MNT: Switch to hatch build backend and update package metadata (#2914)

This PR aims to move away from setuptools+versioneer, which we've been using for a while.

One advantage to this approach is that `_version.py` can be updated by running `hatch build --hooks-only`, which will ensure that patching with `fmriprep-docker --patch fmriprep=...` will get a sensible version instead of the useless `0+unknown` which breaks the reuse of workflow directories.

I have moved to the [hatch](https://hatch.pypa.io/latest/) build system, which has some advantages. This is a plugin-oriented build-system, which means it should be fairly easy for us to find or write additional tools if our needs change. The [hatch-vcs](https://github.com/ofek/hatch-vcs) plugin wraps `setuptools_scm` with only minor changes to the configuration needed.

One additional nice feature of hatch is that you can set different file include/exclude rules for sdists and wheels. In principle, an sdist should be testable without resorting to the original repository, so I have never much liked that we remove a large chunk of data. This allows us to exclude some large data in the `fmriprep/data/tests` directory only in the wheel. This reduces our 5.5MB wheel down to 208K while allowing the sdist to grow to the 24MB monstrosity that it ought to be.

.circleci/config.yml

@@ -4,14 +4,14 @@ _machine_defaults: &machine_defaults
     TZ: "/usr/share/zoneinfo/America/Los_Angeles"
     SCRATCH: "/scratch"
   machine:
-    image: ubuntu-2004:current
+    image: ubuntu-2204:current
     docker_layer_caching: true
   working_directory: /tmp/src/fmriprep
   resource_class: large
 
 _python_defaults: &python_defaults
   docker:
-    - image: circleci/python:3.9.6
+    - image: cimg/python:3.10.9
   working_directory: /tmp/src/fmriprep
 
 _docker_auth: &docker_auth
@@ -84,7 +84,7 @@ _setup_fmriprep_docker: &setup_fmriprep_docker
                   sed -e 's/.* 3\./3./' -e 's/ .*//')
     pyenv local $PY3
     mkdir -p /tmp/${DATASET}/derivatives
-    pip install --upgrade pip setuptools
+    pip install --upgrade pip
     pip install --upgrade /tmp/src/fmriprep/wrapper/
 
 
@@ -159,8 +159,9 @@ jobs:
             export PY3=$(pyenv versions | grep '3\.' |
                          sed -e 's/.* 3\./3./' -e 's/ .*//')
             pyenv local $PY3
+            pip install hatch
             # Get version, update files.
-            THISVERSION=$( python3 get_version.py )
+            THISVERSION=$( hatch version )
             if [[ ${THISVERSION:0:1} == "0" ]] ; then
               echo "WARNING: latest git tag could not be found"
               echo "Please, make sure you fetch all tags from upstream with"
@@ -184,7 +185,7 @@ jobs:
                          sed -e 's/.* 3\./3./' -e 's/ .*//')
             pyenv local $PY3
             # Get version, update files.
-            THISVERSION=$( python3 get_version.py )
+            THISVERSION=$( hatch version )
             BUILT_VERSION=$( docker run --rm nipreps/fmriprep:latest --version )
             BUILT_VERSION=${BUILT_VERSION%$'\r'}
             BUILT_VERSION=${BUILT_VERSION#*"fMRIPrep v"}
@@ -312,7 +313,7 @@ jobs:
           command: |
             mkdir -p /tmp/fslicense
             cd /tmp/fslicense
-            echo "${FS_LICENSE_CONTENT}" | base64 -d | sh
+            echo "cHJpbnRmICJrcnp5c3p0b2YuZ29yZ29sZXdza2lAZ21haWwuY29tXG41MTcyXG4gKkN2dW12RVYzelRmZ1xuRlM1Si8yYzFhZ2c0RVxuIiA+IGxpY2Vuc2UudHh0Cg==" | base64 -d | sh
       - run:
           name: Create Nipype config files
           command: |
@@ -363,28 +364,36 @@ jobs:
               --pyargs fmriprep -svx --doctest-modules
 
       - run:
-          name: Test fmriprep-wrapper (Python 2)
+          name: Build fmriprep-docker wheel
           command: |
-            export PY2=$(pyenv versions | grep '2\.' |
-                         sed -e 's/.* 2\./2./' -e 's/ .*//')
-            pyenv local $PY2
+            export PY3=$(pyenv versions | grep '3\.' |
+                         sed -e 's/.* 3\./3./' -e 's/ .*//')
+            pyenv local $PY3
+            pip install --upgrade pip build
+            python -m build wrapper/
+      - run:
+          name: Install and test fmriprep-docker (Python 3)
+          command: |
+            export PY3=$(pyenv versions | grep '3\.' |
+                         sed -e 's/.* 3\./3./' -e 's/ .*//')
+            pyenv local $PY3
             echo -n "Python version: "
             python --version
-            pip install --upgrade "pip<21" "setuptools<45"
             pip install --upgrade wrapper/
+            pip install wrapper/dist/*.whl
             which fmriprep-docker
             fmriprep-docker -i nipreps/fmriprep:latest --help
             fmriprep-docker -i nipreps/fmriprep:latest --version
       - run:
-          name: Test fmriprep-wrapper (Python 3)
+          name: Install and test fmriprep-docker (Python 2)
           command: |
-            export PY3=$(pyenv versions | grep '3\.' |
-                         sed -e 's/.* 3\./3./' -e 's/ .*//')
-            pyenv local $PY3
+            export PY2=$(pyenv versions | grep '2\.' |
+                         sed -e 's/.* 2\./2./' -e 's/ .*//')
+            pyenv local $PY2
             echo -n "Python version: "
             python --version
-            pip install --upgrade pip setuptools
-            pip install --upgrade wrapper/
+            pip install --upgrade "pip<21"
+            pip install wrapper/dist/*.whl
             which fmriprep-docker
             fmriprep-docker -i nipreps/fmriprep:latest --help
             fmriprep-docker -i nipreps/fmriprep:latest --version
@@ -911,7 +920,7 @@ jobs:
       - checkout
       - run:
           name: Update build tools
-          command: python -m pip install --user pip build twine
+          command: pip install --upgrade build twine hatch
       - run:
           name: Build fMRIPrep
           command: python -m build
@@ -920,8 +929,8 @@ jobs:
       - run:
           name: Check sdist distribution
           command: |
-            THISVERSION=$( python get_version.py )
-            THISVERSION=${THISVERSION%.dirty*}
+            THISVERSION=$( hatch version )
+            THISVERSION=${THISVERSION%.d*}
             THISVERSION=${CIRCLE_TAG:-$THISVERSION}
             python -m twine check dist/fmriprep*.tar.gz
             virtualenv --python=python sdist
@@ -938,8 +947,8 @@ jobs:
       - run:
           name: Check wheel distribution
           command: |
-            THISVERSION=$( python get_version.py )
-            THISVERSION=${THISVERSION%.dirty*}
+            THISVERSION=$( hatch version )
+            THISVERSION=${THISVERSION%.d*}
             THISVERSION=${CIRCLE_TAG:-$THISVERSION}
             python -m twine check dist/fmriprep*.whl
             virtualenv --python=python wheel
@@ -954,11 +963,7 @@ jobs:
             test "$INSTALLED_VERSION" = "$THISVERSION"
       - run:
           name: Build fmriprep-docker
-          command: |
-            THISVERSION=$( python get_version.py )
-            THISVERSION=${THISVERSION%.dirty*}
-            sed -i -E "s/(__version__ = )'[A-Za-z0-9.-]+'/\1'${CIRCLE_TAG:-$THISVERSION}'/" wrapper/fmriprep_docker.py
-            python -m build wrapper/
+          command: python -m build wrapper
       - store_artifacts:
           path: /tmp/src/fmriprep/wrapper/dist
 
@@ -968,21 +973,16 @@ jobs:
       - checkout
       - run:
           name: Update build tools
-          command: python -m pip install --user build twine
+          command: pip install --upgrade build twine
       - run:
           name: Build fMRIPrep
           command: python -m build
       - run:
           name: Build fmriprep-docker
-          command: |
-            THISVERSION=$( python get_version.py )
-            THISVERSION=${THISVERSION%.dirty*}
-            sed -i -E "s/(__version__ = )'[A-Za-z0-9.-]+'/\1'${CIRCLE_TAG:-$THISVERSION}'/" wrapper/fmriprep_docker.py
-            python -m build wrapper/
+          command: python -m build wrapper/
       - run:
           name: Upload packages to PyPI
-          command: |
-            python -m twine upload dist/fmriprep* wrapper/dist/fmriprep*
+          command: python -m twine upload dist/fmriprep* wrapper/dist/fmriprep*
 
   deployable:
     docker:
@@ -1005,8 +1005,6 @@ workflows:
               only: /.*/
 
       - get_data:
-          context:
-            - fs-license
           filters:
             branches:
               ignore:

.git_archival.txt

@@ -0,0 +1,4 @@
+node: $Format:%H$
+node-date: $Format:%cI$
+describe-name: $Format:%(describe:tags=true,match=*[0-9]*)$
+ref-names: $Format:%D$

.gitattributes

@@ -1 +1 @@
-fmriprep/_version.py export-subst
+.git_archival.txt  export-subst

.gitignore

@@ -79,3 +79,5 @@ secrets.py
 local_settings.py
 
 *.swp
+
+_version.py

.maint/ci/install.sh

@@ -18,11 +18,7 @@ if [ -n "$EXTRA_PIP_FLAGS" ]; then
     EXTRA_PIP_FLAGS=${!EXTRA_PIP_FLAGS}
 fi
 
-if [ "$INSTALL_TYPE" == "setup" ]; then
-    python setup.py install
-else
-    pip install $EXTRA_PIP_FLAGS $ARCHIVE
-fi
+pip install $EXTRA_PIP_FLAGS $ARCHIVE
 
 # Basic import check
 python -c 'import fmriprep; print(fmriprep.__version__)'

.pre-commit-config.yaml

@@ -1,3 +1,4 @@
+exclude: ".*/data/.*"
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v2.4.0

.readthedocs.yml

@@ -4,6 +4,9 @@ build:
   os: ubuntu-22.04
   tools:
     python: "3.10"
+  jobs:
+    post_checkout:
+      - git fetch --unshallow
 
 python:
   install:

Dockerfile

@@ -2,7 +2,7 @@
 #
 # MIT License
 #
-# Copyright (c) 2022 The NiPreps Developers
+# Copyright (c) 2023 The NiPreps Developers
 #
 # Permission is hereby granted, free of charge, to any person obtaining a copy
 # of this software and associated documentation files (the "Software"), to deal

Makefile

@@ -14,4 +14,4 @@ docker-build:
 	docker build --rm -t $(tag) \
 	--build-arg BUILD_DATE=`date -u +"%Y-%m-%dT%H:%M:%SZ"` \
 	--build-arg VCS_REF=`git rev-parse --short HEAD` \
-	--build-arg VERSION=`python get_version.py` .
+	--build-arg VERSION=`hatch version` .

NOTICE

@@ -0,0 +1 @@
+fmriprep/data/NOTICE

README.rst

@@ -140,13 +140,13 @@ and some conference posters:
 
 License information
 -------------------
-*fMRIPrep* adheres to the 
+*fMRIPrep* adheres to the
 `general licensing guidelines <https://www.nipreps.org/community/licensing/>`__
 of the *NiPreps framework*.
 
 License
 ~~~~~~~
-Copyright (c) 2022, the *NiPreps* Developers.
+Copyright (c) 2023, the *NiPreps* Developers.
 
 As of the 21.0.x pre-release and release series, *fMRIPrep* is
 licensed under the Apache License, Version 2.0 (the "License");

docs/license.rst

@@ -6,7 +6,7 @@ projects of the framework.
 
 License information
 -------------------
-Copyright (c) 2022, the *NiPreps* Developers.
+Copyright (c) 2023, the *NiPreps* Developers.
 
 As of the 21.0.x pre-release and release series, *fMRIPrep* is
 licensed under the Apache License, Version 2.0 (the "License");
@@ -20,7 +20,7 @@ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 See the License for the specific language governing permissions and
 limitations under the License.
 
-Copyright (c) 2015-2022, the *fMRIPrep* developers and the CRN.
+Copyright (c) 2015-2023, the *fMRIPrep* developers and the CRN.
 All rights reserved.
 
 *fMRIPrep* 20.2 series and earlier are
@@ -32,7 +32,7 @@ All trademarks referenced herein are property of their respective holders.
 
 The ``fmriprep-wrapper`` for Docker
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-Copyright (c) 2020-2022, the *NiPreps* Developers.
+Copyright (c) 2020-2023, the *NiPreps* Developers.
 Copyright (c) 2015-2020, the *fMRIPrep* developers and the CRN.
 All rights reserved.
 

fmriprep/__about__.py

@@ -1,7 +1,7 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 #
-# Copyright 2022 The NiPreps Developers <nipreps@gmail.com>
+# Copyright 2023 The NiPreps Developers <nipreps@gmail.com>
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
@@ -21,13 +21,14 @@
 #     https://www.nipreps.org/community/licensing/
 #
 """Base module variables."""
-from ._version import get_versions
 
-__version__ = get_versions()['version']
-del get_versions
+try:
+    from ._version import __version__
+except ImportError:
+    __version__ == "0+unknown"
 
 __packagename__ = 'fmriprep'
-__copyright__ = 'Copyright 2022, The NiPreps Developers'
+__copyright__ = 'Copyright 2023, The NiPreps Developers'
 __credits__ = (
     'Contributors: please check the ``.zenodo.json`` file at the top-level folder'
     'of the repository'

fmriprep/__main__.py

@@ -1,7 +1,7 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 #
-# Copyright 2022 The NiPreps Developers <nipreps@gmail.com>
+# Copyright 2023 The NiPreps Developers <nipreps@gmail.com>
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.