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changeset 12:ed4996a16f7f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 656ce7ff596a8870b77848469e85b406c7bd9344
author iuc
date Sun, 12 Nov 2023 16:42:25 +0000
parents 3d748954434b
children 7e8c677a7b71
files macros.xml manipulate.xml test-data/addloomout1.loom test-data/addloomout2.loom test-data/addloomout3.loom test-data/converted.loom.test test-data/export.krumsiek11.X.tabular test-data/export.krumsiek11.loom test-data/export.krumsiek11.obs.tabular test-data/export.krumsiek11.obsm.tabular test-data/export.krumsiek11.var.tabular test-data/import.csv.h5ad test-data/import.loom.krumsiek11.h5ad test-data/import.mtx.legacy_10x.h5ad test-data/import.mtx.no_10x.h5ad test-data/import.mtx.v3_10x.h5ad test-data/import.tsv.h5ad test-data/import.umi_tools.h5ad test-data/inspect.X.tabular test-data/inspect.general.txt test-data/inspect.obs.tabular test-data/inspect.var.tabular test-data/krumsiek11.h5ad test-data/krumsiek11.loom test-data/manipulate.add_annotation_obs.h5ad test-data/manipulate.add_annotation_var.h5ad test-data/manipulate.concatenate.h5ad test-data/manipulate.filter_obs_key.h5ad test-data/manipulate.filter_var_index.h5ad test-data/manipulate.obs_names_make_unique.h5ad test-data/manipulate.rename_categories.h5ad test-data/manipulate.save_raw.h5ad test-data/manipulate.strings_to_categoricals.h5ad test-data/manipulate.transpose.h5ad test-data/manipulate.var_names_make_unique.h5ad test-data/obs_add_annotation.tabular test-data/pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad test-data/pp.pca.krumsiek11.h5ad test-data/tl.paga.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad test-data/tl.rank_genes_groups.krumsiek11.h5ad
diffstat 40 files changed, 15 insertions(+), 855 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Wed Jun 22 07:21:03 2022 +0000
+++ b/macros.xml	Sun Nov 12 16:42:25 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>
--- a/manipulate.xml	Wed Jun 22 07:21:03 2022 +0000
+++ b/manipulate.xml	Sun Nov 12 16:42:25 2023 +0000
@@ -20,11 +20,11 @@
         <configfile name="script_file"><![CDATA[
 @CMD_imports@
 
-adata = ad.read('$input')
+adata = ad.read_h5ad('$input')
 
 #if $manipulate.function == 'concatenate'
     #for i, filepath in enumerate($manipulate.other_adatas)
-adata_$i = ad.read('$filepath')
+adata_$i = ad.read_h5ad('$filepath')
     #end for
 adata = adata.concatenate(
     #for i, filepath in enumerate($manipulate.other_adatas)
@@ -174,7 +174,7 @@
                     <option value="var">Variables (var)</option>
                     <option value="obs">Observations (obs)</option>
                 </param>
-                <param name="new_annot" type="data" format="tabular" label="Table with new annotations" 
+                <param name="new_annot" type="data" format="tabular" label="Table with new annotations"
                     help="The new table should have the same number of rows and same order than obs or var. The key names should be in the header (1st line)"/>
             </when>
             <when value="filter">
@@ -289,12 +289,12 @@
             <conditional name="manipulate">
                 <param name="function" value="rename_categories"/>
                 <param name="key" value="cell_type"/>
-                <param name="categories" value="Er,Ml,Mt, Ne, pr"/>
+                <param name="categories" value="Ery, Mk, Mo, progenitor"/>
             </conditional>
             <assert_stdout>
                 <has_text_matching expression="adata.rename_categories"/>
                 <has_text_matching expression="key='cell_type'"/>
-                <has_text_matching expression="categories=\['Er', 'Ml', 'Mt', 'Ne', 'pr'\]"/>
+                <has_text_matching expression="categories=\['Ery', 'Mk', 'Mo', 'progenitor'\]"/>
             </assert_stdout>
             <output name="anndata" value="manipulate.rename_categories.h5ad" ftype="h5ad" compare="sim_size"/>
         </test>
Binary file test-data/addloomout1.loom has changed
Binary file test-data/addloomout2.loom has changed
Binary file test-data/addloomout3.loom has changed
Binary file test-data/converted.loom.test has changed
--- a/test-data/export.krumsiek11.X.tabular	Wed Jun 22 07:21:03 2022 +0000
+++ b/test-data/export.krumsiek11.X.tabular	Sun Nov 12 16:42:25 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
Binary file test-data/export.krumsiek11.loom has changed
--- a/test-data/export.krumsiek11.obs.tabular	Wed Jun 22 07:21:03 2022 +0000
+++ b/test-data/export.krumsiek11.obs.tabular	Sun Nov 12 16:42:25 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
--- a/test-data/export.krumsiek11.obsm.tabular	Wed Jun 22 07:21:03 2022 +0000
+++ b/test-data/export.krumsiek11.obsm.tabular	Sun Nov 12 16:42:25 2023 +0000
@@ -499,143 +499,3 @@
 
 
 
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
--- a/test-data/export.krumsiek11.var.tabular	Wed Jun 22 07:21:03 2022 +0000
+++ b/test-data/export.krumsiek11.var.tabular	Sun Nov 12 16:42:25 2023 +0000
@@ -1,4 +1,4 @@
-index
+""
 Gata2
 Gata1
 Fog1
Binary file test-data/import.csv.h5ad has changed
Binary file test-data/import.loom.krumsiek11.h5ad has changed
Binary file test-data/import.mtx.legacy_10x.h5ad has changed
Binary file test-data/import.mtx.no_10x.h5ad has changed
Binary file test-data/import.mtx.v3_10x.h5ad has changed
Binary file test-data/import.tsv.h5ad has changed
Binary file test-data/import.umi_tools.h5ad has changed
--- a/test-data/inspect.X.tabular	Wed Jun 22 07:21:03 2022 +0000
+++ b/test-data/inspect.X.tabular	Sun Nov 12 16:42:25 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
--- a/test-data/inspect.general.txt	Wed Jun 22 07:21:03 2022 +0000
+++ b/test-data/inspect.general.txt	Sun Nov 12 16:42:25 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'
--- a/test-data/inspect.obs.tabular	Wed Jun 22 07:21:03 2022 +0000
+++ b/test-data/inspect.obs.tabular	Sun Nov 12 16:42:25 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
--- a/test-data/inspect.var.tabular	Wed Jun 22 07:21:03 2022 +0000
+++ b/test-data/inspect.var.tabular	Sun Nov 12 16:42:25 2023 +0000
@@ -1,4 +1,4 @@
-index
+""
 Gata2
 Gata1
 Fog1
Binary file test-data/krumsiek11.h5ad has changed
Binary file test-data/krumsiek11.loom has changed
Binary file test-data/manipulate.add_annotation_obs.h5ad has changed
Binary file test-data/manipulate.add_annotation_var.h5ad has changed
Binary file test-data/manipulate.concatenate.h5ad has changed
Binary file test-data/manipulate.filter_obs_key.h5ad has changed
Binary file test-data/manipulate.filter_var_index.h5ad has changed
Binary file test-data/manipulate.obs_names_make_unique.h5ad has changed
Binary file test-data/manipulate.rename_categories.h5ad has changed
Binary file test-data/manipulate.save_raw.h5ad has changed
Binary file test-data/manipulate.strings_to_categoricals.h5ad has changed
Binary file test-data/manipulate.transpose.h5ad has changed
Binary file test-data/manipulate.var_names_make_unique.h5ad has changed
--- a/test-data/obs_add_annotation.tabular	Wed Jun 22 07:21:03 2022 +0000
+++ b/test-data/obs_add_annotation.tabular	Sun Nov 12 16:42:25 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
Binary file test-data/pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad has changed
Binary file test-data/pp.pca.krumsiek11.h5ad has changed
Binary file test-data/tl.paga.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad has changed
Binary file test-data/tl.rank_genes_groups.krumsiek11.h5ad has changed