Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Update gitpod/workspace-base Docker digest to 12853f7 #3309

Merged
merged 2 commits into from
Dec 2, 2024
Merged

Update gitpod/workspace-base Docker digest to 12853f7 #3309

merged 2 commits into from
Dec 2, 2024
+2 −1

Conversation

renovate[bot]
Copy link
Contributor

@renovate renovate bot commented Dec 2, 2024

This PR contains the following updates:

Package Type Update Change
gitpod/workspace-base final digest 2cc134f -> 12853f7

Configuration

📅 Schedule: Branch creation - "before 4am on the first day of the month" (UTC), Automerge - At any time (no schedule defined).

🚦 Automerge: Enabled.

♻ Rebasing: Whenever PR is behind base branch, or you tick the rebase/retry checkbox.

🔕 Ignore: Close this PR and you won't be reminded about this update again.

  • If you want to rebase/retry this PR, check this box

This PR was generated by Mend Renovate. View the repository job log.

@renovate renovate bot enabled auto-merge (squash) December 2, 2024 03:39
@renovate renovate bot merged commit 800fd8d into dev Dec 2, 2024
88 checks passed
@renovate renovate bot deleted the renovate/gitpod-workspace-base branch December 2, 2024 05:44
jvfe added a commit to sanger-tol/nf-core-tools that referenced this pull request Dec 4, 2024
@jvfe
Merge branch 'dev' into merge-dev-third-rev
9c9c66a 
* dev: (458 commits)
  Apply suggestions from code review
  fix type error
  remove broken test
  loop over list of authors to supply contributors
  combine json parsing code
  test also the main sync function itsel
  Typo in error message.
  Update nf_core/pipeline-template/.github/CONTRIBUTING.md
  fix contributors map
  [automated] Update CHANGELOG.md
  add manifest.contributors to nextflow.config
  also add monochrome_logs if nf-schema is used
  [automated] Update CHANGELOG.md
  update modules and subworkflows
  Update gitpod/workspace-base Docker digest to 12853f7 (nf-core#3309)
  Update pre-commit hook astral-sh/ruff-pre-commit to v0.8.1
  Update dawidd6/action-download-artifact action to v7 (nf-core#3306)
  Changelog.
  Include oras:// regex in download to recognize the paths.
  Add dedicated ORAS image format error.
  ...
jvfe added a commit to sanger-tol/nf-core-tools that referenced this pull request Dec 4, 2024
@jvfe @mashehu
@nf-core-bot @renovate @mribeirodantas @mirpedrol @pinin4fjords @MatthiasZepper @mahesh-panchal @jfy133 @SPPearce @ewels @LouisLeNezet
Merge dev third rev (#20)
c0b51d7 
* write only relevant fields in `.nf-core.yml`

* switch from docstrings to Field descsriptions

* [automated] Update CHANGELOG.md

* update test to new error

* second attempt to add ro crates

* fix import

* first running version

* restructure code and add tests

* add missing dep

* add recommendations from comments

* add git contributors

* fix filename for CI

* better help hint message

* fix class name

* add correct parent directory to faked crate

* add empty ro-crate after sync

* fix tests

* fix ci test

* use github to guess author name, set names as ids if no orcid

* add bioschemas, datecreated and datemodified (only set to current time atm)

* follow `ComputationalWorkflow` schema for main entitty.

* fix date created field

* add "about" field to workflow diagram

* add input as separate entity

* add version to main entity

* fix incorrect type

* switch to add_workflow method to add main entity and add components as datasets with descriptions

* ro_crate -> rocrate

* allow mixed list and dict in lint config

* nested too deeply

* [automated] Update CHANGELOG.md

* use repo2crate to generate the main structure of the crate

* chore(deps): update dependency prompt_toolkit to <=3.0.48

* chore(deps): update pre-commit hook astral-sh/ruff-pre-commit to v0.7.0

* chore(deps): update pre-commit hook pre-commit/mirrors-mypy to v1.12.0

* [automated] Update CHANGELOG.md

* [automated] Update CHANGELOG.md

* Fix typos

* Fix typos (second round)

* Undo accidental typos fixes

* Fix typos (third round)

* Update textual snapshots

* chore(deps): update python:3.12-slim docker digest to 032c526

* [automated] Update CHANGELOG.md

* handle new nf-core.yml structure

* update documentation for `multiqc_config` linting

* parse yaml correctly

* found a better way to handle the ignore file being None

* handle new lint config structure

* add tests with different valid yaml structures

* use correct profile options for sfw test command

* [automated] Update CHANGELOG.md

* remove last traces of LintConfigType

* fix incorrect type

* more type fixes

* Update CHANGELOG.md

* add all lint tests to config

* switch all defaults to None and drop them on dump

* Update nf_core/utils.py

Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>

* Update nf_core/utils.py

* drop None values when checking for test names

* [automated] Fix code linting

* no need for Field value

* fix test_lint tests

* fix worklfow_dispatch trigger and parse more review comments

* [automated] Update CHANGELOG.md

* Update pre-commit hook pre-commit/mirrors-mypy to v1.13.0

* chore(deps): update github actions

* [automated] Update CHANGELOG.md

* remove outdated file

* Revert "Add new command `nf-core rocrate` to create a Research Object (RO) crate for a pipeline"

* move test in correct directory

* fix tests

* Add seqera containers example

* bump ci

* Modify test_find_container_images_modules() for Seqera Containers.

* Enable Seqera Containers download.

* run tests without commiting ro-crate

* add ro-crate creation to pipelines create command

* fix command import

* add rocrate to skip features

* remove schema loading, because it is not needed anymore

* update snapshots

* `modules update`: add a panel around diffs

* add `--dir/-d` option to schema commands

* [automated] Update CHANGELOG.md

* [automated] Update CHANGELOG.md

* try to fix coverage report generation

* fix test_cli

* nf-core download: Fix forgotten symlinks in cache.

* try specifying the coverage output file

* try naming the files directly

* fix variable name

* add hiddnen files for upload-artifact action v4

* group diffs by module

* Update pre-commit hook astral-sh/ruff-pre-commit to v0.7.1

* [automated] Update CHANGELOG.md

* Update GitHub Actions

* Ensure that prioritize_direct_download() retains Seqera Singularity Containers and write additional test.

* make group border blue

* make module names white

* Apply suggestions from code review

Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>

* Add resource limits to Gitpod profile

* Update changelog

* I fix typos for infrastickers

* Fix typo

* Update changelog

* Update Gitpod to use Miniforge instead of Miniconda

* Update Changelog

* Update pre-commit hook astral-sh/ruff-pre-commit to v0.7.3

* [automated] Update CHANGELOG.md

* handle new schema structure in  create-params-file

* add tests

* [automated] Update CHANGELOG.md

* add hint to solve git errors with a synced repo

* run pre-commit when testing linting the template pipeline

* [automated] Update CHANGELOG.md

* [automated] Update CHANGELOG.md

* fix template trailing spaces

* write proper path and raise a UserWarning to avoid printing the error trace

* Apply suggestions from code review

Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>

* remove logging git error from wrong place

* add option to skip .vscode from the template

* update textual snapshots

* update and fix swf patch tests

* Update pre-commit hook astral-sh/ruff-pre-commit to v0.7.4

* [automated] Update CHANGELOG.md

* Update codecov/codecov-action action to v5 (nf-core#3283)

* Update codecov/codecov-action action to v5

* [automated] Update CHANGELOG.md

---------

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
Co-authored-by: nf-core-bot <core@nf-co.re>

* Update python:3.12-slim Docker digest to 2a6386a (nf-core#3284)

* Update python:3.12-slim Docker digest to 2a6386a

* [automated] Update CHANGELOG.md

---------

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
Co-authored-by: nf-core-bot <core@nf-co.re>

* apply patch reverse when linting a patched subworkflow

* update get_patch_fn to work with subworkflows

* move modules_differ.py to components_differ.py

* add subworkflows patch missing tests

* fix subworkflows update test

* update changelog

* add help text for --remove flag

* apply code review suggestions to patch tests

* Update tests/modules/test_patch.py

* apply suggestions by @mashehu

* remove def from nextflow.config and add trace_report_suffix param

* [automated] Update CHANGELOG.md

* Update pre-commit hook astral-sh/ruff-pre-commit to v0.8.0

* [automated] Update CHANGELOG.md

* add validation.monochromeLogs to config

* ignore trace_report_suffix default check

* update snapshots

* add more tests

* enable zip output

* Move modules config import after base.config

* Update nf_core/pipelines/create/template_features.yml

* Update documentation

* Update CHANGELOG

* Update CHANGELOG.md

* Fix linting

* Update CHANGELOG

* Download: Need to deduplicate Seqera Container matches as well, otherwise a race condition emerges.

* Add new function to handle Seqera Container Oras URIs.

* Ensure, that oras:// containers are correctly handled.

* Download: Add test data for oras:// modules.

* Test the new container elimination routine.

* Download: Update the tests.

* Add dedicated ORAS image format error.

* Include oras:// regex in download to recognize the paths.

* Changelog.

* Update dawidd6/action-download-artifact action to v7 (nf-core#3306)

* Update dawidd6/action-download-artifact action to v7

* [automated] Update CHANGELOG.md

---------

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
Co-authored-by: nf-core-bot <core@nf-co.re>

* Update pre-commit hook astral-sh/ruff-pre-commit to v0.8.1

* Update gitpod/workspace-base Docker digest to 12853f7 (nf-core#3309)

* Update gitpod/workspace-base Docker digest to 12853f7

* [automated] Update CHANGELOG.md

---------

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
Co-authored-by: nf-core-bot <core@nf-co.re>

* update modules and subworkflows

* [automated] Update CHANGELOG.md

* also add monochrome_logs if nf-schema is used

* add manifest.contributors to nextflow.config

* [automated] Update CHANGELOG.md

* fix contributors map

* Update nf_core/pipeline-template/.github/CONTRIBUTING.md

Co-authored-by: Phil Ewels <phil.ewels@seqera.io>

* Typo in error message.

Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>

* test also the main sync function itsel

* combine json parsing code

* loop over list of authors to supply contributors

* remove broken test

* fix type error

* Apply suggestions from code review

Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>

---------

Co-authored-by: mashehu <mashehu3@gmail.com>
Co-authored-by: nf-core-bot <core@nf-co.re>
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
Co-authored-by: Marcel Ribeiro-Dantas <marcel.ribeirodantas@seqera.io>
Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>
Co-authored-by: Jonathan Manning <jonathan.manning@seqera.io>
Co-authored-by: Matthias Zepper <MatthiasZepper@users.noreply.github.com>
Co-authored-by: Matthias Zepper <6963520+MatthiasZepper@users.noreply.github.com>
Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
Co-authored-by: Phil Ewels <phil.ewels@seqera.io>
Co-authored-by: Louis LE NEZET <58640615+LouisLeNezet@users.noreply.github.com>
Co-authored-by: Louis Le Nezet <louislenezet@gmail.com>
Co-authored-by: LouisLeNezet <louislenezet@gmaio.com>
jvfe added a commit to sanger-tol/nf-core-tools that referenced this pull request Dec 4, 2024
@jvfe
Merge branch 'dev' into fix/1927
c9d9fa4 
* dev: (458 commits)
  Apply suggestions from code review
  fix type error
  remove broken test
  loop over list of authors to supply contributors
  combine json parsing code
  test also the main sync function itsel
  Typo in error message.
  Update nf_core/pipeline-template/.github/CONTRIBUTING.md
  fix contributors map
  [automated] Update CHANGELOG.md
  add manifest.contributors to nextflow.config
  also add monochrome_logs if nf-schema is used
  [automated] Update CHANGELOG.md
  update modules and subworkflows
  Update gitpod/workspace-base Docker digest to 12853f7 (nf-core#3309)
  Update pre-commit hook astral-sh/ruff-pre-commit to v0.8.1
  Update dawidd6/action-download-artifact action to v7 (nf-core#3306)
  Changelog.
  Include oras:// regex in download to recognize the paths.
  Add dedicated ORAS image format error.
  ...
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@mashehu mashehu mashehu approved these changes

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
2 participants
@mashehu @nf-core-bot