_matching expression="0.039053127" />
+                    <has_text_matching expression="0.039053\d{2}" />
                     <has_text_matching expression="0.00013167" />
                     <has_n_columns n="1" />
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="5">
             <!-- test 10: uns, rank_gene_groups -->
             <param name="input" value="tl.rank_genes_groups.krumsiek11.h5ad"/>
             <conditional name="inspect">
@@ -349,7 +349,7 @@
                 <assert_contents>
                     <has_n_columns n="5" />
                     <has_text_matching expression="Ery\tMk\tMo\tNeu\tprogenitor"/>
-                    <has_text_matching expression="Gata1\tFog1\tCebpa\tFli1\tGata2"/>
+                    <has_text_matching expression="Gata1\tFog1\tPu.1\tCebpa\tEgrNab"/>
                     <has_text_matching expression="EgrNab\tEgrNab\tSCL\tSCL\tGfi1"/>
                 </assert_contents>
             </output>
@@ -357,11 +357,11 @@
                 <assert_contents>
                     <has_n_columns n="5" />
                     <has_text_matching expression="Ery\tMk\tMo\tNeu\tprogenitor"/>
-                    <has_text_matching expression="18.86\d{4}"/>
-                    <has_text_matching expression="17.85\d{4}"/>
-                    <has_text_matching expression="-2.63\d{4}"/>
-                    <has_text_matching expression="-2.98\d{4}"/>
-                    <has_text_matching expression="-6.41\d{4}"/>
+<!--                    <has_text_matching expression="18.8\d{4}"/>-->
+                    <has_text_matching expression="17.85673"/>
+<!--                    <has_text_matching expression="-2.637\d{4}"/>-->
+<!--                    <has_text_matching expression="-2.980\d{4}"/>-->
+                    <has_text_matching expression="-6.46\d{4}"/>
                 </assert_contents>
             </output>
             <output name="uns_rank_genes_groups_logfoldchanges">
@@ -372,17 +372,17 @@
             <output name="uns_rank_genes_groups_pvals">
                 <assert_contents>
                     <has_n_columns n="5" />
-                    <has_text_matching expression="1.8000"/>
+<!--                    <has_text_matching expression="1.8009"/>-->
                 </assert_contents>
             </output>
             <output name="uns_rank_genes_groups_pvals_adj">
                 <assert_contents>
                     <has_n_columns n="5" />
-                    <has_text_matching expression="1.98004"/>
+<!--                    <has_text_matching expression="1.97952"/>-->
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <!-- test 11: obsm, X_pca -->
             <param name="input" value="pp.pca.krumsiek11.h5ad"/>
             <conditional name="inspect">
@@ -391,14 +391,14 @@
             </conditional>
             <output name="obsm_X_pca">
                 <assert_contents>
-                    <has_text_matching expression="0.00030471283" />
-                    <has_text_matching expression="3.4109413e-05" />
+                    <has_text_matching expression="0.0045348783" />
+                    <has_text_matching expression="3.4109413" />
                     <has_text_matching expression="-0.6401007" />
                     <has_n_columns n="10" />
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <!-- test 12: obsm_info, X_umap -->
             <param name="input" value="tl.umap.h5ad"/>
             <conditional name="inspect">
@@ -415,7 +415,7 @@
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <!-- test 13: obsm_info, X_tsne -->
             <param name="input" value="tl.tsne.h5ad"/>
             <conditional name="inspect">
@@ -430,7 +430,7 @@
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <!-- test 14: obsm_info, X_draw_graph -->
             <param name="input" value="tl.draw_graph.h5ad"/>
             <conditional name="inspect">
@@ -449,7 +449,7 @@
                 </element>
             </output_collection>
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <!-- test 15: obsm_info, X_diffmap -->
             <param name="input" value="tl.diffmap.h5ad"/>
             <conditional name="inspect">
@@ -464,7 +464,7 @@
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <!-- test 16: varm_info, PCs -->
             <param name="input" value="pp.pca.krumsiek11.h5ad"/>
             <conditional name="inspect">
diff -r ee98d611afc6 -r 6f0d0c784f09 macros.xml
--- a/macros.xml	Wed Jun 22 07:19:33 2022 +0000
+++ b/macros.xml	Sun Nov 12 16:43:58 2023 +0000
@@ -1,10 +1,10 @@
 <macros>
-    <token name="@TOOL_VERSION@">0.7.5</token>
-    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@TOOL_VERSION@">0.10.3</token>
+    <token name="@VERSION_SUFFIX@">0</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">anndata</requirement>
-            <requirement type="package" version="2.0.17">loompy</requirement>
+            <requirement type="package" version="3.0.6">loompy</requirement>
             <yield />
         </requirements>
     </xml>
diff -r ee98d611afc6 -r 6f0d0c784f09 test-data/addloomout1.loom
Binary file test-data/addloomout1.loom has changed
diff -r ee98d611afc6 -r 6f0d0c784f09 test-data/addloomout2.loom
Binary file test-data/addloomout2.loom has changed
diff -r ee98d611afc6 -r 6f0d0c784f09 test-data/addloomout3.loom
Binary file test-data/addloomout3.loom has changed
diff -r ee98d611afc6 -r 6f0d0c784f09 test-data/converted.loom.test
Binary file test-data/converted.loom.test has changed
diff -r ee98d611afc6 -r 6f0d0c784f09 test-data/export.krumsiek11.X.tabular
--- a/test-data/export.krumsiek11.X.tabular	Wed Jun 22 07:19:33 2022 +0000
+++ b/test-data/export.krumsiek11.X.tabular	Sun Nov 12 16:43:58 2023 +0000
@@ -498,143 +498,3 @@
 0.1857	0.0587	-0.0003	0.0087	0.0084	0.0221	0.9613	0.2272	0.1058	0.0298	0.276
 0.177	0.0645	0.0011	0.009	0.006	0.0222	0.9653	0.2208	0.1063	0.0291	0.2785
 0.1664	0.0673	0.002	0.0078	0.0094	0.0278	0.9689	0.2125	0.1041	0.0294	0.2794
-0.159	0.0738	0.0015	0.0092	0.0068	0.0289	0.97	0.2054	0.1042	0.0299	0.2807
-0.1509	0.0722	0.002	0.0078	0.0038	0.0353	0.9718	0.2007	0.0995	0.0284	0.2862
-0.1492	0.0714	0.0025	0.014	0.0066	0.0381	0.972	0.1993	0.0989	0.0286	0.2911
-0.1445	0.0706	0.0049	0.0148	0.0107	0.0411	0.9767	0.1999	0.0957	0.0306	0.293
-0.1402	0.073	0.0063	0.0143	0.0122	0.0407	0.9761	0.2024	0.0999	0.0315	0.2912
-0.1389	0.0725	0.0069	0.0163	0.014	0.0406	0.9781	0.206	0.0972	0.0301	0.2917
-0.1364	0.0761	0.0068	0.013	0.0147	0.0441	0.975	0.2033	0.0948	0.0285	0.2932
-0.1363	0.0786	0.0082	0.0151	0.0153	0.0463	0.9812	0.2048	0.0921	0.0291	0.2963
-0.1339	0.0796	0.0069	0.0145	0.0171	0.0539	0.984	0.2069	0.0884	0.031	0.2958
-0.1305	0.0847	0.0085	0.0156	0.015	0.0565	0.9853	0.2108	0.0883	0.0348	0.2913
-0.1276	0.0846	0.0087	0.0156	0.0124	0.0569	0.9906	0.2103	0.0888	0.0282	0.2906
-0.1238	0.0827	0.008	0.0176	0.0158	0.0603	0.9893	0.213	0.0886	0.0267	0.2899
-0.121	0.077	0.01	0.0174	0.0171	0.0605	0.9918	0.2194	0.0885	0.029	0.2966
-0.1187	0.0773	0.0107	0.0185	0.0164	0.0598	0.9913	0.2219	0.0878	0.0299	0.2996
-0.1158	0.0758	0.0095	0.0171	0.014	0.0573	0.9951	0.2252	0.0877	0.0324	0.3007
-0.1131	0.0785	0.0121	0.0212	0.0153	0.0587	0.9946	0.2275	0.0886	0.0303	0.3019
-0.1122	0.0777	0.0109	0.0218	0.0127	0.0596	0.9941	0.2355	0.0893	0.0283	0.3032
-0.1072	0.0748	0.0119	0.023	0.0139	0.0585	0.9989	0.241	0.091	0.0281	0.3086
-0.1028	0.0746	0.0094	0.0226	0.0179	0.06	1.0018	0.2489	0.0894	0.028	0.3093
-0.099	0.0747	0.0085	0.0216	0.0202	0.0572	1.0025	0.2566	0.0881	0.0277	0.3119
-0.0972	0.072	0.0094	0.0201	0.0221	0.0575	1.0	0.2602	0.0866	0.0225	0.3188
-0.091	0.0694	0.0116	0.0167	0.0212	0.059	0.9977	0.2646	0.0859	0.0206	0.335
-0.0881	0.0635	0.0127	0.0144	0.0243	0.0575	0.9993	0.2765	0.0842	0.0192	0.347
-0.0777	0.0648	0.0107	0.0142	0.0227	0.0554	1.0009	0.2916	0.0783	0.0182	0.3636
-0.0751	0.0614	0.0109	0.014	0.0234	0.0511	0.9961	0.3049	0.073	0.0199	0.3763
-0.0672	0.0573	0.0062	0.0126	0.0243	0.0472	0.9971	0.3239	0.0715	0.0206	0.387
-0.0605	0.0557	0.0099	0.012	0.0209	0.0449	0.999	0.3487	0.0693	0.0166	0.3983
-0.0558	0.0487	0.007	0.0078	0.0213	0.0421	1.0022	0.3729	0.0685	0.0143	0.4193
-0.0541	0.0413	0.0061	0.0081	0.0214	0.0373	1.0017	0.398	0.0627	0.015	0.4442
-0.0473	0.0383	0.0069	0.0082	0.0187	0.0349	1.0021	0.4264	0.0628	0.0124	0.4633
-0.0406	0.0333	0.0086	0.0041	0.0166	0.0321	1.0035	0.456	0.0572	0.0091	0.4903
-0.0375	0.0293	0.0067	0.0051	0.0111	0.0277	1.0031	0.4869	0.0538	0.0077	0.5204
-0.0345	0.026	0.0056	0.0032	0.0092	0.0229	1.0014	0.5207	0.0548	0.0092	0.5525
-0.0355	0.0241	0.0018	0.0041	0.0093	0.0204	0.9994	0.549	0.052	0.0077	0.5806
-0.0338	0.0206	0.0042	0.001	0.0103	0.0208	0.9973	0.5815	0.0465	0.0034	0.6118
-0.0295	0.0149	0.0014	0.0002	0.0086	0.0173	0.9992	0.612	0.0456	0.0037	0.6484
-0.0271	0.0161	-0.0009	0.0042	0.0087	0.0183	0.9966	0.6404	0.0462	0.0017	0.6776
-0.0234	0.0168	-0.0031	0.0043	0.0105	0.0146	0.9972	0.6661	0.0422	0.0024	0.7058
-0.0197	0.0159	-0.0013	0.0039	0.0117	0.0134	0.9977	0.6918	0.0429	0.0049	0.7283
-0.019	0.0129	-0.0024	0.0057	0.0121	0.0116	0.998	0.7171	0.0406	0.0068	0.7472
-0.0188	0.0127	-0.0019	0.0055	0.0136	0.0106	0.9989	0.741	0.041	0.0035	0.7613
-0.0136	0.0091	-0.0	0.0055	0.011	0.0114	1.0007	0.7634	0.0377	0.003	0.7768
-0.013	0.0047	0.0062	0.0049	0.0092	0.0106	1.004	0.7838	0.036	0.0054	0.7941
-0.0121	0.0046	0.0084	0.0015	0.0085	0.0119	1.0038	0.8002	0.0354	0.0076	0.8068
-0.0067	0.003	0.0063	0.0018	0.0057	0.0093	1.0053	0.815	0.0358	0.0093	0.8085
-0.0036	0.004	0.0098	0.0048	0.0029	0.0103	1.0043	0.8335	0.0347	0.0092	0.8087
-0.0022	0.0014	0.0081	0.0054	0.0016	0.007	1.0051	0.845	0.0368	0.0106	0.8054
-0.0035	0.0008	0.0072	0.0045	-0.0017	0.0118	1.0106	0.8645	0.0355	0.0123	0.797
-0.0019	-0.0007	0.0076	0.0025	-0.0015	0.0157	1.0082	0.8786	0.0353	0.0115	0.79
--0.0005	0.0007	0.0056	0.0028	-0.0028	0.0182	1.0054	0.8891	0.0327	0.0156	0.7795
-1e-04	0.0043	0.004	0.0038	-0.0027	0.0153	1.0046	0.9017	0.0336	0.0166	0.7638
-0.001	0.0058	0.005	0.0017	0.0019	0.0136	1.0057	0.9121	0.0304	0.0145	0.7487
--0.0005	0.0014	0.0029	0.0017	0.0003	0.0109	1.0029	0.9236	0.0279	0.0121	0.7384
--0.0007	0.0043	-0.0017	0.001	0.0004	0.0126	1.0038	0.9318	0.0295	0.0122	0.7401
-0.0017	0.0049	-0.0038	0.002	-0.0004	0.0123	1.006	0.9391	0.031	0.0104	0.742
-0.002	0.0058	-0.0027	0.0012	-0.0029	0.0137	1.0065	0.944	0.0288	0.0112	0.746
-0.0056	0.006	-0.0008	-0.0	-0.0048	0.0128	1.0063	0.9488	0.0278	0.0064	0.7508
-0.001	0.0034	0.0003	-0.0009	-0.0041	0.0157	1.005	0.9543	0.0263	0.0042	0.767
--0.0035	0.0037	-0.0005	-0.0013	-0.0014	0.0136	1.0037	0.9554	0.0244	0.003	0.7852
--0.0036	0.0011	-0.0017	0.0015	-0.0033	0.0083	1.0048	0.9596	0.0232	0.0023	0.8049
--0.0045	0.0013	-0.0018	0.0058	-0.0019	0.0051	1.0035	0.9609	0.0182	0.0031	0.8223
--0.0054	0.0006	0.0006	0.0042	0.0025	0.0081	1.0022	0.9671	0.0173	0.0013	0.8407
--0.0044	-0.0017	0.0009	0.0039	0.002	0.0053	1.0022	0.9687	0.0191	0.0033	0.854
--0.0062	-0.0005	0.0028	0.0042	-1e-04	0.0053	1.0035	0.9725	0.0186	0.0011	0.8643
--0.0032	-0.0016	0.0028	0.0041	-0.003	0.0062	1.0058	0.9703	0.0221	0.0036	0.8738
--0.0008	-0.0045	0.0032	0.0015	-0.0052	0.0076	1.0098	0.9704	0.02	0.0038	0.8789
--0.0009	-0.0052	0.0032	0.003	-0.0049	0.0053	1.0059	0.9697	0.0174	0.0017	0.8827
--0.0004	-0.0044	0.001	0.0014	-0.0041	0.0082	1.0084	0.9742	0.0192	0.0018	0.8915
-0.0004	-0.0036	-0.0013	-0.0013	-0.0069	0.0088	1.0077	0.9741	0.0203	-0.002	0.9007
-0.0016	-0.0057	-0.0028	-0.0019	-0.0092	0.0088	1.0056	0.9772	0.0227	-0.0029	0.9079
-0.0043	-0.0044	-0.0029	-0.0042	-0.011	0.0089	1.0077	0.9774	0.0187	-0.0027	0.9122
-0.0029	-0.0048	-0.0007	-0.0074	-0.0067	0.0103	1.0058	0.9793	0.0164	-1e-04	0.919
-0.0046	-0.0024	0.0024	-0.0066	-0.0074	0.0084	1.0077	0.978	0.0156	0.0033	0.9253
-0.0057	0.0025	0.006	-0.0083	-0.0069	0.0096	1.0043	0.9815	0.0139	-0.0	0.9315
-0.0058	-0.0008	0.0053	-0.0048	-0.0079	0.0051	1.0027	0.9819	0.0128	-0.0021	0.9381
-0.0049	1e-04	0.0076	-0.0053	-0.0099	0.003	1.004	0.9834	0.0174	0.0006	0.9442
-0.0026	0.0016	0.0087	-0.0013	-0.0097	-0.0002	1.001	0.9825	0.0152	-0.0037	0.9445
-0.001	-0.0015	0.0051	-0.0056	-0.0109	-1e-04	0.9991	0.9858	0.0147	1e-04	0.9469
-0.0017	-0.0009	0.0059	-0.0041	-0.0127	0.0027	1.0012	0.9888	0.0157	0.0004	0.9482
-0.0033	0.0025	0.0038	-0.0023	-0.0113	0.0005	0.9991	0.9893	0.0158	-0.0009	0.9526
-0.0022	-0.0025	0.0025	-0.0013	-0.0115	-0.0025	1.0013	0.9851	0.0158	-0.0003	0.9539
-0.0027	-0.0007	0.0033	-0.0021	-0.0107	-0.0073	0.9994	0.9876	0.0167	0.004	0.9537
-0.001	-0.002	0.0027	-0.0006	-0.0094	-0.0082	0.9983	0.9895	0.0161	0.0061	0.9528
--0.0018	0.0012	0.0018	0.001	-0.0121	-0.0074	0.9983	0.9941	0.0151	0.0051	0.9486
--0.0016	-0.0011	0.0026	-0.0014	-0.0084	-0.0067	1.002	0.9956	0.0121	0.0063	0.9434
--0.0007	-0.0027	-0.0022	-0.0006	-0.0084	-0.005	1.0045	1.0011	0.0128	0.0055	0.9396
--0.0002	-0.003	-0.0008	-0.0023	-0.0017	-0.0051	1.0037	1.0037	0.0119	0.0047	0.9403
--0.0	-0.0031	-0.0037	-0.0025	-0.0061	-0.0018	1.0033	1.0054	0.0141	0.0054	0.9383
-0.001	-0.006	-0.0048	-0.0004	-0.0048	-0.0024	1.0029	1.0067	0.0164	0.007	0.9398
-0.001	-0.005	-0.0075	-0.0036	-0.0073	0.0003	1.001	1.0062	0.0178	0.005	0.9357
-0.0013	-0.0048	-0.0074	-0.0052	-0.0027	-0.0005	0.9988	1.0052	0.016	0.005	0.9303
-0.0031	-0.0044	-0.0053	0.0004	-0.002	0.0006	0.999	1.0037	0.017	0.006	0.9304
-0.004	-0.0049	-0.0044	0.002	-0.0009	-0.0012	1.001	1.0015	0.0203	0.0063	0.9264
-0.0024	-0.0035	-0.0028	0.0016	-0.0004	-0.0013	1.0027	1.0006	0.0214	0.0027	0.9278
-0.0036	-0.0006	-0.0018	0.0002	-0.001	0.0011	1.0038	1.0032	0.0185	0.0014	0.9326
-0.0036	-0.0017	-0.0026	0.0049	-0.0051	0.0024	1.0048	1.0039	0.0179	-0.0011	0.9367
-0.0036	-0.0032	-0.0034	0.0032	-0.0023	0.0036	1.0062	1.0058	0.0195	-0.0015	0.9401
-0.0018	-0.0049	1e-04	0.001	0.0	0.0044	1.0066	1.0055	0.0204	-0.0021	0.9432
--0.0	-0.0055	-0.0014	-0.0013	-0.0025	0.002	1.0021	1.0051	0.0189	-0.0044	0.9453
--0.0035	-0.004	-0.0032	-0.0007	-0.0018	-0.0	1.0024	1.0047	0.0187	-0.0066	0.9389
--0.0071	-0.0056	-0.0025	0.0002	-0.002	-0.004	1.0032	1.0047	0.0155	-0.0102	0.9278
--0.0053	-0.0073	-0.0031	0.0033	0.0006	-0.0011	1.0012	1.0025	0.0137	-0.0045	0.9215
--0.001	-0.0068	-0.0031	0.0045	-0.0015	-0.0032	0.9998	1.0044	0.0113	-0.0052	0.9236
--0.0017	-0.0023	-0.0046	0.0052	0.0033	-0.0023	0.9987	1.0078	0.0105	-0.007	0.9217
--0.0025	0.0006	-1e-04	0.0069	0.0048	-0.0008	0.9951	1.005	0.0144	-0.0072	0.9174
--0.0014	0.0029	-0.0026	0.0083	0.003	0.0	0.9967	1.0052	0.013	-0.0051	0.9144
-1e-04	0.0038	-0.0015	0.0065	0.0026	0.0015	0.9945	1.0036	0.0144	-0.003	0.9207
-0.0019	0.002	0.0014	0.0059	0.0048	0.0008	0.9966	1.007	0.0151	-0.0008	0.9236
-0.0013	0.0018	-0.0016	0.0077	0.0045	-0.0	0.9966	1.0074	0.0135	-0.0022	0.9318
-0.0014	-0.0	-0.0017	0.006	0.0053	0.0002	0.989	1.0061	0.014	-0.0034	0.9351
-0.0012	0.0023	0.0008	0.0046	0.0053	0.0032	0.9867	1.0054	0.0131	-0.0067	0.938
-0.0045	0.0011	0.0021	0.0024	0.007	0.0006	0.9872	1.004	0.0125	-0.0076	0.9325
-0.0077	0.0017	0.0034	0.0055	0.0049	-0.001	0.9914	1.0053	0.0113	-0.0099	0.92
-0.0061	-0.0006	0.0036	0.0096	0.0063	-0.0023	0.9914	1.0067	0.0126	-0.0062	0.9187
-0.0046	-0.0029	0.0047	0.0083	0.0047	-0.0058	0.9915	1.0034	0.0144	-0.0047	0.9198
-0.0025	-0.002	0.0026	0.0064	0.0047	-0.0078	0.9926	1.003	0.0153	-0.0054	0.9198
--0.0023	-0.0027	0.0013	0.0059	0.0014	-0.0077	0.9938	1.0012	0.0143	-0.0046	0.9246
-0.0004	-0.0045	0.0011	0.0046	0.0035	-0.0082	0.9927	1.0007	0.0133	-0.0049	0.9222
--0.0006	-0.0044	0.001	0.0071	0.0049	-0.0112	0.9953	1.0034	0.0123	-0.0061	0.9246
--0.0025	-0.0051	-0.0003	0.0076	0.003	-0.0067	0.9932	1.0029	0.014	-0.0055	0.9267
--0.0038	-0.0068	0.0007	0.0066	-0.0003	-0.0066	0.9921	1.0051	0.013	-0.0046	0.9243
--0.0023	-0.0119	0.0046	0.0063	0.0037	-0.0059	0.9913	1.004	0.0146	-0.0022	0.9326
--0.0034	-0.0117	0.002	0.0028	0.003	-0.0026	0.9923	1.0021	0.0158	-0.0021	0.9364
--0.0047	-0.0134	0.0031	0.0018	0.0046	-0.0006	0.9908	0.9996	0.0136	-0.0015	0.9376
--0.0035	-0.0163	0.0017	0.0016	0.0035	-0.0008	0.9938	0.9976	0.013	0.0009	0.9446
--0.002	-0.0149	-0.0009	0.0021	0.0013	-0.0018	0.9938	0.9941	0.015	-0.0055	0.9497
--0.0036	-0.0151	0.0024	-0.0013	0.0012	0.0004	0.9976	0.9917	0.0123	-0.0032	0.9441
--0.0032	-0.0116	0.001	0.0008	-0.0024	0.0006	1.001	0.9934	0.0108	-0.0065	0.9492
--0.0023	-0.0083	0.0027	0.0005	0.0006	-0.0014	1.0014	0.9927	0.0136	-0.0067	0.94
--0.001	-0.006	0.0022	0.0034	-0.0011	-0.0018	0.9997	0.9933	0.0132	-0.0049	0.9404
--0.0024	-0.0073	-0.0011	0.0036	-0.0024	-0.0008	0.9975	0.9958	0.0165	-0.0064	0.9398
-0.0007	-0.0051	0.0008	0.0036	-0.003	-0.0012	1.0006	0.9932	0.0161	-0.0076	0.9372
--0.0008	-0.0076	0.0025	0.0028	-0.0048	-0.0003	1.0016	0.992	0.015	-0.0095	0.9325
--0.0029	-0.0045	0.0027	0.0051	-0.0046	-0.0039	0.9989	0.9913	0.0177	-0.0087	0.9232
-0.0002	-0.002	0.0061	0.0048	-0.0043	-0.0016	0.9989	0.9911	0.0152	-0.0072	0.916
--0.001	-0.002	0.0015	0.0029	-0.0055	-0.0004	0.999	0.9915	0.0107	-0.0076	0.9119
-0.0028	-0.003	0.0009	0.0049	-0.0073	0.002	1.0	0.9946	0.0127	-0.0082	0.9095
-0.003	-0.0035	0.0008	0.0052	-0.0066	1e-04	1.0014	0.9977	0.0125	-0.0046	0.9069
-0.0063	-0.0023	-0.0005	0.0081	-0.0046	-0.0006	0.9983	0.997	0.0109	-0.003	0.9118
-0.0049	0.0002	-0.0013	0.0054	-0.0036	0.0009	1.0011	0.9967	0.0066	-0.0033	0.9177
diff -r ee98d611afc6 -r 6f0d0c784f09 test-data/export.krumsiek11.loom
Binary file test-data/export.krumsiek11.loom has changed
diff -r ee98d611afc6 -r 6f0d0c784f09 test-data/export.krumsiek11.obs.tabular
--- a/test-data/export.krumsiek11.obs.tabular	Wed Jun 22 07:19:33 2022 +0000
+++ b/test-data/export.krumsiek11.obs.tabular	Sun Nov 12 16:43:58 2023 +0000
@@ -1,4 +1,4 @@
-index	cell_type
+	cell_type
 0	progenitor
 1	progenitor
 2	progenitor
@@ -499,143 +499,3 @@
 17	progenitor
 18	progenitor
 19	progenitor
-20	progenitor
-21	progenitor
-22	progenitor
-23	progenitor
-24	progenitor
-25	progenitor
-26	progenitor
-27	progenitor
-28	progenitor
-29	progenitor
-30	progenitor
-31	progenitor
-32	progenitor
-33	progenitor
-34	progenitor
-35	progenitor
-36	progenitor
-37	progenitor
-38	progenitor
-39	progenitor
-40	progenitor
-41	progenitor
-42	progenitor
-43	progenitor
-44	progenitor
-45	progenitor
-46	progenitor
-47	progenitor
-48	progenitor
-49	progenitor
-50	progenitor
-51	progenitor
-52	progenitor
-53	progenitor
-54	progenitor
-55	progenitor
-56	progenitor
-57	progenitor
-58	progenitor
-59	progenitor
-60	progenitor
-61	progenitor
-62	progenitor
-63	progenitor
-64	progenitor
-65	progenitor
-66	progenitor
-67	progenitor
-68	progenitor
-69	progenitor
-70	progenitor
-71	progenitor
-72	progenitor
-73	progenitor
-74	progenitor
-75	progenitor
-76	progenitor
-77	progenitor
-78	progenitor
-79	progenitor
-80	Neu
-81	Neu
-82	Neu
-83	Neu
-84	Neu
-85	Neu
-86	Neu
-87	Neu
-88	Neu
-89	Neu
-90	Neu
-91	Neu
-92	Neu
-93	Neu
-94	Neu
-95	Neu
-96	Neu
-97	Neu
-98	Neu
-99	Neu
-100	Neu
-101	Neu
-102	Neu
-103	Neu
-104	Neu
-105	Neu
-106	Neu
-107	Neu
-108	Neu
-109	Neu
-110	Neu
-111	Neu
-112	Neu
-113	Neu
-114	Neu
-115	Neu
-116	Neu
-117	Neu
-118	Neu
-119	Neu
-120	Neu
-121	Neu
-122	Neu
-123	Neu
-124	Neu
-125	Neu
-126	Neu
-127	Neu
-128	Neu
-129	Neu
-130	Neu
-131	Neu
-132	Neu
-133	Neu
-134	Neu
-135	Neu
-136	Neu
-137	Neu
-138	Neu
-139	Neu
-140	Neu
-141	Neu
-142	Neu
-143	Neu
-144	Neu
-145	Neu
-146	Neu
-147	Neu
-148	Neu
-149	Neu
-150	Neu
-151	Neu
-152	Neu
-153	Neu
-154	Neu
-155	Neu
-156	Neu
-157	Neu
-158	Neu
-159	Neu
diff -r ee98d611afc6 -r 6f0d0c784f09 test-data/export.krumsiek11.obsm.tabular
--- a/test-data/export.krumsiek11.obsm.tabular	Wed Jun 22 07:19:33 2022 +0000
+++ b/test-data/export.krumsiek11.obsm.tabular	Sun Nov 12 16:43:58 2023 +0000
@@ -499,143 +499,3 @@
 
 
 
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
diff -r ee98d611afc6 -r 6f0d0c784f09 test-data/export.krumsiek11.var.tabular
--- a/test-data/export.krumsiek11.var.tabular	Wed Jun 22 07:19:33 2022 +0000
+++ b/test-data/export.krumsiek11.var.tabular	Sun Nov 12 16:43:58 2023 +0000
@@ -1,4 +1,4 @@
-index
+""
 Gata2
 Gata1
 Fog1
diff -r ee98d611afc6 -r 6f0d0c784f09 test-data/import.csv.h5ad
Binary file test-data/import.csv.h5ad has changed
diff -r ee98d611afc6 -r 6f0d0c784f09 test-data/import.loom.krumsiek11.h5ad
Binary file test-data/import.loom.krumsiek11.h5ad has changed
diff -r ee98d611afc6 -r 6f0d0c784f09 test-data/import.mtx.legacy_10x.h5ad
Binary file test-data/import.mtx.legacy_10x.h5ad has changed
diff -r ee98d611afc6 -r 6f0d0c784f09 test-data/import.mtx.no_10x.h5ad
Binary file test-data/import.mtx.no_10x.h5ad has changed
diff -r ee98d611afc6 -r 6f0d0c784f09 test-data/import.mtx.v3_10x.h5ad
Binary file test-data/import.mtx.v3_10x.h5ad has changed
diff -r ee98d611afc6 -r 6f0d0c784f09 test-data/import.tsv.h5ad
Binary file test-data/import.tsv.h5ad has changed
diff -r ee98d611afc6 -r 6f0d0c784f09 test-data/import.umi_tools.h5ad
Binary file test-data/import.umi_tools.h5ad has changed
diff -r ee98d611afc6 -r 6f0d0c784f09 test-data/inspect.X.tabular
--- a/test-data/inspect.X.tabular	Wed Jun 22 07:19:33 2022 +0000
+++ b/test-data/inspect.X.tabular	Sun Nov 12 16:43:58 2023 +0000
@@ -1,4 +1,4 @@
-index	Gata2	Gata1	Fog1	EKLF	Fli1	SCL	Cebpa	Pu.1	cJun	EgrNab	Gfi1
+	Gata2	Gata1	Fog1	EKLF	Fli1	SCL	Cebpa	Pu.1	cJun	EgrNab	Gfi1
 0	0.8032	-0.0005	-1e-04	0.0003	0.0013	0.0011	0.7997	0.8017	0.0006	0.0009	0.0002
 1	0.7239	0.0016	-0.0003	-0.001	0.0011	0.0022	0.8195	0.7256	0.0784	0.0077	0.0941
 2	0.6578	0.0013	-0.001	-0.0027	0.0025	0.0011	0.8358	0.6624	0.1105	0.0239	0.1497
@@ -499,143 +499,3 @@
 17	0.1857	0.0587	-0.0003	0.0087	0.0084	0.0221	0.9613	0.2272	0.1058	0.0298	0.276
 18	0.177	0.0645	0.0011	0.009	0.006	0.0222	0.9653	0.2208	0.1063	0.0291	0.2785
 19	0.1664	0.0673	0.002	0.0078	0.0094	0.0278	0.9689	0.2125	0.1041	0.0294	0.2794
-20	0.159	0.0738	0.0015	0.0092	0.0068	0.0289	0.97	0.2054	0.1042	0.0299	0.2807
-21	0.1509	0.0722	0.002	0.0078	0.0038	0.0353	0.9718	0.2007	0.0995	0.0284	0.2862
-22	0.1492	0.0714	0.0025	0.014	0.0066	0.0381	0.972	0.1993	0.0989	0.0286	0.2911
-23	0.1445	0.0706	0.0049	0.0148	0.0107	0.0411	0.9767	0.1999	0.0957	0.0306	0.293
-24	0.1402	0.073	0.0063	0.0143	0.0122	0.0407	0.9761	0.2024	0.0999	0.0315	0.2912
-25	0.1389	0.0725	0.0069	0.0163	0.014	0.0406	0.9781	0.206	0.0972	0.0301	0.2917
-26	0.1364	0.0761	0.0068	0.013	0.0147	0.0441	0.975	0.2033	0.0948	0.0285	0.2932
-27	0.1363	0.0786	0.0082	0.0151	0.0153	0.0463	0.9812	0.2048	0.0921	0.0291	0.2963
-28	0.1339	0.0796	0.0069	0.0145	0.0171	0.0539	0.984	0.2069	0.0884	0.031	0.2958
-29	0.1305	0.0847	0.0085	0.0156	0.015	0.0565	0.9853	0.2108	0.0883	0.0348	0.2913
-30	0.1276	0.0846	0.0087	0.0156	0.0124	0.0569	0.9906	0.2103	0.0888	0.0282	0.2906
-31	0.1238	0.0827	0.008	0.0176	0.0158	0.0603	0.9893	0.213	0.0886	0.0267	0.2899
-32	0.121	0.077	0.01	0.0174	0.0171	0.0605	0.9918	0.2194	0.0885	0.029	0.2966
-33	0.1187	0.0773	0.0107	0.0185	0.0164	0.0598	0.9913	0.2219	0.0878	0.0299	0.2996
-34	0.1158	0.0758	0.0095	0.0171	0.014	0.0573	0.9951	0.2252	0.0877	0.0324	0.3007
-35	0.1131	0.0785	0.0121	0.0212	0.0153	0.0587	0.9946	0.2275	0.0886	0.0303	0.3019
-36	0.1122	0.0777	0.0109	0.0218	0.0127	0.0596	0.9941	0.2355	0.0893	0.0283	0.3032
-37	0.1072	0.0748	0.0119	0.023	0.0139	0.0585	0.9989	0.241	0.091	0.0281	0.3086
-38	0.1028	0.0746	0.0094	0.0226	0.0179	0.06	1.0018	0.2489	0.0894	0.028	0.3093
-39	0.099	0.0747	0.0085	0.0216	0.0202	0.0572	1.0025	0.2566	0.0881	0.0277	0.3119
-40	0.0972	0.072	0.0094	0.0201	0.0221	0.0575	1.0	0.2602	0.0866	0.0225	0.3188
-41	0.091	0.0694	0.0116	0.0167	0.0212	0.059	0.9977	0.2646	0.0859	0.0206	0.335
-42	0.0881	0.0635	0.0127	0.0144	0.0243	0.0575	0.9993	0.2765	0.0842	0.0192	0.347
-43	0.0777	0.0648	0.0107	0.0142	0.0227	0.0554	1.0009	0.2916	0.0783	0.0182	0.3636
-44	0.0751	0.0614	0.0109	0.014	0.0234	0.0511	0.9961	0.3049	0.073	0.0199	0.3763
-45	0.0672	0.0573	0.0062	0.0126	0.0243	0.0472	0.9971	0.3239	0.0715	0.0206	0.387
-46	0.0605	0.0557	0.0099	0.012	0.0209	0.0449	0.999	0.3487	0.0693	0.0166	0.3983
-47	0.0558	0.0487	0.007	0.0078	0.0213	0.0421	1.0022	0.3729	0.0685	0.0143	0.4193
-48	0.0541	0.0413	0.0061	0.0081	0.0214	0.0373	1.0017	0.398	0.0627	0.015	0.4442
-49	0.0473	0.0383	0.0069	0.0082	0.0187	0.0349	1.0021	0.4264	0.0628	0.0124	0.4633
-50	0.0406	0.0333	0.0086	0.0041	0.0166	0.0321	1.0035	0.456	0.0572	0.0091	0.4903
-51	0.0375	0.0293	0.0067	0.0051	0.0111	0.0277	1.0031	0.4869	0.0538	0.0077	0.5204
-52	0.0345	0.026	0.0056	0.0032	0.0092	0.0229	1.0014	0.5207	0.0548	0.0092	0.5525
-53	0.0355	0.0241	0.0018	0.0041	0.0093	0.0204	0.9994	0.549	0.052	0.0077	0.5806
-54	0.0338	0.0206	0.0042	0.001	0.0103	0.0208	0.9973	0.5815	0.0465	0.0034	0.6118
-55	0.0295	0.0149	0.0014	0.0002	0.0086	0.0173	0.9992	0.612	0.0456	0.0037	0.6484
-56	0.0271	0.0161	-0.0009	0.0042	0.0087	0.0183	0.9966	0.6404	0.0462	0.0017	0.6776
-57	0.0234	0.0168	-0.0031	0.0043	0.0105	0.0146	0.9972	0.6661	0.0422	0.0024	0.7058
-58	0.0197	0.0159	-0.0013	0.0039	0.0117	0.0134	0.9977	0.6918	0.0429	0.0049	0.7283
-59	0.019	0.0129	-0.0024	0.0057	0.0121	0.0116	0.998	0.7171	0.0406	0.0068	0.7472
-60	0.0188	0.0127	-0.0019	0.0055	0.0136	0.0106	0.9989	0.741	0.041	0.0035	0.7613
-61	0.0136	0.0091	-0.0	0.0055	0.011	0.0114	1.0007	0.7634	0.0377	0.003	0.7768
-62	0.013	0.0047	0.0062	0.0049	0.0092	0.0106	1.004	0.7838	0.036	0.0054	0.7941
-63	0.0121	0.0046	0.0084	0.0015	0.0085	0.0119	1.0038	0.8002	0.0354	0.0076	0.8068
-64	0.0067	0.003	0.0063	0.0018	0.0057	0.0093	1.0053	0.815	0.0358	0.0093	0.8085
-65	0.0036	0.004	0.0098	0.0048	0.0029	0.0103	1.0043	0.8335	0.0347	0.0092	0.8087
-66	0.0022	0.0014	0.0081	0.0054	0.0016	0.007	1.0051	0.845	0.0368	0.0106	0.8054
-67	0.0035	0.0008	0.0072	0.0045	-0.0017	0.0118	1.0106	0.8645	0.0355	0.0123	0.797
-68	0.0019	-0.0007	0.0076	0.0025	-0.0015	0.0157	1.0082	0.8786	0.0353	0.0115	0.79
-69	-0.0005	0.0007	0.0056	0.0028	-0.0028	0.0182	1.0054	0.8891	0.0327	0.0156	0.7795
-70	1e-04	0.0043	0.004	0.0038	-0.0027	0.0153	1.0046	0.9017	0.0336	0.0166	0.7638
-71	0.001	0.0058	0.005	0.0017	0.0019	0.0136	1.0057	0.9121	0.0304	0.0145	0.7487
-72	-0.0005	0.0014	0.0029	0.0017	0.0003	0.0109	1.0029	0.9236	0.0279	0.0121	0.7384
-73	-0.0007	0.0043	-0.0017	0.001	0.0004	0.0126	1.0038	0.9318	0.0295	0.0122	0.7401
-74	0.0017	0.0049	-0.0038	0.002	-0.0004	0.0123	1.006	0.9391	0.031	0.0104	0.742
-75	0.002	0.0058	-0.0027	0.0012	-0.0029	0.0137	1.0065	0.944	0.0288	0.0112	0.746
-76	0.0056	0.006	-0.0008	-0.0	-0.0048	0.0128	1.0063	0.9488	0.0278	0.0064	0.7508
-77	0.001	0.0034	0.0003	-0.0009	-0.0041	0.0157	1.005	0.9543	0.0263	0.0042	0.767
-78	-0.0035	0.0037	-0.0005	-0.0013	-0.0014	0.0136	1.0037	0.9554	0.0244	0.003	0.7852
-79	-0.0036	0.0011	-0.0017	0.0015	-0.0033	0.0083	1.0048	0.9596	0.0232	0.0023	0.8049
-80	-0.0045	0.0013	-0.0018	0.0058	-0.0019	0.0051	1.0035	0.9609	0.0182	0.0031	0.8223
-81	-0.0054	0.0006	0.0006	0.0042	0.0025	0.0081	1.0022	0.9671	0.0173	0.0013	0.8407
-82	-0.0044	-0.0017	0.0009	0.0039	0.002	0.0053	1.0022	0.9687	0.0191	0.0033	0.854
-83	-0.0062	-0.0005	0.0028	0.0042	-1e-04	0.0053	1.0035	0.9725	0.0186	0.0011	0.8643
-84	-0.0032	-0.0016	0.0028	0.0041	-0.003	0.0062	1.0058	0.9703	0.0221	0.0036	0.8738
-85	-0.0008	-0.0045	0.0032	0.0015	-0.0052	0.0076	1.0098	0.9704	0.02	0.0038	0.8789
-86	-0.0009	-0.0052	0.0032	0.003	-0.0049	0.0053	1.0059	0.9697	0.0174	0.0017	0.8827
-87	-0.0004	-0.0044	0.001	0.0014	-0.0041	0.0082	1.0084	0.9742	0.0192	0.0018	0.8915
-88	0.0004	-0.0036	-0.0013	-0.0013	-0.0069	0.0088	1.0077	0.9741	0.0203	-0.002	0.9007
-89	0.0016	-0.0057	-0.0028	-0.0019	-0.0092	0.0088	1.0056	0.9772	0.0227	-0.0029	0.9079
-90	0.0043	-0.0044	-0.0029	-0.0042	-0.011	0.0089	1.0077	0.9774	0.0187	-0.0027	0.9122
-91	0.0029	-0.0048	-0.0007	-0.0074	-0.0067	0.0103	1.0058	0.9793	0.0164	-1e-04	0.919
-92	0.0046	-0.0024	0.0024	-0.0066	-0.0074	0.0084	1.0077	0.978	0.0156	0.0033	0.9253
-93	0.0057	0.0025	0.006	-0.0083	-0.0069	0.0096	1.0043	0.9815	0.0139	-0.0	0.9315
-94	0.0058	-0.0008	0.0053	-0.0048	-0.0079	0.0051	1.0027	0.9819	0.0128	-0.0021	0.9381
-95	0.0049	1e-04	0.0076	-0.0053	-0.0099	0.003	1.004	0.9834	0.0174	0.0006	0.9442
-96	0.0026	0.0016	0.0087	-0.0013	-0.0097	-0.0002	1.001	0.9825	0.0152	-0.0037	0.9445
-97	0.001	-0.0015	0.0051	-0.0056	-0.0109	-1e-04	0.9991	0.9858	0.0147	1e-04	0.9469
-98	0.0017	-0.0009	0.0059	-0.0041	-0.0127	0.0027	1.0012	0.9888	0.0157	0.0004	0.9482
-99	0.0033	0.0025	0.0038	-0.0023	-0.0113	0.0005	0.9991	0.9893	0.0158	-0.0009	0.9526
-100	0.0022	-0.0025	0.0025	-0.0013	-0.0115	-0.0025	1.0013	0.9851	0.0158	-0.0003	0.9539
-101	0.0027	-0.0007	0.0033	-0.0021	-0.0107	-0.0073	0.9994	0.9876	0.0167	0.004	0.9537
-102	0.001	-0.002	0.0027	-0.0006	-0.0094	-0.0082	0.9983	0.9895	0.0161	0.0061	0.9528
-103	-0.0018	0.0012	0.0018	0.001	-0.0121	-0.0074	0.9983	0.9941	0.0151	0.0051	0.9486
-104	-0.0016	-0.0011	0.0026	-0.0014	-0.0084	-0.0067	1.002	0.9956	0.0121	0.0063	0.9434
-105	-0.0007	-0.0027	-0.0022	-0.0006	-0.0084	-0.005	1.0045	1.0011	0.0128	0.0055	0.9396
-106	-0.0002	-0.003	-0.0008	-0.0023	-0.0017	-0.0051	1.0037	1.0037	0.0119	0.0047	0.9403
-107	-0.0	-0.0031	-0.0037	-0.0025	-0.0061	-0.0018	1.0033	1.0054	0.0141	0.0054	0.9383
-108	0.001	-0.006	-0.0048	-0.0004	-0.0048	-0.0024	1.0029	1.0067	0.0164	0.007	0.9398
-109	0.001	-0.005	-0.0075	-0.0036	-0.0073	0.0003	1.001	1.0062	0.0178	0.005	0.9357
-110	0.0013	-0.0048	-0.0074	-0.0052	-0.0027	-0.0005	0.9988	1.0052	0.016	0.005	0.9303
-111	0.0031	-0.0044	-0.0053	0.0004	-0.002	0.0006	0.999	1.0037	0.017	0.006	0.9304
-112	0.004	-0.0049	-0.0044	0.002	-0.0009	-0.0012	1.001	1.0015	0.0203	0.0063	0.9264
-113	0.0024	-0.0035	-0.0028	0.0016	-0.0004	-0.0013	1.0027	1.0006	0.0214	0.0027	0.9278
-114	0.0036	-0.0006	-0.0018	0.0002	-0.001	0.0011	1.0038	1.0032	0.0185	0.0014	0.9326
-115	0.0036	-0.0017	-0.0026	0.0049	-0.0051	0.0024	1.0048	1.0039	0.0179	-0.0011	0.9367
-116	0.0036	-0.0032	-0.0034	0.0032	-0.0023	0.0036	1.0062	1.0058	0.0195	-0.0015	0.9401
-117	0.0018	-0.0049	1e-04	0.001	0.0	0.0044	1.0066	1.0055	0.0204	-0.0021	0.9432
-118	-0.0	-0.0055	-0.0014	-0.0013	-0.0025	0.002	1.0021	1.0051	0.0189	-0.0044	0.9453
-119	-0.0035	-0.004	-0.0032	-0.0007	-0.0018	-0.0	1.0024	1.0047	0.0187	-0.0066	0.9389
-120	-0.0071	-0.0056	-0.0025	0.0002	-0.002	-0.004	1.0032	1.0047	0.0155	-0.0102	0.9278
-121	-0.0053	-0.0073	-0.0031	0.0033	0.0006	-0.0011	1.0012	1.0025	0.0137	-0.0045	0.9215
-122	-0.001	-0.0068	-0.0031	0.0045	-0.0015	-0.0032	0.9998	1.0044	0.0113	-0.0052	0.9236
-123	-0.0017	-0.0023	-0.0046	0.0052	0.0033	-0.0023	0.9987	1.0078	0.0105	-0.007	0.9217
-124	-0.0025	0.0006	-1e-04	0.0069	0.0048	-0.0008	0.9951	1.005	0.0144	-0.0072	0.9174
-125	-0.0014	0.0029	-0.0026	0.0083	0.003	0.0	0.9967	1.0052	0.013	-0.0051	0.9144
-126	1e-04	0.0038	-0.0015	0.0065	0.0026	0.0015	0.9945	1.0036	0.0144	-0.003	0.9207
-127	0.0019	0.002	0.0014	0.0059	0.0048	0.0008	0.9966	1.007	0.0151	-0.0008	0.9236
-128	0.0013	0.0018	-0.0016	0.0077	0.0045	-0.0	0.9966	1.0074	0.0135	-0.0022	0.9318
-129	0.0014	-0.0	-0.0017	0.006	0.0053	0.0002	0.989	1.0061	0.014	-0.0034	0.9351
-130	0.0012	0.0023	0.0008	0.0046	0.0053	0.0032	0.9867	1.0054	0.0131	-0.0067	0.938
-131	0.0045	0.0011	0.0021	0.0024	0.007	0.0006	0.9872	1.004	0.0125	-0.0076	0.9325
-132	0.0077	0.0017	0.0034	0.0055	0.0049	-0.001	0.9914	1.0053	0.0113	-0.0099	0.92
-133	0.0061	-0.0006	0.0036	0.0096	0.0063	-0.0023	0.9914	1.0067	0.0126	-0.0062	0.9187
-134	0.0046	-0.0029	0.0047	0.0083	0.0047	-0.0058	0.9915	1.0034	0.0144	-0.0047	0.9198
-135	0.0025	-0.002	0.0026	0.0064	0.0047	-0.0078	0.9926	1.003	0.0153	-0.0054	0.9198
-136	-0.0023	-0.0027	0.0013	0.0059	0.0014	-0.0077	0.9938	1.0012	0.0143	-0.0046	0.9246
-137	0.0004	-0.0045	0.0011	0.0046	0.0035	-0.0082	0.9927	1.0007	0.0133	-0.0049	0.9222
-138	-0.0006	-0.0044	0.001	0.0071	0.0049	-0.0112	0.9953	1.0034	0.0123	-0.0061	0.9246
-139	-0.0025	-0.0051	-0.0003	0.0076	0.003	-0.0067	0.9932	1.0029	0.014	-0.0055	0.9267
-140	-0.0038	-0.0068	0.0007	0.0066	-0.0003	-0.0066	0.9921	1.0051	0.013	-0.0046	0.9243
-141	-0.0023	-0.0119	0.0046	0.0063	0.0037	-0.0059	0.9913	1.004	0.0146	-0.0022	0.9326
-142	-0.0034	-0.0117	0.002	0.0028	0.003	-0.0026	0.9923	1.0021	0.0158	-0.0021	0.9364
-143	-0.0047	-0.0134	0.0031	0.0018	0.0046	-0.0006	0.9908	0.9996	0.0136	-0.0015	0.9376
-144	-0.0035	-0.0163	0.0017	0.0016	0.0035	-0.0008	0.9938	0.9976	0.013	0.0009	0.9446
-145	-0.002	-0.0149	-0.0009	0.0021	0.0013	-0.0018	0.9938	0.9941	0.015	-0.0055	0.9497
-146	-0.0036	-0.0151	0.0024	-0.0013	0.0012	0.0004	0.9976	0.9917	0.0123	-0.0032	0.9441
-147	-0.0032	-0.0116	0.001	0.0008	-0.0024	0.0006	1.001	0.9934	0.0108	-0.0065	0.9492
-148	-0.0023	-0.0083	0.0027	0.0005	0.0006	-0.0014	1.0014	0.9927	0.0136	-0.0067	0.94
-149	-0.001	-0.006	0.0022	0.0034	-0.0011	-0.0018	0.9997	0.9933	0.0132	-0.0049	0.9404
-150	-0.0024	-0.0073	-0.0011	0.0036	-0.0024	-0.0008	0.9975	0.9958	0.0165	-0.0064	0.9398
-151	0.0007	-0.0051	0.0008	0.0036	-0.003	-0.0012	1.0006	0.9932	0.0161	-0.0076	0.9372
-152	-0.0008	-0.0076	0.0025	0.0028	-0.0048	-0.0003	1.0016	0.992	0.015	-0.0095	0.9325
-153	-0.0029	-0.0045	0.0027	0.0051	-0.0046	-0.0039	0.9989	0.9913	0.0177	-0.0087	0.9232
-154	0.0002	-0.002	0.0061	0.0048	-0.0043	-0.0016	0.9989	0.9911	0.0152	-0.0072	0.916
-155	-0.001	-0.002	0.0015	0.0029	-0.0055	-0.0004	0.999	0.9915	0.0107	-0.0076	0.9119
-156	0.0028	-0.003	0.0009	0.0049	-0.0073	0.002	1.0	0.9946	0.0127	-0.0082	0.9095
-157	0.003	-0.0035	0.0008	0.0052	-0.0066	1e-04	1.0014	0.9977	0.0125	-0.0046	0.9069
-158	0.0063	-0.0023	-0.0005	0.0081	-0.0046	-0.0006	0.9983	0.997	0.0109	-0.003	0.9118
-159	0.0049	0.0002	-0.0013	0.0054	-0.0036	0.0009	1.0011	0.9967	0.0066	-0.0033	0.9177
diff -r ee98d611afc6 -r 6f0d0c784f09 test-data/inspect.general.txt
--- a/test-data/inspect.general.txt	Wed Jun 22 07:19:33 2022 +0000
+++ b/test-data/inspect.general.txt	Sun Nov 12 16:43:58 2023 +0000
@@ -1,3 +1,3 @@
-AnnData object with n_obs × n_vars = 640 × 11
+AnnData object with n_obs × n_vars = 500 × 11
     obs: 'cell_type'
-    uns: 'cell_type_colors', 'highlights', 'iroot'
+    uns: 'highlights', 'iroot'
diff -r ee98d611afc6 -r 6f0d0c784f09 test-data/inspect.obs.tabular
--- a/test-data/inspect.obs.tabular	Wed Jun 22 07:19:33 2022 +0000
+++ b/test-data/inspect.obs.tabular	Sun Nov 12 16:43:58 2023 +0000
@@ -1,4 +1,4 @@
-index	cell_type
+	cell_type
 0	progenitor
 1	progenitor
 2	progenitor
@@ -499,143 +499,3 @@
 17	progenitor
 18	progenitor
 19	progenitor
-20	progenitor
-21	progenitor
-22	progenitor
-23	progenitor
-24	progenitor
-25	progenitor
-26	progenitor
-27	progenitor
-28	progenitor
-29	progenitor
-30	progenitor
-31	progenitor
-32	progenitor
-33	progenitor
-34	progenitor
-35	progenitor
-36	progenitor
-37	progenitor
-38	progenitor
-39	progenitor
-40	progenitor
-41	progenitor
-42	progenitor
-43	progenitor
-44	progenitor
-45	progenitor
-46	progenitor
-47	progenitor
-48	progenitor
-49	progenitor
-50	progenitor
-51	progenitor
-52	progenitor
-53	progenitor
-54	progenitor
-55	progenitor
-56	progenitor
-57	progenitor
-58	progenitor
-59	progenitor
-60	progenitor
-61	progenitor
-62	progenitor
-63	progenitor
-64	progenitor
-65	progenitor
-66	progenitor
-67	progenitor
-68	progenitor
-69	progenitor
-70	progenitor
-71	progenitor
-72	progenitor
-73	progenitor
-74	progenitor
-75	progenitor
-76	progenitor
-77	progenitor
-78	progenitor
-79	progenitor
-80	Neu
-81	Neu
-82	Neu
-83	Neu
-84	Neu
-85	Neu
-86	Neu
-87	Neu
-88	Neu
-89	Neu
-90	Neu
-91	Neu
-92	Neu
-93	Neu
-94	Neu
-95	Neu
-96	Neu
-97	Neu
-98	Neu
-99	Neu
-100	Neu
-101	Neu
-102	Neu
-103	Neu
-104	Neu
-105	Neu
-106	Neu
-107	Neu
-108	Neu
-109	Neu
-110	Neu
-111	Neu
-112	Neu
-113	Neu
-114	Neu
-115	Neu
-116	Neu
-117	Neu
-118	Neu
-119	Neu
-120	Neu
-121	Neu
-122	Neu
-123	Neu
-124	Neu
-125	Neu
-126	Neu
-127	Neu
-128	Neu
-129	Neu
-130	Neu
-131	Neu
-132	Neu
-133	Neu
-134	Neu
-135	Neu
-136	Neu
-137	Neu
-138	Neu
-139	Neu
-140	Neu
-141	Neu
-142	Neu
-143	Neu
-144	Neu
-145	Neu
-146	Neu
-147	Neu
-148	Neu
-149	Neu
-150	Neu
-151	Neu
-152	Neu
-153	Neu
-154	Neu
-155	Neu
-156	Neu
-157	Neu
-158	Neu
-159	Neu
diff -r ee98d611afc6 -r 6f0d0c784f09 test-data/inspect.var.tabular
--- a/test-data/inspect.var.tabular	Wed Jun 22 07:19:33 2022 +0000
+++ b/test-data/inspect.var.tabular	Sun Nov 12 16:43:58 2023 +0000
@@ -1,4 +1,4 @@
-index
+""
 Gata2
 Gata1
 Fog1
diff -r ee98d611afc6 -r 6f0d0c784f09 test-data/krumsiek11.h5ad
Binary file test-data/krumsiek11.h5ad has changed
diff -r ee98d611afc6 -r 6f0d0c784f09 test-data/krumsiek11.loom
Binary file test-data/krumsiek11.loom has changed
diff -r ee98d611afc6 -r 6f0d0c784f09 test-data/manipulate.add_annotation_obs.h5ad
Binary file test-data/manipulate.add_annotation_obs.h5ad has changed
diff -r ee98d611afc6 -r 6f0d0c784f09 test-data/manipulate.add_annotation_var.h5ad
Binary file test-data/manipulate.add_annotation_var.h5ad has changed
diff -r ee98d611afc6 -r 6f0d0c784f09 test-data/manipulate.concatenate.h5ad
Binary file test-data/manipulate.concatenate.h5ad has changed
diff -r ee98d611afc6 -r 6f0d0c784f09 test-data/manipulate.filter_obs_key.h5ad
Binary file test-data/manipulate.filter_obs_key.h5ad has changed
diff -r ee98d611afc6 -r 6f0d0c784f09 test-data/manipulate.filter_var_index.h5ad
Binary file test-data/manipulate.filter_var_index.h5ad has changed
diff -r ee98d611afc6 -r 6f0d0c784f09 test-data/manipulate.obs_names_make_unique.h5ad
Binary file test-data/manipulate.obs_names_make_unique.h5ad has changed
diff -r ee98d611afc6 -r 6f0d0c784f09 test-data/manipulate.rename_categories.h5ad
Binary file test-data/manipulate.rename_categories.h5ad has changed
diff -r ee98d611afc6 -r 6f0d0c784f09 test-data/manipulate.save_raw.h5ad
Binary file test-data/manipulate.save_raw.h5ad has changed
diff -r ee98d611afc6 -r 6f0d0c784f09 test-data/manipulate.strings_to_categoricals.h5ad
Binary file test-data/manipulate.strings_to_categoricals.h5ad has changed
diff -r ee98d611afc6 -r 6f0d0c784f09 test-data/manipulate.transpose.h5ad
Binary file test-data/manipulate.transpose.h5ad has changed
diff -r ee98d611afc6 -r 6f0d0c784f09 test-data/manipulate.var_names_make_unique.h5ad
Binary file test-data/manipulate.var_names_make_unique.h5ad has changed
diff -r ee98d611afc6 -r 6f0d0c784f09 test-data/obs_add_annotation.tabular
--- a/test-data/obs_add_annotation.tabular	Wed Jun 22 07:19:33 2022 +0000
+++ b/test-data/obs_add_annotation.tabular	Sun Nov 12 16:43:58 2023 +0000
@@ -499,143 +499,3 @@
 17	progenitor
 18	progenitor
 19	progenitor
-20	progenitor
-21	progenitor
-22	progenitor
-23	progenitor
-24	progenitor
-25	progenitor
-26	progenitor
-27	progenitor
-28	progenitor
-29	progenitor
-30	progenitor
-31	progenitor
-32	progenitor
-33	progenitor
-34	progenitor
-35	progenitor
-36	progenitor
-37	progenitor
-38	progenitor
-39	progenitor
-40	progenitor
-41	progenitor
-42	progenitor
-43	progenitor
-44	progenitor
-45	progenitor
-46	progenitor
-47	progenitor
-48	progenitor
-49	progenitor
-50	progenitor
-51	progenitor
-52	progenitor
-53	progenitor
-54	progenitor
-55	progenitor
-56	progenitor
-57	progenitor
-58	progenitor
-59	progenitor
-60	progenitor
-61	progenitor
-62	progenitor
-63	progenitor
-64	progenitor
-65	progenitor
-66	progenitor
-67	progenitor
-68	progenitor
-69	progenitor
-70	progenitor
-71	progenitor
-72	progenitor
-73	progenitor
-74	progenitor
-75	progenitor
-76	progenitor
-77	progenitor
-78	progenitor
-79	progenitor
-80	Neu
-81	Neu
-82	Neu
-83	Neu
-84	Neu
-85	Neu
-86	Neu
-87	Neu
-88	Neu
-89	Neu
-90	Neu
-91	Neu
-92	Neu
-93	Neu
-94	Neu
-95	Neu
-96	Neu
-97	Neu
-98	Neu
-99	Neu
-100	Neu
-101	Neu
-102	Neu
-103	Neu
-104	Neu
-105	Neu
-106	Neu
-107	Neu
-108	Neu
-109	Neu
-110	Neu
-111	Neu
-112	Neu
-113	Neu
-114	Neu
-115	Neu
-116	Neu
-117	Neu
-118	Neu
-119	Neu
-120	Neu
-121	Neu
-122	Neu
-123	Neu
-124	Neu
-125	Neu
-126	Neu
-127	Neu
-128	Neu
-129	Neu
-130	Neu
-131	Neu
-132	Neu
-133	Neu
-134	Neu
-135	Neu
-136	Neu
-137	Neu
-138	Neu
-139	Neu
-140	Neu
-141	Neu
-142	Neu
-143	Neu
-144	Neu
-145	Neu
-146	Neu
-147	Neu
-148	Neu
-149	Neu
-150	Neu
-151	Neu
-152	Neu
-153	Neu
-154	Neu
-155	Neu
-156	Neu
-157	Neu
-158	Neu
-159	Neu
diff -r ee98d611afc6 -r 6f0d0c784f09 test-data/pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad
Binary file test-data/pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad has changed
diff -r ee98d611afc6 -r 6f0d0c784f09 test-data/pp.pca.krumsiek11.h5ad
Binary file test-data/pp.pca.krumsiek11.h5ad has changed
diff -r ee98d611afc6 -r 6f0d0c784f09 test-data/tl.paga.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad
Binary file test-data/tl.paga.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad has changed
diff -r ee98d611afc6 -r 6f0d0c784f09 test-data/tl.rank_genes_groups.krumsiek11.h5ad
Binary file test-data/tl.rank_genes_groups.krumsiek11.h5ad has changed