From 6e018ce6981548fb11ae5f34e3c476305695ad8f Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Fri, 23 Aug 2024 15:41:07 +0200 Subject: [PATCH 1/3] organise changelog and bump version to 3.0.0dev --- CHANGELOG.md | 55 +++++++++++++++++++++++++++------------------------- setup.py | 2 +- 2 files changed, 30 insertions(+), 27 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index aca2e6f200..42cb2a62aa 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,6 +1,18 @@ # nf-core/tools: Changelog -## v2.14.2dev +## v3.0.0dev + +**Highlights** + +- Pipeline commands are renamed from nf-core to nf-core pipelines +- More customisation for pipeline templates +- A Text User Interface app when running nf-core pipelines create +- The pipeline template will come with the nf-schema plugin +- New command nf-core pipelines rocrate to create a Research Object (RO) crate for a pipeline +- `nf-core licences` command is deprecated. +- Pipeline linting will run with the used version of the template +- The structure of nf-core/tools pytests has been updated +- The structure of the API docs has been updated ### Template @@ -9,14 +21,13 @@ - Remove deprecated syntax ([#3046](https://github.com/nf-core/tools/pull/3046)) - Use filename in code block for `params.yml` ([#3055](https://github.com/nf-core/tools/pull/3055)) - Remove release announcement for non nf-core pipelines ([#3072](https://github.com/nf-core/tools/pull/3072)) +- handle template features with a yaml file ([#3108](https://github.com/nf-core/tools/pull/3108), [#3112](https://github.com/nf-core/tools/pull/3112)) - add option to exclude code linters for custom pipeline template ([#3084](https://github.com/nf-core/tools/pull/3084)) - add option to exclude citations for custom pipeline template ([#3101](https://github.com/nf-core/tools/pull/3101)) - add option to exclude gitpod for custom pipeline template ([#3100](https://github.com/nf-core/tools/pull/3100)) - add option to exclude codespaces from pipeline template ([#3105](https://github.com/nf-core/tools/pull/3105)) - add option to exclude multiqc from pipeline template ([#3103](https://github.com/nf-core/tools/pull/3103)) - add option to exclude changelog from custom pipeline template ([#3104](https://github.com/nf-core/tools/pull/3104)) -- handle template features with a yaml file ([#3108](https://github.com/nf-core/tools/pull/3108)) -- add templatefeatures.yml to python package ([#3112](https://github.com/nf-core/tools/pull/3112)) - add option to exclude license from pipeline template ([#3125](https://github.com/nf-core/tools/pull/3125)) - add option to exclude email from pipeline template ([#3126](https://github.com/nf-core/tools/pull/3126)) @@ -27,53 +38,45 @@ - Restructure pipeline tests and move pipeline linting into subfolder ([#3070](https://github.com/nf-core/tools/pull/3070)) - Fix module linting warning for process_high_memory ([#3086](https://github.com/nf-core/tools/issues/3086)) -### Download +### Pipeline create command + +- Create: allow more special characters on the pipeline name for non-nf-core pipelines ([#3008](https://github.com/nf-core/tools/pull/3008)) +- Create: Mock git cretentials to generate stable textual snapshots ([#3007](https://github.com/nf-core/tools/pull/3007)) +- Create app: display input textbox with equally spaced grid ([#3038](https://github.com/nf-core/tools/pull/3038)) +- Pipelines: allow numbers in custom pipeline name ([#3094](https://github.com/nf-core/tools/pull/3094)) ### Components - The `modules_nfcore` tag in the `main.nf.test` file of modules/subworkflows now displays the organization name in custom modules repositories ([#3005](https://github.com/nf-core/tools/pull/3005)) +- Add `--migrate_pytest` option to `nf-core test` command ([#3085](https://github.com/nf-core/tools/pull/3085)) +- Components: allow spaces at the beginning of include statements ([#3115](https://github.com/nf-core/tools/pull/3115)) ### General -- Update pre-commit hook astral-sh/ruff-pre-commit to v0.4.4 ([#2974](https://github.com/nf-core/tools/pull/2974)) -- Update gitpod/workspace-base Docker digest to 92dd1bc ([#2982](https://github.com/nf-core/tools/pull/2982)) - Update output of generation script for API docs to new structure ([#2988](https://github.com/nf-core/tools/pull/2988)) - Add no clobber and put bash options on their own line ([#2991](https://github.com/nf-core/tools/pull/2991)) - update minimal textual version and snapshots ([#2998](https://github.com/nf-core/tools/pull/2998)) - move pipeline subcommands for v3.0 ([#2983](https://github.com/nf-core/tools/pull/2983)) - return directory if base_dir is the root directory ([#3003](https://github.com/nf-core/tools/pull/3003)) -- Update pre-commit hook astral-sh/ruff-pre-commit to v0.4.6 ([#3006](https://github.com/nf-core/tools/pull/3006)) -- Create: allow more special characters on the pipeline name for non-nf-core pipelines ([#3008](https://github.com/nf-core/tools/pull/3008)) - Remove nf-core licences command ([#3012](https://github.com/nf-core/tools/pull/3012)) - README - absolute image paths ([#3013](https://github.com/nf-core/tools/pull/3013)) -- Update pre-commit hook astral-sh/ruff-pre-commit to v0.4.7 ([#3015](https://github.com/nf-core/tools/pull/3015)) -- Update pre-commit hook astral-sh/ruff-pre-commit to v0.4.8 ([#3017](https://github.com/nf-core/tools/pull/3017)) -- Update python:3.12-slim Docker digest to e3ae8cf ([#3020](https://github.com/nf-core/tools/pull/3020)) -- Update python:3.12-slim Docker digest to 2fba8e7 ([#3023](https://github.com/nf-core/tools/pull/3023)) -- Update pre-commit hook astral-sh/ruff-pre-commit to v0.4.10 ([#3031](https://github.com/nf-core/tools/pull/3031)) - Add warning deprecation message to top-level commands ([#3036](https://github.com/nf-core/tools/pull/3036)) -- Create: Mock git cretentials to generate stable textual snapshots ([#3007](https://github.com/nf-core/tools/pull/3007)) - move pipeline commands to functions to avoid duplication ([#3039](https://github.com/nf-core/tools/pull/3039)) -- Create app: display input textbox with equally spaced grid ([#3038](https://github.com/nf-core/tools/pull/3038)) -- Update python:3.12-slim Docker digest to da2d7af ([#3041](https://github.com/nf-core/tools/pull/3041)) -- Update gitpod/workspace-base Docker digest to 0f38224 ([#3048](https://github.com/nf-core/tools/pull/3048)) - update output_dir for api docs to new website structure ([#3051](https://github.com/nf-core/tools/pull/3051)) -- Update pre-commit hook astral-sh/ruff-pre-commit to v0.5.1 ([#3052](https://github.com/nf-core/tools/pull/3052)) - Add `--limit-output` argument for modules/subworkflow update ([#3047](https://github.com/nf-core/tools/pull/3047)) - update api docs to new structure ([#3054](https://github.com/nf-core/tools/pull/3054)) -- Update to pytest v8 and move it to dev dependencies ([#3058](https://github.com/nf-core/tools/pull/3058)) - handle new jsonschema error type ([#3061](https://github.com/nf-core/tools/pull/3061)) -- Update python:3.12-slim Docker digest to f11725a ([#3071](https://github.com/nf-core/tools/pull/3071)) - Fix number of arguments for pipelines_create within the command_create function ([#3074](https://github.com/nf-core/tools/pull/3074)) -- Update python:3.12-slim Docker digest to 740d94a ([#3079](https://github.com/nf-core/tools/pull/3079)) -- Add `--migrate_pytest` option to `nf-core test` command ([#3085](https://github.com/nf-core/tools/pull/3085)) -- Update pre-commit hook pre-commit/mirrors-mypy to v1.11.1 ([#3091](https://github.com/nf-core/tools/pull/3091)) -- Pipelines: allow numbers in custom pipeline name ([#3094](https://github.com/nf-core/tools/pull/3094)) - Add bot action to update textual snapshots and write bot documentation ([#3102](https://github.com/nf-core/tools/pull/3102)) -- Components: allow spaces at the betinning of include statements ([#3115](https://github.com/nf-core/tools/pull/3115)) +- Update gitpod setup ([#3136](https://github.com/nf-core/tools/pull/3136)) + +## Version updates + - Update pre-commit hook astral-sh/ruff-pre-commit to v0.6.0 ([#3122](https://github.com/nf-core/tools/pull/3122)) +- Update gitpod/workspace-base Docker digest to 92dd1bc ([#2982](https://github.com/nf-core/tools/pull/2982)) - Update python:3.12-slim Docker digest to 59c7332 ([#3124](https://github.com/nf-core/tools/pull/3124)) -- Update gitpod setup ([#3136](https://github.com/nf-core/tools/pull/3136)) +- Update pre-commit hook pre-commit/mirrors-mypy to v1.11.1 ([#3091](https://github.com/nf-core/tools/pull/3091)) +- Update to pytest v8 and move it to dev dependencies ([#3058](https://github.com/nf-core/tools/pull/3058)) ## [v2.14.1 - Tantalum Toad - Patch](https://github.com/nf-core/tools/releases/tag/2.14.1) - [2024-05-09] diff --git a/setup.py b/setup.py index 8f32daa904..45df29b8bc 100644 --- a/setup.py +++ b/setup.py @@ -2,7 +2,7 @@ from setuptools import find_packages, setup -version = "2.14.2dev" +version = "3.0.0dev" with open("README.md") as f: readme = f.read() From 41b2676c8746e92960907c3263f296ea7f606d96 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Fri, 23 Aug 2024 15:52:40 +0200 Subject: [PATCH 2/3] more details! :D --- CHANGELOG.md | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 42cb2a62aa..2a3e98f63b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,13 +4,13 @@ **Highlights** -- Pipeline commands are renamed from nf-core to nf-core pipelines -- More customisation for pipeline templates -- A Text User Interface app when running nf-core pipelines create -- The pipeline template will come with the nf-schema plugin -- New command nf-core pipelines rocrate to create a Research Object (RO) crate for a pipeline +- Pipeline commands are renamed from `nf-core ` to `nf-core pipelines ` to match the structure of modules and subworkflows commands. +- More customisation for pipeline templates. The template has been divided into features which can be skipped, making it easier to avoid annoying merge conflicts, for example, for pipeline which don't have a FastQC module. +- A new Text User Interface app when running nf-core pipelines create +- The pipeline template will come with the `nf-schema` plugin +- Pipeline linting will run with the used version of the template to minimise errors in opened PRs with every new tools release. +- New command `nf-core pipelines rocrate` to create a [Research Object (RO) crate](https://www.researchobject.org/ro-crate/about_ro_crate) for a pipeline - `nf-core licences` command is deprecated. -- Pipeline linting will run with the used version of the template - The structure of nf-core/tools pytests has been updated - The structure of the API docs has been updated From 8000e1f5c31e7903ff72bb2453b67ca8db262f67 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Fri, 23 Aug 2024 16:04:19 +0200 Subject: [PATCH 3/3] add suggestions from @mashehu --- CHANGELOG.md | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 2a3e98f63b..5590abc04a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,12 +4,12 @@ **Highlights** -- Pipeline commands are renamed from `nf-core ` to `nf-core pipelines ` to match the structure of modules and subworkflows commands. -- More customisation for pipeline templates. The template has been divided into features which can be skipped, making it easier to avoid annoying merge conflicts, for example, for pipeline which don't have a FastQC module. -- A new Text User Interface app when running nf-core pipelines create -- The pipeline template will come with the `nf-schema` plugin -- Pipeline linting will run with the used version of the template to minimise errors in opened PRs with every new tools release. -- New command `nf-core pipelines rocrate` to create a [Research Object (RO) crate](https://www.researchobject.org/ro-crate/about_ro_crate) for a pipeline +- Pipeline commands are renamed from `nf-core ` to `nf-core pipelines ` to follow the same command structure as modules and subworkflows commands. +- More customisation for pipeline templates. The template has been divided into features which can be skipped, e.g. you can create a new pipeline without any traces of FastQC in it. +- A new Text User Interface app when running `nf-core pipelines create` to help us guide you through the process better (no worries, you can still use the cli if you give all values as parameters) +- We replaced nf-validation with nf-schema in the pipeline template +- CI tests now lint with the nf-core tools version matching the template version of the pipeline, to minimise errors in opened PRs with every new tools release. +- New command `nf-core pipelines ro-crate` to create a [Research Object (RO) crate](https://www.researchobject.org/ro-crate/) for a pipeline - `nf-core licences` command is deprecated. - The structure of nf-core/tools pytests has been updated - The structure of the API docs has been updated