Quiltcore java preview #122
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…-quilt into quiltcore-java-demo
[](https://renovatebot.com) This PR contains the following updates: | Package | Type | Update | Change | |---|---|---|---| | [actions/checkout](https://togithub.com/actions/checkout) | action | major | `v3` -> `v4` | --- ### Release Notes <details> <summary>actions/checkout (actions/checkout)</summary> ### [`v4`](https://togithub.com/actions/checkout/blob/HEAD/CHANGELOG.md#v400) [Compare Source](https://togithub.com/actions/checkout/compare/v3...v4) - [Support fetching without the --progress option](https://togithub.com/actions/checkout/pull/1067) - [Update to node20](https://togithub.com/actions/checkout/pull/1436) </details> --- ### Configuration 📅 **Schedule**: Branch creation - At any time (no schedule defined), Automerge - At any time (no schedule defined). 🚦 **Automerge**: Disabled by config. Please merge this manually once you are satisfied. ♻ **Rebasing**: Whenever PR becomes conflicted, or you tick the rebase/retry checkbox. 🔕 **Ignore**: Close this PR and you won't be reminded about this update again. --- - [ ] <!-- rebase-check -->If you want to rebase/retry this PR, check this box --- This PR has been generated by [Mend Renovate](https://www.mend.io/free-developer-tools/renovate/). View repository job log [here](https://developer.mend.io/github/quiltdata/nf-quilt). <!--renovate-debug:eyJjcmVhdGVkSW5WZXIiOiIzNi43OC44IiwidXBkYXRlZEluVmVyIjoiMzYuNzguOCIsInRhcmdldEJyYW5jaCI6Im1haW4ifQ==--> Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
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[](https://renovatebot.com) This PR contains the following updates: | Package | Change | Age | Adoption | Passing | Confidence | |---|---|---|---|---|---| | [org.slf4j:slf4j-simple](http://www.slf4j.org) ([source](https://togithub.com/qos-ch/slf4j)) | `2.0.7` -> `2.0.9` | [](https://docs.renovatebot.com/merge-confidence/) | [](https://docs.renovatebot.com/merge-confidence/) | [](https://docs.renovatebot.com/merge-confidence/) | [](https://docs.renovatebot.com/merge-confidence/) | --- ### Configuration 📅 **Schedule**: Branch creation - At any time (no schedule defined), Automerge - At any time (no schedule defined). 🚦 **Automerge**: Disabled by config. Please merge this manually once you are satisfied. ♻ **Rebasing**: Whenever PR becomes conflicted, or you tick the rebase/retry checkbox. 🔕 **Ignore**: Close this PR and you won't be reminded about this update again. --- - [ ] <!-- rebase-check -->If you want to rebase/retry this PR, check this box --- This PR has been generated by [Mend Renovate](https://www.mend.io/free-developer-tools/renovate/). View repository job log [here](https://developer.mend.io/github/quiltdata/nf-quilt). <!--renovate-debug:eyJjcmVhdGVkSW5WZXIiOiIzNi43OC44IiwidXBkYXRlZEluVmVyIjoiMzYuNzguOCIsInRhcmdldEJyYW5jaCI6Im1haW4ifQ==--> Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
wrap hash, namespace, manifest
…-quilt into quiltcore-java-demo
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@dimaryaz Are you okay with me merging this into your quiltcore-java-demo branch? Or should I merge it to master, and have you pull from there? |
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Reviewing it now, but you can merge into my branch if you want. For master, I think it's good to review everything and squash all the commits. |
dimaryaz
reviewed
Sep 8, 2023
| Manifest manifest = packageManifest() | ||
| // get names of entries | ||
| List<String> children = manifest.getEntries().keySet().collect { String key -> | ||
| if (key.startsWith(subpath)) { |
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Make sure that this handles "/" properly? I.e., that filtering for "/a" includes "/a/b", but not "/ab"?
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Can you clarify? Is a leading "/" required? Do we only require the full folder for absolute subpaths?
Specifically, what's the expected result for these subpaths when the package contains ".ipynb_checkpoints/data_products-checkpoint.ipynb"?
subpath | expected_size
'' | 8
'.ipynb_checkpoints' | 1
'/.ipynb_checkpoints' | 1
'.ipynb' | 1
'/.ipynb' | 0
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I am very confused by this. I rewrote the test to make sense for me, which is:
where:
subpath | expected_size
'' | 8
'.ipynb_checkpoints' | 1
'.ipynb_checkpoints/' | 1
'.ipynb' | 1
'.ipynb/' | 0
plugins/nf-quilt/src/main/nextflow/quilt/jep/QuiltPackage.groovy
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drernie
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that referenced
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Sep 18, 2023
commit 016c59f Author: Dima Ryazanov <[email protected]> Date: Mon Sep 18 07:16:20 2023 -0700 Bump quiltcore and use workflows commit 843d22b Author: Ernest Prabhakar <[email protected]> Date: Mon Sep 11 15:35:28 2023 -0700 re-enabled failing workflow tests commit 41d6063 Author: Dr. Ernie Prabhakar <[email protected]> Date: Mon Sep 11 15:23:07 2023 -0700 Quiltcore java preview (#122) Ernie's updates for Sep 6-11 - Added unit and integration tests - Rewrote package to NOT pre-install (instead use Manifest to find relativeChildren) --------- Co-authored-by: Dima Ryazanov <[email protected]> Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
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Ernie's updates for Sep 6