From 9b653a4647451aa2185f54a2bdb3c81dafe23832 Mon Sep 17 00:00:00 2001 From: Kiya Govek Date: Fri, 14 Nov 2025 11:47:00 +0100 Subject: [PATCH 01/13] more info on contributing --- CONTRIBUTING.md | 13 ++++++++++++- README.md | 2 ++ 2 files changed, 14 insertions(+), 1 deletion(-) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index c28075ab..60d665ff 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -10,4 +10,15 @@ https://docs.openmicroscopy.org/contributing/ branch or `develop` * Make your commits and open a PR - \ No newline at end of file +# Contributing to this repository + +## Style Guide +This repository uses Sphinx to publish a ReadTheDocs site at https://ngff.openmicroscopy.org. + +[MyST](https://myst-parser.readthedocs.io/en/latest/) syntax can be used in addition to basic Markdown and HTML. + + +## Previews +Each PR receives a unique preview URL of the format `https://ngff--.org.readthedocs.build/` where `` is the PR number. This link is also posted to each PR by the Github actions bot in an "Automated Review URLs" comment as the "Readthedocs" link. + +Please check that your changes render correctly at this URL. New commits will automatically be live at the PR url after a few minutes. \ No newline at end of file diff --git a/README.md b/README.md index 6ae13169..81d38f6e 100644 --- a/README.md +++ b/README.md @@ -13,6 +13,8 @@ during the Sphinx build step (see conf.py). [Learn more about bikeshed](https://w3c-ccg.github.io/bikeshed_instructions.html) +More information on [contributing](./CONTRIBUTING.md) + ## Reviewing Commits on GitHub can be viewed at PR-numbered URLs provided by readthedocs. From 49592e3a7f07a77258b927f43555bce13eb3abe4 Mon Sep 17 00:00:00 2001 From: Kiya Govek Date: Fri, 14 Nov 2025 13:05:29 +0100 Subject: [PATCH 02/13] adding github button to page --- conf.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/conf.py b/conf.py index d016aada..235f636d 100644 --- a/conf.py +++ b/conf.py @@ -38,6 +38,10 @@ html_theme = "sphinx_book_theme" +html_theme_options = { + github_url = "https://github.com/ome/ngff" +} + html_static_path = ["_static"] html_css_files = [ From 5d022b82d427db0496bf37ed971cfb74e18e64de Mon Sep 17 00:00:00 2001 From: Kiya Govek Date: Fri, 14 Nov 2025 13:09:40 +0100 Subject: [PATCH 03/13] oops meant to be dict --- conf.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf.py b/conf.py index 235f636d..5cb35585 100644 --- a/conf.py +++ b/conf.py @@ -39,7 +39,7 @@ html_theme = "sphinx_book_theme" html_theme_options = { - github_url = "https://github.com/ome/ngff" + "github_url": "https://github.com/ome/ngff" } html_static_path = ["_static"] From a9c7baf3eea9f37a762a9890cf6d4f2468f81911 Mon Sep 17 00:00:00 2001 From: Kiya Govek Date: Fri, 14 Nov 2025 13:41:30 +0100 Subject: [PATCH 04/13] switching to BSD license and testing footer --- LICENSE.md | 19 +++++++++++++------ _templates/github_link.html | 1 + conf.py | 3 ++- 3 files changed, 16 insertions(+), 7 deletions(-) create mode 100644 _templates/github_link.html diff --git a/LICENSE.md b/LICENSE.md index 911bbfb1..9634cd39 100644 --- a/LICENSE.md +++ b/LICENSE.md @@ -1,8 +1,15 @@ -All Reports in this Repository are licensed by Contributors under the [W3C Software and Document -License](https://www.w3.org/Consortium/Legal/2015/copyright-software-and-document). +Copyright (C) 2005 - 2016 Open Microscopy Environment: + - Glencoe Software, Inc. + - University of Dundee + - German BioImaging e.V. +All rights reserved. -Contributions to Specifications are made under the -[W3C CLA](https://www.w3.org/community/about/agreements/cla/). +Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: -Contributions to Software, including sample implementations, are under the -[Apache 2.0 License](https://www.apache.org/licenses/LICENSE-2.0). +1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. + +2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. + +3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS “AS IS” AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. diff --git a/_templates/github_link.html b/_templates/github_link.html new file mode 100644 index 00000000..d5a12c92 --- /dev/null +++ b/_templates/github_link.html @@ -0,0 +1 @@ +
  • Edit on GitHub
    • \ No newline at end of file diff --git a/conf.py b/conf.py index 5cb35585..12c173cf 100644 --- a/conf.py +++ b/conf.py @@ -39,7 +39,8 @@ html_theme = "sphinx_book_theme" html_theme_options = { - "github_url": "https://github.com/ome/ngff" + "github_url": "https://github.com/ome/ngff", + "footer_end": ["github_link.html"] } html_static_path = ["_static"] From acb4823fb3b62b541dea965011d3430b13ceb2de Mon Sep 17 00:00:00 2001 From: Kiya Govek Date: Fri, 14 Nov 2025 14:17:31 +0100 Subject: [PATCH 05/13] reworked readme --- CONTRIBUTING.md | 1 - README.md | 67 +++++++++++-------------------------------------- 2 files changed, 15 insertions(+), 53 deletions(-) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 60d665ff..d838edc3 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -17,7 +17,6 @@ This repository uses Sphinx to publish a ReadTheDocs site at https://ngff.openmi [MyST](https://myst-parser.readthedocs.io/en/latest/) syntax can be used in addition to basic Markdown and HTML. - ## Previews Each PR receives a unique preview URL of the format `https://ngff--.org.readthedocs.build/` where `` is the PR number. This link is also posted to each PR by the Github actions bot in an "Automated Review URLs" comment as the "Readthedocs" link. diff --git a/README.md b/README.md index 81d38f6e..f0b8fc36 100644 --- a/README.md +++ b/README.md @@ -1,67 +1,30 @@ [![DOI](https://zenodo.org/badge/313652456.svg)](https://zenodo.org/badge/latestdoi/313652456) -# ome-ngff +# Contributing -[Next-generation file format (NGFF) specifications](https://ngff.openmicroscopy.org/latest/) for storing bioimaging data in the cloud. - -## Editing - -Specifications are written in markdown, or technically -[bikeshed](https://github.com/tabatkins/bikeshed) -- a markdown document, with -special extensions understood by the bikeshed tool. The bikeshed tool is run -during the Sphinx build step (see conf.py). - -[Learn more about bikeshed](https://w3c-ccg.github.io/bikeshed_instructions.html) +We welcome contributions from anyone! Create Issues and PRs on this repo for content on https://ngff.openmicroscopy.org. -More information on [contributing](./CONTRIBUTING.md) +Content can be created using Markdown, HTML, and [MyST](https://myst-parser.readthedocs.io/en/latest/) syntax. -## Reviewing +See also [CONTRIBUTING.md](./CONTRIBUTING.md) -Commits on GitHub can be viewed at PR-numbered URLs provided by readthedocs. -Additionally, bikeshed pages can be viewed using web services from the W3C: +# Specifications - * Rendered page: http://api.csswg.org/bikeshed/?url=https://raw.githubusercontent.com/ome/ngff/master/0.2/index.bs - * Diff: https://services.w3.org/htmldiff?doc1=https%3A%2F%2Fngff.openmicroscopy.org%2F0.2%2F&doc2=http%3A%2F%2Fapi.csswg.org%2Fbikeshed%2F%3Furl%3Dhttps%3A%2F%2Fraw.githubusercontent.com%2Fome%2Fngff%2Fmaster%2Flatest%2Findex.bs - -## New version - -* Make new changes to `latest/index.bs` -* Update changelog at the bottom of `latest/index.bs` -* Find references to previous version and _in most cases_, bump to the current version. +[Next-generation file format (NGFF) specifications](https://ngff.openmicroscopy.org/latest/) for storing bioimaging data in the cloud. -## JSON schemas +Specifications have been moved to [ome/ngff-spec](https://github.com/ome/ngff-spec). -For each top-level metadata key of the OME-NGFF specification, JSON schemas are maintained -for each version of the specification and stored under `$VERSION/schemas/` or `latest/schemas/`. -Tests validating these schemas must be implemented to follow principles of the -[JSON schema test suite](https://github.com/json-schema-org/JSON-Schema-Test-Suite) -and stored under `$VERSION/tests/` or `latest/tests/` to allow their execution on each CI build. +### Editing specifications -All official example snippets must also be extracted and managed as separate JSON files under -`$VERSION/examples/` or `latest/examples/`, validated by the appropriate schema by adding a -`.config.json` file specifying the JSON schema to use and included in the -specification document using the -[include-code](https://tabatkins.github.io/bikeshed/#including-code) directive. +Specifications are written in markdown, or technically +[bikeshed](https://github.com/tabatkins/bikeshed) -- a markdown document, with +special extensions understood by the bikeshed tool. The bikeshed tool is run +during the Sphinx build step (see conf.py). -The official OME-NGFF JSON schemas are published under -https://ngff.openmicroscopy.org//schemas/.schema. +# RFCs -# Release process +Requests for comments (RFCs) are used to discuss and capture high-level decisions within the NGFF community. -* For patch releases, bump the submodule for the given version. -* For minor and major versions, add a new submodule location for the version branch. -* Check and update: - - copyright.include - - the head matter in the `$VERSION`ed file - * Use: `Status: w3c/CG-FINAL` - * Update `URL: ` - * Use the following `Status Text:`: "This is the $VERSION release of this specification. - Migration scripts will be provided between numbered versions. Data written with the latest version - (an "editor's draft") will not necessarily be supported." - - update the footer matter in the `$VERSION`ed file - - Version in the citation block including release date +RFCs are contained under the `rfc` directory at the moment but may be moved out into a separate repo in the future. -# Citing -Please see https://ngff.openmicroscopy.org/latest#citing for the latest -citation. From d3f9ef640ba68b947c69cb1827d89182f0548910 Mon Sep 17 00:00:00 2001 From: Kiya Govek Date: Fri, 14 Nov 2025 14:21:07 +0100 Subject: [PATCH 06/13] attempting github as icon --- conf.py | 14 +++++++++++++- 1 file changed, 13 insertions(+), 1 deletion(-) diff --git a/conf.py b/conf.py index 12c173cf..ef5be213 100644 --- a/conf.py +++ b/conf.py @@ -40,7 +40,19 @@ html_theme_options = { "github_url": "https://github.com/ome/ngff", - "footer_end": ["github_link.html"] + "footer_end": ["github_link.html"], + "icon_links": [ + { + # Label for this link + "name": "GitHub", + # URL where the link will redirect + "url": "https://github.com/ome/ngff", # required + # Icon class (if "type": "fontawesome"), or path to local image (if "type": "local") + "icon": "fa-brands fa-square-github", + # The type of image to be used (see below for details) + "type": "fontawesome", + } + ] } html_static_path = ["_static"] From 75da5301275da44b90d5dc9d1ea2c4bf1b47331b Mon Sep 17 00:00:00 2001 From: Kiya Govek Date: Fri, 14 Nov 2025 14:24:04 +0100 Subject: [PATCH 07/13] testing edit page button --- _templates/github_link.html | 1 - conf.py | 19 +++++-------------- 2 files changed, 5 insertions(+), 15 deletions(-) delete mode 100644 _templates/github_link.html diff --git a/_templates/github_link.html b/_templates/github_link.html deleted file mode 100644 index d5a12c92..00000000 --- a/_templates/github_link.html +++ /dev/null @@ -1 +0,0 @@ -
  • Edit on GitHub
    • \ No newline at end of file diff --git a/conf.py b/conf.py index ef5be213..3af6e99c 100644 --- a/conf.py +++ b/conf.py @@ -39,20 +39,11 @@ html_theme = "sphinx_book_theme" html_theme_options = { - "github_url": "https://github.com/ome/ngff", - "footer_end": ["github_link.html"], - "icon_links": [ - { - # Label for this link - "name": "GitHub", - # URL where the link will redirect - "url": "https://github.com/ome/ngff", # required - # Icon class (if "type": "fontawesome"), or path to local image (if "type": "local") - "icon": "fa-brands fa-square-github", - # The type of image to be used (see below for details) - "type": "fontawesome", - } - ] + "use_edit_page_button": True +} + +html_context = { + "github_url": "https://github.com/ome/ngff" } html_static_path = ["_static"] From a69a860d0e278fc854c65691c251f15ab2c3db0a Mon Sep 17 00:00:00 2001 From: Kiya Govek Date: Fri, 14 Nov 2025 14:38:29 +0100 Subject: [PATCH 08/13] repo button --- CONTRIBUTING.md | 7 +++++-- conf.py | 7 +++++-- 2 files changed, 10 insertions(+), 4 deletions(-) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index d838edc3..ee873485 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -12,11 +12,14 @@ https://docs.openmicroscopy.org/contributing/ # Contributing to this repository -## Style Guide -This repository uses Sphinx to publish a ReadTheDocs site at https://ngff.openmicroscopy.org. +## Syntax +This repository uses Sphinx to publish a ReadTheDocs site at https://ngff.openmicroscopy.org in the [Sphinx Book Theme](https://sphinx-book-theme.readthedocs.io/en/stable/). [MyST](https://myst-parser.readthedocs.io/en/latest/) syntax can be used in addition to basic Markdown and HTML. +## Configuration +Edit [conf.py](./conf.py) with options from the [Sphinx Book Theme](https://sphinx-book-theme.readthedocs.io/en/stable/). + ## Previews Each PR receives a unique preview URL of the format `https://ngff--.org.readthedocs.build/` where `` is the PR number. This link is also posted to each PR by the Github actions bot in an "Automated Review URLs" comment as the "Readthedocs" link. diff --git a/conf.py b/conf.py index 3af6e99c..3c7e7e66 100644 --- a/conf.py +++ b/conf.py @@ -39,11 +39,14 @@ html_theme = "sphinx_book_theme" html_theme_options = { - "use_edit_page_button": True + "use_repository_button": True } html_context = { - "github_url": "https://github.com/ome/ngff" + "repository_url": "https://github.com/ome/ngff" + # "github_user": "ome", + # "github_repo": "ngff", + # "github_version" } html_static_path = ["_static"] From dc35f08aba0fdd61030429dfbbebd31e28aa80e0 Mon Sep 17 00:00:00 2001 From: Kiya Govek Date: Fri, 14 Nov 2025 14:41:55 +0100 Subject: [PATCH 09/13] trying with new way of specifying path --- conf.py | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/conf.py b/conf.py index 3c7e7e66..75073365 100644 --- a/conf.py +++ b/conf.py @@ -43,10 +43,9 @@ } html_context = { - "repository_url": "https://github.com/ome/ngff" - # "github_user": "ome", - # "github_repo": "ngff", - # "github_version" + "github_user": "ome", + "github_repo": "ngff", + "github_version": "main" } html_static_path = ["_static"] From 47bde05f904798156b60043b340639a3f4f48fe4 Mon Sep 17 00:00:00 2001 From: Kiya Govek Date: Fri, 14 Nov 2025 14:49:26 +0100 Subject: [PATCH 10/13] trying more config for button --- CONTRIBUTING.md | 2 +- conf.py | 2 ++ 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index ee873485..86dbd094 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -18,7 +18,7 @@ This repository uses Sphinx to publish a ReadTheDocs site at https://ngff.openmi [MyST](https://myst-parser.readthedocs.io/en/latest/) syntax can be used in addition to basic Markdown and HTML. ## Configuration -Edit [conf.py](./conf.py) with options from the [Sphinx Book Theme](https://sphinx-book-theme.readthedocs.io/en/stable/). +Edit [conf.py](./conf.py) with options from the [Sphinx Book Theme](https://sphinx-book-theme.readthedocs.io/en/stable/). The [PyData Sphinx Theme](https://pydata-sphinx-theme.readthedocs.io/en/stable/user_guide) user guide may also have more up to date instructions for configuration properties. ## Previews Each PR receives a unique preview URL of the format `https://ngff--.org.readthedocs.build/` where `` is the PR number. This link is also posted to each PR by the Github actions bot in an "Automated Review URLs" comment as the "Readthedocs" link. diff --git a/conf.py b/conf.py index 75073365..31df0bcc 100644 --- a/conf.py +++ b/conf.py @@ -43,6 +43,8 @@ } html_context = { + "repository_provider": "github", + "repository_url": "https://github.com/ome/ngff", "github_user": "ome", "github_repo": "ngff", "github_version": "main" From 96dc6eefa37144c2c36c6211ae8b59de335412f7 Mon Sep 17 00:00:00 2001 From: Kiya Govek Date: Fri, 14 Nov 2025 14:56:08 +0100 Subject: [PATCH 11/13] removing github for now --- conf.py | 12 ------------ 1 file changed, 12 deletions(-) diff --git a/conf.py b/conf.py index 31df0bcc..d016aada 100644 --- a/conf.py +++ b/conf.py @@ -38,18 +38,6 @@ html_theme = "sphinx_book_theme" -html_theme_options = { - "use_repository_button": True -} - -html_context = { - "repository_provider": "github", - "repository_url": "https://github.com/ome/ngff", - "github_user": "ome", - "github_repo": "ngff", - "github_version": "main" -} - html_static_path = ["_static"] html_css_files = [ From f6c68d7fbd4f2ef52b72077cc3f94e311ad484dc Mon Sep 17 00:00:00 2001 From: Kiya Govek Date: Fri, 14 Nov 2025 15:42:34 +0100 Subject: [PATCH 12/13] update contributing page --- contributing/index.md | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/contributing/index.md b/contributing/index.md index 59e91a3c..0ca43720 100644 --- a/contributing/index.md +++ b/contributing/index.md @@ -24,6 +24,4 @@ relevant RFC. A template is also available for formatting your comment: ## Changes to this website -Any minor fixes/improvements to these pages should be opened as an issue in the -[`ome/ngff repository`](https://github.com/ome/ngff), and be fixed/implemented -with a pull request in the [`ome/ngff` repository](https://github.com/ome/ngff). +The repository for this website is [ome/ngff](https://github.com/ome/ngff). Contributions to these pages are welcome as issues or PRs. Please read the [contributing guide](https://github.com/ome/ngff/blob/main/CONTRIBUTING.md). From 5fd91526bbbf8d2fc57e8366bfdee6e1906b11c5 Mon Sep 17 00:00:00 2001 From: Kiya Govek Date: Fri, 14 Nov 2025 15:48:47 +0100 Subject: [PATCH 13/13] added all contributors --- .all-contributorsrc | 4 ++++ README.md | 11 +++++++++++ 2 files changed, 15 insertions(+) create mode 100644 .all-contributorsrc diff --git a/.all-contributorsrc b/.all-contributorsrc new file mode 100644 index 00000000..e3488061 --- /dev/null +++ b/.all-contributorsrc @@ -0,0 +1,4 @@ +{ + "projectName": "ngff", + "projectOwner": "ome" +} \ No newline at end of file diff --git a/README.md b/README.md index f0b8fc36..d0d38d56 100644 --- a/README.md +++ b/README.md @@ -27,4 +27,15 @@ Requests for comments (RFCs) are used to discuss and capture high-level decision RFCs are contained under the `rfc` directory at the moment but may be moved out into a separate repo in the future. +# Contributors + + + + + + + + + +