diff --git a/CHANGELOG.md b/CHANGELOG.md index ec7410ce6..1527f5ba4 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 ` 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 ### 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)) @@ -28,53 +39,45 @@ - 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 8f32daa90..45df29b8b 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()