diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 4f20ab1..b690145 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -60,7 +60,7 @@ repos: rev: v1.11.1 hooks: - id: mypy - additional_dependencies: [types-all, pydantic] + additional_dependencies: [pydantic, numpy] files: bidsmreye args: [--config-file, pyproject.toml] @@ -75,7 +75,7 @@ repos: rev: 7.1.1 hooks: - id: flake8 - exclude: tests_.*.py|version.*.py|setup.py # ignore tests and versioneer related code + exclude: tests_.*.py|version.*.py|setup.py # ignore tests and versioneer related code args: [--config, .flake8, --verbose] additional_dependencies: [flake8-docstrings, flake8-use-fstring, flake8-functions, flake8-bugbear] diff --git a/docs/source/CHANGELOG.md b/docs/source/CHANGELOG.md new file mode 100644 index 0000000..db7e6dd --- /dev/null +++ b/docs/source/CHANGELOG.md @@ -0,0 +1,116 @@ +# Changelog + +All notable changes to this project will be documented in this file. + +The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), +and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). + + + +## [Unreleased] + +### Added + +### Changed + +### Deprecated + +### Removed + +### Fixed + +### Security + + +## [0.4.0] - 20234-08-05 + +* [FIX] update file naming when run indices are padded by @Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/146 +* [MAINT] move most of the config to pyproject.toml by @Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/147 +* [MAINT] update packaging by @Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/165 +* [MAINT] pin pooch dependency by @Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/166 +* [STY] use isort by @Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/191 +* [FIX] pin keras and fix make file by @Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/197 +* [FIX] fix deploy to github on Circle CI by @Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/210 +* [ENH] improve error messages for invalid input data by @Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/150 +* [ENH] turn `--action` into subcommands by @Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/215 +* [ENH] Skip prepare and QC if output already exists by @Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/216 +* [FIX] handle exceptions for QC at group level when participants are missing QC data by @Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/217 +* [FIX] Use repetition time from BIDS metadata instead of nifti header by @Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/218 +* [FIX] save models in output dir by @Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/219 +* [FIX] improve help for missing subject / task by @Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/220 + +**Full Changelog**: https://github.com/cpp-lln-lab/bidsMReye/compare/0.3.1...0.4.0 + +## [0.3.1] - 2023-01-23 + +* [ENH] update config by @Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/126 +* [MNT] update docker and doc by @Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/118 +* [FMT] format yml by @Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/120 +* [INFRA] improve docker by @Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/122 +* [DOC] update FAQ by @Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/121 +* [DOC] add CLI info for group level by @Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/128 + +**Full Changelog**: https://github.com/cpp-lln-lab/bidsMReye/compare/0.3.0...0.4.0 + +## [0.3.0] - 2022-12-29 + +* [ENH] run QC on input data by @Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/113 +* [ENH] add group level QA plot and table by @Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/115 + +**Full Changelog**: https://github.com/cpp-lln-lab/bidsMReye/compare/0.2.0...0.3.0 + +## [0.2.0] - 2022-12-19 + +* [DOC] add logo by @Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/89 +* [MISC] by @Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/92 +* [MNT] add workflow to run on openneuro data by @Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/90 +* [ENH] improve log and change verbosity parameter by @Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/96 +* [ENH] improve model download by @Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/97 +* [ENH] improve methods by @Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/98 +* [ENH] add CCO license by default by @Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/99 +* [ENH] add possibility to used ANTs non linear registration by @Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/100 +* [ENH] add basic QC by @Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/102 + +**Full Changelog**: https://github.com/cpp-lln-lab/bidsMReye/compare/0.1.2...0.2.0 + +## [0.1.0] - 2022-12-08 + +* [MNT] coverage, doc, config by @Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/20 +* [ENH] save one output per subject by @Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/26 +* [ENH] add CLI by @Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/28 +* [REF] use Path instead of os.path by @Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/31 +* [MNT] set up dev docker by @Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/32 +* [ENH] use logging by @Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/34 +* [ENH] Dockerfile make by @WeeXee in https://github.com/cpp-lln-lab/bidsMReye/pull/40 +* [ENH] method section and vscode extensions by @Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/45 +* [ENH] set up config class (Sourcery refactored) by @sourcery-ai in https://github.com/cpp-lln-lab/bidsMReye/pull/50 +* [ENH] set up config class by @Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/48 +* [ENH] run on several files by @Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/52 +* [MISC] openneuro demo, add run argument, use pybids database... by @Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/58 +* [ENH] downloads all models by @Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/60 +* [FIX] do not specify nb args in argparse of CLI as leads to failure of constructing the config by @Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/63 +* [MNT] prepare for pypi release by @Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/85 + +### New Contributors + +* @pre-commit-ci made their first contribution in https://github.com/cpp-lln-lab/bidsMReye/pull/1 +* @Remi-Gau made their first contribution in https://github.com/cpp-lln-lab/bidsMReye/pull/20 +* @sourcery-ai made their first contribution in https://github.com/cpp-lln-lab/bidsMReye/pull/27 +* @WeeXee made their first contribution in https://github.com/cpp-lln-lab/bidsMReye/pull/40 +* @allcontributors made their first contribution in https://github.com/cpp-lln-lab/bidsMReye/pull/46 +* @Naubody made their first contribution in https://github.com/cpp-lln-lab/bidsMReye/pull/66 +* @dependabot made their first contribution in https://github.com/cpp-lln-lab/bidsMReye/pull/70 + +**Full Changelog**: https://github.com/cpp-lln-lab/bidsMReye/commits/0.1.0 diff --git a/docs/source/index.rst b/docs/source/index.rst index 00e3961..0b0d901 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -11,6 +11,7 @@ Welcome to bidsMReye's documentation! FAQ modules references + CHANGELOG Indices and tables ================== diff --git a/pyproject.toml b/pyproject.toml index 04fb59c..d382650 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -141,7 +141,10 @@ disallow_untyped_defs = true # enable_error_code = ["ignore-without-code", "redundant-expr", "truthy-bool"] exclude = ['tests/'] no_implicit_optional = true -plugins = "pydantic.mypy" +plugins = [ + "pydantic.mypy", + "numpy.typing.mypy_plugin" +] warn_redundant_casts = true warn_unused_ignores = true