Merge pull request #2775 from chriswyatt1/main

Minor fix (NOTE in list)
nf-core · Oct 17, 2024 · ace587d · ace587d
2 parents 7665fbc + 11f9199
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diff --git a/sites/docs/src/content/docs/checklists/pipeline_release.md b/sites/docs/src/content/docs/checklists/pipeline_release.md
@@ -10,63 +10,62 @@ markdownPlugin: checklist
 If this is your first release, make sure to follow the [first release tutorial](/docs/tutorials/adding_a_pipeline/first_release) for extra review requirements!
 :::
 
-1. [ ] Check the pipeline follows [nf-core guidelines](/docs/guidelines/pipelines/overview).
-2. [ ] All continuous-integration tests on the `dev` branch should be passing
-   - [ ] Check the output of `nf-core pipelines lint` for warnings and address all that you can
-   - [ ] Update any software dependencies that are out of date.
-         The linting will warn about available updates via automated API calls to (bio-)conda
-3. [ ] Check that there are no outstanding issues that need to be addressed, especially bug reports.
-4. [ ] Finalize the description of the pipeline in the GitHub repository and ensure that you remove any "under development" labels in the description. This wording will be used when a new pipeline gets announced on Twitter.
-5. [ ] If there is a [release milestone](https://help.github.com/en/github/managing-your-work-on-github/about-milestones),
-       have a look and see if all issues are closed, or can be resolved
-   - [ ] It's fine to decide that some things should be postponed until the next release - just move them on to the next milestone
+- [ ] Check the pipeline follows [nf-core guidelines](/docs/guidelines/pipelines/overview).
+- [ ] All continuous-integration tests on the `dev` branch should be passing
+  - [ ] Check the output of `nf-core pipelines lint` for warnings and address all that you can
+  - [ ] Update any software dependencies that are out of date.
+        The linting will warn about available updates via automated API calls to (bio-)conda
+- [ ] Check that there are no outstanding issues that need to be addressed, especially bug reports.
+- [ ] Finalize the description of the pipeline in the GitHub repository and ensure that you remove any "under development" labels in the description. This wording will be used when a new pipeline gets announced on Twitter.
+- [ ] If there is a [release milestone](https://help.github.com/en/github/managing-your-work-on-github/about-milestones), have a look and see if all issues are closed, or can be resolved
+  - [ ] It's fine to decide that some things should be postponed until the next release - just move them on to the next milestone
 
 ## Steps to release
 
-1. [ ] On your fork, bump the version number of the `dev` branch to a release version
-   - [ ] For example, `1.0.0dev` becomes `1.0.0`
-   - [ ] Use the `nf-core pipelines bump-version` command to make the changes, eg: navigate to the pipeline directory and run `nf-core pipelines bump-version 1.0.0`
-   - [ ] Please make sure to use strictly numeric release numbers
-   - [ ] Use [Semantic Versioning](https://semver.org/)
-   - [ ] Make sure to update the version in any pipeline diagrams and other figures
-2. [ ] Run `nf-core pipelines lint --release` and check that there are no test failures for release.
-3. [ ] Check that `CHANGELOG.md` includes everything that has been added/fixed in this release, update the version number above the changes, and optionally add a human-readable release name (e.g. using a [code name generator](http://www.codenamegenerator.com/))
-   - [ ] We recommend you also add the GitHub handle of the main contributors of each CHANGELOG entry (author, and significant reviewers etc.). This will mean each release on GitHub will display each contributors icons for extra visibility and recognition.
-4. [ ] [Open a Pull Request (PR)](https://help.github.com/en/articles/creating-a-pull-request) with these changes from your fork to the `dev` branch on the nf-core repository.
-5. [ ] Once merged, open another PR from the nf-core `dev` branch to the nf-core `master`
-   - [ ] Make sure that all of the CI tests are passing - this is a special case PR and the tests are different
-   - [ ] Request PR reviews from at least two people
-   - [ ] Once approved by two reviewers, merge your PR into `master`
-   - [ ] And finally delete any label of types: "under development", "under construction" or variants of these
-6. [ ] If this is a first release, ask a core team member to activate the Zenodo functionality for this repository, which will be used to generate a DOI.
-7. [ ] Go to GitHub and [create a new release for your pipeline](https://help.github.com/en/articles/creating-releases)
-       :::note
-       Use _exactly_ the same version as in the code (e.g. `1.0.0`) - **do not prefix with v** (e.g. not `v1.0.0`).
-       :::
-   - [ ] Optional: Also include your [nice code name](http://www.codenamegenerator.com/) in your pipeline release title (see above with `CHANGELOG.md`)
-         For example releases in nf-core/rnaseq follow the pattern: - Prefix = Metal - Dictionary = Animals - Suffix = Don't use a suffix
-8. [ ] Celebrate! But not too much - you still have a few things left to do...
+- [ ] On your fork, bump the version number of the `dev` branch to a release version
+  - [ ] For example, `1.0.0dev` becomes `1.0.0`
+  - [ ] Use the `nf-core pipelines bump-version` command to make the changes, eg: navigate to the pipeline directory and run `nf-core pipelines bump-version 1.0.0`
+  - [ ] Please make sure to use strictly numeric release numbers
+  - [ ] Use [Semantic Versioning](https://semver.org/)
+  - [ ] Make sure to update the version in any pipeline diagrams and other figures
+- [ ] Run `nf-core pipelines lint --release` and check that there are no test failures for release.
+- [ ] Check that `CHANGELOG.md` includes everything that has been added/fixed in this release, update the version number above the changes, and optionally add a human-readable release name (e.g. using a [code name generator](http://www.codenamegenerator.com/))
+  - [ ] We recommend you also add the GitHub handle of the main contributors of each CHANGELOG entry (author, and significant reviewers etc.). This will mean each release on GitHub will display each contributors icons for extra visibility and recognition.
+- [ ] [Open a Pull Request (PR)](https://help.github.com/en/articles/creating-a-pull-request) with these changes from your fork to the `dev` branch on the nf-core repository.
+- [ ] Once merged, open another PR from the nf-core `dev` branch to the nf-core `master`
+  - [ ] Make sure that all of the CI tests are passing - this is a special case PR and the tests are different
+  - [ ] Request PR reviews from at least two people
+  - [ ] Once approved by two reviewers, merge your PR into `master`
+  - [ ] And finally delete any label of types: "under development", "under construction" or variants of these
+- [ ] If this is a first release, ask a core team member to activate the Zenodo functionality for this repository, which will be used to generate a DOI.
+- [ ] Go to GitHub and [create a new release for your pipeline](https://help.github.com/en/articles/creating-releases)
+      :::note
+      Use _exactly_ the same version as in the code (e.g. `1.0.0`) - **do not prefix with v** (e.g. not `v1.0.0`).
+      :::
+  - [ ] Optional: Also include your [nice code name](http://www.codenamegenerator.com/) in your pipeline release title (see above with `CHANGELOG.md`)
+        For example releases in nf-core/rnaseq follow the pattern: - Prefix = Metal - Dictionary = Animals - Suffix = Don't use a suffix
+- [ ] Celebrate! But not too much - you still have a few things left to do...
 
 ### Automated events
 
 A number of events are automatically triggered after the pipeline is released:
 
-1. [ ] The [nf-core website](https://nf-co.re/pipelines) will be updated automatically with the release information.
-2. [ ] The [`@nf_core` twitter account](https://twitter.com/nf_core) will send out an automated tweet about the pipeline release within minutes.
-3. [ ] A [Zenodo DOI](https://zenodo.org/) is automatically generated that provides a persistent means with which to cite the pipeline.
+- [ ] The [nf-core website](https://nf-co.re/pipelines) will be updated automatically with the release information.
+- [ ] The [`@nf_core` twitter account](https://twitter.com/nf_core) will send out an automated tweet about the pipeline release within minutes.
+- [ ] A [Zenodo DOI](https://zenodo.org/) is automatically generated that provides a persistent means with which to cite the pipeline.
 
 ## After release
 
 The last step is to bump up the pipeline version number in the development branch:
 
-1. [ ] Make sure the dev branch on your fork is up to date
-2. [ ] On a new branch, bump to a new `dev` version
-   - [ ] For example, `1.0.0` becomes `1.1.0dev`
-   - [ ] Use the `nf-core pipelines bump-version` command to make the changes, eg: navigate to the pipeline directory and run `nf-core pipelines bump-version 1.1.0dev`
-3. [ ] Update the `CHANGELOG.md` to include a new section for this new version
-4. [ ] [Open a Pull Request (PR)](https://help.github.com/en/articles/creating-a-pull-request) with these changes from your fork to the `dev` branch on the nf-core repository.
-5. [ ] (first release only) After the first release of the pipeline you will need to add the DOI manually into the main `README.md` for the pipeline:
-   - [ ] Search for your pipeline on Zenodo and find the DOI that allows you to _"Cite all versions"_ of the pipeline.
-   - [ ] Ask a core member to copy the DOI information you added to dev via the PR above to the master branch. The core member will uncomment the Zenodo-related `TODO` statement in the `Citation` section of the main `README.md` and add the DOI, as well as as updating the badge for the Zenodo DOI at the top of the main `README.md` e.g. [nf-core/atacseq](https://github.com/nf-core/atacseq/blob/fa1e3f8993cd20e249b9df09d29c5498eff311d2/README.md).
-6. [ ] (first release only) Ask a core member to change default branch from `dev` to `master`.
-7. [ ] (publication only) If a publication of the pipeline is being prepared, recommended [nf-core guidelines](/docs/guidelines/pipelines/recommendations/publication_credit) are followed.
+- [ ] Make sure the dev branch on your fork is up to date
+- [ ] On a new branch, bump to a new `dev` version
+  - [ ] For example, `1.0.0` becomes `1.1.0dev`
+  - [ ] Use the `nf-core pipelines bump-version` command to make the changes, eg: navigate to the pipeline directory and run `nf-core pipelines bump-version 1.1.0dev`
+- [ ] Update the `CHANGELOG.md` to include a new section for this new version
+- [ ] [Open a Pull Request (PR)](https://help.github.com/en/articles/creating-a-pull-request) with these changes from your fork to the `dev` branch on the nf-core repository.
+- [ ] (first release only) After the first release of the pipeline you will need to add the DOI manually into the main `README.md` for the pipeline:
+  - [ ] Search for your pipeline on Zenodo and find the DOI that allows you to _"Cite all versions"_ of the pipeline.
+  - [ ] Ask a core member to copy the DOI information you added to dev via the PR above to the master branch. The core member will uncomment the Zenodo-related `TODO` statement in the `Citation` section of the main `README.md` and add the DOI, as well as as updating the badge for the Zenodo DOI at the top of the main `README.md` e.- [nf-core/atacseq](https://github.com/nf-core/atacseq/blob/fa1e3f8993cd20e249b9df09d29c5498eff311d2/README.md).
+- [ ] (first release only) Ask a core member to change default branch from `dev` to `master`.
+- [ ] (publication only) If a publication of the pipeline is being prepared, recommended [nf-core guidelines](/docs/guidelines/pipelines/recommendations/publication_credit) are followed.
diff --git a/sites/main-site/src/components/markdown/MarkdownWrapper.svelte b/sites/main-site/src/components/markdown/MarkdownWrapper.svelte
@@ -1,5 +1,5 @@
 <script lang="ts">
-    import { currentHeading } from '@components/store';
+    import { currentHeading, Checkboxes } from '@components/store';
     import * as icons from 'file-icons-js';
     import 'file-icons-js/css/style.css';
     import mermaid from 'mermaid';
@@ -98,6 +98,16 @@
             }
             block.prepend(icon);
         });
+
+        // Update Checkboxes store when checkboxes are clicked
+        const checkboxes = document.querySelectorAll('input[type="checkbox"]');
+        checkboxes.forEach((checkbox) => {
+            checkbox.addEventListener('change', () => {
+                const checked = Array.from(checkboxes).filter((checkbox) => (checkbox as HTMLInputElement).checked);
+
+                Checkboxes.set(checked);
+            });
+        });
     });
 </script>
 

diff --git a/sites/main-site/src/components/sidebar/ProgressIndicator.svelte b/sites/main-site/src/components/sidebar/ProgressIndicator.svelte
@@ -15,7 +15,6 @@
 
     // Calculate the circumference of the circle
     const circumference = 2 * Math.PI * (size - strokeWidth);
-
     if (onScroll) {
         onMount(() => {
             isCurrent = true;
@@ -31,9 +30,6 @@
 
 <a class="text-decoration-none" {href} data-bs-title={`${progress}% of items are checked`} data-bs-toggle="tooltip">
     <span>
-        {#if confetti && progress === 100}
-            <Confetti rounded={true} />
-        {/if}
         <svg width={size} height={size} viewBox={`0 0 ${size * 2} ${size * 2}`}>
             <!-- rotate the circle to start from the top -->
             <g transform={`rotate(-90 ${size} ${size})`}>
@@ -81,8 +77,12 @@
             >
         </svg>
     </span>
+
     {title}
 </a>
+{#if confetti && progress === 100}
+    <Confetti rounded={true} />
+{/if}
 
 <style>
     /* Define a CSS class for the circle */

diff --git a/sites/main-site/src/components/sidebar/SidebarToc.svelte b/sites/main-site/src/components/sidebar/SidebarToc.svelte
@@ -111,6 +111,7 @@
                                             size={25}
                                             strokeWidth={7}
                                             isCurrent={true}
+                                            confetti={hCheckboxes.every((check) => check.checked)}
                                         />
                                     </span>
                                 {/if}