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Dir schema major/minor versions #1312

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merged 20 commits into from
Apr 10, 2024
Merged

Dir schema major/minor versions #1312

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abaab7e
initial work to get dir schema minor versions
gesinaphillips Mar 12, 2024
d66b522
ran tests, updated dir schema location logic
gesinaphillips Mar 15, 2024
2f78347
small updates to formatting, bugfixes
gesinaphillips Mar 18, 2024
b4cde99
clarifying comment
gesinaphillips Mar 18, 2024
3218525
save minor dir schema and report via get_info
gesinaphillips Mar 21, 2024
9b173d2
updated readmes
gesinaphillips Mar 21, 2024
ffe9af9
made sorting more reliable
gesinaphillips Mar 21, 2024
059898b
changed dir schema names, docs broken
gesinaphillips Mar 25, 2024
fbfcb25
updated docs, still need to update readmes
gesinaphillips Mar 25, 2024
89862cc
updating readmes, all codex broken because assayclassifier still retu…
gesinaphillips Mar 25, 2024
288ad64
testing around codex
gesinaphillips Mar 25, 2024
5271f10
mocked up good codex data to test, will need to re-test when assaycla…
gesinaphillips Mar 25, 2024
e692913
linter fix
gesinaphillips Mar 25, 2024
a8db90b
merging incl. changes to shared upload dir validation; updated more t…
gesinaphillips Mar 26, 2024
5b9e8ad
updated testing
gesinaphillips Mar 26, 2024
5cc3e8b
fixing logic
gesinaphillips Mar 26, 2024
bc40bb0
merge
gesinaphillips Mar 28, 2024
ab43f4c
updating tests, added command line arg to test using DEV
gesinaphillips Apr 9, 2024
3ff1512
merge
gesinaphillips Apr 9, 2024
32fa080
merge
gesinaphillips Apr 10, 2024
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1 change: 1 addition & 0 deletions CHANGELOG.md
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## v0.0.19 (in progress)
- Directory validation changes for "shared" uploads
- Accommodate dir schema minor versions

## v0.0.18

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2 changes: 1 addition & 1 deletion docs/10x-multiome/current/index.md
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Expand Up @@ -28,7 +28,7 @@ REQUIRED - For this assay, you must also prepare and submit two additional metad
<br>

## Directory schemas
<summary><b>Version 2 (use this one)</b></summary>
<summary><b>Version 2.0 (use this one)</b></summary>

| pattern | required? | description |
| --- | --- | --- |
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2 changes: 1 addition & 1 deletion docs/af/current/index.md
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<br>

## Directory schemas
<summary><b>Version 2 (use this one)</b></summary>
<summary><b>Version 2.0 (use this one)</b></summary>

| pattern | required? | description | dependent on |
| --- | --- | --- | --- |
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2 changes: 1 addition & 1 deletion docs/af/deprecated/index.md
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<br>

## Directory schemas
<summary><b>Version 0 (use this one)</b></summary>
<summary><b>Version 0.0 (use this one)</b></summary>

| pattern | required? | description |
| --- | --- | --- |
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2 changes: 1 addition & 1 deletion docs/atacseq/current/index.md
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Expand Up @@ -30,7 +30,7 @@ For additional documentation on this dataset type, please visit [here](https://d
<br>

## Directory schemas
<summary><b>Version 2 (use this one)</b></summary>
<summary><b>Version 2.0 (use this one)</b></summary>

| pattern | required? | description |
| --- | --- | --- |
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2 changes: 1 addition & 1 deletion docs/bodyct/current/index.md
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<br>

## Directory schemas
<summary><b>Version 2 (use this one)</b></summary>
<summary><b>Version 2.0 (use this one)</b></summary>

| pattern | required? | description |
| --- | --- | --- |
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2 changes: 1 addition & 1 deletion docs/bulkatacseq/deprecated/index.md
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<br>

## Directory schemas
<summary><b>Version 0 (use this one)</b></summary>
<summary><b>Version 0.0 (use this one)</b></summary>

| pattern | required? | description |
| --- | --- | --- |
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2 changes: 1 addition & 1 deletion docs/bulkrnaseq/deprecated/index.md
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<br>

## Directory schemas
<summary><b>Version 0 (use this one)</b></summary>
<summary><b>Version 0.0 (use this one)</b></summary>

| pattern | required? | description |
| --- | --- | --- |
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2 changes: 1 addition & 1 deletion docs/celldive/current/index.md
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<br>

## Directory schemas
<summary><a href="https://docs.google.com/spreadsheets/d/1pZD2e51e4QkxzIk6xjHPPu1RBZpx5mzoykMmlaDK8rA"><b>Version 2 (use this one)</b> (draft - submission of data prepared using this schema will be supported by Sept. 30) </a></summary>
<summary><a href="https://docs.google.com/spreadsheets/d/1pZD2e51e4QkxzIk6xjHPPu1RBZpx5mzoykMmlaDK8rA"><b>Version 2.0 (use this one)</b> (draft - submission of data prepared using this schema will be supported by Sept. 30) </a></summary>

2 changes: 1 addition & 1 deletion docs/celldive/deprecated/index.md
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<br>

## Directory schemas
<summary><b>Version 0 (use this one)</b></summary>
<summary><b>Version 0.0 (use this one)</b></summary>

| pattern | required? | description |
| --- | --- | --- |
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2 changes: 1 addition & 1 deletion docs/cems/deprecated/index.md
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<br>

## Directory schemas
<summary><b>Version 0 (use this one)</b></summary>
<summary><b>Version 0.0 (use this one)</b></summary>

| pattern | required? | description |
| --- | --- | --- |
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2 changes: 1 addition & 1 deletion docs/codex/current/index.md
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<br>

## Directory schemas
<summary><b>Version 2 (use this one)</b></summary>
<summary><b>Version 2.0 (use this one)</b></summary>

| pattern | required? | description | dependent on |
| --- | --- | --- | --- |
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4 changes: 2 additions & 2 deletions docs/codex/deprecated/index.md
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<br>

## Directory schemas
<summary><b>Version 1-with-dataset-json (use this one)</b></summary>
<summary><b>Version 1.1 (use this one)</b></summary>

| pattern | required? | description |
| --- | --- | --- |
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| <code>extras/dir-schema-v1-with-dataset-json</code> | ✓ | Empty file whose presence indicates the version of the directory schema in use |
| <code>extras\/.*</code> | | Folder for general lab-specific files related to the dataset. [Exists in all assays] |

<summary><b>Version 0</b></summary>
<summary><b>Version 0.0</b></summary>

| pattern | required? | description |
| --- | --- | --- |
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2 changes: 1 addition & 1 deletion docs/confocal/current/index.md
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<br>

## Directory schemas
<summary><b>Version 2 (use this one)</b></summary>
<summary><b>Version 2.0 (use this one)</b></summary>

| pattern | required? | description | dependent on |
| --- | --- | --- | --- |
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2 changes: 1 addition & 1 deletion docs/cosmx/current/index.md
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<br>

## Directory schemas
<summary><a href="https://docs.google.com/spreadsheets/d/1LE-iyY2E6eP4E8jhgP6rhsvjESrdHXWYrMwKTvNkI5Y"><b>Version 2 (use this one)</b> (draft - submission of data prepared using this schema will be supported by Sept. 30) </a></summary>
<summary><a href="https://docs.google.com/spreadsheets/d/1LE-iyY2E6eP4E8jhgP6rhsvjESrdHXWYrMwKTvNkI5Y"><b>Version 2.0 (use this one)</b> (draft - submission of data prepared using this schema will be supported by Sept. 30) </a></summary>

2 changes: 1 addition & 1 deletion docs/cycif/current/index.md
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<br>

## Directory schemas
<summary><a href="https://docs.google.com/spreadsheets/d/1pZD2e51e4QkxzIk6xjHPPu1RBZpx5mzoykMmlaDK8rA"><b>Version 2 (use this one)</b> (draft - submission of data prepared using this schema will be supported by Sept. 30) </a></summary>
<summary><a href="https://docs.google.com/spreadsheets/d/1pZD2e51e4QkxzIk6xjHPPu1RBZpx5mzoykMmlaDK8rA"><b>Version 2.0 (use this one)</b> (draft - submission of data prepared using this schema will be supported by Sept. 30) </a></summary>

2 changes: 1 addition & 1 deletion docs/dbit/current/index.md
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<br>

## Directory schemas
<summary><a href="https://docs.google.com/spreadsheets/d/1LE-iyY2E6eP4E8jhgP6rhsvjESrdHXWYrMwKTvNkI5Y"><b>Version 2 (use this one)</b> (draft - submission of data prepared using this schema will be supported by Sept. 30) </a></summary>
<summary><a href="https://docs.google.com/spreadsheets/d/1LE-iyY2E6eP4E8jhgP6rhsvjESrdHXWYrMwKTvNkI5Y"><b>Version 2.0 (use this one)</b> (draft - submission of data prepared using this schema will be supported by Sept. 30) </a></summary>

2 changes: 1 addition & 1 deletion docs/desi/current/index.md
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<br>

## Directory schemas
<summary><b>Version 2 (use this one)</b></summary>
<summary><b>Version 2.0 (use this one)</b></summary>

| pattern | required? | description |
| --- | --- | --- |
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2 changes: 1 addition & 1 deletion docs/enhanced-srs/current/index.md
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<br>

## Directory schemas
<summary><b>Version 2 (use this one)</b></summary>
<summary><b>Version 2.0 (use this one)</b></summary>

| pattern | required? | description | dependent on |
| --- | --- | --- | --- |
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2 changes: 1 addition & 1 deletion docs/gcms/deprecated/index.md
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<br>

## Directory schemas
<summary><b>Version 0 (use this one)</b></summary>
<summary><b>Version 0.0 (use this one)</b></summary>

| pattern | required? | description |
| --- | --- | --- |
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2 changes: 1 addition & 1 deletion docs/geomx-ncounter/current/index.md
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<br>

## Directory schemas
<summary><a href="https://docs.google.com/spreadsheets/d/1LE-iyY2E6eP4E8jhgP6rhsvjESrdHXWYrMwKTvNkI5Y"><b>Version 2 (use this one)</b> (draft - submission of data prepared using this schema will be supported by Sept. 30) </a></summary>
<summary><a href="https://docs.google.com/spreadsheets/d/1LE-iyY2E6eP4E8jhgP6rhsvjESrdHXWYrMwKTvNkI5Y"><b>Version 2.0 (use this one)</b> (draft - submission of data prepared using this schema will be supported by Sept. 30) </a></summary>

2 changes: 1 addition & 1 deletion docs/geomx-ngs/current/index.md
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<br>

## Directory schemas
<summary><b>Version 2 (use this one)</b></summary>
<summary><b>Version 2.0 (use this one)</b></summary>

| pattern | required? | description |
| --- | --- | --- |
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2 changes: 1 addition & 1 deletion docs/hifi-slide/current/index.md
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<br>

## Directory schemas
<summary><b>Version 2 (use this one)</b></summary>
<summary><b>Version 2.0 (use this one)</b></summary>

| pattern | required? | description |
| --- | --- | --- |
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2 changes: 1 addition & 1 deletion docs/histology/current/index.md
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<br>

## Directory schemas
<summary><b>Version 2 (use this one)</b></summary>
<summary><b>Version 2.0 (use this one)</b></summary>

| pattern | required? | description | dependent on |
| --- | --- | --- | --- |
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2 changes: 1 addition & 1 deletion docs/imc-2d/current/index.md
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<br>

## Directory schemas
<summary><b>Version 2 (use this one)</b></summary>
<summary><b>Version 2.0 (use this one)</b></summary>

| pattern | required? | description | dependent on |
| --- | --- | --- | --- |
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2 changes: 1 addition & 1 deletion docs/imc/deprecated/index.md
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<br>

## Directory schemas
<summary><b>Version 0 (use this one)</b></summary>
<summary><b>Version 0.0 (use this one)</b></summary>

| pattern | required? | description |
| --- | --- | --- |
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2 changes: 1 addition & 1 deletion docs/imc3d/deprecated/index.md
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<br>

## Directory schemas
<summary><b>Version 0 (use this one)</b></summary>
<summary><b>Version 0.0 (use this one)</b></summary>

| pattern | required? | description |
| --- | --- | --- |
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2 changes: 1 addition & 1 deletion docs/ims/deprecated/index.md
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<br>

## Directory schemas
<summary><b>Version 0 (use this one)</b></summary>
<summary><b>Version 0.0 (use this one)</b></summary>

| pattern | required? | description |
| --- | --- | --- |
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2 changes: 1 addition & 1 deletion docs/lcms/current/index.md
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<br>

## Directory schemas
<summary><b>Version 2 (use this one)</b></summary>
<summary><b>Version 2.0 (use this one)</b></summary>

| pattern | required? | description |
| --- | --- | --- |
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<br>

## Directory schemas
<summary><b>Version 0 (use this one)</b></summary>
<summary><b>Version 0.0 (use this one)</b></summary>

| pattern | required? | description |
| --- | --- | --- |
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2 changes: 1 addition & 1 deletion docs/lightsheet/current/index.md
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<br>

## Directory schemas
<summary><b>Version 2 (use this one)</b></summary>
<summary><b>Version 2.0 (use this one)</b></summary>

| pattern | required? | description | dependent on |
| --- | --- | --- | --- |
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4 changes: 2 additions & 2 deletions docs/lightsheet/deprecated/index.md
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<br>

## Directory schemas
<summary><b>Version 1 (use this one)</b></summary>
<summary><b>Version 1.0 (use this one)</b></summary>

| pattern | required? | description |
| --- | --- | --- |
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| <code>Level3/Merged/MergedChannel[^/]+/[^/]+\.ome.tiff</code> | | Merged image file. |
| <code>extras\/.*</code> | | Folder for general lab-specific files related to the dataset. [Exists in all assays] |

<summary><b>Version 0</b></summary>
<summary><b>Version 0.0</b></summary>

| pattern | required? | description |
| --- | --- | --- |
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2 changes: 1 addition & 1 deletion docs/maldi/current/index.md
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<br>

## Directory schemas
<summary><b>Version 2 (use this one)</b></summary>
<summary><b>Version 2.0 (use this one)</b></summary>

| pattern | required? | description |
| --- | --- | --- |
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2 changes: 1 addition & 1 deletion docs/mc/current/index.md
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<br>

## Directory schemas
<summary><a href="https://docs.google.com/spreadsheets/d/1LE-iyY2E6eP4E8jhgP6rhsvjESrdHXWYrMwKTvNkI5Y"><b>Version 2 (use this one)</b> (draft - submission of data prepared using this schema will be supported by Sept. 30) </a></summary>
<summary><a href="https://docs.google.com/spreadsheets/d/1LE-iyY2E6eP4E8jhgP6rhsvjESrdHXWYrMwKTvNkI5Y"><b>Version 2.0 (use this one)</b> (draft - submission of data prepared using this schema will be supported by Sept. 30) </a></summary>

2 changes: 1 addition & 1 deletion docs/merfish/current/index.md
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<br>

## Directory schemas
<summary><b>Version 2 (use this one)</b></summary>
<summary><b>Version 2.0 (use this one)</b></summary>

| pattern | required? | description |
| --- | --- | --- |
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2 changes: 1 addition & 1 deletion docs/mibi/current/index.md
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<br>

## Directory schemas
<summary><b>Version 2 (use this one)</b></summary>
<summary><b>Version 2.0 (use this one)</b></summary>

| pattern | required? | description |
| --- | --- | --- |
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2 changes: 1 addition & 1 deletion docs/mibi/deprecated/index.md
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<br>

## Directory schemas
<summary><b>Version 0 (use this one)</b></summary>
<summary><b>Version 0.0 (use this one)</b></summary>

| pattern | required? | description |
| --- | --- | --- |
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2 changes: 1 addition & 1 deletion docs/microct/current/index.md
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<br>

## Directory schemas
<summary><b>Version 2 (use this one)</b></summary>
<summary><b>Version 2.0 (use this one)</b></summary>

| pattern | required? | description |
| --- | --- | --- |
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2 changes: 1 addition & 1 deletion docs/mri/current/index.md
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<br>

## Directory schemas
<summary><b>Version 2 (use this one)</b></summary>
<summary><b>Version 2.0 (use this one)</b></summary>

| pattern | required? | description |
| --- | --- | --- |
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2 changes: 1 addition & 1 deletion docs/mxif/deprecated/index.md
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<br>

## Directory schemas
<summary><b>Version 0 (use this one)</b></summary>
<summary><b>Version 0.0 (use this one)</b></summary>

| pattern | required? | description |
| --- | --- | --- |
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2 changes: 1 addition & 1 deletion docs/nano-splits/current/index.md
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<br>

## Directory schemas
<summary><a href="https://docs.google.com/spreadsheets/d/1eQrEby95rrvyCFMAgrrpqGOBZ7VAcA_nih-SnM47u44"><b>Version 2 (use this one)</b> (draft - submission of data prepared using this schema will be supported by Sept. 30) </a></summary>
<summary><a href="https://docs.google.com/spreadsheets/d/1eQrEby95rrvyCFMAgrrpqGOBZ7VAcA_nih-SnM47u44"><b>Version 2.0 (use this one)</b> (draft - submission of data prepared using this schema will be supported by Sept. 30) </a></summary>

2 changes: 1 addition & 1 deletion docs/nano/deprecated/index.md
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<br>

## Directory schemas
<summary><b>Version 0 (use this one)</b></summary>
<summary><b>Version 0.0 (use this one)</b></summary>
<details markdown="1"><summary>Deprecated</summary>

| pattern | required? | description |
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2 changes: 1 addition & 1 deletion docs/oct/current/index.md
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<br>

## Directory schemas
<summary><b>Version 2 (use this one)</b></summary>
<summary><b>Version 2.0 (use this one)</b></summary>

| pattern | required? | description |
| --- | --- | --- |
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2 changes: 1 addition & 1 deletion docs/phenocycler/current/index.md
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<br>

## Directory schemas
<summary><b>Version 2 (use this one)</b></summary>
<summary><b>Version 2.0 (use this one)</b></summary>

| pattern | required? | description |
| --- | --- | --- |
Expand Down
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