From e97a1975e8d7f633357b715140ba3a5a8de9c4b5 Mon Sep 17 00:00:00 2001 From: Josh Moore Date: Wed, 13 Mar 2024 09:26:33 +0100 Subject: [PATCH 01/11] rename review --- rfc/1/{review_1.md => comment_1.md} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename rfc/1/{review_1.md => comment_1.md} (100%) diff --git a/rfc/1/review_1.md b/rfc/1/comment_1.md similarity index 100% rename from rfc/1/review_1.md rename to rfc/1/comment_1.md From f364253d85c9fb6221b77a7988f1dfd18286ba98 Mon Sep 17 00:00:00 2001 From: Josh Moore Date: Wed, 13 Mar 2024 09:29:46 +0100 Subject: [PATCH 02/11] List reviews & comments --- rfc/1/index.md | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/rfc/1/index.md b/rfc/1/index.md index 05384ad6..7076204d 100644 --- a/rfc/1/index.md +++ b/rfc/1/index.md @@ -7,9 +7,13 @@ Definition of the NGFF RFC process This RFC is currently under review (D4). -| Name | GitHub Handle | Institution | Date | Status | -|------------|---------------|-------------------|------------|--------| -| Josh Moore | joshmoore | German BioImaging | 2023-12-23 | Author | +| Name | GitHub Handle | Institution | Date | Status | +|----------------------------------------|-------------------------|----------------------|------------|---------------------------| +| Josh Moore | joshmoore | German BioImaging | 2023-12-23 | Author | +| Virginia Scarlett, _et al._ | | Janelia | 2024-02-26 | Review requested | +| Kevin Yamauchi, Virginie Uhlmann | | ETH, BiovisionCenter | 2024-03-05 | Review requested | +| Matthew Hartley | | EMBL-EBI | 2024-03-05 | Review requested | +| Wouter-Michiel Vierdag, Luca Marconato | melonora, LucaMarconato | EMBL | 2024-01-13 | [Comment](comment_1.html) | ## Overview From ba5fe21a91eebac8a046a140e2ceb01c82b7b770 Mon Sep 17 00:00:00 2001 From: Josh Moore Date: Wed, 13 Mar 2024 09:48:38 +0100 Subject: [PATCH 03/11] in-person Wouter/Luca feedback --- rfc/1/index.md | 33 +++++++++++++++++++++++++++++---- 1 file changed, 29 insertions(+), 4 deletions(-) diff --git a/rfc/1/index.md b/rfc/1/index.md index 7076204d..7e2dabd3 100644 --- a/rfc/1/index.md +++ b/rfc/1/index.md @@ -71,7 +71,7 @@ process and making that readily visible (c) ultimately driving the implementation of specifications in order to get working solutions into the hands of the bioimaging community. The process should **NOT** prevent future discussions on any adopted RFCs but instead will encourage continued -improvement and evolution through discussions of _further_RFCs. +improvement and evolution through discussions of _further_ RFCs. ## Requirements @@ -83,7 +83,7 @@ interpreted as described in IETF RFC 2119. This section lists the major stakeholders in the RFC process and provides an overview of their responsibilities and involvement in the process. For more -details, see the “Implementation” section below. +details, see the "Implementation" section below. **Authors** propose an idea for the RFC process and socialize the idea, e.g., through an issue or community call, gaining **Endorsers** They then submit a @@ -93,8 +93,8 @@ document under the `rfc/` subdirectory and it SHOULD follow the template provided. As described under the "DRAFT" section below, this document can be discussed for clarity following the standard PR process. However, once the draft has reached a certain stage that it is ready for comments, **Editors** -will merge it as a record of the fact that the suggestion. It will then become -available on https://ngff.openmicroscopy.org. +will merge it as a record of the fact that the suggestion has been made, and +it will then become available on https://ngff.openmicroscopy.org. **Endorsers** are non-**Author** supporters of an RFC, listed in a table. **Reviewers** who have given an "Accept" recommendation are also added to the @@ -131,6 +131,15 @@ This description of the RFC process will refer frequently to the [visual diagram Readers may want to familiar themselves with it at this point. Identifiers such as "D1", "R2", "S3", refer to steps in that diagram. +### Legend + +Notes regarding specific requirements are called out throughout the text +with the following symbols: + +> * 🕑 The clock symbol specifies definitive wait times within the process. +> * 📂 The folder symbol specifies requirements on additions to the repository, +> for example an implementation or failing test. + ### Phases The overall process is broken down into three phases: DRAFT phase before a @@ -242,6 +251,8 @@ progress (S1) to the SPEC phase below. If there are no "Major" objections but still no consensus, the decision falls to the **Editors** (R7) who may also move the RFC to the SPEC phase (S0). +> 📂 Two in-progress implementations required for progressing to S1. + Otherwise, the RFC iterates through the process again. If the changes made by the **Authors** are significant, **Reviewers** may be asked to respond again (R2). Alternatively, **Editors** may send the text back to the **Authors** for @@ -274,6 +285,20 @@ listed, the specification will be considered "adopted". The adopted specification will be slotted into a release version by the **Editors** and the **Authors** are encouraged to be involved in that release. +> 📂 Two released implementations required for being adopted. + +### Decision-making + +Unless otherwise specified in the text, the following considerations are taken +into account when making decisions regarding RFCs: + + * **Prefer working examples**: whether an implementation of an RFC or a + failing test which exposes an issue in a proposal, working examples will + tend to carry more weight in decision making. + * **technical expertise**: all other considerations being equal, feedback + from stakeholders with more technical expertise in a matter under + consideration will tend to carry more weight in decision making. + ## Drawbacks, risks, alternatives, and unknowns The primary **drawbacks**, **risks**, and **unknowns** of the proposal revolve From 480e1731c46403494900f8a98730a812c449a1bf Mon Sep 17 00:00:00 2001 From: Josh Moore Date: Wed, 13 Mar 2024 09:50:58 +0100 Subject: [PATCH 04/11] Remove use of 'Editor' in the main text post-RFC-1 --- 0.1/index.bs | 6 +++--- 0.2/index.bs | 2 +- 0.3/index.bs | 8 ++++---- 0.4/index.bs | 8 ++++---- latest/index.bs | 8 ++++---- 5 files changed, 16 insertions(+), 16 deletions(-) diff --git a/0.1/index.bs b/0.1/index.bs index 52a33115..3d14ff7d 100644 --- a/0.1/index.bs +++ b/0.1/index.bs @@ -12,8 +12,8 @@ Local Boilerplate: header yes Local Boilerplate: copyright yes Boilerplate: style-darkmode off Markup Shorthands: markdown yes -Editor: Josh Moore, Open Microscopy Environment (OME) https://www.openmicroscopy.org -Editor: Sébastien Besson, Open Microscopy Environment (OME) https://www.openmicroscopy.org +Author: Josh Moore, Open Microscopy Environment (OME) https://www.openmicroscopy.org +Author: Sébastien Besson, Open Microscopy Environment (OME) https://www.openmicroscopy.org Abstract: This document contains next-generation file format (NGFF) Abstract: specifications for storing bioimaging data in the cloud. Abstract: All specifications are submitted to the https://image.sc community for review. @@ -513,7 +513,7 @@ Citing {#citing} ================ [Next-generation file format (NGFF) specifications for storing bioimaging data in the cloud.](https://ngff.openmicroscopy.org/0.1) -J. Moore, *et al*. Editors. Open Microscopy Environment Consortium, 20 November 2020. +J. Moore, *et al*. Open Microscopy Environment Consortium, 20 November 2020. This edition of the specification is [https://ngff.openmicroscopy.org/0.1/](https://ngff.openmicroscopy.org/0.1/]). The latest edition is available at [https://ngff.openmicroscopy.org/latest/](https://ngff.openmicroscopy.org/latest/). [(doi:10.5281/zenodo.4282107)](https://doi.org/10.5281/zenodo.4282107) diff --git a/0.2/index.bs b/0.2/index.bs index 126eae10..e8e5a7bd 100644 --- a/0.2/index.bs +++ b/0.2/index.bs @@ -571,7 +571,7 @@ Citing {#citing} ================ [Next-generation file format (NGFF) specifications for storing bioimaging data in the cloud.](https://ngff.openmicroscopy.org/0.2) -J. Moore, *et al*. Editors. Open Microscopy Environment Consortium, 29 March, 2021. +J. Moore, *et al*. Open Microscopy Environment Consortium, 29 March, 2021. This edition of the specification is [https://ngff.openmicroscopy.org/0.2/](https://ngff.openmicroscopy.org/0.2/]). The latest edition is available at [https://ngff.openmicroscopy.org/latest/](https://ngff.openmicroscopy.org/latest/). [(doi:10.5281/zenodo.4282107)](https://doi.org/10.5281/zenodo.4282107) diff --git a/0.3/index.bs b/0.3/index.bs index d50db957..48da447e 100644 --- a/0.3/index.bs +++ b/0.3/index.bs @@ -12,9 +12,9 @@ Local Boilerplate: header yes Local Boilerplate: copyright yes Boilerplate: style-darkmode off Markup Shorthands: markdown yes -Editor: Josh Moore, Open Microscopy Environment (OME) https://www.openmicroscopy.org -Editor: Sébastien Besson, Open Microscopy Environment (OME) https://www.openmicroscopy.org -Editor: Constantin Pape, European Molecular Biology Laboratory (EMBL) https://www.embl.org/sites/heidelberg/ +Author: Josh Moore, Open Microscopy Environment (OME) https://www.openmicroscopy.org +Author: Sébastien Besson, Open Microscopy Environment (OME) https://www.openmicroscopy.org +Author: Constantin Pape, European Molecular Biology Laboratory (EMBL) https://www.embl.org/sites/heidelberg/ Abstract: This document contains next-generation file format (NGFF) Abstract: specifications for storing bioimaging data in the cloud. Abstract: All specifications are submitted to the https://image.sc community for review. @@ -581,7 +581,7 @@ Citing {#citing} ================ [Next-generation file format (NGFF) specifications for storing bioimaging data in the cloud.](https://ngff.openmicroscopy.org/0.3) -J. Moore, *et al*. Editors. Open Microscopy Environment Consortium, 20 November 2020. +J. Moore, *et al*. Open Microscopy Environment Consortium, 20 November 2020. This edition of the specification is [https://ngff.openmicroscopy.org/0.3/](https://ngff.openmicroscopy.org/0.3/]). The latest edition is available at [https://ngff.openmicroscopy.org/latest/](https://ngff.openmicroscopy.org/latest/). [(doi:10.5281/zenodo.4282107)](https://doi.org/10.5281/zenodo.4282107) diff --git a/0.4/index.bs b/0.4/index.bs index 065a79cb..a8cc6760 100644 --- a/0.4/index.bs +++ b/0.4/index.bs @@ -13,9 +13,9 @@ Local Boilerplate: header yes Local Boilerplate: copyright yes Boilerplate: style-darkmode off Markup Shorthands: markdown yes -Editor: Josh Moore, University of Dundee (UoD) https://www.dundee.ac.uk, https://orcid.org/0000-0003-4028-811X -Editor: Sébastien Besson, University of Dundee (UoD) https://www.dundee.ac.uk, https://orcid.org/0000-0001-8783-1429 -Editor: Constantin Pape, European Molecular Biology Laboratory (EMBL) https://www.embl.org/sites/heidelberg/, https://orcid.org/0000-0001-6562-7187 +Author: Josh Moore, University of Dundee (UoD) https://www.dundee.ac.uk, https://orcid.org/0000-0003-4028-811X +Author: Sébastien Besson, University of Dundee (UoD) https://www.dundee.ac.uk, https://orcid.org/0000-0001-8783-1429 +Author: Constantin Pape, European Molecular Biology Laboratory (EMBL) https://www.embl.org/sites/heidelberg/, https://orcid.org/0000-0001-6562-7187 Abstract: This document contains next-generation file format (NGFF) Abstract: specifications for storing bioimaging data in the cloud. Abstract: All specifications are submitted to the https://image.sc community for review. @@ -657,7 +657,7 @@ Citing {#citing} ================ [Next-generation file format (NGFF) specifications for storing bioimaging data in the cloud.](https://ngff.openmicroscopy.org/0.4) -J. Moore, *et al*. Editors. Open Microscopy Environment Consortium, 8 February 2022. +J. Moore, *et al*. Open Microscopy Environment Consortium, 8 February 2022. This edition of the specification is [https://ngff.openmicroscopy.org/0.4/](https://ngff.openmicroscopy.org/0.4/]). The latest edition is available at [https://ngff.openmicroscopy.org/latest/](https://ngff.openmicroscopy.org/latest/). [(doi:10.5281/zenodo.4282107)](https://doi.org/10.5281/zenodo.4282107) diff --git a/latest/index.bs b/latest/index.bs index d1672042..834c7d89 100644 --- a/latest/index.bs +++ b/latest/index.bs @@ -13,9 +13,9 @@ Local Boilerplate: header yes Local Boilerplate: copyright yes Boilerplate: style-darkmode off Markup Shorthands: markdown yes -Editor: Josh Moore, University of Dundee (UoD) https://www.dundee.ac.uk, https://orcid.org/0000-0003-4028-811X -Editor: Sébastien Besson, University of Dundee (UoD) https://www.dundee.ac.uk, https://orcid.org/0000-0001-8783-1429 -Editor: Constantin Pape, European Molecular Biology Laboratory (EMBL) https://www.embl.org/sites/heidelberg/, https://orcid.org/0000-0001-6562-7187 +Author: Josh Moore, University of Dundee (UoD) https://www.dundee.ac.uk, https://orcid.org/0000-0003-4028-811X +Author: Sébastien Besson, University of Dundee (UoD) https://www.dundee.ac.uk, https://orcid.org/0000-0001-8783-1429 +Author: Constantin Pape, European Molecular Biology Laboratory (EMBL) https://www.embl.org/sites/heidelberg/, https://orcid.org/0000-0001-6562-7187 Text Macro: NGFFVERSION 0.5-dev Abstract: This document contains next-generation file format (NGFF) Abstract: specifications for storing bioimaging data in the cloud. @@ -609,7 +609,7 @@ Citing {#citing} ================ [Next-generation file format (NGFF) specifications for storing bioimaging data in the cloud.](https://ngff.openmicroscopy.org/0.4) -J. Moore, *et al*. Editors. Open Microscopy Environment Consortium, 8 February 2022. +J. Moore, *et al*. Open Microscopy Environment Consortium, 8 February 2022. This edition of the specification is [https://ngff.openmicroscopy.org/0.4/](https://ngff.openmicroscopy.org/0.4/]). The latest edition is available at [https://ngff.openmicroscopy.org/latest/](https://ngff.openmicroscopy.org/latest/). [(doi:10.5281/zenodo.4282107)](https://doi.org/10.5281/zenodo.4282107) From 8cd4b57763fde7a15e761fe6aa7bf90affc0a82b Mon Sep 17 00:00:00 2001 From: Josh Moore Date: Wed, 13 Mar 2024 09:59:09 +0100 Subject: [PATCH 05/11] Prefix custom bikeshed field --- 0.1/index.bs | 4 ++-- 0.3/index.bs | 6 +++--- 0.4/index.bs | 6 +++--- latest/index.bs | 6 +++--- 4 files changed, 11 insertions(+), 11 deletions(-) diff --git a/0.1/index.bs b/0.1/index.bs index 3d14ff7d..535b706b 100644 --- a/0.1/index.bs +++ b/0.1/index.bs @@ -12,8 +12,8 @@ Local Boilerplate: header yes Local Boilerplate: copyright yes Boilerplate: style-darkmode off Markup Shorthands: markdown yes -Author: Josh Moore, Open Microscopy Environment (OME) https://www.openmicroscopy.org -Author: Sébastien Besson, Open Microscopy Environment (OME) https://www.openmicroscopy.org +!Author: Josh Moore, Open Microscopy Environment (OME) https://www.openmicroscopy.org +!Author: Sébastien Besson, Open Microscopy Environment (OME) https://www.openmicroscopy.org Abstract: This document contains next-generation file format (NGFF) Abstract: specifications for storing bioimaging data in the cloud. Abstract: All specifications are submitted to the https://image.sc community for review. diff --git a/0.3/index.bs b/0.3/index.bs index 48da447e..542ee397 100644 --- a/0.3/index.bs +++ b/0.3/index.bs @@ -12,9 +12,9 @@ Local Boilerplate: header yes Local Boilerplate: copyright yes Boilerplate: style-darkmode off Markup Shorthands: markdown yes -Author: Josh Moore, Open Microscopy Environment (OME) https://www.openmicroscopy.org -Author: Sébastien Besson, Open Microscopy Environment (OME) https://www.openmicroscopy.org -Author: Constantin Pape, European Molecular Biology Laboratory (EMBL) https://www.embl.org/sites/heidelberg/ +!Author: Josh Moore, Open Microscopy Environment (OME) https://www.openmicroscopy.org +!Author: Sébastien Besson, Open Microscopy Environment (OME) https://www.openmicroscopy.org +!Author: Constantin Pape, European Molecular Biology Laboratory (EMBL) https://www.embl.org/sites/heidelberg/ Abstract: This document contains next-generation file format (NGFF) Abstract: specifications for storing bioimaging data in the cloud. Abstract: All specifications are submitted to the https://image.sc community for review. diff --git a/0.4/index.bs b/0.4/index.bs index a8cc6760..b2c8c9e3 100644 --- a/0.4/index.bs +++ b/0.4/index.bs @@ -13,9 +13,9 @@ Local Boilerplate: header yes Local Boilerplate: copyright yes Boilerplate: style-darkmode off Markup Shorthands: markdown yes -Author: Josh Moore, University of Dundee (UoD) https://www.dundee.ac.uk, https://orcid.org/0000-0003-4028-811X -Author: Sébastien Besson, University of Dundee (UoD) https://www.dundee.ac.uk, https://orcid.org/0000-0001-8783-1429 -Author: Constantin Pape, European Molecular Biology Laboratory (EMBL) https://www.embl.org/sites/heidelberg/, https://orcid.org/0000-0001-6562-7187 +!Author: Josh Moore, University of Dundee (UoD) https://www.dundee.ac.uk, https://orcid.org/0000-0003-4028-811X +!Author: Sébastien Besson, University of Dundee (UoD) https://www.dundee.ac.uk, https://orcid.org/0000-0001-8783-1429 +!Author: Constantin Pape, European Molecular Biology Laboratory (EMBL) https://www.embl.org/sites/heidelberg/, https://orcid.org/0000-0001-6562-7187 Abstract: This document contains next-generation file format (NGFF) Abstract: specifications for storing bioimaging data in the cloud. Abstract: All specifications are submitted to the https://image.sc community for review. diff --git a/latest/index.bs b/latest/index.bs index 834c7d89..61a09a5a 100644 --- a/latest/index.bs +++ b/latest/index.bs @@ -13,9 +13,9 @@ Local Boilerplate: header yes Local Boilerplate: copyright yes Boilerplate: style-darkmode off Markup Shorthands: markdown yes -Author: Josh Moore, University of Dundee (UoD) https://www.dundee.ac.uk, https://orcid.org/0000-0003-4028-811X -Author: Sébastien Besson, University of Dundee (UoD) https://www.dundee.ac.uk, https://orcid.org/0000-0001-8783-1429 -Author: Constantin Pape, European Molecular Biology Laboratory (EMBL) https://www.embl.org/sites/heidelberg/, https://orcid.org/0000-0001-6562-7187 +!Author: Josh Moore, University of Dundee (UoD) https://www.dundee.ac.uk, https://orcid.org/0000-0003-4028-811X +!Author: Sébastien Besson, University of Dundee (UoD) https://www.dundee.ac.uk, https://orcid.org/0000-0001-8783-1429 +!Author: Constantin Pape, European Molecular Biology Laboratory (EMBL) https://www.embl.org/sites/heidelberg/, https://orcid.org/0000-0001-6562-7187 Text Macro: NGFFVERSION 0.5-dev Abstract: This document contains next-generation file format (NGFF) Abstract: specifications for storing bioimaging data in the cloud. From b87c1ccd3ee8f5a5178d8bfdc91ac11734356e9f Mon Sep 17 00:00:00 2001 From: Josh Moore Date: Wed, 13 Mar 2024 10:20:01 +0100 Subject: [PATCH 06/11] Revert to 'Editor:' in header --- 0.1/index.bs | 4 ++-- 0.3/index.bs | 6 +++--- 0.4/index.bs | 6 +++--- latest/index.bs | 6 +++--- 4 files changed, 11 insertions(+), 11 deletions(-) diff --git a/0.1/index.bs b/0.1/index.bs index 535b706b..7cb79539 100644 --- a/0.1/index.bs +++ b/0.1/index.bs @@ -12,8 +12,8 @@ Local Boilerplate: header yes Local Boilerplate: copyright yes Boilerplate: style-darkmode off Markup Shorthands: markdown yes -!Author: Josh Moore, Open Microscopy Environment (OME) https://www.openmicroscopy.org -!Author: Sébastien Besson, Open Microscopy Environment (OME) https://www.openmicroscopy.org +Editor: Josh Moore, Open Microscopy Environment (OME) https://www.openmicroscopy.org +Editor: Sébastien Besson, Open Microscopy Environment (OME) https://www.openmicroscopy.org Abstract: This document contains next-generation file format (NGFF) Abstract: specifications for storing bioimaging data in the cloud. Abstract: All specifications are submitted to the https://image.sc community for review. diff --git a/0.3/index.bs b/0.3/index.bs index 542ee397..ed424f62 100644 --- a/0.3/index.bs +++ b/0.3/index.bs @@ -12,9 +12,9 @@ Local Boilerplate: header yes Local Boilerplate: copyright yes Boilerplate: style-darkmode off Markup Shorthands: markdown yes -!Author: Josh Moore, Open Microscopy Environment (OME) https://www.openmicroscopy.org -!Author: Sébastien Besson, Open Microscopy Environment (OME) https://www.openmicroscopy.org -!Author: Constantin Pape, European Molecular Biology Laboratory (EMBL) https://www.embl.org/sites/heidelberg/ +Editor: Josh Moore, Open Microscopy Environment (OME) https://www.openmicroscopy.org +Editor: Sébastien Besson, Open Microscopy Environment (OME) https://www.openmicroscopy.org +Editor: Constantin Pape, European Molecular Biology Laboratory (EMBL) https://www.embl.org/sites/heidelberg/ Abstract: This document contains next-generation file format (NGFF) Abstract: specifications for storing bioimaging data in the cloud. Abstract: All specifications are submitted to the https://image.sc community for review. diff --git a/0.4/index.bs b/0.4/index.bs index b2c8c9e3..0cc02bac 100644 --- a/0.4/index.bs +++ b/0.4/index.bs @@ -13,9 +13,9 @@ Local Boilerplate: header yes Local Boilerplate: copyright yes Boilerplate: style-darkmode off Markup Shorthands: markdown yes -!Author: Josh Moore, University of Dundee (UoD) https://www.dundee.ac.uk, https://orcid.org/0000-0003-4028-811X -!Author: Sébastien Besson, University of Dundee (UoD) https://www.dundee.ac.uk, https://orcid.org/0000-0001-8783-1429 -!Author: Constantin Pape, European Molecular Biology Laboratory (EMBL) https://www.embl.org/sites/heidelberg/, https://orcid.org/0000-0001-6562-7187 +Editor: Josh Moore, University of Dundee (UoD) https://www.dundee.ac.uk, https://orcid.org/0000-0003-4028-811X +Editor: Sébastien Besson, University of Dundee (UoD) https://www.dundee.ac.uk, https://orcid.org/0000-0001-8783-1429 +Editor: Constantin Pape, European Molecular Biology Laboratory (EMBL) https://www.embl.org/sites/heidelberg/, https://orcid.org/0000-0001-6562-7187 Abstract: This document contains next-generation file format (NGFF) Abstract: specifications for storing bioimaging data in the cloud. Abstract: All specifications are submitted to the https://image.sc community for review. diff --git a/latest/index.bs b/latest/index.bs index 61a09a5a..9d633d1f 100644 --- a/latest/index.bs +++ b/latest/index.bs @@ -13,9 +13,9 @@ Local Boilerplate: header yes Local Boilerplate: copyright yes Boilerplate: style-darkmode off Markup Shorthands: markdown yes -!Author: Josh Moore, University of Dundee (UoD) https://www.dundee.ac.uk, https://orcid.org/0000-0003-4028-811X -!Author: Sébastien Besson, University of Dundee (UoD) https://www.dundee.ac.uk, https://orcid.org/0000-0001-8783-1429 -!Author: Constantin Pape, European Molecular Biology Laboratory (EMBL) https://www.embl.org/sites/heidelberg/, https://orcid.org/0000-0001-6562-7187 +Editor: Josh Moore, University of Dundee (UoD) https://www.dundee.ac.uk, https://orcid.org/0000-0003-4028-811X +Editor: Sébastien Besson, University of Dundee (UoD) https://www.dundee.ac.uk, https://orcid.org/0000-0001-8783-1429 +Editor: Constantin Pape, European Molecular Biology Laboratory (EMBL) https://www.embl.org/sites/heidelberg/, https://orcid.org/0000-0001-6562-7187 Text Macro: NGFFVERSION 0.5-dev Abstract: This document contains next-generation file format (NGFF) Abstract: specifications for storing bioimaging data in the cloud. From 79d6743c6bd02b388dd5889f026bfa0e0c7cc8ec Mon Sep 17 00:00:00 2001 From: Josh Moore Date: Wed, 13 Mar 2024 10:45:27 +0100 Subject: [PATCH 07/11] Move to single editor per RFC-1 --- latest/index.bs | 2 -- 1 file changed, 2 deletions(-) diff --git a/latest/index.bs b/latest/index.bs index 9d633d1f..26e27b3c 100644 --- a/latest/index.bs +++ b/latest/index.bs @@ -14,8 +14,6 @@ Local Boilerplate: copyright yes Boilerplate: style-darkmode off Markup Shorthands: markdown yes Editor: Josh Moore, University of Dundee (UoD) https://www.dundee.ac.uk, https://orcid.org/0000-0003-4028-811X -Editor: Sébastien Besson, University of Dundee (UoD) https://www.dundee.ac.uk, https://orcid.org/0000-0001-8783-1429 -Editor: Constantin Pape, European Molecular Biology Laboratory (EMBL) https://www.embl.org/sites/heidelberg/, https://orcid.org/0000-0001-6562-7187 Text Macro: NGFFVERSION 0.5-dev Abstract: This document contains next-generation file format (NGFF) Abstract: specifications for storing bioimaging data in the cloud. From b072ae3945f8bf79639c4ac62207e62dcb1e2aeb Mon Sep 17 00:00:00 2001 From: Josh Moore Date: Wed, 13 Mar 2024 10:52:52 +0100 Subject: [PATCH 08/11] Fix link to comment --- rfc/1/index.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/rfc/1/index.md b/rfc/1/index.md index 7e2dabd3..114e14fd 100644 --- a/rfc/1/index.md +++ b/rfc/1/index.md @@ -13,7 +13,7 @@ This RFC is currently under review (D4). | Virginia Scarlett, _et al._ | | Janelia | 2024-02-26 | Review requested | | Kevin Yamauchi, Virginie Uhlmann | | ETH, BiovisionCenter | 2024-03-05 | Review requested | | Matthew Hartley | | EMBL-EBI | 2024-03-05 | Review requested | -| Wouter-Michiel Vierdag, Luca Marconato | melonora, LucaMarconato | EMBL | 2024-01-13 | [Comment](comment_1.html) | +| Wouter-Michiel Vierdag, Luca Marconato | melonora, LucaMarconato | EMBL | 2024-01-13 | [Comment](./comment_1.html) | ## Overview From 96a94981d9a5361cb967df7afc75d4ae06f6c238 Mon Sep 17 00:00:00 2001 From: Josh Moore Date: Wed, 13 Mar 2024 10:57:03 +0100 Subject: [PATCH 09/11] Formatting for comment 1 --- rfc/1/comment_1.md | 19 ++++++++++++------- 1 file changed, 12 insertions(+), 7 deletions(-) diff --git a/rfc/1/comment_1.md b/rfc/1/comment_1.md index 7cf729a2..1d5d8cbc 100644 --- a/rfc/1/comment_1.md +++ b/rfc/1/comment_1.md @@ -1,8 +1,12 @@ -# RFC 1 -*Review to RFC 1 from @LucaMarconato and @melonora.* +# Comment to [RFC 1](../1) from @LucaMarconato and @melonora.* + +| Name | GitHub Handle | Institution | +|------------------------|---------------|----------------------| +| Wouter-Michiel Vierdag | melonora | EMBL | +| Luca Marconato | LucaMarconato | EMBL | + +## Comments on implementations -## Comments -### Comments on implementations - Currently diagram does not reflect text. Text says *"If sufficient endorsements, including two in-progress implementations, are available, then the RFC can progress (S1) to the SPEC phase below."*. The "code" checks are not visible in the diagram which could make someone think that implementation is only of importance at the end of the RFC @@ -38,11 +42,12 @@ based on this example in which case the comment would have the status of address author I would prefer the meaning "the review process lasts maximum 4 weeks", while as a reviewer I would prefer "I have up to 4 weeks to submit the review". -### Typos/minor edits +## Typos/minor edits + - This sentence under section 'Stakeholders' paragraph 2 is truncated: "However, once the draft has reached a certain stage that it is ready for comments, Editors will merge it as a record of the fact that the suggestion." -### Consistency between the diagram and text description +## Consistency between the diagram and text description - The sentence "However, once the draft has reached a certain stage that it is ready for comments, Editors will merge it as a record of the fact that the suggestion." seems not to be reflected in the diagram. @@ -52,4 +57,4 @@ already in the RFC phase. - Related to above, we suggest to use the same wording in the diagram and in the text: for instance the "RFC persists" wording is not present in the text. - The diagram doesn't contain the equivalent points for the 🕐 comments that are present in the text. I would consider -unifying the clocks and the traffic lights. \ No newline at end of file +unifying the clocks and the traffic lights. From 047a96de3bda7b14be21b5879554183af386b7f9 Mon Sep 17 00:00:00 2001 From: Josh Moore Date: Wed, 24 Apr 2024 17:11:00 +0200 Subject: [PATCH 10/11] Add Matt's comment from #222 --- rfc/1/comment_2.md | 61 ++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 61 insertions(+) create mode 100644 rfc/1/comment_2.md diff --git a/rfc/1/comment_2.md b/rfc/1/comment_2.md new file mode 100644 index 00000000..647a7dee --- /dev/null +++ b/rfc/1/comment_2.md @@ -0,0 +1,61 @@ +# Comment to [RFC 1](../1) from @thewtex + +| Name | GitHub Handle | Institution | +|------------------------|---------------|----------------------| +| Matt McCormick | thewtex | ITK | + +## Comments from the original issue + +Wow, spectacular @joshmoore ! + +I love :heart_eyes: : + +- The well-defined process! +- Building on the process of arguably the most successful and impactful efforts for interoperability, the internet. +- Multiple stages for incremental evolution and improvements. +- A process that promotes a "defaults to yes" as opposed to "defaults to no" so we can progress and effort is not wasted. +- Artifacts that result in a clear record of what has been proposed and discussed. +- The diagram that provides a succinct high-level overview. +- The time limits at stages. +- A recognition in the process that full consensus is not what will allow the community to move forward, which is what we all really want. +- The process essentially utilizes the same GitHub pull request-based system, but formalizes the phases and content, and ensures drafts and reviews and responses are more easily navigated. + +Regarding possible areas of improvement, there are a few tweaks we could make +to have the intended effect. In particular, I am thinking of dynamics common in +specification development where: + +- Changes are prematurely or unjustifiably suppressed because reviewers do not personally have interest in or and understanding of the change. +- Strong-willed, arm-chair speculation on how a change should work without experience in implementation or usage. +- Overly complex proposals that are difficult to implement. +- Changes are rejected too early in an incubation stage. + +Another successful community process to cite that I think has lessons to learn +from, also a W3C project, is the [WebAssembly +process](https://github.com/WebAssembly/meetings/blob/main/process/phases.md). + +In particular, I think it is helpful to specify expectations on different +degrees of implementations throughout the process. As we know, speculation on +what should work well or how it should work is often clarified or modified +during implementation and usage. There is also an iterative, evolutionary +process to a final specification and implementation for good specifications. It +is also helpful to clarify the specifics of a proposal to reviewers with a +concrete example. And concerns about the impact of the complexity of a change +on practical deployment are often resolved with reference implementation(s). By +evolving an implementation with the spec, even if the implementation lags a +bit, this helps avoid inconsistencies, which can be problematic even if it is +just schema / documentation inconsistencies. + +The following changes could help address these issues with this in mind: + +1. Reserve input from Reviewers and Commenters until a spec has gone into the + RFC stage (I am afraid we may not see a practical difference with the status + quo otherwise). +2. Before exiting the DRAFT phase, request some *partial* implementation + reference to link to. +3. Before exiting the RFC phase, a *full* implementation with a *test suite* is + required. +4. Before entering the SPEC adopted status, there must be at least two + implementations for the spec in the community. + +*Editor's note: See https://github.com/ome/ngff/pull/222 for the further +discussion of these issues.* From f8fb94ab6d41c6a057828527fe51ee7e32254c05 Mon Sep 17 00:00:00 2001 From: Josh Moore Date: Wed, 24 Apr 2024 17:20:56 +0200 Subject: [PATCH 11/11] Update rfc 1 status and changelog --- rfc/1/index.md | 23 +++++++++++++++-------- 1 file changed, 15 insertions(+), 8 deletions(-) diff --git a/rfc/1/index.md b/rfc/1/index.md index 114e14fd..edac9a11 100644 --- a/rfc/1/index.md +++ b/rfc/1/index.md @@ -5,15 +5,16 @@ Definition of the NGFF RFC process ## Status -This RFC is currently under review (D4). +This RFC is currently being responded to (R4). -| Name | GitHub Handle | Institution | Date | Status | -|----------------------------------------|-------------------------|----------------------|------------|---------------------------| -| Josh Moore | joshmoore | German BioImaging | 2023-12-23 | Author | -| Virginia Scarlett, _et al._ | | Janelia | 2024-02-26 | Review requested | -| Kevin Yamauchi, Virginie Uhlmann | | ETH, BiovisionCenter | 2024-03-05 | Review requested | -| Matthew Hartley | | EMBL-EBI | 2024-03-05 | Review requested | -| Wouter-Michiel Vierdag, Luca Marconato | melonora, LucaMarconato | EMBL | 2024-01-13 | [Comment](./comment_1.html) | +| Name | GitHub Handle | Institution | Date | Status | +| ---------------------------------------- | ------------------------- | ---------------------- | ------------ | --------------------------------------------------- | +| Josh Moore | joshmoore | German BioImaging | 2023-12-23 | Author ([PR](https://github.com/ome/ngff/pull/222)) | +| Virginia Scarlett, _et al._ | | Janelia | 2024-02-26 | [Review](./review_2.html) | +| Kevin Yamauchi, Virginie Uhlmann | | ETH, BiovisionCenter | 2024-03-05 | [Review](./review_1.html) | +| Matthew Hartley | | EMBL-EBI | 2024-03-05 | [Review](./review_3.html) | +| Wouter-Michiel Vierdag, Luca Marconato | melonora, LucaMarconato | EMBL | 2024-01-13 | [Comment](./comment_1.html) | +| Matt McCormick | thewtex | ITK | 2024-01-09 | [Comment](./comment_2.html) | ## Overview @@ -538,6 +539,12 @@ Definitions for terms used throughout this RFC have been collected below. * ZEP ("Zarr Enhancement Proposal") Decision-making process for the Zarr specification +## Changelog + +| Date | Description | Link | +| ---------- | --------------------------------------- | --------------------------------------- | +| 2024-04-24 | Apply changes from comment 1 | | + [dia]: diagram.png [tmpl]: template.md [iab]: https://www.ietf.org/about/groups/iab/