[DOC] add changelog (#224)

* add changelog

* use numpy type annotations

.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]
 

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).
+
+<!--
+### Added
+
+### Changed
+
+### Deprecated
+
+### Removed
+
+### Fixed
+
+### Security
+-->
+
+## [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

docs/source/index.rst

@@ -11,6 +11,7 @@ Welcome to bidsMReye's documentation!
    FAQ
    modules
    references
+   CHANGELOG
 
 Indices and tables
 ==================

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