.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" }
+        ]
+    }
+}

.gitlab-ci.yml

-test:2.7:
-  image: wxpython-python2.7:4.0.0a2
+#############################################################################
+# 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:
-    - cat requirements.txt | xargs -n 1 pip install
-    - xvfb-run python setup.py test
-    - coverage report -m
+    - 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
 
-test:3.5:
-  image: wxpython-python3.6:4.0.0a2
   script:
-    - cat requirements.txt | xargs -n 1 pip install
-    - xvfb-run python setup.py test
-    - coverage report -m
+    - 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

COPYRIGHT

-Copyright 2016-2017 University of Oxford, Oxford, UK
+Copyright 2016-2023 University of Oxford, Oxford, UK

LICENSE

 The fslpy library
 
-Copyright 2016-2017 University of Oxford, Oxford, UK.
+Copyright 2016-2023 University of Oxford, Oxford, UK.
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.

MANIFEST.in

-include           LICENSE
+include           AUTHOR
+include           CHANGELOG.rst
 include           COPYRIGHT
-include           README.md
-include           requirements.txt
-recursive-include doc *
-recursive-include tests *
+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/).
-
-
-Dependencies
-------------
-
-
-All of the dependencies of `fslpy` are listed in the
-[requirements.txt](requirements.txt) file. Some `fslpy` modules require
-[wxPython](http://www.wxpython.org) 3.0.2.0.
-
-
-Documentation
--------------
-
-`fslpy` is documented using [sphinx](http://http://sphinx-doc.org/). You can
-build the API documentation by installing `sphinx` and `sphinx-rtd-theme`, and
-running:
-
-    python setup.py doc
-
-The HTML documentation will be generated and saved in the `doc/html/` directory.
-
-
-If you are interested in contributing to `fslpy`, check out the [contributing
-guide](doc/contributing.rst).
-
-
-Tests
------
-
-To run the tests, install `mock`, `pytest`, `pytest-runner`, `pytest-html`,
-and `pytest-cov`, and then run:
-
-    python setup.py test
-
-A test report will be generated at `report.html`, and a code coverage report
-will be generated in `htmlcov/`.

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.

tests/conftest.py → conftest.py

@@ -14,42 +14,24 @@ import numpy as np
 
 
 def pytest_addoption(parser):
-    parser.addoption('--niters',
-                     type=int,
-                     action='store',
-                     default=50,
-                     help='Number of test iterations for imagewrapper')
-    
     parser.addoption('--testdir',
                      action='store',
                      help='FSLeyes test data directory')
 
     parser.addoption('--seed',
                      type=int,
-                     help='Seed for random number generator') 
+                     help='Seed for random number generator')
 
 
-    
-@pytest.fixture
-def testdir(request):
-    """FSLeyes test data directory."""
-    return op.expanduser(request.config.getoption('--testdir'))
-
-
-@pytest.fixture
-def niters(request):
-    """Number of test iterations."""
-    return request.config.getoption('--niters')
-
 
 @pytest.fixture
 def seed(request):
-    
+
     seed = request.config.getoption('--seed')
 
     if seed is None:
-        seed = np.random.randint(2 ** 32)
-        
+        seed = np.random.randint(2 ** 30)
+
     np.random.seed(seed)
     random   .seed(seed)
     print('Seed for random number generator: {}'.format(seed))

doc/_static/theme_overrides.css

+/* override table width restrictions */
+.wy-table-responsive table td, .wy-table-responsive table th {
+    white-space: normal;
+}
+
+.wy-table-responsive {
+    margin-bottom: 24px;
+    max-width: 100%;
+    overflow: visible;
+}