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changeset 11:2411ca833c18 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
author iuc
date Sat, 14 Sep 2024 19:55:32 +0000
parents 87254cd3a609
children 155982133d99
files export.xml macros.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.diffmap.h5ad test-data/tl.draw_graph.h5ad test-data/tl.paga.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad test-data/tl.rank_genes_groups.krumsiek11.h5ad test-data/tl.tsne.h5ad test-data/tl.umap.h5ad
diffstat 44 files changed, 30 insertions(+), 942 deletions(-) [+]
line wrap: on
line diff
--- a/export.xml	Wed Jun 22 07:18:12 2022 +0000
+++ b/export.xml	Sat Sep 14 19:55:32 2024 +0000
@@ -1,90 +1,33 @@
-<tool id="anndata_export" name="Export AnnData and loom files" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
-    <description>Interconvert AnnData and Loom formats</description>
+<tool id="anndata_export" name="Export AnnData" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>matrix and annotations</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements"/>
     <expand macro="version_command"/>
     <command detect_errors="exit_code"><![CDATA[
-#if $hd5_format.filetype == 'anndata':
-    @CMD@
-#else:
-    @LOOMCMD@
-#end if
+@CMD@
       ]]></command>
     <configfiles>
         <configfile name="script_file"><![CDATA[
 @CMD_imports@
-#if $hd5_format.filetype == 'anndata':
-adata = ad.read('$hd5_format.input')
-    #if $hd5_format.output_format == 'loom':
-adata.write_loom('anndata.loom')
-    #else if $hd5_format.output_format == 'tabular':
+adata = ad.read_h5ad('$input')
 adata.write_csvs('.', sep="\t", skip_data = False)
-    #end if
-#end if
     ]]></configfile>
 </configfiles>
     <inputs>
-        <conditional name="hd5_format">
-            <param name="filetype" type="select" label="hd5 format">
-                <option value="anndata" selected="true">Anndata file</option>
-                <option value="loom">Loom file</option>
-            </param>
-            <when value="anndata">
-                <param name="input" type="data" format="h5ad" label="Annotated data matrix"/>
-                <param name="output_format" type="select" label="Format to write the annotated data matrix">
-                    <option value="loom">loom</option>
-                    <option value="tabular">Tabular</option>
-                </param>
-            </when>
-            <when value="loom">
-                <param name="input" type="data" format="loom" label="Loom file to be exported to a series of tabular files."/>
-            </when>
-        </conditional>
+        <param name="input" type="data" format="h5ad" label="Annotated data matrix to export" help="Create individual tabular files for matrix, obs, obsm, var and varm annotations"/>
     </inputs>
     <outputs>
-        <data name="loom_output" format="loom" from_work_dir="anndata.loom" label="${tool.name} on ${on_string}: Annotated data matrix">
-            <filter>hd5_format['filetype'] == 'anndata' and hd5_format['output_format'] == 'loom'</filter>
-        </data>
-        <data name="tabular_x" format="tabular" from_work_dir="X.csv" label="${tool.name} on ${on_string}: Matrix table (X)">
-            <filter>hd5_format['filetype'] == 'anndata' and hd5_format['output_format'] == 'tabular'</filter>
-        </data>
-        <data name="tabular_obs" format="tabular" from_work_dir="obs.csv" label="${tool.name} on ${on_string}: Key-indexed one-dimensional observations annotation (obs)">
-            <filter>hd5_format['filetype'] == 'anndata' and hd5_format['output_format'] == 'tabular'</filter>
-        </data>
-        <data name="tabular_obsm" format="tabular" from_work_dir="obsm.csv" label="${tool.name} on ${on_string}: Key-indexed multi-dimensional observations annotation (obsm)">
-            <filter>hd5_format['filetype'] == 'anndata' and hd5_format['output_format'] == 'tabular'</filter>
-        </data>
-        <data name="tabular_var" format="tabular" from_work_dir="var.csv" label="${tool.name} on ${on_string}: Key-indexed one-dimensional variables annotation (var)">
-            <filter>hd5_format['filetype'] == 'anndata' and hd5_format['output_format'] == 'tabular'</filter>
-        </data>
-        <data name="tabular_varm" format="tabular" from_work_dir="varm.csv" label="${tool.name} on ${on_string}: Key-indexed multi-dimensional variables annotation (varm)">
-            <filter>hd5_format['filetype'] == 'anndata' and hd5_format['output_format'] == 'tabular'</filter>
-        </data>
-        <collection name="layer_tsvs" type="list" label="Layer matrices" >
-            <filter>hd5_format['filetype'] == 'loom'</filter>
-            <discover_datasets pattern="__designation__" format="tabular" directory="output" visible="false" />
-        </collection>
-        <collection name="attribute_tsvs" type="list" label="Attribute matrices" >
-            <filter>hd5_format['filetype'] == 'loom'</filter>
-            <discover_datasets pattern="__designation__" format="tabular" directory="attributes" visible="false" />
-        </collection>
+        <data name="tabular_x" format="tabular" from_work_dir="X.csv" label="${tool.name} on ${on_string}: Matrix table (X)"/>
+        <data name="tabular_obs" format="tabular" from_work_dir="obs.csv" label="${tool.name} on ${on_string}: Key-indexed one-dimensional observations annotation (obs)"/>
+        <data name="tabular_obsm" format="tabular" from_work_dir="obsm.csv" label="${tool.name} on ${on_string}: Key-indexed multi-dimensional observations annotation (obsm)"/>
+        <data name="tabular_var" format="tabular" from_work_dir="var.csv" label="${tool.name} on ${on_string}: Key-indexed one-dimensional variables annotation (var)"/>
+        <data name="tabular_varm" format="tabular" from_work_dir="varm.csv" label="${tool.name} on ${on_string}: Key-indexed multi-dimensional variables annotation (varm)"/>
     </outputs>
     <tests>
-        <test expect_num_outputs="1">
-            <param name="filetype" value="anndata"/>
+        <test expect_num_outputs="5">
             <param name="input" value="krumsiek11.h5ad"/>
-            <param name="output_format" value="loom"/>
-            <assert_stdout>
-                <has_text_matching expression="adata.write_loom"/>
-            </assert_stdout>
-            <output name="loom_output" value="export.krumsiek11.loom" ftype="loom" compare="sim_size"/>
-        </test>
-        <test expect_num_outputs="5">
-            <param name="filetype" value="anndata"/>
-            <param name="input" value="krumsiek11.h5ad"/>
-            <param name="output_format" value="tabular"/>
             <assert_stdout>
                 <has_text_matching expression="adata.write_csvs"/>
             </assert_stdout>
@@ -94,26 +37,9 @@
             <output name="tabular_var" value="export.krumsiek11.var.tabular" ftype="tabular"/>
             <output name="tabular_varm" value="export.krumsiek11.varm.tabular" ftype="tabular"/>
         </test>
-        <test expect_num_outputs="2">
-            <param name="filetype" value="loom"/>
-            <param name="input" value="loomtest.loom"/>
-            <output_collection name="layer_tsvs" type="list">
-                <element name="mainmatrix.tsv" value="firstlayer.tsv" ftype="tabular"/>
-                <element name="extralayer.tsv" value="secondlayer.tsv" ftype="tabular"/>
-                <element name="thirdlayer.tsv" value="finallayer.tsv" ftype="tabular"/>
-            </output_collection>
-            <output_collection name="attribute_tsvs" type="list">
-                <element name="row_attr.tsv" value="rows.tsv" ftype="tabular"/>
-                <element name="col_attr.tsv" value="cols.tsv" ftype="tabular"/>
-            </output_collection>
-        </test>
     </tests>
     <help><![CDATA[
-This tool exports an AnnData dataset to a Loom file
-(`write_loom method <https://anndata.readthedocs.io/en/latest/generated/anndata.AnnData.write_loom.html>`__)
-or a Tabular file (`write_csvs method <https://anndata.readthedocs.io/en/latest/generated/anndata.AnnData.write_csvs.html>`__)
-
-It can also create a series of tabular files from an input loom dataset.
+This tool exports an AnnData dataset to a tabular files (`write_csvs method <https://anndata.readthedocs.io/en/latest/generated/anndata.AnnData.write_csvs.html>`__)
 
 @HELP@
     ]]></help>
--- a/macros.xml	Wed Jun 22 07:18:12 2022 +0000
+++ b/macros.xml	Sat Sep 14 19:55:32 2024 +0000
@@ -1,10 +1,11 @@
 <macros>
-    <token name="@TOOL_VERSION@">0.7.5</token>
-    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@TOOL_VERSION@">0.10.9</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@PROFILE@">21.09</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>
@@ -21,12 +22,6 @@
 python '$script_file'
     ]]>
     </token>
-    <token name="@LOOMCMD@"><![CDATA[
-mkdir ./output &&
-mkdir ./attributes &&
-python '$__tool_directory__/loompy_to_tsv.py' -f '${hd5_format.input}'
-    ]]>
-    </token>
     <token name="@CMD_imports@"><![CDATA[
 import anndata as ad
     ]]>
@@ -76,4 +71,11 @@
             </when>
         </conditional>
     </xml>
+    <xml name="sanitize_query" token_validinitial="string.printable">
+        <sanitizer>
+            <valid initial="@VALIDINITIAL@">
+                <remove value="&apos;" />
+            </valid>
+       </sanitizer>
+    </xml>
 </macros>
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 07:18:12 2022 +0000
+++ b/test-data/export.krumsiek11.X.tabular	Sat Sep 14 19:55:32 2024 +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 07:18:12 2022 +0000
+++ b/test-data/export.krumsiek11.obs.tabular	Sat Sep 14 19:55:32 2024 +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 07:18:12 2022 +0000
+++ b/test-data/export.krumsiek11.obsm.tabular	Sat Sep 14 19:55:32 2024 +0000
@@ -499,143 +499,3 @@
 
 
 
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
--- a/test-data/export.krumsiek11.var.tabular	Wed Jun 22 07:18:12 2022 +0000
+++ b/test-data/export.krumsiek11.var.tabular	Sat Sep 14 19:55:32 2024 +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 07:18:12 2022 +0000
+++ b/test-data/inspect.X.tabular	Sat Sep 14 19:55:32 2024 +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 07:18:12 2022 +0000
+++ b/test-data/inspect.general.txt	Sat Sep 14 19:55:32 2024 +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 07:18:12 2022 +0000
+++ b/test-data/inspect.obs.tabular	Sat Sep 14 19:55:32 2024 +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 07:18:12 2022 +0000
+++ b/test-data/inspect.var.tabular	Sat Sep 14 19:55:32 2024 +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 07:18:12 2022 +0000
+++ b/test-data/obs_add_annotation.tabular	Sat Sep 14 19:55:32 2024 +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.diffmap.h5ad has changed
Binary file test-data/tl.draw_graph.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
Binary file test-data/tl.tsne.h5ad has changed
Binary file test-data/tl.umap.h5ad has changed