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Refactor Config and ROCrateWriter #18

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merged 9 commits into from
Aug 1, 2024
Merged

Refactor Config and ROCrateWriter #18

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d2a4f41
Support bioformats2raw.layout
joshmoore Aug 1, 2024
d795a73
Fix argument handling
joshmoore Aug 1, 2024
af78c62
Fix binary files
joshmoore Aug 1, 2024
865209d
Refactor configs and stores
joshmoore Aug 1, 2024
635fa89
Minor fixes and more tests
joshmoore Aug 1, 2024
915e330
Refactor ROCrateWriter
joshmoore Aug 1, 2024
fad4317
Re-add full test with org/modality
joshmoore Aug 1, 2024
71c61a3
Update README in preparation for 0.0.5 release
joshmoore Aug 1, 2024
8f35e53
Fix minor linting issues
joshmoore Aug 1, 2024
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23 changes: 21 additions & 2 deletions README.md
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Original file line number Diff line number Diff line change
@@ -1,8 +1,6 @@
# ome2024-ngff-challenge

[![Actions Status][actions-badge]][actions-link]
[![Documentation Status][rtd-badge]][rtd-link]

[![PyPI version][pypi-version]][pypi-link]
[![PyPI platforms][pypi-platforms]][pypi-link]
[![Image.SC Zulip][zulip-badge]][zulip-link]
Expand Down Expand Up @@ -43,6 +41,27 @@ Data generated within the challenge will have:
- a top-level `ro-crate-metadata.json` file with minimal metadata (specimen and
imaging modality)

You can example the contents of a sample dataset by using
[the minio client](https://github.com/minio/mc):

```
$ mc config host add uk1anon https://uk1s3.embassy.ebi.ac.uk "" ""
Added `uk1anon` successfully.
$ mc ls -r uk1anon/idr/share/ome2024-ngff-challenge/0.0.5/6001240.zarr/
[2024-08-01 14:24:35 CEST] 24MiB STANDARD 0/c/0/0/0/0
[2024-08-01 14:24:28 CEST] 598B STANDARD 0/zarr.json
[2024-08-01 14:24:32 CEST] 6.0MiB STANDARD 1/c/0/0/0/0
[2024-08-01 14:24:28 CEST] 598B STANDARD 1/zarr.json
[2024-08-01 14:24:29 CEST] 1.6MiB STANDARD 2/c/0/0/0/0
[2024-08-01 14:24:28 CEST] 592B STANDARD 2/zarr.json
[2024-08-01 14:24:28 CEST] 1.2KiB STANDARD ro-crate-metadata.json
[2024-08-01 14:24:28 CEST] 2.7KiB STANDARD zarr.json
```

The dataset can be inspected using a development version of the OME-NGFF
Validator available at
<https://deploy-preview-36--ome-ngff-validator.netlify.app/?source=https://uk1s3.embassy.ebi.ac.uk/idr/share/ome2024-ngff-challenge/0.0.4/6001240.zarr>

## Converting your data

### Getting started
Expand Down
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