Ecosyste.ms: OpenCollective

An open API service for software projects hosted on Open Collective.

github.com/ome/ngff

Next-generation file format (NGFF) specifications for storing bioimaging data in the cloud.
https://github.com/ome/ngff

Update to review.yml to pull_request_target

97551e9b52a0058f6936e87edd0ce8680705cd2d authored over 2 years ago by Josh Moore <[email protected]>
Add no-op review.yml workflow for activation

7a411473cfef96ac34fb661a1be3530e436d7e81 authored over 2 years ago by Josh Moore <[email protected]>
Use integer for id, starttime, endtime, fieldcount in plate.schemas

09ab485d2869fbae8e3346f0694b399613e79b9e authored over 2 years ago by William Moore <[email protected]>
Update 0.2/schemas/plate.schema

Co-authored-by: Sébastien Besson <[email protected]>

bf748c3ed40dda4f34d97b05fd5340ccb5d28969 authored over 2 years ago by Will Moore <[email protected]>
Update 0.3/schemas/well.schema

Co-authored-by: Sébastien Besson <[email protected]>

2be816c24416a2dc2c2b86d0394df58e8a805471 authored over 2 years ago by Will Moore <[email protected]>
Update 0.3/schemas/plate.schema

Co-authored-by: Sébastien Besson <[email protected]>

9e3e8ed484af4323d38c1c39f3f1132e3a479ba9 authored over 2 years ago by Will Moore <[email protected]>
Update 0.2/schemas/plate.schema

Co-authored-by: Sébastien Besson <[email protected]>

a2718c5cb06339b5cf441b1714a643d81341acec authored over 2 years ago by Will Moore <[email protected]>
Update 0.2/schemas/well.schema

Co-authored-by: Sébastien Besson <[email protected]>

119bbdc8729595f8dc93b9d9613a4dc4c44c6209 authored over 2 years ago by Will Moore <[email protected]>
Update 0.1/schemas/well.schema

Co-authored-by: Sébastien Besson <[email protected]>

83f1ffdfabfcb007f05635183d5a030fce36e634 authored over 2 years ago by Will Moore <[email protected]>
Merge pull request #126 from sbesson/plate_specification_2

Clarify types and requirements levels for the plate/well specification

e26e20663f0f0e839c185bbf2c558fa760d252c3 authored over 2 years ago by Sébastien Besson <[email protected]>
Correct a few remaining typos

c889ffa77ea07eeff220104404719c3721feb824 authored over 2 years ago by Sebastien Besson <[email protected]>
Port plate/well updates to latest specification

d950f3af5d37fecedecda1754fde828c2bf6ba50 authored over 2 years ago by Sebastien Besson <[email protected]>
Add acquisition description to the plate schema

cbefa91a7fe569a89cad7b8b797a1dcab2108cc5 authored over 2 years ago by Sebastien Besson <[email protected]>
Improve wording as per Melissa's suggestions

bbc46783e7ee3ae144654b86e7cce382aba2d7f6 authored over 2 years ago by Sebastien Besson <[email protected]>
Add missing plate and well schemas for 0.1, 0.2, 0.3

77cf470aa8408c95a6b1eb3775a9762c7485ea7c authored over 2 years ago by William Moore <[email protected]>
Clarify types and requirements levels for the plate/well specification

This commit rewrites the section and ensures that:
- each key has a requirement level specified ...

4ee4fa18872a90d2fea6cfefbf444b331b5f2f83 authored over 2 years ago by Sebastien Besson <[email protected]>
Merge pull request #124 from yarikoptic/bf-codeowners

RF: take the "burden" off @kimdhamilton shoulders

ff6317039dfc037749c28f6563492a9745525674 authored over 2 years ago by Josh Moore <[email protected]>
RF: take the "burden" off @kimdhamilton shoulders -- remove CODEOWNERS

https://github.com/w3c-ccg/markdown-to-spec
template for the ngff repository.

Decision was made...

f1e8925f1386c9a04387576ff7e4f15126148183 authored over 2 years ago by Yaroslav Halchenko <[email protected]>
Merge pull request #122 from sbesson/plate_schemas_latest

Plate/well JSON schemas (latest specification)

1b9ef48a63bf90ca5aa0d42694a25a6514fd661d authored over 2 years ago by Josh Moore <[email protected]>
Merge pull request #123 from yarikoptic/enh-mailmap

ENH: add .mailmap to harmonize contributors names etc

52ccf2319e8ac251fa6c884bcff3652620b57e18 authored over 2 years ago by Sébastien Besson <[email protected]>
ENH: add .mailmap to harmonize contributors names etc

$> git shortlog -sn
78 Sebastien Besson
58 jmoore
49 William Moore
36 Constantin Pa...

a19883c88407697849b4af3d29aabfe10652ecb3 authored over 2 years ago by Yaroslav Halchenko <[email protected]>
Extract plate/well snippets under examples

8a4bd123f0a87b264171bacdadd970cd9f7baa0a authored over 2 years ago by Sebastien Besson <[email protected]>
Add plate/well test suite and update validation tests

0f397185c923a7c6c1c4ca388fdc2b6d0a10b84c authored over 2 years ago by Sebastien Besson <[email protected]>
Port plate/well JSON schemas to latest specification

06b07a48ea5e8d749f60d5c23ab2e6c84d8fe481 authored over 2 years ago by Sebastien Besson <[email protected]>
Merge pull request #120 from sbesson/plate_specification

Add JSON schemas for plate and well specification

e0a439786eab1b0ffef446ee232b0e69b132df56 authored over 2 years ago by Sébastien Besson <[email protected]>
Clarify that timestamps are epoch times

38c3eb27722269a7f7bee2f49eb2172f63a2592f authored over 2 years ago by Sebastien Besson <[email protected]>
Ensure acquisition id, starttime and endtime are positive integers

30d0156ac773c43d79c5892c29a6ae063dc7aeeb authored over 2 years ago by Sebastien Besson <[email protected]>
Add JSON schemas and JSON tests for well specification

495ac5dab312493bf6f4c1c72718ea2af5a7890b authored over 2 years ago by Sebastien Besson <[email protected]>
Extract well specification snippets under examples

295971de2bf33f2bce191c4d9e310490d25bcbb5 authored over 2 years ago by Sebastien Besson <[email protected]>
Add trailing newlines

d745d71712493a7f037fbf77b49b6d0f68b521ce authored over 2 years ago by Sebastien Besson <[email protected]>
Disallow non-unique rows/columns/wells

1bb8a07aa15d87e258c8b014c4940b92da1992dc authored over 2 years ago by Sebastien Besson <[email protected]>
Disallow empty rows/columns/wells

95a5162add1c2b3e4892f538afbb9685085c7506 authored over 2 years ago by Sebastien Besson <[email protected]>
Fix internal reference

bf021038f7b02a44765fc91ee1b2e6fd337cc511 authored over 2 years ago by Sebastien Besson <[email protected]>
Test examples with strict plate schema

c97eddcc2ae1e04e08baad9d27e9482aaa364ca6 authored over 2 years ago by Sebastien Besson <[email protected]>
Add tests for strict plate JSON schema

8a807f728a055c69049407e182706217bd8bb0e3 authored over 2 years ago by Sebastien Besson <[email protected]>
Add suite of test for plate schema

448bc5934b67073a32b3cfea7299dbdbd565f5bd authored over 2 years ago by Sebastien Besson <[email protected]>
test_validation: construct global schema store

At the moment, each test suite is creating its own internal schema
store with a single schema.
T...

949a3528b58fd78cb7c970da99222ad856def179 authored over 2 years ago by Sebastien Besson <[email protected]>
Add first version of strict plate JSON schema

0cdc99aa52ddb259c7940ac7e7274c899ef6239d authored over 2 years ago by Sebastien Besson <[email protected]>
Only test the examples in the same folder as .config.json

e49f12628499b3eeabb34625e8cfa72fcadaa242 authored over 2 years ago by Sebastien Besson <[email protected]>
Add first version of plate JSON schema

6852d5e16a28acaf93874f10e05790e6053d897f authored over 2 years ago by Sebastien Besson <[email protected]>
Extract plate snippets under plate_strict

f5aa76f4350e51c5e881ec645a569dcd60e571c9 authored over 2 years ago by Sebastien Besson <[email protected]>
Merge pull request #119 from sbesson/0.4_test_refactor

Refactor 0.4 schema validation tests

052ccf2a21833b3674e7b9bca49f0f980dba1d19 authored over 2 years ago by Sébastien Besson <[email protected]>
Refactor 0.4 schema validation tests

Ports changes made against the latest version of the specification to
consolidate the JSON test ...

7d329713ca4bba202176b82a60841e9d537c906a authored over 2 years ago by Sebastien Besson <[email protected]>
Merge pull request #118 from joshmoore/test-refactor

f17bbab393b17d79a544845cc6a225bbc336ffa1 authored over 2 years ago by Josh Moore <[email protected]>
Remove 'invalid but doesn't fail' test

e151ae06b96fb2e40c5827ba11b079c39bd1830b authored over 2 years ago by Josh Moore <[email protected]>
Upgrade jsonschema to use Draft202012Validator

67384348048135fc15ff34644d2c7c0f6e7b58b9 authored over 2 years ago by Josh Moore <[email protected]>
Fix TBDs in strict json

7c5e989aec1ae6035eb15f20bcb7fb382f9a2e8f authored over 2 years ago by Josh Moore <[email protected]>
Recombine test classes

9d602747fbf606e62a68ef72fdcf461266b133fa authored over 2 years ago by Josh Moore <[email protected]>
Remove unused examples

7c1cd6edca42c0d54937d01bb29724dd2b5ba4ea authored over 2 years ago by Josh Moore <[email protected]>
Update examples tests

06672cea5b7d1ab0a70ec6c62c55dda3f4d6abbc authored over 2 years ago by Josh Moore <[email protected]>
Proposal: use test suite structure

fad4a86c93c2e05bb992cf0b65346b7f64e8303d authored over 2 years ago by Josh Moore <[email protected]>
Add applicable versions statement

2b67a36515b8eaeab643f217167e6cb8ad4d9bcc authored over 2 years ago by Josh Moore <[email protected]>
Merge 'origin/main' into bf2raw

b09928105043fdb6fa86c084874d9ec5664fc2b2 authored over 2 years ago by jmoore <[email protected]>
Merge pull request #113 from sbesson/schemas_publication

Consume main branch of ome/spec-prod action

895d88a631555a472da2c5d51dc0e3bfee5d51a3 authored over 2 years ago by Josh Moore <[email protected]>
Add missing schema file

890e8a281daac0bf00ed3e32a864f24d1fc72168 authored over 2 years ago by jmoore <[email protected]>
Add schema & test for bf2raw metadata

6403d883aa1ca559cc0b37368b5f78a84245e22f authored over 2 years ago by jmoore <[email protected]>
Clarify contents of METADATA.ome.xml, thanks to Melissa

c8e98e4c390d1a2d12f33377e2a21e37a4567247 authored over 2 years ago by jmoore <[email protected]>
Improve wording of "SHOULD parse multiple images", thanks to Ilan

see: https://github.com/ome/ngff/issues/104#issuecomment-1092706651

ee1545552bac2758e55574f6c55cedbda2d15624 authored over 2 years ago by jmoore <[email protected]>
Consume main branch of ome/spec-prod action

This should include the latest changes allowing to publish the JSON
schemas under ngff.openmicro...

f24828335845ab22791bdb68457ef574e4a0cc7a authored over 2 years ago by Sebastien Besson <[email protected]>
Merge pull request #110 from sbesson/json_snippets_latest

Extract specification snippets as standalone JSON files (latest)

caa7e8eb83291947e4168539d30a7afc967f6f4f authored over 2 years ago by Josh Moore <[email protected]>
Add layout example

8ee02d1e60e216496ccd0ffb30f80892057269e7 authored over 2 years ago by jmoore <[email protected]>
First draft of bioformats2raw.layout

d7c0556029ab514fadedda40086f4d1de64efe42 authored over 2 years ago by jmoore <[email protected]>
Replace version in JSON snippets

4feebbcf41a56380712bdf4f592996487645ddf0 authored over 2 years ago by Sebastien Besson <[email protected]>
Defined NGFFVERSION text macro

dd5d5553583b4af418192a605b8c6cdd714b63f7 authored over 2 years ago by Sebastien Besson <[email protected]>
Use 0.5-dev rather than 0.4

866dd01dbf39cdd48123bd0dd06febdf0c61fe80 authored over 2 years ago by Sebastien Besson <[email protected]>
Add validation test infrastructure under latest specification

ff936b894f9047508849bee8072b6388d0ac935a authored almost 3 years ago by Sebastien Besson <[email protected]>
Copy 0.4 JSON schemas under latest

0765b4d4aa00509e0263887a425f38f7a930028e authored almost 3 years ago by Sebastien Besson <[email protected]>
Port changes from 0.4 specification (conventions, json inclusion)

663c3693cbc2ce3415ce3bfc9813a6ddcf46e1e6 authored almost 3 years ago by Sebastien Besson <[email protected]>
Copy 0.4 examples under latest

1fbc2503aa2126f3185107818ff7b2962e001daf authored almost 3 years ago by Sebastien Besson <[email protected]>
Merge pull request #98 from sbesson/json_snippets

Extract specification snippets as standalone JSON files

8dec6918ee6630f43f339b281b66043e0a797ca4 authored almost 3 years ago by Sébastien Besson <[email protected]>
Update 0.4/index.bs

Co-authored-by: Josh Moore <[email protected]>

51ccdd9471e8059fc6e1949734f98f42ce513dc7 authored almost 3 years ago by Sébastien Besson <[email protected]>
Do not allow comments in JSON objects

551aab770bee91681ba8c90f7afc4da5b0920504 authored almost 3 years ago by Sebastien Besson <[email protected]>
Update tests to strip out comments

ae8839c35bd2fc4e35d6be4ea77b80b12ec8db78 authored almost 3 years ago by Sebastien Besson <[email protected]>
Convert back into comments

fbf4aee3b2ee6deb9ba411eacab7a2cc0bc28304 authored almost 3 years ago by Sebastien Besson <[email protected]>
Tentatively capture comments as custom description key/values

0e5d65211a64f8f5ce5756f179ab5aaea6026ceb authored almost 3 years ago by Sebastien Besson <[email protected]>
Split the coordinateTransformations for readability

6e3a0a38a4809675e980d32e213a23e693b30134 authored almost 3 years ago by Sebastien Besson <[email protected]>
Extract the multiscales snippet into a JSON file validated by the schema

e5c20b219bf524d4923e2d5fa0cac7007374b6b1 authored almost 3 years ago by Sebastien Besson <[email protected]>
Fix invalid JSON elements (comments, missing parenthesis)

c460f1222dcbb5b9d6ecfa193526dcaa754456c2 authored almost 3 years ago by Sebastien Besson <[email protected]>
Add document conventions

a7038b6fc518b2f23c6c1ad08c47a27268caa999 authored almost 3 years ago by Sebastien Besson <[email protected]>
Merge pull request #106 from sbesson/default_scale

Clarifies that scale should always capture the downsampling factor

047bc0b8ec5cf5ab0f1dd2174e1baa1772a93928 authored almost 3 years ago by Sébastien Besson <[email protected]>
alongside -> along

637a98a0efc1139596d0174f64d74654c638832b authored almost 3 years ago by Sebastien Besson <[email protected]>
Clarify dataset.coordinateTransformations relationship

9e1eba93638670dbff18eef67bcbdad4c760fbb5 authored almost 3 years ago by Sebastien Besson <[email protected]>
Clarifies that scale should always capture the downsampling factor

For instance in the case of a synthetic 5D dataset downsampled by a
factor of 2 alongside the la...

e19d4dffc2ca0c7cea998a150e10cb57bfeb8162 authored almost 3 years ago by Sebastien Besson <[email protected]>
Merge pull request #97 from sbesson/0.4_publication

Publish 0.4 specification

a5162078c93ca7f11249523435e4d13b8d9f4c12 authored almost 3 years ago by Sébastien Besson <[email protected]>
Use v4 of spec-prod action

174876360b804586d3804f6e1c10e6bb475c0e2e authored almost 3 years ago by Sebastien Besson <[email protected]>
Review versions numbers and add history

0f03373888f3103978843d5d0a896521807f2637 authored almost 3 years ago by Sebastien Besson <[email protected]>
Copy 0.4 specification under versioned folder

5067681721cc73ddf8b64692456cdda604cc659a authored almost 3 years ago by Sebastien Besson <[email protected]>
Merge pull request #96 from sbesson/0.4_xarray

Remove requirement for xarray-compatible metadata

1848aff766d2a485a468e1cd03d754805153b25b authored almost 3 years ago by Sébastien Besson <[email protected]>
Merge pull request #95 from joshmoore/fix-1

Minor updates around copyright, etc.

d973d475976ecce20eb8d9e8e1a7128b4f9f564a authored almost 3 years ago by Sébastien Besson <[email protected]>
Rollback to spec-prod@v3

0fb3b33e04b42d820f57f4515203c73c78fdc0a3 authored almost 3 years ago by jmoore <[email protected]>
Remove requirement for xarray-compatible metadata

08da947a8d5c955e8075738eae107335410b5f76 authored almost 3 years ago by Sebastien Besson <[email protected]>
Merge pull request #92 from sbesson/0.4_schemas_strict_validation

0.4 schemas: add testing infrastructure for strict and base validation

12acbb69dba91da09f162eb806c59161601dc1c0 authored almost 3 years ago by Sébastien Besson <[email protected]>
Add xfail tests for invalid metadata not flagged by the JSON schema

96bfeacd0094ecdc637b8a6200571f87981d22d2 authored almost 3 years ago by Sebastien Besson <[email protected]>
Also ensure that invalid files fail the strict validator

f0f3930cd2ee841fbb8ed0f5c341e6fcd4110d63 authored almost 3 years ago by Sebastien Besson <[email protected]>
Revert "Remove duplicate_axes_name example"

This reverts commit d3a1c38a7181a8eca8bfb4800b6ea238d3a83f9e.

f01657995d38da50665340a853da5105e87e66ce authored almost 3 years ago by Sebastien Besson <[email protected]>
Add more details on release process

d88dba7bde457db2580c9b031afd9753b87ee5e2 authored almost 3 years ago by jmoore <[email protected]>
Use migrated spec-prod repo

298ef4eb73c1eb32e08b942d07a5b585985124d4 authored almost 3 years ago by jmoore <[email protected]>
Use UoD for authorship

dc968114a19d892b7cba922b0958fd4882080854 authored almost 3 years ago by jmoore <[email protected]>
Add another new-version-todo to the README

a17a7e68b2e02cb657d602b20686252d2ad101f5 authored almost 3 years ago by jmoore <[email protected]>
Update copyright, add to 0.3, and include in README

1e4a32ba12c0e36284d431ce504c421ff03c5520 authored almost 3 years ago by jmoore <[email protected]>