.ci/build_doc.sh

+#!/usr/bin/env /bash
+
+set -e
+
+source /test.venv/bin/activate
+pip install ".[doc]"
+sphinx-build doc public

.ci/build_pypi_dist.sh

+#!/usr/bin/env bash
+
+set -e
+
+pip install --upgrade pip wheel setuptools twine build
+
+python -m build
+twine check dist/*
+
+# do a test install from both source and wheel
+sdist=`find dist -maxdepth 1 -name *.tar.gz`
+wheel=`find dist -maxdepth 1 -name *.whl`
+
+for target in $sdist $wheel; do
+    python -m venv test.venv
+    . test.venv/bin/activate
+    pip install --upgrade pip setuptools
+    pip install $target
+    deactivate
+    rm -r test.venv
+done

.ci/check_version.sh

+#!/usr/bin/env bash
+
+set -e
+
+cat fsl/version.py | egrep "^__version__ += +'$CI_COMMIT_REF_NAME' *$"

.ci/deploy_pypi.sh

+#!/usr/bin/env BASH
+
+set -e
+
+pip install setuptools wheel twine
+twine upload dist/*

.ci/setup_ssh.sh

+#!/usr/bin/env /bash
+
+set -e
+
+##########################################################
+# The setup_ssh script does the following:
+#
+#  - Sets up key-based SSH login, and
+#    installs the private keys, so
+#    we can connect to servers.
+#
+#  - Configures git, and adds the
+#    upstream repo as a remote
+#
+# (see https://docs.gitlab.com/ce/ci/ssh_keys/README.html)
+#
+# NOTE: It is assumed that non-docker
+#       executors are already configured
+#       (or don't need any configuration).
+##########################################################
+
+if [[ -f /.dockerenv ]]; then
+
+ # We have to use different host names to connect
+ # to the docker daemon host on mac as opposed
+ # to on linux.
+ #
+ # On linux (assuming the docker job is running
+ # with --net=host), we can connect via
+ # username@localhost.
+ #
+ # On mac, we have to connect via
+ # username@host.docker.internal
+ if [[ "$CI_RUNNER_TAGS" == *"macOS"* ]]; then
+  if [[ "$FSL_HOST" == *"@localhost" ]]; then
+   FSL_HOST=${FSL_HOST/localhost/host.docker.internal}
+  fi
+ fi
+
+ apt-get update -y                           || yum -y check-update                     || true;
+ apt-get install -y openssh-client rsync git || yum install -y openssh-client rsync git || true;
+
+ eval $(ssh-agent -s);
+ mkdir -p $HOME/.ssh;
+
+ # for downloading FSL atlases/standards
+ echo "$SSH_PRIVATE_KEY_FSL_DOWNLOAD" > $HOME/.ssh/id_fsl_download;
+
+ chmod go-rwx $HOME/.ssh/id_*;
+
+ ssh-add $HOME/.ssh/id_fsl_download;
+
+ ssh-keyscan ${FSL_HOST##*@} >> $HOME/.ssh/known_hosts;
+
+ touch $HOME/.ssh/config;
+
+ echo "Host fsldownload"                            >> $HOME/.ssh/config;
+ echo "    HostName ${FSL_HOST##*@}"                >> $HOME/.ssh/config;
+ echo "    User ${FSL_HOST%@*}"                     >> $HOME/.ssh/config;
+ echo "    IdentityFile $HOME/.ssh/id_fsl_download" >> $HOME/.ssh/config;
+
+ echo "Host *"                                      >> $HOME/.ssh/config;
+ echo "    IdentitiesOnly yes"                      >> $HOME/.ssh/config;
+
+ git config --global user.name  "Gitlab CI";
+ git config --global user.email "gitlabci@localhost";
+
+ if [[ `git remote -v` == *"upstream"* ]]; then
+     git remote remove upstream;
+ fi;
+ git remote add upstream "$UPSTREAM_URL:$UPSTREAM_PROJECT";
+fi

.ci/test_template.sh

+#!/usr/bin/env bash
+
+set -e
+
+source /test.venv/bin/activate
+
+pip install ".[extra,test,style]"
+
+# style stage
+if [ "$TEST_STYLE"x != "x" ]; then flake8                           fsl || true; fi;
+if [ "$TEST_STYLE"x != "x" ]; then pylint --output-format=colorized fsl || true; fi;
+if [ "$TEST_STYLE"x != "x" ]; then exit 0;                                       fi;
+
+# We need the FSL atlases for the atlas
+# tests, and need $FSLDIR to be defined
+export FSLDIR=/fsl/
+mkdir -p $FSLDIR/data/
+rsync -rv "fsldownload:$FSL_ATLAS_DIR" "$FSLDIR/data/atlases/"
+
+# Run the tests. Suppress coverage
+# reporting until after we're finished.
+TEST_OPTS="--cov-report= --cov-append"
+
+# pytest struggles with my organisation of
+# the fslpy package, where all tests are in
+# fsl.tests, and fsl is a namespace package
+touch fsl/__init__.py
+
+# We run some tests under xvfb-run
+# because they invoke wx. Sleep in
+# between, otherwise xvfb gets upset.
+xvfb-run -a pytest $TEST_OPTS fsl/tests/test_idle.py
+sleep 5
+xvfb-run -a pytest $TEST_OPTS fsl/tests/test_platform.py
+
+# We run the immv/imcp tests as the nobody
+# user because some tests expect permission
+# denied errors when looking at files, and
+# root never gets denied. Make everything in
+# this directory writable by anybody (which,
+# unintuitively, includes nobody)
+chmod -R a+w `pwd`
+cmd="source /test.venv/bin/activate && pytest"
+cmd="$cmd $TEST_OPTS fsl/tests/test_scripts/test_immv_imcp.py fsl/tests/test_immv_imcp.py"
+su -s /bin/bash -c "$cmd" nobody
+
+# All other tests can be run as normal.
+pytest $TEST_OPTS -m 'not longtest'         \
+       --ignore=fsl/tests/test_idle.py      \
+       --ignore=fsl/tests/test_platform.py  \
+       --ignore=fsl/tests/test_immv_imcp.py \
+       --ignore=fsl/tests/test_scripts/test_immv_imcp.py
+
+# Long tests are only run on release branches
+if [[ $CI_COMMIT_REF_NAME == v* ]]; then
+    pytest $TEST_OPTS -m 'longtest'
+fi
+
+python -m coverage report -i

.ci/zenodo.py

+#!/usr/bin/env python
+#
+# Deposit a new version of something on zenodo.
+#
+# It is assumed that a deposit already exists on zenodo - you must
+# specify the deposit ID of that original deposit.
+#
+# http://developers.zenodo.org/#rest-api
+
+
+import os.path as op
+import sys
+import json
+
+import jinja2 as j2
+import requests
+
+
+def deposit(zenodo_url, access_token, dep_id, upload_file, meta):
+
+    urlbase = '{}/api/deposit/depositions'.format(zenodo_url)
+    headers = {'Content-Type': 'application/json'}
+    params  = {'access_token' : access_token}
+
+    # Create a new deposit
+    url = '{}/{}/actions/newversion'.format(urlbase, dep_id)
+    print('Creating new deposit: {}'.format(url))
+    r   = requests.post(url, params=params)
+    if r.status_code != 201:
+        raise RuntimeError('POST {} failed: {}'.format(url, r.status_code))
+
+    newurl = r.json()['links']['latest_draft']
+    dep_id = newurl.split('/')[-1]
+
+    print("New deposition ID: {}".format(dep_id))
+
+    # Upload the file
+    data   = {'filename': op.basename(upload_file)}
+    files  = {'file': open(upload_file, 'rb')}
+    url    = '{}/{}/files'.format(urlbase, dep_id)
+    print('Uploading file: {}'.format(url))
+    r   = requests.post(url, params=params, data=data, files=files)
+
+    if r.status_code != 201:
+        raise RuntimeError('POST {} failed: {}'.format(url, r.status_code))
+
+    # Upload the metadata
+
+    url  = '{}/{}?access_token={}'.format(urlbase, dep_id, access_token)
+    print('Uploading metadata: {}'.format(url))
+    r = requests.put(url, data=json.dumps(meta), headers=headers)
+
+    if r.status_code != 200:
+        print(r.json())
+        raise RuntimeError('PUT {} failed: {}'.format(url, r.status_code))
+
+    # Publish
+    url = '{}/{}/actions/publish'.format(urlbase, dep_id)
+    print('Publishing: {}'.format(url))
+    r = requests.post(url, params=params)
+
+    if r.status_code != 202:
+        raise RuntimeError('POST {} failed: {}'.format(url, r.status_code))
+
+
+def make_meta(templatefile, version, date):
+    with open(templatefile, 'rt') as f:
+        template = f.read()
+
+    template = j2.Template(template)
+
+    env = {
+        'VERSION' : version,
+        'DATE'    : date,
+    }
+
+    return json.loads(template.render(**env))
+
+
+if __name__ == '__main__':
+
+    zurl       = sys.argv[1]
+    tkn        = sys.argv[2]
+    depid      = sys.argv[3]
+    upfile     = sys.argv[4]
+    metafile   = sys.argv[5]
+    version    = sys.argv[6]
+    date       = sys.argv[7]
+
+    meta = make_meta(metafile, version, date)
+
+    deposit(zurl, tkn, depid, upfile, meta)

.ci/zenodo_deposit.sh

+#!/bin/bash
+
+tmp=`dirname $0`
+pushd $tmp > /dev/null
+thisdir=`pwd`
+popd > /dev/null
+
+zenodo_url=$1
+zenodo_tkn=$2
+zenodo_depid=$3
+
+version=$(cat fsl/version.py      |
+          egrep '^__version__ +=' |
+          cut -d "=" -f 2         |
+          tr -d "'"               |
+          tr -d ' ')
+upfile=$(pwd)/dist/fslpy-"$version".tar.gz
+metafile=$(pwd)/.ci/zenodo_meta.json.jinja2
+date=$(date +"%Y-%m-%d")
+
+pip install --retries 10 requests jinja2
+
+python "$thisdir"/zenodo.py \
+       "$zenodo_url" \
+       "$zenodo_tkn" \
+       "$zenodo_depid" \
+       "$upfile" \
+       "$metafile" \
+       "$version" \
+       "$date"

.ci/zenodo_meta.json.jinja2

+{
+    "metadata" : {
+        "title"            : "fslpy",
+        "upload_type"      : "software",
+        "version"          : "{{VERSION}}",
+        "publication_date" : "{{DATE}}",
+        "description"      : "<p>The fslpy project is a <a href=\"https://fsl.fmrib.ox.ac.uk/fsl/fslwiki\">FSL</a> programming library written in Python. It is used by <a href=\"http://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/\">FSLeyes</a>.</p>\n\n<p>The fslpy library is developed at the Wellcome Centre for Integrative Neuroimaging (FMRIB), at the University of Oxford. It is hosted at <a href=\"https://git.fmrib.ox.ac.uk/fsl/fslpy/\">https://git.fmrib.ox.ac.uk/fsl/fslpy/</a>.</p>",
+        "keywords"         : ["python", "mri", "neuroimaging", "neuroscience"],
+        "access_right"     : "open",
+        "license"          : "Apache-2.0",
+        "creators"         : [
+           { "name" : "McCarthy, Paul" },
+           { "name" : "Cottaar, Michiel" },
+           { "name" : "Webster, Matthew" },
+           { "name" : "Fitzgibbon, Sean" },
+           { "name" : "Craig, Martin" }
+        ]
+    }
+}

.dir-locals.el

-((python-mode . ((project-venv-name . "fslpy")))
-
- ; make our bodgy wx widgets installation work nicely with emacs
- (nil . ((eval . (setenv "PYTHONPATH" "/Users/paulmc/Projects/props"))))
- (nil . ((eval . (setenv "PYTHONHOME" "/Users/paulmc/.virtualenvs/fslpy")))))

.gitignore

 *.pyc
-apidoc/html
-fsleyes_doc/html
+.projectile
+.dir-locals.el
+.cache
+.coverage
+.eggs
+fslpy.egg-info
+htmlcov
+doc/html

.gitlab-ci.yml

+#############################################################################
+# This file defines the build process for fslpy, as hosted at:
+#
+#    https://git.fmrib.ox.ac.uk/fsl/fslpy
+#
+# The build pipeline comprises the following stages:
+#
+#    1. test:   Unit tests
+#
+#    2. style:  Check coding style
+#
+#    3. doc:    Building and upload API documentation using GitLab Pages.
+#
+#    4. build:  Building source and wheel distributions
+#
+#    5. deploy: Uploading the build outputs to pypi/hosting servers.
+#
+#
+# Custom docker images are used for several jobs - these images are
+# available at:
+#
+#    https://hub.docker.com/u/pauldmccarthy/
+#
+# The test and style stages are executed on all branches of upstream and fork
+# repositories.
+#
+# The doc stage is executed on release branches of the upstream repository.
+#
+# The build and deploy stages are executed on tags on the upstream
+# repository, and the deploy stage must be manually instantiated.
+#
+# Most of the logic for each job is defined in shell scripts in the .ci
+# sub-directory.
+#############################################################################
+
+
+stages:
+ - test
+ - style
+ - doc
+ - build
+ - deploy
+
+
+#################################################################################
+# A number of variables must be set for the jobs to work. The following
+# variables are implicitly defined in any gitlab CI job:
+#
+#   - CI_PROJECT_PATH    - gitlab namespace/project
+#   - CI_COMMIT_REF_NAME - branch name, provided by gitlab
+#   - CI_COMMIT_TAG      - present if build is running on a tag
+#
+# These variables must be explicitly set as "secret" variables:
+#
+#   - SSH_PRIVATE_KEY_GIT            - private key for git login to remote host
+#                                      (UPSTREAM_URL)
+#
+#   - SSH_PRIVATE_KEY_FSL_DOWNLOAD   - private key for downloading some FSL
+#                                      files from a remote server (FSL_HOST)
+#
+#   - SSH_SERVER_HOSTKEYS            - List of trusted SSH hosts
+#
+#   - FSL_HOST:                      - Username@host to download FSL data from
+#                                      (most likely "paulmc@localhost")
+#
+#   - FSL_ATLAS_DIR:                 - Location of the FSL atlas data on
+#                                      FSL_HOST.
+#
+#   - TWINE_USERNAME:                - Username to use when uploading to pypi
+#
+#   - TWINE_PASSWORD:                - Password to use when uploading to pypi
+#
+#   - TWINE_REPOSITORY_URL:          - Pypi repository to upload to
+#
+#   - ZENODO_URL:                    - Zenodo URL to deposit release file to.
+#
+#   - ZENODO_TOKEN:                  - Zenodo access token.
+#
+#   - ZENODO_DEPOSIT_ID:             - Deposit ID of previous Zenodo deposit.
+###############################################################################
+
+
+variables:
+  UPSTREAM_PROJECT: "fsl/fslpy"
+  UPSTREAM_URL:     "git@git.fmrib.ox.ac.uk"
+
+
+####################################
+# These anchors are used to restrict
+# when and where jobs are executed.
+####################################
+
+
+.only_release_branches: &only_release_branches
+  only:
+    - /^v.+$/@fsl/fslpy
+
+
+.only_releases: &only_releases
+  only:
+    - tags@fsl/fslpy
+
+
+.setup_ssh: &setup_ssh
+  before_script:
+    - bash ./.ci/setup_ssh.sh
+
+
+###################################################
+# The check_version anchor contains a before_script
+# section which is run on release builds, and makes
+# sure that the version in the code is up to date
+# (i.e. equal to the tag name).
+###################################################
+
+
+.check_version: &check_version
+  before_script:
+    - bash ./.ci/check_version.sh
+
+
+############
+# Test stage
+############
+
+.test_rules: &test_rules
+  # We only run tests on MRs, and on release branches
+  # (a more substantial test suite is run on release
+  # branches - see .ci/test_template.sh). We don't run
+  # on upstream/main, as all merges are fast-forwards,
+  # so the tests will have already been run on the MR
+  # branch. We also allow manually running a pipeline
+  # via the web interface.
+  rules:
+    - if:   $SKIP_TESTS != null
+      when: never
+    - if:   $CI_COMMIT_MESSAGE =~ /\[skip-tests\]/
+      when: never
+    - if:   $CI_PIPELINE_SOURCE == "merge_request_event"
+      when: on_success
+    - if:   $CI_PROJECT_PATH == $UPSTREAM_PROJECT && $CI_COMMIT_BRANCH =~ /^v.+$/
+      when: on_success
+    - if:   $CI_PIPELINE_SOURCE == "web"
+      when: on_success
+    - when: never
+
+
+.test: &test_template
+  <<: *setup_ssh
+  <<: *test_rules
+
+  tags:
+    - docker
+
+  script:
+    - bash ./.ci/test_template.sh
+
+
+test:3.10:
+  stage: test
+  image: pauldmccarthy/fsleyes-py310-wxpy4-gtk3
+  <<: *test_template
+
+
+test:3.11:
+  stage: test
+  image: pauldmccarthy/fsleyes-py311-wxpy4-gtk3
+  <<: *test_template
+
+
+test:3.12:
+  stage: test
+  image: pauldmccarthy/fsleyes-py312-wxpy4-gtk3
+  <<: *test_template
+
+
+test:3.13:
+  stage: test
+  image: pauldmccarthy/fsleyes-py313-wxpy4-gtk3
+  <<: *test_template
+
+
+test:build-pypi-dist:
+  stage: test
+  image: python:3.10
+  <<: *test_rules
+
+  tags:
+    - docker
+
+  script:
+   - bash ./.ci/build_pypi_dist.sh
+
+
+#############
+# Style stage
+#############
+
+
+style:
+  stage: style
+  image: pauldmccarthy/fsleyes-py310-wxpy4-gtk3
+  <<: *test_template
+  variables:
+    TEST_STYLE:  "true"
+
+
+#############
+# Pages stage
+#############
+
+# I would like to have separate doc deploys for
+# both the main and latest release branches,
+# but this is awkward with gitlab pages. So
+# currently the most recently executed pages
+# job is the one that gets deployed.
+
+pages:
+  <<: *only_release_branches
+
+  tags:
+   - docker
+
+  stage: doc
+  image: pauldmccarthy/fsleyes-py310-wxpy4-gtk3
+
+  script:
+    - bash ./.ci/build_doc.sh
+
+  artifacts:
+    paths:
+      - public
+
+
+#############
+# Build stage
+#############
+
+
+build-pypi-dist:
+  <<: *only_releases
+  <<: *check_version
+
+  stage: build
+  image: python:3.10
+
+  tags:
+    - docker
+
+  script:
+   - bash ./.ci/build_pypi_dist.sh
+
+  artifacts:
+    expire_in: 1 day
+    paths:
+      - dist/*
+
+
+##############
+# Deploy stage
+##############
+
+
+deploy-pypi:
+  <<: *only_releases
+  <<: *setup_ssh
+  stage: deploy
+  when:  manual
+  image: python:3.10
+
+  tags:
+    - docker
+
+  dependencies:
+    - build-pypi-dist
+
+  script:
+    - bash ./.ci/deploy_pypi.sh
+
+
+deploy-zenodo:
+  <<: *only_releases
+  <<: *setup_ssh
+  stage: deploy
+  when:  manual
+  image: python:3.10
+
+  tags:
+    - docker
+
+  dependencies:
+    - build-pypi-dist
+
+  script:
+    - bash ./.ci/zenodo_deposit.sh "$ZENODO_URL" "$ZENODO_TOKEN" "$ZENODO_DEPOSIT_ID"

.pylintrc

+[MASTER]
+
+# A comma-separated list of package or module names from where C extensions may
+# be loaded. Extensions are loading into the active Python interpreter and may
+# run arbitrary code
+extension-pkg-whitelist=numpy,wx,scipy
+
+# Add files or directories to the blacklist. They should be base names, not
+# paths.
+ignore=CVS
+
+# Add files or directories matching the regex patterns to the blacklist. The
+# regex matches against base names, not paths.
+ignore-patterns=
+
+# Python code to execute, usually for sys.path manipulation such as
+# pygtk.require().
+#init-hook=
+
+# Use multiple processes to speed up Pylint.
+jobs=1
+
+# List of plugins (as comma separated values of python modules names) to load,
+# usually to register additional checkers.
+load-plugins=
+
+# Pickle collected data for later comparisons.
+persistent=yes
+
+# Specify a configuration file.
+#rcfile=
+
+# Allow loading of arbitrary C extensions. Extensions are imported into the
+# active Python interpreter and may run arbitrary code.
+unsafe-load-any-extension=no
+
+
+[MESSAGES CONTROL]
+
+# Only show warnings with the listed confidence levels. Leave empty to show
+# all. Valid levels: HIGH, INFERENCE, INFERENCE_FAILURE, UNDEFINED
+confidence=
+
+# Disable the message, report, category or checker with the given id(s). You
+# can either give multiple identifiers separated by comma (,) or put this
+# option multiple times (only on the command line, not in the configuration
+# file where it should appear only once).You can also use "--disable=all" to
+# disable everything first and then reenable specific checks. For example, if
+# you want to run only the similarities checker, you can use "--disable=all
+# --enable=similarities". If you want to run only the classes checker, but have
+# no Warning level messages displayed, use"--disable=all --enable=classes
+# --disable=W"
+disable=blacklisted-name,invalid-name,missing-docstring,empty-docstring,unneeded-not,singleton-comparison,misplaced-comparison-constant,unidiomatic-typecheck,consider-using-enumerate,consider-iterating-dictionary,bad-classmethod-argument,bad-mcs-method-argument,bad-mcs-classmethod-argument,single-string-used-for-slots,line-too-long,too-many-lines,trailing-whitespace,missing-final-newline,trailing-newlines,multiple-statements,superfluous-parens,bad-whitespace,mixed-line-endings,unexpected-line-ending-format,bad-continuation,wrong-spelling-in-comment,wrong-spelling-in-docstring,invalid-characters-in-docstring,multiple-imports,wrong-import-order,ungrouped-imports,wrong-import-position,old-style-class,len-as-condition,print-statement,parameter-unpacking,unpacking-in-except,old-raise-syntax,backtick,long-suffix,old-ne-operator,old-octal-literal,import-star-module-level,raw-checker-failed,bad-inline-option,locally-disabled,locally-enabled,file-ignored,suppressed-message,useless-suppression,deprecated-pragma,literal-comparison,no-self-use,no-classmethod-decorator,no-staticmethod-decorator,cyclic-import,duplicate-code,too-many-ancestors,too-many-instance-attributes,too-few-public-methods,too-many-public-methods,too-many-return-statements,too-many-branches,too-many-arguments,too-many-locals,too-many-statements,too-many-boolean-expressions,consider-merging-isinstance,too-many-nested-blocks,simplifiable-if-statement,redefined-argument-from-local,no-else-return,consider-using-ternary,trailing-comma-tuple,fixme,broad-except,logging-format-interpolation,apply-builtin,basestring-builtin,buffer-builtin,cmp-builtin,coerce-builtin,execfile-builtin,file-builtin,long-builtin,raw_input-builtin,reduce-builtin,standarderror-builtin,unicode-builtin,xrange-builtin,coerce-method,delslice-method,getslice-method,setslice-method,no-absolute-import,old-division,dict-iter-method,dict-view-method,next-method-called,metaclass-assignment,indexing-exception,raising-string,reload-builtin,oct-method,hex-method,nonzero-method,cmp-method,input-builtin,round-builtin,intern-builtin,unichr-builtin,map-builtin-not-iterating,zip-builtin-not-iterating,range-builtin-not-iterating,filter-builtin-not-iterating,using-cmp-argument,eq-without-hash,div-method,idiv-method,rdiv-method,exception-message-attribute,invalid-str-codec,sys-max-int,bad-python3-import,deprecated-string-function,deprecated-str-translate-call
+
+# Enable the message, report, category or checker with the given id(s). You can
+# either give multiple identifier separated by comma (,) or put this option
+# multiple time (only on the command line, not in the configuration file where
+# it should appear only once). See also the "--disable" option for examples.
+enable=
+
+
+[REPORTS]
+
+# Python expression which should return a note less than 10 (10 is the highest
+# note). You have access to the variables errors warning, statement which
+# respectively contain the number of errors / warnings messages and the total
+# number of statements analyzed. This is used by the global evaluation report
+# (RP0004).
+evaluation=10.0 - ((float(5 * error + warning + refactor + convention) / statement) * 10)
+
+# Template used to display messages. This is a python new-style format string
+# used to format the message information. See doc for all details
+#msg-template=
+
+# Set the output format. Available formats are text, parseable, colorized, json
+# and msvs (visual studio).You can also give a reporter class, eg
+# mypackage.mymodule.MyReporterClass.
+output-format=colorized
+
+# Tells whether to display a full report or only the messages
+reports=no
+
+# Activate the evaluation score.
+score=yes
+
+
+[REFACTORING]
+
+# Maximum number of nested blocks for function / method body
+max-nested-blocks=5
+
+
+[BASIC]
+
+# Naming hint for argument names
+argument-name-hint=(([a-z][a-z0-9_]{2,30})|(_[a-z0-9_]*))$
+
+# Regular expression matching correct argument names
+argument-rgx=(([a-z][a-z0-9_]{2,30})|(_[a-z0-9_]*))$
+
+# Naming hint for attribute names
+attr-name-hint=(([a-z][a-z0-9_]{2,30})|(_[a-z0-9_]*))$
+
+# Regular expression matching correct attribute names
+attr-rgx=(([a-z][a-z0-9_]{2,30})|(_[a-z0-9_]*))$
+
+# Bad variable names which should always be refused, separated by a comma
+bad-names=foo,bar,baz,toto,tutu,tata
+
+# Naming hint for class attribute names
+class-attribute-name-hint=([A-Za-z_][A-Za-z0-9_]{2,30}|(__.*__))$
+
+# Regular expression matching correct class attribute names
+class-attribute-rgx=([A-Za-z_][A-Za-z0-9_]{2,30}|(__.*__))$
+
+# Naming hint for class names
+class-name-hint=[A-Z_][a-zA-Z0-9]+$
+
+# Regular expression matching correct class names
+class-rgx=[A-Z_][a-zA-Z0-9]+$
+
+# Naming hint for constant names
+const-name-hint=(([A-Z_][A-Z0-9_]*)|(__.*__))$
+
+# Regular expression matching correct constant names
+const-rgx=(([A-Z_][A-Z0-9_]*)|(__.*__))$
+
+# Minimum line length for functions/classes that require docstrings, shorter
+# ones are exempt.
+docstring-min-length=-1
+
+# Naming hint for function names
+function-name-hint=(([a-z][a-z0-9_]{2,30})|(_[a-z0-9_]*))$
+
+# Regular expression matching correct function names
+function-rgx=(([a-z][a-z0-9_]{2,30})|(_[a-z0-9_]*))$
+
+# Good variable names which should always be accepted, separated by a comma
+good-names=i,j,k,ex,Run,_
+
+# Include a hint for the correct naming format with invalid-name
+include-naming-hint=no
+
+# Naming hint for inline iteration names
+inlinevar-name-hint=[A-Za-z_][A-Za-z0-9_]*$
+
+# Regular expression matching correct inline iteration names
+inlinevar-rgx=[A-Za-z_][A-Za-z0-9_]*$
+
+# Naming hint for method names
+method-name-hint=(([a-z][a-z0-9_]{2,30})|(_[a-z0-9_]*))$
+
+# Regular expression matching correct method names
+method-rgx=(([a-z][a-z0-9_]{2,30})|(_[a-z0-9_]*))$
+
+# Naming hint for module names
+module-name-hint=(([a-z_][a-z0-9_]*)|([A-Z][a-zA-Z0-9]+))$
+
+# Regular expression matching correct module names
+module-rgx=(([a-z_][a-z0-9_]*)|([A-Z][a-zA-Z0-9]+))$
+
+# Colon-delimited sets of names that determine each other's naming style when
+# the name regexes allow several styles.
+name-group=
+
+# Regular expression which should only match function or class names that do
+# not require a docstring.
+no-docstring-rgx=^_
+
+# List of decorators that produce properties, such as abc.abstractproperty. Add
+# to this list to register other decorators that produce valid properties.
+property-classes=abc.abstractproperty
+
+# Naming hint for variable names
+variable-name-hint=(([a-z][a-z0-9_]{2,30})|(_[a-z0-9_]*))$
+
+# Regular expression matching correct variable names
+variable-rgx=(([a-z][a-z0-9_]{2,30})|(_[a-z0-9_]*))$
+
+
+[FORMAT]
+
+# Expected format of line ending, e.g. empty (any line ending), LF or CRLF.
+expected-line-ending-format=
+
+# Regexp for a line that is allowed to be longer than the limit.
+ignore-long-lines=^\s*(# )?<?https?://\S+>?$
+
+# Number of spaces of indent required inside a hanging  or continued line.
+indent-after-paren=4
+
+# String used as indentation unit. This is usually "    " (4 spaces) or "\t" (1
+# tab).
+indent-string='    '
+
+# Maximum number of characters on a single line.
+max-line-length=100
+
+# Maximum number of lines in a module
+max-module-lines=1000
+
+# List of optional constructs for which whitespace checking is disabled. `dict-
+# separator` is used to allow tabulation in dicts, etc.: {1  : 1,\n222: 2}.
+# `trailing-comma` allows a space between comma and closing bracket: (a, ).
+# `empty-line` allows space-only lines.
+no-space-check=trailing-comma,dict-separator
+
+# Allow the body of a class to be on the same line as the declaration if body
+# contains single statement.
+single-line-class-stmt=no
+
+# Allow the body of an if to be on the same line as the test if there is no
+# else.
+single-line-if-stmt=no
+
+
+[LOGGING]
+
+# Logging modules to check that the string format arguments are in logging
+# function parameter format
+logging-modules=logging
+
+
+[MISCELLANEOUS]
+
+# List of note tags to take in consideration, separated by a comma.
+notes=FIXME,XXX,TODO
+
+
+[SIMILARITIES]
+
+# Ignore comments when computing similarities.
+ignore-comments=yes
+
+# Ignore docstrings when computing similarities.
+ignore-docstrings=yes
+
+# Ignore imports when computing similarities.
+ignore-imports=no
+
+# Minimum lines number of a similarity.
+min-similarity-lines=4
+
+
+[SPELLING]
+
+# Spelling dictionary name. Available dictionaries: none. To make it working
+# install python-enchant package.
+spelling-dict=
+
+# List of comma separated words that should not be checked.
+spelling-ignore-words=
+
+# A path to a file that contains private dictionary; one word per line.
+spelling-private-dict-file=
+
+# Tells whether to store unknown words to indicated private dictionary in
+# --spelling-private-dict-file option instead of raising a message.
+spelling-store-unknown-words=no
+
+
+[TYPECHECK]
+
+# List of decorators that produce context managers, such as
+# contextlib.contextmanager. Add to this list to register other decorators that
+# produce valid context managers.
+contextmanager-decorators=contextlib.contextmanager
+
+# List of members which are set dynamically and missed by pylint inference
+# system, and so shouldn't trigger E1101 when accessed. Python regular
+# expressions are accepted.
+generated-members=np.int8,np.uint8,np.int16,np.uint16,np.int32,np.uint32,np.int64,np.uint64,np.float32,np.float64,np.float128,wx.PyDeadObjectError
+
+# Tells whether missing members accessed in mixin class should be ignored. A
+# mixin class is detected if its name ends with "mixin" (case insensitive).
+ignore-mixin-members=yes
+
+# This flag controls whether pylint should warn about no-member and similar
+# checks whenever an opaque object is returned when inferring. The inference
+# can return multiple potential results while evaluating a Python object, but
+# some branches might not be evaluated, which results in partial inference. In
+# that case, it might be useful to still emit no-member and other checks for
+# the rest of the inferred objects.
+ignore-on-opaque-inference=yes
+
+# List of class names for which member attributes should not be checked (useful
+# for classes with dynamically set attributes). This supports the use of
+# qualified names.
+ignored-classes=optparse.Values,thread._local,_thread._local
+
+# List of module names for which member attributes should not be checked
+# (useful for modules/projects where namespaces are manipulated during runtime
+# and thus existing member attributes cannot be deduced by static analysis. It
+# supports qualified module names, as well as Unix pattern matching.
+ignored-modules=
+
+# Show a hint with possible names when a member name was not found. The aspect
+# of finding the hint is based on edit distance.
+missing-member-hint=yes
+
+# The minimum edit distance a name should have in order to be considered a
+# similar match for a missing member name.
+missing-member-hint-distance=1
+
+# The total number of similar names that should be taken in consideration when
+# showing a hint for a missing member.
+missing-member-max-choices=1
+
+
+[VARIABLES]
+
+# List of additional names supposed to be defined in builtins. Remember that
+# you should avoid to define new builtins when possible.
+additional-builtins=
+
+# Tells whether unused global variables should be treated as a violation.
+allow-global-unused-variables=yes
+
+# List of strings which can identify a callback function by name. A callback
+# name must start or end with one of those strings.
+callbacks=cb_,_cb
+
+# A regular expression matching the name of dummy variables (i.e. expectedly
+# not used).
+dummy-variables-rgx=_+$|(_[a-zA-Z0-9_]*[a-zA-Z0-9]+?$)|dummy|^ignored_|^unused_
+
+# Argument names that match this expression will be ignored. Default to name
+# with leading underscore
+ignored-argument-names=_.*|^ignored_|^unused_
+
+# Tells whether we should check for unused import in __init__ files.
+init-import=no
+
+# List of qualified module names which can have objects that can redefine
+# builtins.
+redefining-builtins-modules=six.moves,future.builtins
+
+
+[CLASSES]
+
+# List of method names used to declare (i.e. assign) instance attributes.
+defining-attr-methods=__init__,__new__,setUp
+
+# List of member names, which should be excluded from the protected access
+# warning.
+exclude-protected=_asdict,_fields,_replace,_source,_make
+
+# List of valid names for the first argument in a class method.
+valid-classmethod-first-arg=cls
+
+# List of valid names for the first argument in a metaclass class method.
+valid-metaclass-classmethod-first-arg=mcs
+
+
+[DESIGN]
+
+# Maximum number of arguments for function / method
+max-args=5
+
+# Maximum number of attributes for a class (see R0902).
+max-attributes=7
+
+# Maximum number of boolean expressions in a if statement
+max-bool-expr=5
+
+# Maximum number of branch for function / method body
+max-branches=12
+
+# Maximum number of locals for function / method body
+max-locals=15
+
+# Maximum number of parents for a class (see R0901).
+max-parents=7
+
+# Maximum number of public methods for a class (see R0904).
+max-public-methods=20
+
+# Maximum number of return / yield for function / method body
+max-returns=6
+
+# Maximum number of statements in function / method body
+max-statements=50
+
+# Minimum number of public methods for a class (see R0903).
+min-public-methods=2
+
+
+[IMPORTS]
+
+# Allow wildcard imports from modules that define __all__.
+allow-wildcard-with-all=no
+
+# Analyse import fallback blocks. This can be used to support both Python 2 and
+# 3 compatible code, which means that the block might have code that exists
+# only in one or another interpreter, leading to false positives when analysed.
+analyse-fallback-blocks=no
+
+# Deprecated modules which should not be used, separated by a comma
+deprecated-modules=optparse,tkinter.tix
+
+# Create a graph of external dependencies in the given file (report RP0402 must
+# not be disabled)
+ext-import-graph=
+
+# Create a graph of every (i.e. internal and external) dependencies in the
+# given file (report RP0402 must not be disabled)
+import-graph=
+
+# Create a graph of internal dependencies in the given file (report RP0402 must
+# not be disabled)
+int-import-graph=
+
+# Force import order to recognize a module as part of the standard
+# compatibility libraries.
+known-standard-library=
+
+# Force import order to recognize a module as part of a third party library.
+known-third-party=enchant
+
+
+[EXCEPTIONS]
+
+# Exceptions that will emit a warning when being caught. Defaults to
+# "Exception"
+overgeneral-exceptions=Exception

AUTHOR

+Paul McCarthy <pauldmccarthy@gmail.com>
+Michiel Cottaar <michiel.cottaar@ndcn.ox.ac.uk>
+Matthew Webster <matthew.webster@ndcn.ox.ac.uk>
+Sean Fitzgibbon <sean.fitzgibbon@ndcn.ox.ac.uk>
+Martin Craig <martin.craig@eng.ox.ac.uk>
+Taylor Hanayik <taylor.hanayik@ndcn.ox.ac.uk>
+Evan Edmond <evan.edmond@ndcn.ox.ac.uk>
+Christoph Arthofer <christoph.arthofer@ndcn.oxc.ac.uk>
+Fidel Alfaro Almagro <fidel.alfaroalmagro@ndcn.ox.ac.uk>
\ No newline at end of file

CHANGELOG.rst

+This document contains the ``fslpy`` release history in reverse chronological
+order.
+
+XXX (Under development)
+-----------------------
+
+
+Fixed
+^^^^^
+
+* Adjusted the :func:`.featdesign.loadFEATDesignFile` function to handle missing
+  values (!469).
+* Fix to the :class:`.Notifier` class involving handling of callback functions
+  that have been garbage-collected (!470).
+
+
+3.22.0 (Monday 17th February 2025)
+----------------------------------
+
+
+Changed
+^^^^^^^
+
+
+* The :meth:`.Nifti.getAffine` method now supports the ``'scaled'`` coordinate
+  system, which is equivalent to the ``'fsl'`` coordinate system, but without
+  any flip along the first axis (!466).
+
+
+Deprecated
+^^^^^^^^^^
+
+* Deprecated the :meth:`.Nifti.voxToScaledVoxMat` and
+  :meth:`.Nifti.caledVoxToVoxMat` properties in favour of using the
+  :meth:`.Nifti.getAffine` method (!466).
+
+
+3.21.1 (Friday 27th September 2024)
+-----------------------------------
+
+
+Changed
+^^^^^^^
+
+* The :func:`.fixlabels.loadLabelFile` and :func:`.fixlabels.saveLabelFile`
+  functions now support FIX label files which contain classification
+  probabilities, as generated by pyfix >= 0.9.0, and old FIX >= 1.069 (!464).
+
+
+3.21.0 (Tuesday 23rd July 2024)
+-------------------------------
+
+
+Changed
+^^^^^^^
+
+
+* Behaviour of the ``imcp`` / ``immv`` commands has been adjusted so that
+  when an image file is copied/moved, and converted to a different format
+  (e.g. ``.nii`` to ``.nii.gz``), the image data and header slope/intercept
+  fields are not modified (!462).
+
+
+3.20.0 (Wednesday 10th July 2024)
+---------------------------------
+
+
+Added
+^^^^^
+
+
+* New functions/methods in the :mod:`.featanalysis` module and
+  :class:`.FEATImage` class for accessing F-test results (!460).
+
+
+3.19.1 (Wednesday 26th June 2024)
+---------------------------------
+
+
+Fixed
+^^^^^
+
+
+* Minor Updates for compatibility with ``numpy`` 2.0 (!458).
+
+
+3.19.0 (Friday 24th May 2024)
+-----------------------------
+
+
+Added
+^^^^^
+
+
+* New :func:`.bedpostx` and :func:`.bedpostx_gpu` wrapper functions (!455).
+* New :meth:`.Platform.wsl` property for detecting whether we are running
+  under Microsoft WSL (!456).
+
+
+Deprecated
+^^^^^^^^^^
+
+
+* Deprecated the :func:`.bedpostx_postproc_gpu` wrapper function - the
+  ``bedpostx_postproc_gpu.sh`` and ``bedpostx_postproc.sh`` scripts are not
+  intended to be called directly (!455).
+
+
+3.18.3 (Saturday 4th May 2024)
+------------------------------
+
+
+Fixed
+^^^^^
+
+
+* Fixed an issue with :mod:``fsl.wrappers`` functions not finding output files
+  when ``$FSLOUTPUTTYPE`` is set to something other than ``NIFTI_GZ`` (!452).
+
+
+3.18.2 (Wednesday 3rd April 2024)
+---------------------------------
+
+
+Fixed
+^^^^^
+
+
+* Made some changes to the :mod:`fsl.utils.run` module to improve
+  compatibility with [`dill`](https://github.com/uqfoundation/dill/) (!449).
+
+
+
+3.18.1 (Tuesday 5th March 2024)
+-------------------------------
+
+
+Fixed
+^^^^^
+
+
+* Fixed an issue which could cause :mod:`fsl.wrappers` functions to crash
+  when being executed concurrently (!446).
+
+
+3.18.0 (Thursdday 22nd February 2024)
+-------------------------------------
+
+
+Added
+^^^^^
+
+* New wrapper function for the FLIRT `midtrans` command (!443).
+* The :class:`.Image` class now accepts a ``version`` parameter, as an
+  easy way of specifying the NIfTI file format version (!443).
+
+
+3.17.0 (Friday 9th February 2024)
+---------------------------------
+
+
+
+Added
+^^^^^
+
+* New wrapper function for the FLIRT `makerot` command (!441).
+* New wrapper functions for the `imcp`, `immv`, `imrm`, `imln`, `imglob` and
+  `imtest` commands. These are all implemented within fslpy, so the wrapper
+  functions invoke them directly (i.e. within the same process) (!441).
+
+
+3.16.1 (Wednesday 17th January 2024)
+------------------------------------
+
+
+Added
+^^^^^
+
+
+* The :func:`run` function now allows the ``log{'stdout']`` and
+  ``log{'stderr'}`` options (used for capturing the standard output/error
+  streams of a called process) to be either file-likes or callables (!438).
+
+
+3.16.0 (Thursday 21st December 2023)
+------------------------------------
+
+
+Added
+^^^^^
+
+
+* Added more functions to the :class:`.fslmaths` wrapper (!431).
+* New :func:`.smoothest` wrapper function (!432).
+* New :func:`.get_standard` wrapper function (!433).
+* New :func:`.vecreg` wrapper function (!434).
+
+
+3.15.4 (Monday 27th November 2023)
+----------------------------------
+
+
+Added
+^^^^^
+
+
+* New `silent` option to the :func:`.run` function = passing ``silent=True`` is
+  equivalent to passing ``log={'tee':False}`` (!428).
+* New `prefix` option to the :func:`.tempdir` function, which is passed through
+  to ``tempfile.mkdtemp`` (!429).
+
+
+3.15.3 (Thursday 16th November 2023)
+------------------------------------
+
+
+Changed
+^^^^^^^
+
+
+* Adjusted the :func:`.loadLabelFile` function to accept files with missing
+  entries, and files which only contain the MELODIC directory path and list of
+  noisy components (!424, !425).
+
+
+Fixed
+^^^^^
+
+* Fixed a bug in the :func:`.run.hold` function (!426).
+
+
+3.15.2 (Wednesday 4th October 2023)
+-----------------------------------
+
+
+Fixed
+^^^^^
+
+
+* Removed the obsolete :func:`fsl.wrappers.misc.cluster` wrapper function
+  (!422).
+
+
+3.15.1 (Monday 25th September 2023)
+-----------------------------------
+
+
+Fixed
+^^^^^
+
+
+* Fixed a problem with some unit tests (!420).
+
+
+3.15.0 (Monday 25th September 2023)
+-----------------------------------
+
+
+Added
+^^^^^
+
+* New :func:`.cluster` wrapper function for the FSL ``cluster`` /
+  ``fsl-cluster`` command (!417).
+
+Changed
+^^^^^^^
+
+
+* All metadata stored in GIfTI files is now copied by :class:`.GiftiMesh`
+  instances into their :class:`.Meta` store (!416).
+
+
+3.14.1 (Thursday 31st August 2023)
+----------------------------------
+
+
+Fixed
+^^^^^
+
+
+* Fixed a bug in :meth:`.Image.__setitem__` - change listeners were being
+  passed an un-normalised ``slice`` object (with slices for trailing
+  dimensions of length 1 present) (!414).
+
+
+3.14.0 (Wednesday 30th August 2023)
+-----------------------------------
+
+
+Added
+^^^^^
+
+
+* New :func:`.affine.flip` function, for applying a flip/inversion to the
+  axes of an affine transformation (!403).
+
+
+Changed
+^^^^^^^
+
+
+* The ``sform``/``qform`` fields of a :class:`.DeformationField` instance are
+  automatically set from the reference image if they are not already set (!402).
+* Replaced ``setup.py``-based build system with ``pyproject.toml`` (!402).
+* Tests have been moved into the ``fsl/tests/`` package (!402).
+* Updated the ```immv``/``imcp`` scripts to support ``FSLOUTPUTTYPE=ANALYZE``
+  (!405).
+
+
+Fixed
+^^^^^
+
+
+* Updated the ```immv``/``imcp`` scripts to honour the ``$FSLOUTPUTTYPE``
+  environment variable more closely - conversions between NIFTI1 and
+  NIFTI2 were not being performed correctly (!405).
+
+
+3.13.3 (Monday 17th July 2023)
+------------------------------
+
+
+Changed
+^^^^^^^
+
+
+* Callback functions registered with :class:`.Notifier` instances no longer
+  need to accept three arguments (!400).
+
+
+3.13.2 (Monday 3rd July 2023)
+-----------------------------
+
+
+Added
+^^^^^
+
+
+* New ``scaleAtOrigin`` option to the :func:`.affine.compose` function, which
+  allows the origin to be preserved by scaling parameters (!398).
+
+
+
+3.13.1 (Tuesday 13th June 2023)
+-------------------------------
+
+
+Fixed
+^^^^^
+
+
+* Fixed some minor issues with API documentation (!396).
+
+
+3.13.0 (Monday 12th June 2023)
+------------------------------
+
+
+Added
+^^^^^
+
+* New :func:`.runfunc` function which can be used to execute a Python function
+  in a separate process (or as a submitted cluster job), via the
+  :func:`~fsl.utils.run.func_to_cmd` function (!390).
+* New ``keys()``, ``values()``, and ``items()`` methods on the :class:`.Cache`
+  class (!391).
+
+
+Changed
+^^^^^^^
+
+
+* The :func:`.run.func_to_cmd`, :func:`.run.hold`, and :func:`.run.job_output`
+  functions have been moved from :mod:`fsl.utils.fslsub` to the
+  :mod:`fsl.utils.run` module (!390).
+
+
+Deprecated
+^^^^^^^^^^
+
+
+* The :mod:`fsl.utils.fslsub`  module has been deprecated, and scheduled for
+  removal in ``fslpy 4.0.0`` (!390).
+
+
+3.12.1 (Tuesday 23rd May 2023)
+------------------------------
+
+
+Fixed
+^^^^^
+
+
+* The :mod:`fsl.scripts.Text2Vest` now handles column vector inputs
+  correctly (!387, !388).
+* The :func:`.tempdir` function was not changing back to the original
+  working directory when the ``override`` argument was used (!388).
+
+
+
+3.12.0 (Friday 19th May 2023)
+-----------------------------
+
+
+Added
+^^^^^
+
+
+* New :func:`.randomise` wrapper function.
+
+
+Changed
+^^^^^^^
+
+
+* The :func:`.fslmaths` wrapper function now allows the ``-dt`` and
+  ``-odt`` options to be set (!381).
+* Assertions (from the :mod:`.assertions` module) called within wrapper
+  functions are now disabled if the command is to be submitted via
+  ``fsl_sub`` (!382).
+* The :class:`.Image` class will now resolve symlinks when loading images
+  from file (!383).
+
+
+Fixed
+^^^^^
+
+
+* The :func:`.fslstats` wrapper no longer overwrites the ``log`` option that
+  is passed to :func:`~.run.run`, if a :func:`.wrapperconfig` context is
+  active (!381).
+
+
+
+3.11.3 (Thursday 2nd March 2023)
+--------------------------------
+
+
+Fixed
+^^^^^
+
+
+* Fixed another bug in the :func:`.dcm2niix` function (!379).
+
+
+3.11.2 (Monday 27th February 2023)
+----------------------------------
+
+
+Fixed
+^^^^^
+
+
+* Fixed a bug in the :func:`.dcm2niix` function (!376).
+* Adjusted the :mod:`.imrm` and :mod:`.imglob` scripts to support incomplete
+  wildcard patterns (e.g. ``img_??`` matching ``img_01.nii.gz``) (!377).
+
+
+3.11.1 (Friday 24th February 2023)
+----------------------------------
+
+
+Added
+^^^^^
+
+
+* New :func:`.featquery` wrapper function (!374).
+
+
+Fixed
+^^^^^
+
+
+* fixed the :class:`.fslstats` wrapper to handle index masks (the ``-K``
+  option) with missing label values (!374).
+
+
+
+3.11.0 (Monday 20th February 2023)
+----------------------------------
+
+
+Added
+^^^^^
+
+
+* New :func:`.standard_space_roi`, :func:`.fslswapdim`, :func:`.fslmerge`,
+  :func:`.fslsplit`, :func:`fslselectvols`, and :func:`.fslcpgeom` wrapper
+  functions (!351, !354, !364).
+* New :mod:`fsl.wrappers.first` wrapper functions (!355).
+* New :mod:`fsl.wrappers.bianca` and :mod:`fsl.wrappers.avwutils` wrapper
+  functions (!358).
+* New :mod:`fsl.wrappers.bedpostx` and :mod:`~.wrappers.dtifit` wrapper
+  functions (!364).
+* New :func:`~fsl.wrappers.feat.feat`, :func:`~.melodic.fsl_regfilt` and
+  :func:`~.melodic.fsl_glm` wrapper functions (!364).
+* New :func:`.oxford_asl` and :func:`asl_file` wrapper functions (!368).
+* New :func:`.wrapperconfig` context manager function, which allows the
+  default values for arguments passed by the :mod:`fsl.wrappers` functions to
+  the :func:`fsl.utils.run.run` function to be changed (!352, !356).
+* New :func:`.affine.mergeBounds` function (!360).
+
+
+Changed
+^^^^^^^
+
+
+* The :class:`fsl.wrappers.fslmaths.fslmaths` and
+  :class:`fsl.wrappers.fslstats.fslstats` wrapper functions have been updated
+  to accept arguments destined for :func:`fsl.utils.run.run` (!352).
+* :class:`.Mesh` objects can now be created without indices/triangles - they
+  can be assigned after creation (!360).
+* The :mod:`.dicom` module will now preferentially call
+  ``$FSLDIR/bin/dcm2niix``, instead of calling the first ``dcm2niix`` on the
+  ``$PATH`` (!365).
+* The :func:`.applyArgStyle` ``argmap`` argument can now be a callable which
+  defines a rule which will be applied to all argument names (!366).
+* The :func:`.applyArgStyle` ``valmap`` argument now accepts a new
+  ``EXPAND_LIST`` option, which allows sequences to be expanded as separate
+  command-line options (!366).
+* :class:`.Image` objects can now be created without passing a
+  ``nibabel.Nifti1Image`` (or similar) object, as long as a
+  ``nibabel.Nifti1Header`` and a :class:`.DataManager` are provided (!362).
+
+
+Fixed
+^^^^^
+
+
+* Fixed a bug in the :meth:`.Image.strval` method (!353).
+
+
+3.10.0 (Wednesday 29th June 2022)
+---------------------------------
+
+
+Added
+^^^^^
+
+
+* New :func:`fsl.wrappers.eddy.eddy` function, to replace :func:`.eddy_cuda`.
+  Note that this function will not work with FSL versions 6.0.5.2 or older
+  (!348).
+
+
+Deprecated
+^^^^^^^^^^
+
+
+* The :func:`fsl.wrappers.eddy.eddy_cuda` function has been deprecated in
+  favour of the ``eddy`` function (!348).
+
+
+3.9.6 (Wednesday 15th June 2022)
+--------------------------------
+
+
+Added
+^^^^^
+
+
+* The `.fslmaths` wrapper now supports the ``-roi`` option, via the
+  :meth:`.fslmaths.roi` method (!346).
+
+
+3.9.5 (Thursday 2nd June 2022)
+------------------------------
+
+
+Changed
+^^^^^^^
+
+
+* Updated the :func:`.ensureIsImage` function to support ``pathlib.Path``
+  objects (!343).
+
+
+Fixed
+^^^^^
+
+
+* Some fixes in the :mod:`.wrappers` module (specifically in the
+  :class:`.FileOrThing` class) to better support ``pathlib.Path`` objects
+  (!343).
+
+
+3.9.4 (Friday 27th May 2022)
+----------------------------
+
+
+Changed
+^^^^^^^
+
+
+* Changed the behaviour of :meth:`.Image.__getitem__` so that, if image
+  data is accessed with a boolean mask array (e.g. ``image[mask > 0]``),
+  the image data is loaded into memory (!341).
+
+
+3.9.3 (Friday 27th May 2022)
+----------------------------
+
+
+Fixed
+^^^^^
+
+
+* Fixed an issue in the :func:`~.fslsub.func_to_cmd` function (!339).
+
+
+3.9.2 (Friday 20th May 2022)
+----------------------------
+
+
+Changed
+^^^^^^^
+
+
+* Added the :data:`.NIFTI_XFORM_TEMPLATE_OTHER` identifier, an extension to the
+  NIfTI standard (!337).
+
+
+3.9.1 (Friday 13th May 2022)
+----------------------------
+
+
+Changed
+^^^^^^^
+
+
+* Adjusted the :func:`.applyArgStyle` function so that it allows separate
+  specification of the style to use for single-character arguments. This
+  fixes some usage issues with commands such as FSL ``fast``, which have
+  regular ``--=`` arguments, but also single-character arguments which
+  expect multiple positional values (!335).
+
+
+3.9.0 (Tuesday 12th April 2022)
+-------------------------------
+
+
+Added
+^^^^^
+
+
+* New :meth:`.Image.niftiDataTypeSize` method, which reports the number
+  of bits per voxel, according to the NIfTI data type (!327).
+
+
+Changed
+^^^^^^^
+
+
+* The :class:`.Image` class no longer uses an :class:`.ImageWrapper` to
+  manage data access and assignment (!327).
+* Semantics for accessing and modifying image data have changed. By default,
+  image data access is now delegated to the underlying ``nibabel.Nifti1Image``
+  object (and so remains on disk by default). Image data can be loaded into
+  memory by accessing the :meth:`.Image.data` property, or by modifying the
+  data through :meth:`.Image.__setitem__` (!327).
+* The :func:`~.fslsub.func_to_cmd` function now uses `dill
+  <https://dill.readthedocs.io/en/latest/>`_ instead of ``pickle`` for
+  serialisation (!328).
+
+
+Fixed
+^^^^^
+
+
+* Fixes to the :mod:`.melodic` and :meth:`.eddy` wrapper functions.
+
+
+Deprecated
+^^^^^^^^^^
+
+
+* The :mod:`.imagewrapper` module (and the :class:`.ImageWrapper` class) is
+  being migrated to FSLeyes (!327).
+* The ``loadData``, ``calcRange``, and ``threaded`` arguments to the
+  :class:`.Image` class are deprecated and no longer have any effect (!327).
+* The :meth:`.Nifti.mapIndices` method is deprecated (!327).
+* The :meth:`.Image.getImageWrapper`, :meth:`.Image.calcRange` and
+  :meth:`.Image.loadData` methods are deprecated and no longer have any effect
+  (!327).
+
+
+3.8.2 (Tuesday 15th February 2022)
+----------------------------------
+
+
+Fixed
+^^^^^
+
+
+* The the :func:`.topup` wrapper function now allows multiple file names to
+  be passed to the ``--imain`` argument (!324).
+
+
+3.8.1 (Tuesday 28th December 2021)
+----------------------------------
+
+
+Fixed
+^^^^^
+
+
+* The :func:`.melodic` wrapper function no longer requires its ``input``
+  argument to be a NIFTI image or file (!321).
+
+
+
+3.8.0 (Thursday 23rd December 2021)
+-----------------------------------
+
+
+Added
+^^^^^
+
+
+* New :func:`.fslorient` wrapper function (!315).
+* The :class:`.Bitmap` class has basic support for loading JPEG2000 images
+  (!316).
+
+
+Fixed
+^^^^^
+
+
+* Fixed an issue with API  documentation generation (!317).
+
+
+
+3.7.1 (Friday 12th November 2021)
+---------------------------------
+
+
+Changed
+^^^^^^^
+
+
+* BIDS and ``dcm2niix`` ``.json`` sidecar files with control characters
+  are now accepted (!312).
+
+
+Fixed
+^^^^^
+
+
+* Fixed an issue with temporary input files created by :mod:`fsl.wrappers`
+  functions not being deleted (!313).
+
+
+3.7.0 (Friday 20th August 2021)
+-------------------------------
+
+
+Added
+^^^^^
+
+
+* New :mod:`fsl.wrappers.fsl_sub` wrapper function for the ``fsl_sub``
+  command (!309).
+
+
+Changed
+^^^^^^^
+
+
+* Performance of the :mod:`.imglob`, :mod:`.imln`, :mod:`imtest`, :mod:`.imrm`
+  and :mod:`.remove_ext` scripts has been improved, by re-organising them to
+  avoid unnecessary and expensive imports such as ``numpy`` (!310).
+* The default behaviour of the :func:`fsl.utils.run.run` function (and hence
+  that of all :mod:`fsl.wrappers` functions) has been changed so that the
+  standard output and error of the called command is now forwarded to the
+  calling Python process, in addition to being returned from ``run`` as
+  strings. In other words, the default behaviour of ``run('cmd')``, is now
+  equivalent to ``run('cmd', log={"tee":True})``. The previous default
+  behaviour can be achieved with ``run('cmd', log={"tee":False})`` (!309).
+* The :func:`fsl.utils.run.run` and :func:`fsl.utils.run.runfsl` functions
+  (and hence all :mod:`fsl.wrappers` functions) have been modified to use
+  ``fsl.wrappers.fsl_sub`` instead of ``fsl.utils.fslsub.submit``. This is an
+  internal change which should not affect the usage of the ``run``, ``runfsl``
+  or wrapper functions (!309).
+
+
+Deprecated
+^^^^^^^^^^
+
+
+* :class:`fsl.utils.fslsub.SubmitParams` and :func:`fsl.utils.fslsub.submit`
+  have been deprecated in favour of using the ``fsl.wrappers.fsl_sub`` wrapper
+  function (!309).
+* The :func:`fsl.utils.fslsub.info` function has been deprecated in favour of
+  using the ``fsl_sub.report`` function, from the separate `fsl_sub
+  <https://git.fmrib.ox.ac.uk/fsl/fsl_sub>`_ Python library (!309).
+
+
+3.6.4 (Tuesday 3rd August 2021)
+-------------------------------
+
+
+Added
+^^^^^
+
+
+* New :func:`.epi_reg` wrapper function (!306).
+* New :meth:`.fslmaths.kernel` and :meth:`.fslmaths.fmeanu` options on the
+  :class:`.fslmaths` wrapper (!304).
+
+
+3.6.3 (Wednesday 28th July 2021)
+--------------------------------
+
+
+Changed
+^^^^^^^
+
+
+* When creating an ``Image`` object with ``loadData=False``, the ``calcRange``
+  argument is ignored, as it would otherwise cause the data to be loaded
+  (!301).
+
+
+3.6.2 (Wednesday 23rd June 2021)
+--------------------------------
+
+
+Changed
+^^^^^^^
+
+
+* The ``fsl.wrappers.fast`` wrapper passes ``-v`` to ``fast`` if ``v=True`` or
+  ``verbose=True`` is specified.
+
+
+3.6.1 (Thursday 27th May 2021)
+------------------------------
+
+
+Changed
+^^^^^^^
+
+
+* Removed the ``dataclasses`` backport from requirements (!297).
+
+
+3.6.0 (Monday 19th April 2021)
+------------------------------
+
+
+Changed
+^^^^^^^
+
+
+* The ``fslpy`` API ocumentation is now hosted at
+  https://open.win.ox.ac.uk/pages/fsl/fslpy (!290).
+* The :mod:`fsl` and :mod:`fsl.scripts` packages have been changed from being
+  `pkgutil-style
+  <https://packaging.python.org/guides/packaging-namespace-packages/#pkgutil-style-namespace-packages>`_
+  namespace packages to now being `native
+  <https://packaging.python.org/guides/packaging-namespace-packages/#native-namespace-packages>`_
+  namespace packages (!290).
+* The :class:`.TaskThread` now allows an error handler function to be
+  specified, which is run on the :mod:`.idle` loop (!283).
+* The :func:`.bids.loadMetadata` function no long resolves sym-links when
+  determining whether a file is contained within a BIDS data set (!287).
+* The :class:`.Image` class can now be created from a ``pathlib.Path`` object
+  (!292).
+* Some functions in the :mod:`.path` module can now be used with
+  ``pathlib.Path`` objects (!293).
+
+
+Deprecated
+^^^^^^^^^^
+
+
+* Deprecated a number of GUI-specific properties in the
+  :mod:`fsl.utils.platform` module, including ``frozen``, ``haveGui``,
+  ``canHaveGui``, ``inSSHSession``, ``inVNCSession``, ``wxPlatform``,
+  ``wxFlavour``, ``glVersion``, ``glRenderer``, and ``glIsSoftwareRenderer``.
+  Equivalent functions are being added to the ``fsleyes-widgets`` library
+  (!285).
+* The :mod:`fsl.utils.filetree` package has been deprecated, and will be
+  removed in a future version of ``fslpy`` - it is now published as a separate
+  library on [PyPI](https://pypi.org/project/file-tree/) (!286).
+
+
+Fixed
+^^^^^
+
+* Fixed an edge-case in the :mod:`.gifti` module, where a surface with a
+  single triangle was being loaded incorrectly (!288).
+* Fixed an issue in the :func:`~.fslsub.func_to_cmd` function, where it was
+  unintentionally leaving flie handles open (!291).
+
+
+3.5.3 (Tuesday 9th February 2021)
+---------------------------------
+
+
+Fixed
+^^^^^
+
+
+* Fixed a bug in :func:`.featanalysis.loadClusterResults` (!281).
+
+
+3.5.2 (Friday 29th January 2021)
+---------------------------------
+
+
+Fixed
+^^^^^
+
+
+* Adjusted the :func:`.dicom.scanDir` function so that it will set a
+  default value for ``SeriesDescription`` if it is not present in the
+  ``dcm2niix`` ``json`` output (!279).
+* Fixed some issues with API documentation generation (!279).
+
+
+3.5.1 (Thursday 21st January 2021)
+----------------------------------
+
+
+Added
+^^^^^
+
+
+* New :func:`.featanalysis.loadFsf` function, for loading arbitrary ``.fsf``
+  files (!276).
+
+
+Fixed
+^^^^^
+
+
+* Adjustments to :mod:`.dicom` tests to work with different versions of
+  ``dcm2niix`` (!277).
+
+
+3.5.0 (Wednesday 20th January 2021)
+-----------------------------------
+
+
+Added
+^^^^^
+
+
+* New ``fsl_anat.tree``, for use with the :mod:`~fsl.utils.filetree` package
+  (!264).
+* New :func:`.fsl_prepare_fieldmap` wrapper function (!265).
+* The :class:`.fslmaths` wrapper now supports the ``fslmaths -s`` option
+  via the :meth:`.fslmaths.smooth` method (!271).
+
+
+Fixed
+^^^^^
+
+
+* Windows/WSL-specific workaround to the :func:`fsl.utils.run.run` function to
+  avoid console windows from popping up, when used from a graphical program
+  (!272).
+
+
+3.4.0 (Tuesday 20th October 2020)
+---------------------------------
+
+
+Added
+^^^^^
+
+
+* New :mod:`.tbss` wrapper functions for `TBSS
+  <https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/TBSS>`_ commands.
+
+
+Changed
+^^^^^^^
+
+
+* Calls to functions in the :mod:`.assertions` module are disabled when a
+  wrapper function is called with ``cmdonly=True``.
+
+
+3.3.3 (Wednesday 13th October 2020)
+-----------------------------------
+
+
+Changed
+^^^^^^^
+
+
+* The :func:`.fileOrImage` (and related) decorators will not manipulate the
+  return value of a decorated function if an argument ``cmdonly=True`` is
+  passed. This is so that wrapper functions will directly return the command
+  that would be executed when ``cmdonly=True``.
+
+
+3.3.2 (Tuesday 12th October 2020)
+---------------------------------
+
+
+Changed
+^^^^^^^
+
+
+* Most :func:`.wrapper` functions now accept an argument called ``cmdonly``
+  which, if ``True``, will cause the generated command-line call to be
+  returned, instead of executed.
+
+
+3.3.1 (Thursday 8th October 2020)
+---------------------------------
+
+
+Changed
+^^^^^^^
+
+
+* The :func:`.affine.decompose` and :func:`.affine.compose` functions now
+  have the ability to return/accept shear components.
+
+
+Fixed
+^^^^^
+
+
+* Fixed a bug in the :func:`.affine.decompose` function which was corrupting
+  the scale estimates when given an affine containing shears.
+
+
+3.3.0 (Tuesday 22nd September 2020)
+-----------------------------------
+
+
+Added
+^^^^^
+
+* New ported versions of various core FSL tools, including ``imrm``, ``imln``,
+  ``imtest``, ``fsl_abspath``, ``remove_ext``, ``Text2Vest``, and
+  ``Vest2Text``.
+* New :func:`.gps` function, wrapping the FSL ``gps`` command.
+* New :func:`.vest.loadVestFile` and :func:`.vest.generateVest` functions.
+
+
+Changed
+^^^^^^^
+
+
+* Updates to the BIDS filetree specification.
+
+
+Fixed
+^^^^^
+
+
+* The :class:`.CoefficientField` class now works with alternate reference
+  images (i.e. a reference image with different dimensions to that which
+  was originally used when the non-linear transformation was calculated).
+
+
+3.2.2 (Thursday 9th July 2020)
+------------------------------
+
+
+Changed
+^^^^^^^
+
+
+* The :func:`.fslsub.func_to_cmd` function allows more fine-grained control
+  over whether the script file is removed after the job has finished running.
+
+
+3.2.1 (Tuesday 23rd June 2020)
+------------------------------
+
+
+Changed
+^^^^^^^
+
+
+* Minor updates to documentation.
+
+
+3.2.0 (Thursday 11th June 2020)
+-------------------------------
+
+
+Added
+^^^^^
+
+
+* A new :func:`.fslsub.hold` function to wait on previously submitted jobs, to
+  be used in place of the ``wait`` function.
+
+
+Removed
+^^^^^^^
+
+
+* The :func:`.fslsub.wait` (and :func:`.run.wait`) function has been removed, as
+  repeated calls to ``qstat`` can adversely affect the cluster job submission
+  system.
+
+
+3.1.0 (Thursday 21st May 2020)
+------------------------------
+
+
+Added
+^^^^^
+
+
+* New :mod:`.cifti` module, providing classes and functions for working with
+  `CIFTI <https://www.nitrc.org/projects/cifti/>`_ data.
+* New :func:`.winpath` and :func:`wslpath` functions for working with paths
+  when using FSL in a Windows Subsystem for Linux (WSL) environment.
+* New :func:`.wslcmd` function for generating a path to a FSL command installed
+  in a WSL environment.
+* New :meth:`.Platform.fslwsl` attribute for detecting whether FSL is installed
+  in a WSL environment.
+* New :meth:`.Image.niftiDataType` property.
+* The :class:`.FileTree` class has been updated to allow creation of
+  deep copies via the new :meth:`.FileTree.copy` method.
+
+
+Changed
+^^^^^^^
+
+
+* :func:`.Image` objects created from ``numpy`` arrays will be NIFTI1 or
+  NIFTI2, depending on the value of the ``$FSLOUTPUTTYPE`` environment
+  variable.
+
+
+Fixed
+^^^^^
+
+
+* Updated the :func:`.fast` wrapper to support some single-character
+  command-line flags.
+
+
+3.0.1 (Wednesday 15th April 2020)
+---------------------------------
+
+
+Changed
+^^^^^^^
+
+
+* The :func:`.isMelodicDir` function now accepts directories that do not end
+  with ``.ica``, as long as all required files are present.
+* Added the ``dataclasses`` backport, so ``fslpy`` is now compatible with
+  Python 3.6 again.
+
+
+3.0.0 (Sunday 29th March 2020)
+------------------------------
+
+
+Added
+^^^^^
+
+
+* New wrapper functions for the FSL :class:`.fslstats`, :func:`.prelude` and
+  :func:`applyxfm4D` commands.
+* New ``firstDot`` option to the :func:`.path.getExt`,
+  :func:`.path.removeExt`, and :func:`.path.splitExt`, functions, offering
+  rudimentary support for double-barrelled filenames.
+* The :func:`.nonlinear.applyDeformation` function now accepts a ``premat``
+  affine, which is applied to the input image before the deformation field.
+* New :class:`.SubmitParams` class, providing a higer level interface for
+  cluster submission.
+* New :meth:`.FileTree.load_json` and  :meth:`.FileTree.save_json` methods.
+
+
+Changed
+^^^^^^^
+
+
+* ``fslpy`` now requires a minimum Python version of 3.7.
+* The default value for the ``partial_fill`` option to :meth:`.FileTree.read`
+  has been changed to ``False``. Accordingly, the :class:`.FileTreeQuery`
+  calls the :meth:`.FileTree.partial_fill` method on the ``FileTree`` it is
+  given.
+* The :func:`.gifti.relatedFiles` function now supports files with
+  BIDS-style naming conventions.
+* The :func:`.run.run` and :func:`.run.runfsl` functions now pass through any
+  additional keyword arguments to ``subprocess.Popen`` or, if ``submit=True``,
+  to :func:`fslsub.submit`.
+* The :func:`.fslsub.submit` function now accepts an ``env`` option, allowing
+  environment variables to be specified.
+* The :func:`.run.runfsl` function now raises an error on attempts to
+  run a command which is not present in ``$FSLDIR/bin/`` (e.g. ``ls``).
+* The :mod:`.bids` module has been updated to support files with any
+  extension, not just those in the core BIDS specification (``.nii``,
+  ``.nii.gz``, ``.json``, ``.tsv``).
+* The return value of a function decorated with :func:`.fileOrImage`,
+  :func:`.fileOrArray`, or :func:`.fileOrText` is now accessed via an attribute
+  called ``stdout``, instead of ``output``.
+* Output files of functions decorated with :func:`.fileOrImage`,
+  :func:`.fileOrArray`, or :func:`.fileOrText`, which have been loaded via the
+  :attr:`.LOAD` symbol, can now be accessed as attributes of the returned
+  results object, in addition to being accessed as dict items.
+* Wrapper functions decorated with the :func:`.fileOrImage`,
+  :func:`.fileOrArray`, or :func:`.fileOrText` decorators will now pass all
+  arguments and return values through unchanged if an argument called ``submit``
+  is passed in, and is set to ``True`` (or any non-``False``
+  value). Furthermore, in such a scenario a :exc:`ValueError` will be raised if
+  any in-memory objects or ``LOAD`` symbols are passed.
+* The :func:`.fileOrText` decorator has been updated to work with input
+  values - file paths must be passed in as ``pathlib.Path`` objects, so they
+  can be differentiated from input values.
+* Loaded :class:`.Image` objects returned by :mod:`fsl.wrappers` functions
+  are now named according to the wrapper function argument name.
+
+
+Fixed
+^^^^^
+
+
+* Updated the :func:`.prepareArgs` function to use ``shlex.split`` when
+  preparing shell command arguments, instead of performing a naive whitespace
+  split.
+* Fixed some bugs in the :func:`.fslsub.info` and :func:`.fslinfo.wait`
+  functions.
+* Fixed the :func:`.DeformationField.transform` method so it works with
+  a single set of coordinates.
+* :class:`.Image` creation does not fail if ``loadMeta`` is set, and a
+  sidecar file containing invalid JSON is present.
+
+Removed
+^^^^^^^
+
+
+* Removed the deprecated ``.StatisticAtlas.proportions``,
+  ``.StatisticAtlas.coordProportions``, and
+  ``.StatisticAtlas.maskProportions`` methods.
+* Removed the deprecated ``indexed`` option to :meth:`.Image.__init__`.
+* Removed the deprecated ``.Image.resample`` method.
+* Removed the deprecated ``.image.loadIndexedImageFile`` function.
+* Removed the deprecatd ``.FileTreeQuery.short_names`` and
+  ``.Match.short_name`` properties.
+* Removed the deprecated ``.idle.inIdle``, ``.idle.cancelIdle``,
+  ``.idle.idleReset``, ``.idle.getIdleTimeout``, and
+  ``.idle.setIdleTimeout`` functions.
+* Removed the deprecated ``resample.calculateMatrix`` function.
+
+
+2.8.4 (Monday 2nd March 2020)
+-----------------------------
+
+
+Added
+^^^^^
+
+
+* Added a new ``partial_fill`` option to :meth:`.FileTree.read`, which
+  effectively eliminates any variables which only have one value. This was
+  added to accommodate some behavioural changes that were introduced in 2.8.2.
+
+
+
+2.8.3 (Friday 28th February 2020)
+---------------------------------
+
+
+Fixed
+^^^^^
+
+
+* Fixed a bug in the :meth:`.Image.save` method.
+
+
+2.8.2 (Thursday 27th February 2020)
+-----------------------------------
+
+
+Fixed
+^^^^^
+
+
+* Fixed some subtle bugs in the :func:`.filetree.utils.get_all` function.
+
+
+2.8.1 (Thursday 20th February 2020)
+-----------------------------------
+
+
+Fixed
+^^^^^
+
+
+* Fixed a bug where an error would be raised on attempts to load an image file
+  without a BIDS-compatible name from a BIDS-like directory.
+
+
+2.8.0 (Wednesday 29th January 2020)
+-----------------------------------
+
+
+Added
+^^^^^
+
+
+* New :meth:`.Nifti.adjust` method, for creating a copy of a :class:`.Nifti`
+  header with adjusted shape, pixdims, and affine. This can be useful for
+  creating a resampling reference.
+* New :func:`.affine.rescale` function, for adjusting a scaling matrix.
+* New :func:`.mghimage.voxToSurfMat` function, for creating a
+  voxel-to-freesurfer affine transform from any image.
+
+
+Changed
+^^^^^^^
+
+
+* The :class:`.ImageWrapper` now maintains its own image data cache, rather
+  than depending on ``nibabel``.
+* Internal changes to avoid using the deprecated
+  ``nibabel.dataobj_images.DataobjImage.get_data`` method.
+
+
+Fixed
+^^^^^
+
+
+* Improved the algorithm used by the :func:`.mesh.needsFixing` function.
+* The :meth:`.fslmaths.run` method now accepts :attr:`.wrappers.LOAD` as an
+  output specification.
+* Fixed a bug in the :class:`.Mesh` class to prevent indices from being loaded
+  as floating point type.
+* Fixed a bug in the :func:`.resample` function.
+* Fixed a bug in the :class:`.MGHImage` class, which was causing pixdims to
+  be overridden by scales derived from the affine.
+
+
+Deprecated
+^^^^^^^^^^
+
+
+* :func:`.calculateMatrix` - its functionality has been moved to the
+  :func:`.affine.rescale` function.
+
+
+2.7.0 (Wednesday 6th November 2019)
+-----------------------------------
+
+
+Added
+^^^^^
+
+
+* New ``until`` option to the :func:`.idle.block` function.
+* New :meth:`.Idle.neverQueue` setting, which can be used to force all
+  tasks passed to :func:`.idle.idle` to be executed synchronously.
+* New :meth:`.IdleLoop.synchronous` context manager, to temporarily change the
+  value of :meth:`.IdleLoop.neverQueue`.
+* New :mod:`.bids` module, containing a few simple functions for working with
+  `BIDS <https://bids.neuroimaging.io>`_ datasets.
+* New :func:`.image.loadMetadata` function, and ``loadMeta`` option to the
+  :class:`.Image` class, to automatically find and load any sidecar JSON files
+  associated with an image file.
+
+
+Changed
+^^^^^^^
+
+
+* Internal reorganisation in the :mod:`.idle` module.
+
+
+Fixed
+^^^^^
+
+
+* Fixed incorrect usage of ``setuptools.find_packages``, which was causing
+  unit tests to be installed.
+
+
+Deprecated
+^^^^^^^^^^
+
+
+* :func:`.idle.inIdle` - replaced by :meth:`.IdleLoop.inIdle`.
+* :func:`.idle.cancelIdle` - replaced by :meth:`.IdleLoop.cancelIdle`.
+* :func:`.idle.idleReser` - replaced by :meth:`.IdleLoop.idleReset`.
+* :func:`.idle.getIdleTimeout` - replaced by :meth:`.IdleLoop.callRate`.
+* :func:`.idle.setIdleTimeout` - replaced by :meth:`.IdleLoop.callRate`.
+
+
+2.6.2 (Monday 7th October 2019)
+-------------------------------
+
+
+Changed
+^^^^^^^
+
+
+* Added a debugging hook in the :mod:`.idle` module.
+* The :func:`.fslsub.submit` function is now more flexible in the way it
+  accepts the command and input arguments.
+* The :func:`.run.prepareArgs` function has been renamed (from
+  ``_prepareArgs``).
+
+
+2.6.1 (Thursday 19th September 2019)
+------------------------------------
+
+
+Changed
+^^^^^^^
+
+
+* ``fslpy`` is no longer tested against Python 3.5, and is now tested against
+  Python 3.6, 3.7, and 3.8.
+
+
+2.6.0 (Tuesday 10th September 2019)
+-----------------------------------
+
+
+Added
+^^^^^
+
+
+* New :meth:`.Image.iscomplex` attribute.
+* Support for a new ``Statistic`` atlas type.
+
+
+Changed
+^^^^^^^
+
+
+* The :class:`.Cache` class has a new ``lru`` option, allowing it to be used
+  as a least-recently-used cache.
+* The :mod:`fsl.utils.filetree` module has been refactored to make it easier
+  for the :mod:`.query` module to work with file tree hierarchies.
+* The :meth:`.LabelAtlas.get` method has a new ``binary`` flag, allowing
+  either a binary mask, or a mask with the original label value, to be
+  returned.
+* The :mod:`.dicom` module has been updated to work with the latest version of
+  ``dcm2niix``.
+
+
+Deprecated
+^^^^^^^^^^
+
+
+* :meth:`.ProbabilisticAtlas.proportions`,
+  :meth:`.ProbabilisticAtlas.maskProportions`, and
+  :meth:`.ProbabilisticAtlas.labelProportions` have been deprecated in favour
+  of :meth:`.StatisticAtlas.values`, :meth:`.StatisticAtlas.maskValues`, and
+  :meth:`.StatisticAtlas.labelValues`
+
+
+2.5.0 (Tuesday 6th August 2019)
+-------------------------------
+
+
+Added
+^^^^^
+
+
+* New :meth:`.Image.getAffine` method, for retrieving an affine between any of
+  the voxel, FSL, or world coordinate systems.
+* New :mod:`fsl.transforms` package, which contains classes and functions for
+  working with linear and non-linear FLIRT and FNIRT transformations.
+* New static methods :meth:`.Nifti.determineShape`,
+  :meth:`.Nifti.determineAffine`, :meth:`.Nifti.generateAffines`, and
+  :meth:`.Nifti.identifyAffine`.
+* New prototype :mod:`fsl.transforms.x5`  module, for reading/writing linear
+  and non-linear X5 files (*preliminary release, subject to change*).
+* New prototype :mod:`.fsl_convert_x5` :mod:`.fsl_apply_x5` programs, for
+  working with X5 transformations (*preliminary release, subject to change*).
+
+
+
+Changed
+^^^^^^^
+
+
+* The :mod:`.vest.looksLikeVestLutFile` function has been made slightly more
+  lenient.
+* `h5py <https://www.h5py.org/>`_ has been added to the ``fslpy`` dependencies.
+
+
+Deprecated
+^^^^^^^^^^
+
+
+* The :mod:`fsl.utils.transform` module has been deprecated; its functions can
+  now be found in the :mod:`fsl.transforms.affine` and
+  :mod:`fsl.transform.flirt` modules.
+
+
+2.4.0 (Wednesday July 24th 2019)
+--------------------------------
+
+
+Added
+^^^^^
+
+
+* New :mod:`.image.roi` module, for extracting an ROI of an image, or expanding
+  its field-of-view.
+
+
+Changed
+^^^^^^^
+
+
+* The :mod:`.resample_image` script has been updated to support resampling of
+  images with more than 3 dimensions.
+
+
+2.3.1 (Friday July 5th 2019)
+----------------------------
+
+
+Fixed
+^^^^^
+
+
+* The :class:`.Bitmap` class now supports greyscale images and palette images.
+
+
+2.3.0 (Tuesday June 25th 2019)
+------------------------------
+
+
+Added
+^^^^^
+
+
+* New :class:`.Bitmap` class, for loading bitmap images. The
+  :meth:`.Bitmap.asImage` method can be used to convert a ``Bitmap`` into
+  an :class:`.Image`.
+* The :class:`.Image` class now has support for the ``RGB24`` and ``RGBA32``
+  NIfTI data types.
+* New :attr:`.Image.nvals` property, for use with ``RGB24``/``RGBA32``
+  images.
+* New :meth:`.LabelAtlas.get` and :meth:`ProbabilisticAtlas.get` methods,
+  which return an :class:`.Image` for a specific region.
+* The :meth:`.AtlasDescription.find` method also now a ``name`` parameter,
+  allowing labels to be looked up by name.
+* New :meth:`.FileTree.defines` and :meth:`.FileTree.on_disk` methods, to
+  replace the :func:`.FileTree.exists` method.
+
+
+Fixed
+^^^^^
+
+
+* The :func:`.makeWriteable` function will always create a copy of an
+  ``array`` if its base is a ``bytes`` object.
+* Fixed a bug in the :meth:`.GitfitMesh.loadVertices` method.
+* Fixed a bug in the :meth:`.Mesh.addVertices` method where the wrong face
+  normals could be used for newly added vertex sets.
+
+
+2.2.0 (Wednesday May 8th 2019)
+------------------------------
+
+
+Added
+^^^^^
+
+
+* New :mod:`.resample_image` script.
+* New :mod:`.resample` module (replacing the :func:`.Image.resample` method),
+  containing functions to resample an :class:`.Image`.
+* New :func:`.resample.resampleToPixdim` and
+  :func:`.resample.resampleToReference` functions, convenience wrappers around
+  :func:`.resample.resample`.
+* New :func:`.idle.block` function.
+
+
+Changed
+^^^^^^^
+
+
+* The :func:`.resample` function (formerly :meth:`.Image.resample`) now
+  accepts ``origin`` and ``matrix`` parameters, which can be used to adjust
+  the alignment of the voxel grids of the input and output images.
+* The :func:`.transform.decompose` function now accepts both ``(3, 3)``
+  and ``(4, 4)`` matrices.
+
+
+Fixed
+^^^^^
+
+
+* Minor fixes to some :mod:`.filetree.filetree` tree definitions.
+
+
+Deprecated
+^^^^^^^^^^
+
+
+* The :meth:`.Image.resample` method has been deprecated in favour of the
+  :func:`.resample.resample` function.
+
+
+2.1.0 (Saturday April 13th 2019)
+--------------------------------
+
+
+Added
+^^^^^
+
+
+* New tensor conversion routines in the :mod:`~fsl.data.dtifit` module
+  (Michiel Cottaar).
+* New :func:`.makeWriteable` function which ensures that a ``numpy.array`` is
+  writeable, and creates a copy if necessary
+
+
+Changed
+^^^^^^^
+
+
+* The :class:`.GiftiMesh` class no longer creates copies of the mesh
+  vertex/index arrays. This means that, these arrays will be flagged as
+  read-only.
+* The :class:`.Mesh` class handles vertex data sets requiring different
+  triangle unwinding orders, at the cost of potentially having to store
+  two copies of the mesh indices.
+
+
+Fixed
+^^^^^
+
+
+* The :class:`.FeatDesign` class now handles "compressed" voxelwise EV files,
+  such as those generated by `PNM
+  <https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/PNM>`_.
+
+
+2.0.1 (Monday April 1st 2019)
+-----------------------------
+
+
+Fixed
+^^^^^
+
+
+* Fixed a bug with the :func:`.gifti.relatedFiles` function returning
+  duplicate files.
+
+
+2.0.0 (Friday March 20th 2019)
+------------------------------
+
+
+Added
+^^^^^
+
+* New :mod:`fsl.utils.filetree` package for defining and working with
+  file/directory templates (Michiel Cottaar).
+* Simple built-in :mod:`.deprecated` decorator.
+* New :mod:`fsl.data.utils` module, which currently contains one function
+  :func:`.guessType`, which guesses the data type of a file/directory path.
+* New :func:`.commonBase` function for finding the common prefix of a set of
+  file/directory paths.
+
+
+Changed
+^^^^^^^
+
+
+* Removed support for Python 2.7 and 3.4.
+* Minimum required version of ``nibabel`` is now 2.3.
+* The :class:`.Image` class now fully delegates to ``nibabel`` for managing
+  file handles.
+* The :class:`.GiftiMesh` class can now load surface files which contain
+  vertex data, and will accept surface files which end in ``.gii``, rather
+  than requiring files which end in ``.surf.gii``.
+* The ``name`` property of :class:`.Mesh` instances can now be updated.
+
+
+Removed
+^^^^^^^
+
+* Many deprecated items removed.
+
+
+Deprecated
+^^^^^^^^^^
+
+
+* Deprecated the :func:`.loadIndexedImageFile`  function, and the ``indexed``
+  flag to the :class:`.Image` constructor.
+
+
+1.13.3 (Friday February 8th 2019)
+---------------------------------
+
+
+Fixed
+^^^^^
+
+
+* Fixed an issue with the :func:`.dicom.loadSeries` using memory-mapping for
+  image files that would subsequently be deleted.
+* Fixed an issue in the :class:`.GiftiMesh` class, where
+  ``numpy``/``nibabel`` was returning read-only index arrays.
+
+
+1.13.2 (Friday November 30th 2018)
+----------------------------------
+
+
+Changed
+^^^^^^^
+
+
+* The :meth:`.Image.resample` method now supports images with more than three
+  dimensions.
+* The :func:`fsl.utils.fslsub.submit` now returns the job-id as a string
+  rather than a one-element tuple. It now also accepts a nested sequence
+  of job ids rather than just a flat sequence. This will also changes the
+  output from the function wrappers in :mod:`fsl.wrappers` if submitted.
+
+
+Fixed
+^^^^^
+
+
+* Fix to the :class:`.ImageWrapper` regarding complex data types.
+
+
+1.13.1 (Friday November 23rd 2018)
+----------------------------------
+
+
+Fixed
+^^^^^
+
+
+* Added a missing ``image`` attribute in the :class:`.VoxelwiseConfoundEV`
+  class.
+* Make sure that FEAT ``Cluster`` objects (created by the
+  :func:`.loadClusterResults` function) contain ``p`` and ``logp`` attributes,
+  even when cluster thresholding was not used.
+
+
+1.13.0 (Thursday 22nd November 2018)
+------------------------------------
+
+
+Added
+^^^^^
+
+* New wrapper functions for :func:`.fsl_anat`, :func:`.applytopup` (Martin
+  Craig).
+* New :func:`.fileOrText` decorator for use in wrapper functions (Martin
+  Craig).
+
+
+Changed
+^^^^^^^
+
+* Various minor changes and enhancements to the FSL function :mod:`.wrappers`
+  interfaces (Martin Craig).
+
+
+Fixed
+^^^^^
+
+* The ``immv`` and ``imcp`` scripts now accept incorrect file extensions on
+  input arguments.
+
+
+1.12.0 (Sunday October 21st 2018)
+---------------------------------
+
+
+Changed
+^^^^^^^
+
+
+* The ``extract_noise`` script has been renamed to :mod:`.fsl_ents`.
+* Increased the minimum required version of ``dcm2niix`` in the
+  :mod:`fsl.data.dicom` module.
+
+
+Deprecated
+^^^^^^^^^^
+
+
+* The ``extract_noise`` script.
+
+
+1.11.1 (Friday September 14th 2018
+----------------------------------
+
+
+Fixed
+^^^^^
+
+
+* Fixed a Python 2 incompatibility in the :mod:`.settings` module.
+
+
+1.11.0 (Thursday September 13th 2018)
+-------------------------------------
+
+
+Added
+^^^^^
+
+
+* A couple of new convenience functions to the :mod:`.settings` module.
+
+
+Changed
+^^^^^^^
+
+
+* Development (test and documentation dependencies) are no longer listed
+  in ``setup.py`` - they now need to be installed manually.
+* Removed conda build infrastructure.
+
+
+1.10.3 (Sunday September 9th 2018)
+----------------------------------
+
+
+Added
+^^^^^
+
+
+* The :func:`.parseVersionString` function accepts (and ignores) `local
+  version identifer
+  <https://www.python.org/dev/peps/pep-0440/#local-version-identifiers>`_
+  strings.
+
+
+1.10.2 (Friday September 7th 2018)
+----------------------------------
+
+
+Fixed
+^^^^^
+
+
+* The :meth:`.Image.save` method was not handling memory-mapped images
+  correctly.
+
+
+1.10.1 (Friday August 3rd 2018)
+-------------------------------
+
+
+Changed
+^^^^^^^
+
+
+* Minor adjustmenets to improve Windows compatibility.
+
+
+Fixed
+^^^^^
+
+* The :mod:`.FEATImage.getCOPE` method was returning PE images.
+
+
+1.10.0 (Wednesday July 18th 2018)
+---------------------------------
+
+
+Added
+^^^^^
+
+
+* A new script, :mod:`.extract_noise`, which can be used to extract ICA
+  component time courses from a MELODIC ICA analysis.
+* New :func:`.path.allFiles` function which returns all files underneath a
+  directory.
+* The :func:`.fileOrImage` and :func:`.fileOrArray` decorators now support
+  loading of files which are specified with an output basename.
+* New :mod:`.fast` wrapper function for the FSL FAST tool.
+
+
+Changed
+^^^^^^^
+
+
+* When using the :func:`.run.run` function, the command output/error streams
+  are now forwarded immediately.
+* Removed dependency on ``pytest-runner``.
+
+
+1.9.0 (Monday June 4th 2018)
+----------------------------
+
+
+Added
+^^^^^
+
+
+* New :meth:`.Image.data` property method, for easy access to image data
+  as a ``numpy`` array.
+* New ``log`` option to the :func:`.run.run` function, allowing more
+  fine-grained control over sub-process output streams.
+* New :meth:`.Platform.fsldevdir` property, allowing the ``$FSLDEVDIR``
+  environment variable to be queried/changed.
+
+
+Changed
+^^^^^^^
+
+
+* :meth:`.Image.ndims` has been renamed to :meth:`.Image.ndim`, to align
+  more closely with ``numpy`` naming conventions.
+* The ``err`` and ``ret`` parameters to the :func:`.run.run` function have
+  been renamed to ``stderr`` and ``exitcode`` respectively.
+* The :func:`.runfsl` function will give priority to the ``$FSLDEVDIR``
+  environment variable if it is set.
+
+
+Deprecated
+^^^^^^^^^^
+
+
+* :meth:`.Image.ndims`.
+* The ``err`` and ``ret`` parameters to :func:`.run.run`.
+
+
+1.8.1 (Friday May 11th 2018)
+----------------------------
+
+
+Changed
+^^^^^^^
+
+
+* The :func:`.fileOrImage` decorator function now accepts :class:`.Image`
+  objects as well as ``nibabel`` image objects.
+
+
+1.8.0 (Thursday May 3rd 2018)
+-----------------------------
+
+
+Added
+^^^^^
+
+
+* New :mod:`.wrappers` package, containing wrapper functions for a range of
+  FSL tools.
+* New :mod:`fsl.utils.run` module, to replace the :mod:`fsl.utils.callfsl`
+  module.
+* New :mod:`fsl.utils.fslsub` module, containing a :func:`.fslsub.submit`
+  function which submits a cluster job via ``fsl_sub``.
+* Assertions (in the :mod:`.assertions` module) can be disabled with the
+  new :func:`.assertions.disabled` context manager.
+* New :mod:`fsl.utils.parse_data` module containing various neuroimaging
+  data constructors for use with ``argparse``.
+* The :func:`.memoize.skipUnchanged` decorator has an ``invalidate`` function
+  which allows its cache to be cleared.
+
+
+Changed
+^^^^^^^
+
+
+* The :func:`.tempdir` function has an option to not change to the newly
+  created directory.
+
+
+Deprecated
+^^^^^^^^^^
+
+
+* The :mod:`fsl.utils.callfsl` module (replaced with :mod:`fsl.utils.run`).
+
+
+1.7.2 (Monday March 19th 2018)
+------------------------------
+
+
+Added
+^^^^^
+
+
+* Added the :meth:`.MGHImage.voxToSurfMat` and related properties, giving
+  access to the voxel-to-surface affine for an MGH image.
+
+
+1.7.1 (Monday March 12th 2018)
+------------------------------
+
+
+
+Changed
+^^^^^^^
+
+
+* Adjusted :func:`.parseVersionString` so it accepts ``.dev*`` suffixes.
+
+
+Fixed
+^^^^^
+
+
+* Removed deprecated use of :func:`.imagewrapper.canonicalShape`.
+
+
+1.7.0 (Tuesday March 6th 2018)
+------------------------------
+
+
+Added
+^^^^^
+
+
+* The :mod:`fsl.utils.assertions` module contains a range of functions
+  which can be used to assert that some condition is met.
+* The :mod:`fsl.utils.ensure` module contains a range of functions (currently
+  just one) which can be used to ensure that some condiution is met.
+
+
+Changed
+^^^^^^^
+
+
+* The :mod:`.settings` module now saves its files in a format that is
+  compatible with Python 2 and 3.
+* The :func:`.tempdir` function now accepts a ``root`` argument, which
+  specifies the location in which the temporary directory should be created.
+* An image's data source can now be set via  :meth:`.Image.__init__`.
+* :meth:`.MGHImage` objects now have a :meth:`.MGHImage.save` method.
+* Adjustments to the ``conda`` package build and deployment process.
+* The :func:`.ImageWrapper.canonicalShape` function has been moved
+  to the :mod:`.data.image` class.
+* The :func:`.ImageWrapper.naninfrange` function has been moved
+  into its own :mod:`.naninfrange` module.
+
+
+Fixed
+^^^^^
+
+
+* Fixed a bug in the :class:`.MutexFactory` class.
+
+
+Deprecated
+^^^^^^^^^^
+
+
+* :func:`.ImageWrapper.canonicalShape` (moved to the :mod:`.data.image` module)
+* :func:`.ImageWrapper.naninfrange` function (moved to the :mod:`.naninfrange`
+  module)
+
+
+1.6.8 (Monday February 12th 2018)
+---------------------------------
+
+
+* The `atlasq`, `immv`, `imcp` and `imglob` scripts suppress some warnings.
+
+
+1.6.7 (Friday February 9th 2018)
+--------------------------------
+
+
+* More further adjustments to the ``conda`` package build.
+* Adjustments to pypi source distribution - the ``requirements-extra.txt`` file
+  was not being included.
+
+
+1.6.6 (Thursday February 8th 2018)
+----------------------------------
+
+
+* Further adjustments to the ``conda`` package build.
+
+
+1.6.5 (Tuesday February 6th 2018)
+---------------------------------
+
+
+* Adjustments to the ``conda`` package build.
+
+
+1.6.4 (Monday February 5th 2018)
+--------------------------------
+
+
+* The :mod:`.platform` module emits a warning if it cannot import ``wx``.
+
+
+1.6.3 (Friday February 2nd 2018)
+--------------------------------
+
+
+* Minor enhancements to the :class:`.WeakFunctionRef` class.
+* Some bugfixes to the :mod:`fsl.utils.imcp` module, with respect to handling
+  relative path names, moving file groups (e.g. `.img`/`.hdr` pairs), and
+  non-existent directories.
+
+
+1.6.2 (Tuesday January 30th 2018)
+---------------------------------
+
+
+* Updates to the ``conda`` installation process.
+* A new script is installed when ``fslpy`` is installed via ``pip`` or
+  ``conda`` - ``atlasquery``, which emulates the FSL ``atlasquery`` tool.
+
+
+1.6.1 (Monday January 29th 2018)
+--------------------------------
+
+
+* Removed ``lxml`` as a dependency - this was necessary in older versions of
+  ``trimesh``.
+
+
+1.6.0 (Friday January 26th 2018)
+--------------------------------
+
+
+* The new :class:`.Mesh` class is now the base class for all mesh types. It
+  has been written to allow multiple sets of vertices to be associated with a
+  mesh object (to support e.g. white matter, inflated, spherical models for a
+  GIFTI/freeusrfer mesh).
+* The new :class:`.VTKMesh` class must now be used for loading VTK model files,
+  instead of the old :class:`.TriangleMesh` class.
+* The new :class:`.Mesh` class uses the ``trimesh`` library
+  (https://github.com/mikedh/trimesh) to perform various geometrical
+  operations, accessible via new :meth:`.Mesh.rayIntersection`,
+  :meth:`.Mesh.planeIntersection`, :meth:`.Mesh.nearestVertex` methods.
+* The :class:`.Nifti` and :class:`.Mesh` classes have new methods allowing
+  arbitrary metadata to be stored with the image, as key-value
+  pairs. These are provided by a new mixin class, :class:`.Meta`.
+* Freesurer surface files and vertex data can now be loaded via the
+  :class:`.FreesurferMesh` class, in the new :mod:`.freesurfer` module.
+* Freesurfer ``mgz`` / ``mgh`` image files can now be loaded via the new
+  :mod:`.mghimage` module. Internally, these image files are converted to NIFTI
+  - the :class:`.MGHImage` class derives from the :class:`.Image` class.
+* Meta-data access methods on the :class:`.DicomImage` class have been
+  deprecated, as their functionality is provided by the new :class:`.Meta`
+  mixin.
+* The :class:`.TriangleMesh` class has been deprecated in favour of the new
+  :class:`.Mesh` class.
+* Optional dependencies ``wxpython``, ``indexed_gzip``, ``trimesh``, and
+  ``rtree`` are now listed separately, so ``fslpy`` can be used without them
+  (although relevant functionality will be disabled if they are not present).
+
+
+1.5.4 (Wednesday January 10th 2018)
+-----------------------------------
+
+
+* Actually included the fix that was supposed to be in version 1.5.3.
+
+
+1.5.3 (Tuesday January 9th 2018)
+--------------------------------
+
+
+* Bug fix to :meth:`.ImageWrapper.__expandCoverage` - was not correctly handling
+  large images with lots of ``nan`` values.
+
+
+1.5.2 (Tuesday January 2nd 2018)
+--------------------------------
+
+
+* Fixed issue with ``MANIFEST.in`` file.
+
+
+1.5.1 (Thursday December 14th 2017)
+-----------------------------------
+
+
+* Fixed bug in :func:`.dicom.scanDir` function related to data series ordering.
+
+
+1.5.0 (Wednesday December 13th 2017)
+------------------------------------
+
+
+* New module :mod:`.dicom`, which provides a thin wrapper on top of Chris
+  Rorden's `dcm2niix <https://github.com/rordenlab/dcm2niix>`_.
+* New module :mod:`.tempdir`, which has a convenience function for creating
+  temporary directories.
+* Fixed small issue in :meth:`.Image.dtype` - making sure that it access
+  image data via the :class:`.ImageWrapper`, rather than via the `Nifti1Image`
+  object.
+
+
+1.4.2 (Tuesday December 5th 2017)
+---------------------------------
+
+
+* New function :func:`.transform.rmsdev` function, which implements the RMS
+  deviation equation for comparing two affine transformations (FMRIB Technical
+  Report TR99MJ1, available at https://www.fmrib.ox.ac.uk/datasets/techrep/).
+* Some small bugfixes to the :mod:`.atlasq` and :mod:`.atlases` moduless.
+
+
+1.4.1 (Thursday November 9th 2017)
+----------------------------------
+
+
+* Fixed bug in ``setup.py``.
+
+
+1.4.0 (Thursday November 9th 2017)
+----------------------------------
+
+
+* The :func:`.uniquePrefix` function now raises a :exc:`~.path.PathError`
+  instead of a :exc:`.ValueError`, when an invalid path is provided.
+* The :mod:`fsl.utils.async` module is now deprecated, as ``async`` will
+  become a reserved word in Python 3.7. It has been renamed to
+  ``fsl.utils.idle``, with no other API changes.
+* For image file pairs, the ``hdr`` extension now takes precedence over the
+  ``img`` extension, when using the :func:`fsl.data.image.addExt` (and
+  related) functions.
+* The :func:`fsl.utils.path.addExt` function accepts a new parameter,
+  ``unambiguous`` which causes it to allow an ambiguous prefix, and return
+  all matching paths.
+* New :mod:`~fsl.scripts.atlasq` application, intended to replace the FSL
+  ``atlasquery`` tool.
+* New :mod:`~fsl.scripts.imglob` application, intended to replace the FSL
+  ``imglob`` tool.
+* The :meth:`.Image.resample` method explicitly raises a ``ValueError``
+  if incompatible shapes are provided.
+
+
+1.3.1 (Wednesday October 25th 2017)
+-----------------------------------
+
+
+* Fixed bug in :meth:`.Platform.wxPlatform` causing it to always return
+  ``WX_UNKNOWN``.
+
+
+1.3.0 (Wednesday October 25th 2017)
+-----------------------------------
+
+
+* :class:`.Atlas` classes can now pass ``kwargs`` through to the
+  :class:`.Image` constructor.
+* :class:`.LabelAtlas` image values no longer need to match the index of the
+  label into the :class:`.AtlasDescription` ``labels`` list. This means that
+  label atlas XML files may contain non-sequential label values.
+* :class:`.Cache` now implements ``__getitem__`` and ``__setitem__``
+* The :func:`.image.read_segments` function (monkey-patched into ``nibabel``)
+  is deprecated, as it is no longer necessary as of ``nibabel`` 2.2.0.
+* :func:`.platform.isWidgetAlive` is deprecated in favour of an equivalent
+  function in the ``fsleyes-widgets`` library.
+* ``scipy`` is now explicitly listed as a requirement (this should have been
+  done in 1.2.1).
+
+
+
+1.2.2 (Saturday October 21st 2017)
+----------------------------------
+
+
+* The :func:`.image.read_segments` function is only monkey-patched into
+  ``nibabel`` 2.1.0, as it breaks when used with 2.2.0.
+
+
+1.2.1 (Saturday October 7th 2017)
+---------------------------------
+
+
+* If an :class:`.Image` is passed an existing ``nibabel`` header object,
+  it creates a copy, rather than using the original.
+* New :meth:`.Image.resample` method, which resamples the image data to a
+  different resolution.
+* New :meth:`.LabelAtlas.coordLabel`, :meth:`.LabelAtlas.maskLabel`,
+  :meth:`.ProbabilisticAtlas.coordProportions` and
+  :meth:`.ProbabilisticAtlas.maskProportions` methods. The ``coord``
+  methods perform coordinate queries in voxel or world coordinates,
+  and the ``mask`` methods perform mask-based queries.
+
+
+1.2.0 (Thursday September 21st 2017)
+------------------------------------
+
+
+* :meth:`fsl.data.image.Nifti.voxelsToScaledVoxels` method deprecated in
+  favour of new :meth:`.Nifti.voxToScaledVoxMat` and
+  :meth:`Nifti.scaledVoxToVoxMat` properties.
+
+
+1.1.0 (Monday September 11th 2017)
+----------------------------------
+
+
+* The :mod:`fsl` package is now a ``pkgutil``-style `namespace package
+  <https://packaging.python.org/guides/packaging-namespace-packages/>`_, so it
+  can be used for different projects.
+* Updates to :class:`fsl.data.image.Nifti` and :class:`fsl.data.image.Image`
+  to add support for images with more than 4 dimensions:
+  - New ``ndims`` property
+  - ``is4DImage`` method deprecated
+
+
+1.0.5 (Thursday August 10th 2017)
+---------------------------------
+
+
+* New functions and further adjustments in :mod:`fsl.utils.transform` module:
+
+ - :func:`.transform.rotMatToAffine` converts a ``(3, 3)`` rotation matrix
+   into a ``(4, 4)`` affine.
+ - :func:`.transform.transformNormal` applies an affine transform to one or
+   more vectors.
+ - :func:`.transform.veclength` calculates the length of a vector
+ - :func:`.transform.normalise` normalises a vector
+ - :func:`.transform.scaleOffsetXform` adjusted to have more flexibility with
+   respect to inputs.
+ - :func:`.transform.decompose` can return rotations either as three
+   axis-angles, or as a rotation matrix
+
+* Updates to :class:`fsl.data.mesh.TriangleMesh` - ``vertices`` and ``indices``
+  are now ``property`` attributes. New lazily generated ``normals`` and
+  ``vnormals`` properties (face and vertex normals respectively). Option
+  to ``__init__`` to fix the face winding order of a mesh.
+* :func:`fsl.utils.memoize.memoize` decorator made into a class rather than a
+  function. The new :class:`.Memoize` class has an ``invalidate`` method, which
+  clears the cache.
+
+
+1.0.4 (Friday July 14th 2017)
+-----------------------------
+
+
+* Python 2/3 compatibility fix to :mod:`fsl.utils.callfsl`.
+* Fix to :func:`fsl.utils.transform.scaleOffsetXform` - accepts inputs
+  that are not lists.
+* :func:`fsl.utils.transform.compose` accepts either a sequence of three
+  axis angles, or a ``(3, 3)`` rotation matrix.
+
+
+1.0.3 (Sunday June 11th 2017)
+-----------------------------
+
+
+* Fix to :mod:`fsl.utils.async` which was breaking environments where multiple
+  ``wx.App`` instances were being created.
+
+
+1.0.2 (Thursday June 8th 2017)
+------------------------------
+
+
+* Python 2/3 compatibility fixes
+* New :func:`fsl.version.patchVersion` function.
+
+
+1.0.1 (Sunday 4th June 2017)
+----------------------------
+
+
+* New version number parsing functions in :mod:`fsl.version`.
+
+
+1.0.0 (Saturday May 27th 2017)
+------------------------------
+
+
+* Removed many GUI-related modules - they have been moved to the
+  ``fsleyes-widgets`` project. The following modules have been removed:
+  - :mod:`fsl.utils.colourbarbitmap`
+  - :mod:`fsl.utils.dialog`
+  - :mod:`fsl.utils.imagepanel`
+  - :mod:`fsl.utils.layout`
+  - :mod:`fsl.utils.platform`
+  - :mod:`fsl.utils.runwindow`
+  - :mod:`fsl.utils.status`
+  - :mod:`fsl.utils.textbitmap`
+  - :mod:`fsl.utils.typedict`
+  - :mod:`fsl.utils.webpage`
+* :mod:`fsl.utils.settings` module rewritten. It no longer uses ``wx``,
+  but instead stores plain-text and ``pickle`` files in the user's home
+  directory.
+* Software GL renderer test in :mod:`fsl.utils.platform` is more lenient
+* New :class:`.AtlasLabel` class
+* :meth:`.Image.__init__` allows arguments to be passed through to
+  ``nibabel.load``.
+* New :meth:`.Nifti.strval` method to handle escaped strings in NIFTI headers.
+* Python 2/3 compatibility fixes
+
+
+0.11.0 (Thursday April 20th 2017)
+---------------------------------
+
+
+* First public release as part of FSL 5.0.10

COPYRIGHT

+Copyright 2016-2023 University of Oxford, Oxford, UK

LICENSE

-FSLeyes, (c) 2016, The University of Oxford (the "Software")
+The fslpy library
 
-The Software remains the property of the University of Oxford ("the
-University").
+Copyright 2016-2023 University of Oxford, Oxford, UK.
 
-The Software is distributed "AS IS" under this Licence solely for
-non-commercial use in the hope that it will be useful, but in order
-that the University as a charitable foundation protects its assets for
-the benefit of its educational and research purposes, the University
-makes clear that no condition is made or to be implied, nor is any
-warranty given or to be implied, as to the accuracy of the Software,
-or that it will be suitable for any particular purpose or for use
-under any specific conditions. Furthermore, the University disclaims
-all responsibility for the use which is made of the Software. It
-further disclaims any liability for the outcomes arising from using
-the Software.
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
 
-The Licensee agrees to indemnify the University and hold the
-University harmless from and against any and all claims, damages and
-liabilities asserted by third parties (including claims for
-negligence) which arise directly or indirectly from the use of the
-Software or the sale of any products based on the Software.
+    http://www.apache.org/licenses/LICENSE-2.0
 
-No part of the Software may be reproduced, modified, transmitted or
-transferred in any form or by any means, electronic or mechanical,
-without the express permission of the University. The permission of
-the University is not required if the said reproduction, modification,
-transmission or transference is done without financial return, the
-conditions of this Licence are imposed upon the receiver of the
-product, and all original and amended source code is included in any
-transmitted product. You may be held legally responsible for any
-copyright infringement that is caused or encouraged by your failure to
-abide by these terms and conditions.
-
-You are not permitted under this Licence to use this Software
-commercially. Use for which any financial return is received shall be
-defined as commercial use, and includes (1) integration of all or part
-of the source code or the Software into a product for sale or license
-by or on behalf of Licensee to third parties or (2) use of the
-Software or any derivative of it for research with the final aim of
-developing software products for sale or license to a third party or
-(3) use of the Software or any derivative of it for research with the
-final aim of developing non-software products for sale or license to a
-third party, or (4) use of the Software to provide any service to an
-external organisation for which payment is received. If you are
-interested in using the Software commercially, please contact Isis
-Innovation Limited ("Isis"), the technology transfer company of the
-University, to negotiate a licence. Contact details are:
-innovation@isis.ox.ac.uk quoting reference BS/9564.
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+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.

MANIFEST.in

+include           AUTHOR
+include           CHANGELOG.rst
+include           COPYRIGHT
+include           LICENSE
+include           README.rst
+include           conftest.py
+recursive-include doc       *
+recursive-include fsl/tests *

README.md

-fslpy
-=====
-
-The `fslpy` project is a [FSL](http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/)
-programming library written in Python. It is used by
-[FSLeyes](https://git.fmrib.ox.ac.uk/paulmc/fsleyes/).
-
-
-Documentation
--------------
-
-
-Take a look at the [Documentation for
-developers](http://users.fmrib.ox.ac.uk/~paulmc/fslpy/index.html) if you want
-to program with `fslpy`.
-
-
-Dependencies
-------------
-
-
-`fslpy` depends upon the following libraries:
-
-
-| Library                                           | Version |
-| ------------------------------------------------- | ------- |
-| [props](https://git.fmrib.ox.ac.uk/paulmc/props/) | Latest  |
-| [numpy](http://www.numpy.org/)                    | 1.8.1   |
-| [scipy](http://www.scipy.org/)                    | 0.14.0  |
-| [matplotlib](http://matplotlib.org/)              | 1.4.3   |
-| [nibabel](http://nipy.org/nibabel/)               | 1.3.0   |
-| [six](https://pythonhosted.org/six/)              | 1.10.0  |
-| [Sphinx](http://www.sphinx-doc.org/en/stable/)    | 1.3.5   |
-| [wxPython](http://wxpython.org/)                  | 3.0.2.0 |
-
- > Notes:
- >   - Sphinx is only needed for building the documentation.
- > 
- >   - If you are installing `fslpy` manually, don't worry too much about 
- >     having the exact version of each of the packages - just try with 
- >     the latest version, and roll-back if you have problems.

README.rst

+fslpy
+=====
+
+.. image:: https://img.shields.io/pypi/v/fslpy.svg
+   :target: https://pypi.python.org/pypi/fslpy/
+
+.. image:: https://anaconda.org/conda-forge/fslpy/badges/version.svg
+   :target: https://anaconda.org/conda-forge/fslpy
+
+.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.1470750.svg
+   :target: https://doi.org/10.5281/zenodo.1470750
+
+.. image:: https://git.fmrib.ox.ac.uk/fsl/fslpy/badges/master/coverage.svg
+   :target: https://git.fmrib.ox.ac.uk/fsl/fslpy/commits/master/
+
+
+The ``fslpy`` project is a `FSL <http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/>`_
+programming library written in Python. It is used by `FSLeyes
+<https://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/>`_.
+
+
+``fslpy`` is tested against Python versions 3.10, 3.11, 3.12, and 3.13.
+
+
+Installation
+------------
+
+
+Install ``fslpy`` and its core dependencies via pip::
+
+    pip install fslpy
+
+
+``fslpy`` is also available on `conda-forge <https://conda-forge.org/>`_::
+
+    conda install -c conda-forge fslpy
+
+
+Dependencies
+------------
+
+
+All of the core dependencies of ``fslpy`` are listed in the
+`pyproject.toml <pyproject.toml>`_ file.
+
+Some optional dependencies (labelled ``extra`` in ``pyproject.toml``) provide
+addditional functionality:
+
+- ``wxPython``: The `fsl.utils.idle <fsl/utils/idle.py>`_ module has
+  functionality  to schedule functions on the ``wx`` idle loop.
+
+- ``indexed_gzip``: The `fsl.data.image.Image <fsl/data/image.py>`_ class
+  can use ``indexed_gzip`` to keep large compressed images on disk instead
+  of decompressing and loading them into memory..
+
+- ``trimesh``/``rtree``: The `fsl.data.mesh.TriangleMesh <fsl/data/mesh.py>`_
+  class has some methods which use ``trimesh`` to perform geometric queries
+  on the mesh.
+
+- ``Pillow``: The `fsl.data.bitmap.Bitmap <fsl/data/bitmap.py>`_ class uses
+  ``Pillow`` to load image files.
+
+
+If you are using Linux, you need to install wxPython first, as binaries are
+not available on PyPI. Install wxPython like so, changing the URL for your
+specific platform::
+
+    pip install -f https://extras.wxpython.org/wxPython4/extras/linux/gtk2/ubuntu-16.04/ wxpython
+
+
+Once wxPython has been installed, you can type the following to install the
+remaining optional dependencies::
+
+    pip install "fslpy[extra]"
+
+
+Dependencies for testing and documentation are also listed in ``pyproject.toml``,
+and are respectively labelled as ``test`` and ``doc``.
+
+
+Non-Python dependencies
+^^^^^^^^^^^^^^^^^^^^^^^
+
+
+The `fsl.data.dicom <fsl/data/dicom.py>`_ module requires the presence of
+Chris Rorden's `dcm2niix <https://github.com/rordenlab/dcm2niix>`_ program.
+
+
+The ``rtree`` library assumes that ``libspatialindex`` is installed on
+your system.
+
+
+The `fsl.transform.x5 <fsl/transform/x5.py>`_ module uses `h5py
+<https://www.h5py.org/>`_, which requires ``libhdf5``.
+
+
+Documentation
+-------------
+
+API documentation for ``fslpy`` is hosted at
+https://open.win.ox.ac.uk/pages/fsl/fslpy/.
+
+``fslpy`` is documented using `sphinx <http://http://sphinx-doc.org/>`_. You
+can build the API documentation by running::
+
+    pip install ".[doc]"
+    sphinx-build doc html
+
+The HTML documentation will be generated and saved in the ``html/``
+directory.
+
+
+Tests
+-----
+
+Run the test suite via::
+
+    pip install ".[test]"
+    pytest
+
+
+Some tests will only pass if the test environment meets certain criteria -
+refer to the ``tool.pytest.init_options`` section of
+[``pyproject.toml``](pyproject.toml) for a list of [pytest
+marks](https://docs.pytest.org/en/7.1.x/example/markers.html) which can be
+selectively enabled or disabled.
+
+
+Contributing
+------------
+
+
+If you are interested in contributing to ``fslpy``, check out the
+`contributing guide <doc/contributing.rst>`_.
+
+
+Credits
+-------
+
+
+The `fsl.data.dicom <fsl/data/dicom.py>`_ module is little more than a thin
+wrapper around Chris Rorden's `dcm2niix
+<https://github.com/rordenlab/dcm2niix>`_ program.
+
+
+The `example.mgz <tests/testdata/example.mgz>`_ file, used for testing,
+originates from the ``nibabel`` test data set.