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Merge in preparation for new release #939

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merged 354 commits into from
Jun 5, 2024
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e94668b
Clean up test debugging code
IanCa Jan 11, 2024
6de556c
Replace carriage returns with new lines when reading schema as a string
IanCa Jan 11, 2024
8488682
Bump spec_tests/hed-examples from `3508e5d` to `98da8ed`
dependabot[bot] Jan 11, 2024
1d48e95
Merge pull request #832 from IanCa/develop
VisLab Jan 11, 2024
df75b54
Merge pull request #833 from hed-standard/dependabot/submodules/devel…
VisLab Jan 11, 2024
6a4e889
Added jsonschema to the docs requirements
VisLab Jan 19, 2024
2b8b467
Merge pull request #835 from VisLab/develop
VisLab Jan 19, 2024
82ee48a
Bump spec_tests/hed-examples from `98da8ed` to `bd1e089`
dependabot[bot] Jan 22, 2024
32c1ef9
Bump actions/cache from 3 to 4
dependabot[bot] Jan 22, 2024
0176068
Merge pull request #836 from hed-standard/dependabot/submodules/devel…
VisLab Jan 22, 2024
8ebd0a2
Merge pull request #837 from hed-standard/dependabot/github_actions/d…
VisLab Jan 22, 2024
47a18f5
Bump spec_tests/hed-examples from `bd1e089` to `79de656`
dependabot[bot] Jan 23, 2024
2062282
Merge pull request #838 from hed-standard/dependabot/submodules/devel…
VisLab Jan 23, 2024
8ebdb3d
Require a verison number when loading schemas
IanCa Jan 30, 2024
1952ab3
Fix test runner
IanCa Jan 30, 2024
14beefe
Merge pull request #841 from IanCa/develop
VisLab Jan 30, 2024
eacdb8e
Bump spec_tests/hed-examples from `79de656` to `c9a7eb6`
dependabot[bot] Jan 31, 2024
e6f5f1d
Merge pull request #842 from hed-standard/dependabot/submodules/devel…
VisLab Jan 31, 2024
39a58dd
Fix bug in column mapper dicts could be returned wrong
IanCa Jan 31, 2024
37133bb
Merge pull request #844 from IanCa/develop
VisLab Jan 31, 2024
eda15ae
Remove some URL calls in test code, try to update token for workflow
IanCa Jan 31, 2024
41c9604
Fix/supress some pandas future warnings
IanCa Feb 1, 2024
013a7fa
fix typo
IanCa Feb 1, 2024
98c6146
Bump spec_tests/hed-examples from `c9a7eb6` to `7b047e3`
dependabot[bot] Feb 1, 2024
a7252b1
Merge pull request #845 from IanCa/develop
VisLab Feb 1, 2024
f7a1bdf
Merge pull request #846 from hed-standard/dependabot/submodules/devel…
VisLab Feb 1, 2024
5098840
Updated type_values in factor operation to be optional
VisLab Feb 1, 2024
bd148b7
Updated the remodeling to correct check optional arguments
VisLab Feb 2, 2024
c9f6254
Merge pull request #847 from VisLab/develop
VisLab Feb 2, 2024
f087d7f
Switch over most settings to .toml file
IanCa Feb 2, 2024
085e09c
Restore setup.py, delete setup.cfg
IanCa Feb 2, 2024
7130705
Merge pull request #848 from IanCa/develop
VisLab Feb 2, 2024
b40e686
Bump spec_tests/hed-examples from `7b047e3` to `94dc628`
dependabot[bot] Feb 5, 2024
55801fd
Merge pull request #849 from hed-standard/dependabot/submodules/devel…
VisLab Feb 5, 2024
839c234
Implemented context handling for factor by hed tags
VisLab Feb 5, 2024
c27ce63
Merge pull request #850 from VisLab/develop
VisLab Feb 5, 2024
8a6223c
Fix toml install, make sure installer test works
IanCa Feb 5, 2024
fcf7704
Tweak installer test
IanCa Feb 5, 2024
623f753
Need venv in more steps
IanCa Feb 5, 2024
bf462e2
Run installer test in a different folder
IanCa Feb 5, 2024
6338bf5
Merge pull request #851 from IanCa/develop
VisLab Feb 5, 2024
74f6507
Corrected minor doc indentation error
VisLab Feb 5, 2024
7c05a54
Merge pull request #852 from VisLab/develop
VisLab Feb 5, 2024
7147d09
add wordcloud to setup requirements. Restore init file
IanCa Feb 6, 2024
b733f97
Merge pull request #853 from IanCa/develop
VisLab Feb 6, 2024
c00e650
Bump spec_tests/hed-examples from `94dc628` to `64c7c94`
dependabot[bot] Feb 7, 2024
f1e4749
Merge pull request #854 from hed-standard/dependabot/submodules/devel…
VisLab Feb 7, 2024
3df2dab
Allow validation of files with out of order onsets. Rename expressio…
IanCa Feb 7, 2024
d6f3b73
Merge pull request #855 from IanCa/develop
VisLab Feb 7, 2024
c981b97
Updated the docs
VisLab Feb 7, 2024
788c13b
Finished merging
VisLab Feb 7, 2024
392a881
Completely re-write schema comparison summary
IanCa Feb 8, 2024
c18fcfe
Merge pull request #856 from IanCa/develop
VisLab Feb 9, 2024
456a3c5
Merge branch 'develop' of https://github.com/hed-standard/hed-python …
VisLab Feb 9, 2024
8aff712
Minor changes to the documentation and implementation
VisLab Feb 12, 2024
f3465b7
Merge pull request #857 from VisLab/develop
VisLab Feb 12, 2024
cb96692
Word cloud added and starting a pass through docs
VisLab Feb 15, 2024
d8f4a94
Documentation cleanup
VisLab Feb 15, 2024
59e983c
Finished initial pass on the docs
VisLab Feb 16, 2024
0ecd8c9
Merge pull request #858 from VisLab/develop
VisLab Feb 16, 2024
1db4823
Minor fixes to install/misc
IanCa Feb 16, 2024
569e5a8
Merge pull request #859 from IanCa/develop
VisLab Feb 17, 2024
daf23c4
Various cleanup of comments, removing some unused functions
IanCa Feb 17, 2024
9766bea
Merge pull request #860 from IanCa/develop
VisLab Feb 17, 2024
a91a4dd
Updating word cloud visualization in HED tag summary to have parameters
VisLab Feb 19, 2024
0e771eb
Fixed word-cloud save file name
VisLab Feb 19, 2024
83eec02
Merge pull request #861 from VisLab/develop
VisLab Feb 19, 2024
2412fe1
Remove new line from comment for now
IanCa Feb 19, 2024
8f5e93d
Merge pull request #862 from IanCa/develop
VisLab Feb 19, 2024
df8c82e
Allow adjust size/color of svg contour in wordcloud
IanCa Feb 19, 2024
82ede45
Merge pull request #863 from IanCa/develop
VisLab Feb 19, 2024
0285ad8
Allow tag cloud to take a transparent mask
IanCa Feb 20, 2024
32946c5
Merge pull request #864 from IanCa/develop
VisLab Feb 20, 2024
ef825fd
Added minor logging facility for exceptions
VisLab Feb 20, 2024
63a5dfc
Merge pull request #865 from VisLab/develop
VisLab Feb 20, 2024
f506fb6
Pin wordcloud, switch to python 3.8 minimum
IanCa Feb 21, 2024
2b04113
Merge pull request #866 from IanCa/dev_installer
VisLab Feb 21, 2024
c8c9614
Turn on allowed character support in > 8.3
IanCa Feb 22, 2024
e5cbdc4
Make sure older < 8.2 utf banned support remains
IanCa Feb 22, 2024
dbe4f32
Update wordcloud to better support different fonts
IanCa Feb 22, 2024
b722e5f
Siwtch to a font matplotlib should have by default
IanCa Feb 22, 2024
34c418a
Merge pull request #867 from IanCa/develop
VisLab Feb 22, 2024
7342e5b
Update/improve deprecatedFrom support
IanCa Feb 23, 2024
43ec7fa
Merge pull request #869 from IanCa/develop
VisLab Feb 24, 2024
d0e8717
Added EventManager raises exception when onsets unordered
VisLab Feb 25, 2024
0759e41
Incorporated font path into remodeling ops
VisLab Feb 25, 2024
4281249
Merge pull request #870 from VisLab/develop
VisLab Feb 25, 2024
a31a6b0
Bump spec_tests/hed-specification from `9a22f15` to `cd2428e`
dependabot[bot] Feb 26, 2024
9910f1b
Merge pull request #872 from hed-standard/dependabot/submodules/devel…
VisLab Feb 26, 2024
5e3516e
Removed set_path parameter from word cloud creation
VisLab Feb 26, 2024
68e9606
Merge pull request #873 from VisLab/develop
VisLab Feb 26, 2024
5010a11
Updated for mixed case extensions
VisLab Feb 26, 2024
59a0e9f
Merge pull request #874 from VisLab/develop
VisLab Feb 26, 2024
9b4110a
Only flag spaces in units if they aren't deprecated
IanCa Feb 26, 2024
dac5220
Merge pull request #875 from IanCa/develop
VisLab Feb 26, 2024
3fb34a2
Bump spec_tests/hed-examples from `64c7c94` to `0206613`
dependabot[bot] Feb 27, 2024
869458e
Merge pull request #876 from hed-standard/dependabot/submodules/devel…
VisLab Feb 27, 2024
bbe7cce
Update deprecatedFrom validation and tests
IanCa Feb 29, 2024
47b06a6
Merge pull request #877 from IanCa/dev_deprecated
VisLab Feb 29, 2024
3af84d4
Bump spec_tests/hed-specification from `cd2428e` to `0a5e8b5`
dependabot[bot] Mar 1, 2024
0b23b2a
Merge pull request #878 from hed-standard/dependabot/submodules/devel…
VisLab Mar 1, 2024
a03e803
Add support for Duration tag, and validation support for Delay
IanCa Mar 5, 2024
cbfd00a
Rename Onset error to TEMPORAL_TAG_ERROR
IanCa Mar 5, 2024
50a6df1
Merge pull request #879 from IanCa/develop
VisLab Mar 5, 2024
a7fd57e
Update sidecar validation to check fully combined hed strings
IanCa Mar 6, 2024
55490f2
Fix unrelated test
IanCa Mar 7, 2024
173bba0
Bump spec_tests/hed-specification from `0a5e8b5` to `595701b`
dependabot[bot] Mar 7, 2024
f000099
Merge pull request #880 from IanCa/develop
VisLab Mar 7, 2024
b982688
Merge pull request #881 from hed-standard/dependabot/submodules/devel…
VisLab Mar 7, 2024
9048ae5
Lazy load definition entries when creating tags(tests run ~25 faster …
IanCa Mar 8, 2024
e1139cc
Bump spec_tests/hed-specification from `595701b` to `9a3ed49`
dependabot[bot] Mar 8, 2024
fd20109
Merge pull request #882 from IanCa/develop
VisLab Mar 8, 2024
6c9b45a
Merge pull request #883 from hed-standard/dependabot/submodules/devel…
VisLab Mar 8, 2024
0568209
Allow mixed case in non unitsymbol units
IanCa Mar 9, 2024
7286dd6
Merge pull request #884 from IanCa/develop
VisLab Mar 11, 2024
d4bea7c
Add validation/function to Delay and Duration tags.
IanCa Mar 19, 2024
601383a
Merge pull request #885 from IanCa/develop
VisLab Mar 19, 2024
c3a26c9
Bump spec_tests/hed-specification from `9a3ed49` to `3ad49f9`
dependabot[bot] Mar 19, 2024
7246f32
Minor cleanup/documentation cleanup of schema and models
IanCa Mar 20, 2024
9178dbe
Merge pull request #886 from hed-standard/dependabot/submodules/devel…
VisLab Mar 20, 2024
5ff33c8
Bump spec_tests/hed-specification from `3ad49f9` to `111b0ad`
dependabot[bot] Mar 20, 2024
f6fbfb5
Update schema_attribute_validators.py
IanCa Mar 20, 2024
a74eb54
Add doc strings back
IanCa Mar 20, 2024
c93eb00
Comment out owl related code pending new version
IanCa Mar 20, 2024
05e80c0
Merge pull request #887 from IanCa/develop
VisLab Mar 21, 2024
71ba0cc
Merge pull request #888 from hed-standard/dependabot/submodules/devel…
VisLab Mar 21, 2024
166a1a3
Minor updates to documentation
VisLab Mar 23, 2024
d74696b
Added description fields to JSON schema for remodeler
VisLab Mar 25, 2024
86172d9
Merge pull request #889 from VisLab/develop
VisLab Mar 25, 2024
bf0020e
Bump spec_tests/hed-specification from `111b0ad` to `0289e6d`
dependabot[bot] Mar 25, 2024
6565a34
Fix check if that should be top level when writing
IanCa Mar 25, 2024
b8a6a62
Merge pull request #890 from hed-standard/dependabot/submodules/devel…
VisLab Mar 25, 2024
757d570
Merge pull request #891 from hed-standard/dev_fix_wiki_write
VisLab Mar 25, 2024
1dfa011
Fix source_format when using a mix of xml/mediawiki sources
IanCa Mar 26, 2024
0efe5b4
Merge pull request #892 from hed-standard/dev_fix_source_format
VisLab Mar 27, 2024
4c0f327
Update spec tests output
IanCa Mar 27, 2024
9e4b99a
Merge pull request #893 from IanCa/dev_update_output2
VisLab Mar 28, 2024
efad7dc
Bump spec_tests/hed-specification from `0289e6d` to `8e796da`
dependabot[bot] Mar 28, 2024
a8c48e6
Merge pull request #894 from hed-standard/dependabot/submodules/devel…
VisLab Mar 28, 2024
5c22158
Bump spec_tests/hed-specification from `8e796da` to `afa4a8b`
dependabot[bot] Mar 29, 2024
e7d8701
Merge pull request #895 from hed-standard/dependabot/submodules/devel…
VisLab Mar 29, 2024
8604bef
Improve schema character validation to match the new spec/utf8 support
IanCa Mar 29, 2024
f198b6b
Switch to .casefold in most places
IanCa Mar 30, 2024
cfa831c
Merge pull request #896 from IanCa/develop
VisLab Mar 30, 2024
b76c65e
Bump spec_tests/hed-specification from `afa4a8b` to `1ebd8eb`
dependabot[bot] Apr 1, 2024
501925d
Merge pull request #897 from hed-standard/dependabot/submodules/devel…
VisLab Apr 1, 2024
71b5623
Bump spec_tests/hed-specification from `1ebd8eb` to `a659865`
dependabot[bot] Apr 3, 2024
a7ccd3a
Implement validation with new 83 schema properties/rules
IanCa Apr 4, 2024
9bf38b8
fix typos
IanCa Apr 4, 2024
1329ebc
Move schema_83_props to baseclass
IanCa Apr 4, 2024
8a4b955
Merge pull request #899 from hed-standard/dependabot/submodules/devel…
VisLab Apr 4, 2024
3eaaff5
Merge pull request #900 from IanCa/develop
VisLab Apr 4, 2024
dff36c6
Add support for caching prerelease schemas. Generates a warning on v…
IanCa Apr 4, 2024
12750cf
Merge pull request #901 from IanCa/develop
VisLab Apr 5, 2024
7c1b456
Bump spec_tests/hed-specification from `a659865` to `3c034a4`
dependabot[bot] Apr 12, 2024
205a0f9
Merge pull request #903 from hed-standard/dependabot/submodules/devel…
VisLab Apr 14, 2024
f57cce9
Bump spec_tests/hed-specification from `3c034a4` to `208fe68`
dependabot[bot] Apr 15, 2024
ef93447
Merge pull request #904 from hed-standard/dependabot/submodules/devel…
VisLab Apr 15, 2024
a733b31
Bump spec_tests/hed-specification from `208fe68` to `9044516`
dependabot[bot] Apr 16, 2024
151266e
Initial commit of saving/loading .tsv.
IanCa Apr 18, 2024
f9fcc80
Merge pull request #905 from hed-standard/dependabot/submodules/devel…
VisLab Apr 18, 2024
cec8527
Merge pull request #906 from IanCa/develop
VisLab Apr 18, 2024
5c2066b
Fix spec tests/minor error tweaks for tests
IanCa Apr 18, 2024
d63872c
Merge pull request #907 from IanCa/develop
VisLab Apr 18, 2024
99fb8bf
Corrected argument on summarize column values
VisLab Apr 18, 2024
095a713
Merge pull request #908 from VisLab/develop
VisLab Apr 18, 2024
cdf0766
Bump spec_tests/hed-specification from `2976edd` to `32b3eb2`
dependabot[bot] Apr 19, 2024
c0e4532
Merge pull request #909 from hed-standard/dependabot/submodules/devel…
VisLab Apr 19, 2024
f8efcee
Added a strs_to_sidecar
VisLab Apr 21, 2024
cb0a104
Bump spec_tests/hed-specification from `32b3eb2` to `6182ab9`
dependabot[bot] Apr 22, 2024
ebf650e
Updated sidecars
VisLab Apr 22, 2024
f6a388f
Merge pull request #911 from VisLab/develop
VisLab Apr 22, 2024
7437024
Move cache test to spec_tests
IanCa Apr 22, 2024
07bd207
Merge pull request #912 from IanCa/develop
VisLab Apr 22, 2024
f260b83
Merge pull request #910 from hed-standard/dependabot/submodules/devel…
VisLab Apr 22, 2024
f00f6bd
Added utilities for accessing sidecars and tabular input
VisLab Apr 23, 2024
3d30f8e
Merge pull request #913 from VisLab/develop
VisLab Apr 23, 2024
8daebfa
Added a get_sidecar to TabularInput
VisLab Apr 24, 2024
94671fe
Added a str_list to annotation utilities to handle None for MATLAB
VisLab Apr 25, 2024
100fa96
Updated the strlist renamed to_strlist
VisLab Apr 25, 2024
ef9c006
Merge pull request #914 from VisLab/develop
VisLab Apr 25, 2024
1908087
Changed the behavior of None in to_strlist
VisLab Apr 25, 2024
43e344f
Merge pull request #915 from VisLab/develop
VisLab Apr 25, 2024
144de72
Updated cached testlib and added helper to convert to factor list
VisLab Apr 27, 2024
9c0b3d3
Updated the to_factor helper to also handle DataFrame
VisLab Apr 27, 2024
1c5e6f7
Remove tabs in wiki format
IanCa Apr 27, 2024
3c09e1b
Bump paambaati/codeclimate-action from 5.0.0 to 6.0.0
dependabot[bot] Apr 29, 2024
b5389fc
Bump spec_tests/hed-specification from `6182ab9` to `2b727a8`
dependabot[bot] Apr 29, 2024
ba22418
Merge pull request #916 from hed-standard/IanCa-patch-1
VisLab Apr 30, 2024
623ed17
Merge pull request #917 from hed-standard/dependabot/github_actions/d…
VisLab Apr 30, 2024
1bf129a
Second pass dataframe/omn schema handling
IanCa May 7, 2024
0eaa723
Fix typos
IanCa May 7, 2024
d3191ac
slightly improve ontology test
IanCa May 7, 2024
ba258f3
Merge pull request #918 from hed-standard/dependabot/submodules/devel…
VisLab May 7, 2024
714d6c4
Merge pull request #919 from IanCa/develop
VisLab May 7, 2024
f8ac3c9
Replace removeprefix with 3.7 compatible
IanCa May 7, 2024
d87aa9b
Loosen matplotlib requirement for 3.8
IanCa May 7, 2024
219f729
Merge pull request #920 from IanCa/develop
VisLab May 7, 2024
79b2dc7
Merge branch 'develop' of https://github.com/hed-standard/hed-python …
VisLab May 8, 2024
e200406
Bump spec_tests/hed-examples from `0206613` to `db1eb80`
dependabot[bot] May 8, 2024
ce87684
Add more robust hedID validation, minor ontology code tweaks
IanCa May 8, 2024
6bb4d57
Merge pull request #921 from hed-standard/dependabot/submodules/devel…
VisLab May 9, 2024
f2e340a
Merge pull request #922 from IanCa/develop
VisLab May 9, 2024
9ad66ca
Updated the __init__ for visibility in matlab
VisLab May 13, 2024
8f08ebd
Added a get_bids_dataset
VisLab May 13, 2024
5dfa7ab
Updated the main init
VisLab May 13, 2024
39ff3da
Worked on the init to make functions available to MATLAB
VisLab May 13, 2024
159d0a5
Make assigning ID's optional in script
IanCa May 13, 2024
c374130
Merge pull request #923 from IanCa/develop
VisLab May 14, 2024
845a524
Updated the imports
VisLab May 14, 2024
a98db20
Merge branch 'develop' of https://github.com/hed-standard/hed-python …
VisLab May 14, 2024
cc813a6
Fixed conflict
VisLab May 14, 2024
67450cc
Imported jsonschema rather than directly imported the validator
VisLab May 14, 2024
cb0fae5
Updated the imports
VisLab May 14, 2024
1a62ba9
Merge pull request #924 from VisLab/develop
VisLab May 14, 2024
7325839
Updated
VisLab May 14, 2024
9877540
Updated imports
VisLab May 14, 2024
d5fef61
Updated return value on strs_sidecar
VisLab May 14, 2024
1d880ed
Updated allowed font extensions
VisLab May 15, 2024
10eae28
Updated annotation_util formating
VisLab May 15, 2024
3194e77
Merge pull request #925 from VisLab/develop
VisLab May 15, 2024
98bd6d7
delete test hed cache
IanCa May 15, 2024
b5deece
update error message per kay
IanCa May 15, 2024
c61c7af
Merge pull request #926 from IanCa/develop
VisLab May 15, 2024
b7ab42f
Update dataframe loading/saving to allow passing a folder name
IanCa May 16, 2024
b768dc9
add tests
IanCa May 16, 2024
40964c2
Access matplotlib color map in a different way
IanCa May 16, 2024
7fb7317
Merge pull request #928 from IanCa/develop
VisLab May 17, 2024
bf952d7
Move schema scripts over to hed-python
IanCa May 20, 2024
b9ffbb6
Add debug print
IanCa May 20, 2024
56524c9
Update print, better handle non lowercase
IanCa May 20, 2024
c02af7f
Fix add_extension for None
IanCa May 20, 2024
d601d8b
Restore add_extension
IanCa May 20, 2024
d80e069
Merge pull request #929 from IanCa/develop
VisLab May 20, 2024
533d8fd
---
dependabot[bot] May 22, 2024
aff55a7
Merge pull request #930 from hed-standard/dependabot/submodules/devel…
VisLab May 23, 2024
317c381
Minor tweaks to spreadsheet script/code
IanCa May 23, 2024
a11d217
Bump spec_tests/hed-examples from `db1eb80` to `a32e00e`
dependabot[bot] May 24, 2024
73ba583
Merge pull request #931 from IanCa/develop
VisLab May 24, 2024
9c201e5
Merge pull request #932 from hed-standard/dependabot/submodules/devel…
VisLab May 24, 2024
3bcc505
Fix for codespell and documentation errors
IanCa May 24, 2024
f38f9d5
Add assertIn to codespell filter
IanCa May 24, 2024
1c9d69e
Ontology fixes
IanCa May 28, 2024
aa3d27d
Merge pull request #934 from IanCa/develop
VisLab May 28, 2024
09350f0
Bump spec_tests/hed-specification from `9a1574e` to `0d8303e`
dependabot[bot] May 30, 2024
1151024
Merge pull request #936 from hed-standard/dependabot/submodules/devel…
VisLab May 31, 2024
a45226d
Fix tests on windows/with new 8.3
IanCa Jun 4, 2024
6ce29e2
First pass create_ontology script
IanCa Jun 4, 2024
d5d5f26
Add debug print
IanCa Jun 4, 2024
193696a
remove debug print
IanCa Jun 4, 2024
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Bump spec_tests/hed-examples from bd1e089 to 79de656
Bumps [spec_tests/hed-examples](https://github.com/hed-standard/hed-examples) from `bd1e089` to `79de656`.
- [Release notes](https://github.com/hed-standard/hed-examples/releases)
- [Commits](hed-standard/hed-examples@bd1e089...79de656)

---
updated-dependencies:
- dependency-name: spec_tests/hed-examples
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <[email protected]>
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dependabot[bot] authored Jan 23, 2024
commit 47a18f51d940e76c2d606e35f0422f5c81e3efb0