diff --git a/.gitpod.yml b/.gitpod.yml index d5948695b..db31d01be 100644 --- a/.gitpod.yml +++ b/.gitpod.yml @@ -1,4 +1,4 @@ -image: nfcore/gitpod:dev +image: nfcore/gitpod:latest tasks: - name: install current state of nf-core/tools and setup pre-commit command: | diff --git a/CHANGELOG.md b/CHANGELOG.md index 682a67652..6369cedd2 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,13 +1,19 @@ # nf-core/tools: Changelog -## v3.0.3dev +## [v3.1.0 - Brass Boxfish](https://github.com/nf-core/tools/releases/tag/3.1.0) - [2024-12-09] + +**Highlights** + +- We added the new `contributors` field to the pipeline template `manifest`. +- The `nf-core pipelines download` command supports ORAS container URIs. +- New command `nf-core subworkflows patch`. ### Template - Keep pipeline name in version.yml file ([#3223](https://github.com/nf-core/tools/pull/3223)) - Fix Manifest DOI text ([#3224](https://github.com/nf-core/tools/pull/3224)) - Do not assume pipeline name is url ([#3225](https://github.com/nf-core/tools/pull/3225)) -- fix workflow_dispatch trigger and parse more review comments in awsfulltest ([#3235](https://github.com/nf-core/tools/pull/3235)) +- fix `workflow_dispatch` trigger and parse more review comments in awsfulltest ([#3235](https://github.com/nf-core/tools/pull/3235)) - Add resource limits to Gitpod profile([#3255](https://github.com/nf-core/tools/pull/3255)) - Fix a typo ([#3268](https://github.com/nf-core/tools/pull/3268)) - Remove `def` from `nextflow.config` and add `trace_report_suffix` param ([#3296](https://github.com/nf-core/tools/pull/3296)) @@ -18,14 +24,14 @@ ### Download -- First steps towards fixing [#3179](https://github.com/nf-core/tools/issues/3179): Modify `prioritize_direct_download()` to retain Seqera Singularity https:// Container URIs and hardcode Seqera Containers into `gather_registries()` ([#3244](https://github.com/nf-core/tools/pull/3244)). +- First steps towards fixing [#3179](https://github.com/nf-core/tools/issues/3179): Modify `prioritize_direct_download()` to retain Seqera Singularity `https://` Container URIs and hardcode Seqera Containers into `gather_registries()` ([#3244](https://github.com/nf-core/tools/pull/3244)). - Further steps towards fixing [#3179](https://github.com/nf-core/tools/issues/3179): Enable limited support for `oras://` container paths (_only absolute URIs, no flexible registries like with Docker_) and prevent unnecessary image downloads for Seqera Container modules with `reconcile_seqera_container_uris()` ([#3293](https://github.com/nf-core/tools/pull/3293)). - Update dawidd6/action-download-artifact action to v7 ([#3306](https://github.com/nf-core/tools/pull/3306)) ### Linting - allow mixed `str` and `dict` entries in lint config ([#3228](https://github.com/nf-core/tools/pull/3228)) -- fix meta_yml linting test failing due to module.process_name always being "" ([#3317](https://github.com/nf-core/tools/pull/3317)) +- fix `meta_yml` linting test failing due to `module.process_name` always being `""` ([#3317](https://github.com/nf-core/tools/pull/3317)) - fix module section regex matching wrong things ([#3321](https://github.com/nf-core/tools/pull/3321)) ### Modules @@ -39,32 +45,28 @@ ### General -- Include .nf-core.yml in `nf-core pipelines bump-version` ([#3220](https://github.com/nf-core/tools/pull/3220)) +- Include `.nf-core.yml` in `nf-core pipelines bump-version` ([#3220](https://github.com/nf-core/tools/pull/3220)) - create: add shortcut to toggle all switches ([#3226](https://github.com/nf-core/tools/pull/3226)) - Remove unrelated values when saving `.nf-core` file ([#3227](https://github.com/nf-core/tools/pull/3227)) -- chore(deps): update pre-commit hook pre-commit/mirrors-mypy to v1.12.0 ([#3230](https://github.com/nf-core/tools/pull/3230)) -- chore(deps): update pre-commit hook astral-sh/ruff-pre-commit to v0.7.0 ([#3229](https://github.com/nf-core/tools/pull/3229)) -- Update python:3.12-slim Docker digest to 032c526 ([#3232](https://github.com/nf-core/tools/pull/3232)) - use correct `--profile` options for `nf-core subworkflows test` ([#3233](https://github.com/nf-core/tools/pull/3233)) - Update GitHub Actions ([#3237](https://github.com/nf-core/tools/pull/3237)) - add `--dir/-d` option to schema commands ([#3247](https://github.com/nf-core/tools/pull/3247)) -- Update pre-commit hook astral-sh/ruff-pre-commit to v0.7.1 ([#3250](https://github.com/nf-core/tools/pull/3250)) - fix headers in api docs ([#3323](https://github.com/nf-core/tools/pull/3323)) - handle new schema structure in `nf-core pipelines create-params-file` ([#3276](https://github.com/nf-core/tools/pull/3276)) - Update Gitpod image to use Miniforge instead of Miniconda([#3274](https://github.com/nf-core/tools/pull/3274)) -- Update pre-commit hook astral-sh/ruff-pre-commit to v0.7.3 ([#3275](https://github.com/nf-core/tools/pull/3275)) - Add hint to solve git errors with a synced repo ([#3279](https://github.com/nf-core/tools/pull/3279)) -- Update pre-commit hook astral-sh/ruff-pre-commit to v0.7.4 ([#3282](https://github.com/nf-core/tools/pull/3282)) -- Update codecov/codecov-action action to v5 ([#3283](https://github.com/nf-core/tools/pull/3283)) -- Update python:3.12-slim Docker digest to 2a6386a ([#3284](https://github.com/nf-core/tools/pull/3284)) -- Update pre-commit hook astral-sh/ruff-pre-commit to v0.8.0 ([#3299](https://github.com/nf-core/tools/pull/3299)) -- Update gitpod/workspace-base Docker digest to 12853f7 ([#3309](https://github.com/nf-core/tools/pull/3309)) - Run pre-commit when testing linting the template pipeline ([#3280](https://github.com/nf-core/tools/pull/3280)) -- Update pre-commit hook astral-sh/ruff-pre-commit to v0.8.2 ([#3325](https://github.com/nf-core/tools/pull/3325)) - Make CLI prompt less nf-core specific ([#3326](https://github.com/nf-core/tools/pull/3326)) - Update gitpod vscode extensions to use nf-core extension pack ([#3327](https://github.com/nf-core/tools/pull/3327)) - Remove toList() channel operation from inside onComplete block ([#3304](https://github.com/nf-core/tools/pull/3304)) - build: Setup VS Code tests ([#3292](https://github.com/nf-core/tools/pull/3292)) + +### Version updates + +- chore(deps): update pre-commit hook pre-commit/mirrors-mypy to v1.12.0 ([#3230](https://github.com/nf-core/tools/pull/3230)) +- Update codecov/codecov-action action to v5 ([#3283](https://github.com/nf-core/tools/pull/3283)) +- Update gitpod/workspace-base Docker digest to 12853f7 ([#3309](https://github.com/nf-core/tools/pull/3309)) +- Update pre-commit hook astral-sh/ruff-pre-commit to v0.8.2 ([#3325](https://github.com/nf-core/tools/pull/3325)) - Update dependency textual-dev to v1.7.0 ([#3308](https://github.com/nf-core/tools/pull/3308)) ## [v3.0.2 - Titanium Tapir Patch](https://github.com/nf-core/tools/releases/tag/3.0.2) - [2024-10-11] diff --git a/setup.py b/setup.py index 11b302249..6b68973a6 100644 --- a/setup.py +++ b/setup.py @@ -2,7 +2,7 @@ from setuptools import find_packages, setup -version = "3.0.3dev" +version = "3.1.0" with open("README.md") as f: readme = f.read()