.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

-###########################################################################
+#############################################################################
 # This file defines the build process for fslpy, as hosted at:
 #
 #    https://git.fmrib.ox.ac.uk/fsl/fslpy
@@ -9,24 +9,29 @@
 #
 #    2. style:  Check coding style
 #
-#    3. doc:    Building API documentation
+#    3. doc:    Building and upload API documentation using GitLab Pages.
 #
-#    4. build:  Building source distributions and wheels
+#    4. build:  Building source and wheel distributions
 #
-#    5. deploy: Uploading the build outputs to pypi, and the documentation
-#               to a hosting server.
+#    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, and the deploy-doc job, is executed on all branches of the
-# upstream repository.
+# The doc stage is executed on release branches of the upstream repository.
 #
-# The build stage, and the remaining jobs in the  deploy stage, are only
-# executed on the upstream repository, and only for release tags.
+# The build and deploy stages are executed on tags on the upstream
+# repository, and the deploy stage must be manually instantiated.
 #
-# The deploy stages are manually instantiated.
-###########################################################################
+# Most of the logic for each job is defined in shell scripts in the .ci
+# sub-directory.
+#############################################################################
 
 
 stages:
@@ -53,16 +58,13 @@ stages:
 #   - SSH_PRIVATE_KEY_FSL_DOWNLOAD   - private key for downloading some FSL
 #                                      files from a remote server (FSL_HOST)
 #
-#   - SSH_PRIVATE_KEY_DOC_DEPLOY     - private key for rsyncing documentation
-#                                      to remote host (DOC_HOST)
-#
 #   - SSH_SERVER_HOSTKEYS            - List of trusted SSH hosts
 #
-#   - DOC_HOST:                      - Username@host to upload documentation to
-#                                      (e.g. "paulmc@jalapeno.fmrib.ox.ac.uk")
-#
 #   - FSL_HOST:                      - Username@host to download FSL data from
-#                                      (e.g. "paulmc@jalapeno.fmrib.ox.ac.uk")
+#                                      (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
 #
@@ -70,18 +72,17 @@ stages:
 #
 #   - TWINE_REPOSITORY_URL:          - Pypi repository to upload to
 #
-#   - WXPYTHON_UBUNTU1404_URL:       - Url to a location containg binary wheels
-#                                      for wxPython/ubuntu 14.04
+#   - ZENODO_URL:                    - Zenodo URL to deposit release file to.
 #
-#   - WXPYTHON_UBUNTU1604_URL:       - Url to a location containg binary wheels
-#                                      for wxPython/ubuntu 16.04
+#   - 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"
-  TEST_OPTS:            "--cov-report= --cov-append"
+  UPSTREAM_PROJECT: "fsl/fslpy"
+  UPSTREAM_URL:     "git@git.fmrib.ox.ac.uk"
 
 
 ####################################
@@ -90,14 +91,9 @@ variables:
 ####################################
 
 
-.only_upstream: &only_upstream
+.only_release_branches: &only_release_branches
   only:
-    - branches@fsl/fslpy
-
-
-.only_master: &only_master
-  only:
-    - master@fsl/fslpy
+    - /^v.+$/@fsl/fslpy
 
 
 .only_releases: &only_releases
@@ -105,233 +101,95 @@ variables:
     - tags@fsl/fslpy
 
 
-.except_releases: &except_releases
-  except:
-    - tags
-
-
-##########################################################
-# The setup_ssh anchor contains a before_script section
-# which 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).
-##########################################################
-
-
 .setup_ssh: &setup_ssh
   before_script:
-
-    - if [[ -f /.dockerenv ]]; then
-
-        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 $HOME/.ssh;
-
-        echo "$SSH_PRIVATE_KEY_GIT"          > $HOME/.ssh/id_git;
-        echo "$SSH_PRIVATE_KEY_FSL_DOWNLOAD" > $HOME/.ssh/id_fsl_download;
-
-        if [[ "$CI_PROJECT_PATH" == "$UPSTREAM_PROJECT" ]]; then
-          echo "$SSH_PRIVATE_KEY_DOC_DEPLOY" > $HOME/.ssh/id_doc_deploy;
-        fi;
-
-        chmod go-rwx $HOME/.ssh/id_*;
-
-        ssh-add $HOME/.ssh/id_git;
-        ssh-add $HOME/.ssh/id_fsl_download;
-
-        if [[ "$CI_PROJECT_PATH" == "$UPSTREAM_PROJECT" ]]; then
-          ssh-add $HOME/.ssh/id_doc_deploy;
-        fi
-
-        echo "$SSH_SERVER_HOSTKEYS" > $HOME/.ssh/known_hosts;
-
-        touch $HOME/.ssh/config;
-
-        echo "Host ${UPSTREAM_URL##*@}"                    >> $HOME/.ssh/config;
-        echo "    User ${UPSTREAM_URL%@*}"                 >> $HOME/.ssh/config;
-        echo "    IdentityFile $HOME/.ssh/id_git"          >> $HOME/.ssh/config;
-
-        echo "Host docdeploy"                              >> $HOME/.ssh/config;
-        echo "    HostName ${DOC_HOST##*@}"                >> $HOME/.ssh/config;
-        echo "    User ${DOC_HOST%@*}"                     >> $HOME/.ssh/config;
-        echo "    IdentityFile $HOME/.ssh/id_doc_deploy"   >> $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
+    - bash ./.ci/setup_ssh.sh
 
 
 ###################################################
-# The patch_version anchor contains a before_script
+# 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).
 ###################################################
 
 
-.patch_version: &patch_version
+.check_version: &check_version
   before_script:
-
-    - if [[ "x$CI_COMMIT_TAG" != "x" ]]; then
-        echo "Release detected - patching version - $CI_COMMIT_REF_NAME";
-        python -c "import fsl.version as v; v.patchVersion('fsl/version.py', '$CI_COMMIT_REF_NAME')";
-      fi
+    - 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
-
-  # Releases are just tags on a release
-  # branch, so we don't need to test them.
-  <<: *except_releases
+  <<: *test_rules
 
   tags:
     - docker
 
   script:
+    - bash ./.ci/test_template.sh
 
-    # Install $PY_VERSION, xvfb, and all
-    # of the wxpython dependencies.
-    - apt-get update -y || true
-    - apt-get install -y software-properties-common python-software-properties xvfb libgtk2.0-0 libnotify4 freeglut3 libsdl1.2debian
-    - add-apt-repository -y ppa:deadsnakes/ppa
-    - apt-get update -y || true
-    - apt-get install -y $PY_VERSION "$PY_VERSION"-dev $PY_PACKAGES
-    - $PY_VENV test.venv
-    - source test.venv/bin/activate
-    - pip install --upgrade pip setuptools
-
-    # If running on a fork repository, we merge in the
-    # upstream/master branch. This is done so that merge
-    # requests from fork to the parent repository will
-    # have unit tests run on the merged code, something
-    # which gitlab CE does not currently do for us.
-    - if [[ "$CI_PROJECT_PATH" != "$UPSTREAM_PROJECT" ]]; then
-        git fetch upstream;
-        git merge --no-commit --no-ff upstream/master;
-      fi;
-
-    - $INSTALL_WX
-
-    # All other deps can be installed as normal.
-    # We install test dependenciesd through pip,
-    # because if we let setuptools do it, it
-    # will build/install everything from source,
-    # rather than using wheels.
-    - pip install -r requirements.txt
-    - pip install sphinx sphinx-rtd-theme
-    - pip install pytest pytest-cov pytest-html pytest-runner mock coverage
-
-    # style stage
-    - if [ "$TEST_STYLE"x != "x" ]; then pip install pylint flake8; fi;
-    - 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 $FSLDIR/data/
-    - rsync -rv "fsldownload:data/atlases/" "$FSLDIR/data/atlases/"
-
-    # Finally, run the damned tests.
-
-    # We run some tests under xvfb-run
-    # because they invoke wx. Sleep in
-    # between, otherwise xvfb gets upset.
-    - xvfb-run python setup.py test --addopts="$TEST_OPTS tests/test_async.py"
-    - sleep 5
-    - xvfb-run python setup.py test --addopts="$TEST_OPTS tests/test_platform.py"
-
-    # We run the immv/imcpy 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`
-    - su -s /bin/bash -c 'source test.venv/bin/activate && python setup.py test --addopts="$TEST_OPTS tests/test_immv_imcp.py"' nobody
-
-    # All other tests can be run as normal
-    - python setup.py test --addopts="$TEST_OPTS --ignore=tests/test_async.py --ignore=tests/test_platform.py --ignore=tests/test_immv_imcp.py"
-    - python -m coverage report
-
-
-test:2.7:
+
+test:3.10:
   stage: test
-  image: ubuntu:16.04
+  image: pauldmccarthy/fsleyes-py310-wxpy4-gtk3
   <<: *test_template
-  variables:
-    PY_VERSION:  "python2.7"
-    PY_PACKAGES: "python-pip python-virtualenv"
-    PY_VENV:     "virtualenv"
-    INSTALL_WX:  "pip install --only-binary wxpython -f $WXPYTHON_UBUNTU1604_URL wxpython"
 
 
-# we use ubuntu:14.04 for python 3.4, because
-# wxpython is not available for 16.04/3.4
-test:3.4:
+test:3.11:
   stage: test
-  image: ubuntu:14.04
+  image: pauldmccarthy/fsleyes-py311-wxpy4-gtk3
   <<: *test_template
-  variables:
-    PY_VERSION:  "python3.4"
-    PY_PACKAGES: "python3-pip python3.4-venv"
-    PY_VENV:     "python3.4 -m venv"
-    INSTALL_WX:  "pip install --pre -f $WXPYTHON_UBUNTU1404_URL wxpython"
 
 
-test:3.5:
+test:3.12:
   stage: test
-  image: ubuntu:16.04
+  image: pauldmccarthy/fsleyes-py312-wxpy4-gtk3
   <<: *test_template
-  variables:
-    PY_VERSION:  "python3.5"
-    PY_PACKAGES: "python3-pip python3-venv"
-    PY_VENV:     "python3.5 -m venv"
-    INSTALL_WX:  "pip install --only-binary wxpython -f $WXPYTHON_UBUNTU1604_URL wxpython"
 
 
-test:3.6:
+test:3.13:
   stage: test
-  image: ubuntu:16.04
+  image: pauldmccarthy/fsleyes-py313-wxpy4-gtk3
   <<: *test_template
-  variables:
-    PY_VERSION:  "python3.6"
-    PY_PACKAGES: "python3-pip python3.6-venv"
-    PY_VENV:     "python3.6 -m venv"
-    INSTALL_WX:  "pip install --only-binary wxpython -f $WXPYTHON_UBUNTU1604_URL wxpython"
+
+
+test:build-pypi-dist:
+  stage: test
+  image: python:3.10
+  <<: *test_rules
+
+  tags:
+    - docker
+
+  script:
+   - bash ./.ci/build_pypi_dist.sh
 
 
 #############
@@ -341,37 +199,37 @@ test:3.6:
 
 style:
   stage: style
-  image: ubuntu:16.04
+  image: pauldmccarthy/fsleyes-py310-wxpy4-gtk3
   <<: *test_template
   variables:
-    PY_VERSION:  "python3.5"
-    PY_PACKAGES: "python3-pip python3-venv"
-    PY_VENV:     "python3.5 -m venv"
-    INSTALL_WX:  "pip install --only-binary wxpython -f $WXPYTHON_UBUNTU1604_URL wxpython"
     TEST_STYLE:  "true"
 
 
-###########
-# Doc stage
-###########
+#############
+# 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.
 
-build-doc:
-  <<: *only_upstream
-  <<: *patch_version
+pages:
+  <<: *only_release_branches
 
   tags:
    - docker
 
   stage: doc
-  image: python:3.5
+  image: pauldmccarthy/fsleyes-py310-wxpy4-gtk3
 
   script:
-    - python setup.py doc
-    - mv doc/html doc/"$CI_COMMIT_REF_NAME"
+    - bash ./.ci/build_doc.sh
+
   artifacts:
-    expire_in: 1 day
     paths:
-      - doc/$CI_COMMIT_REF_NAME
+      - public
 
 
 #############
@@ -379,20 +237,18 @@ build-doc:
 #############
 
 
-build-dist:
+build-pypi-dist:
   <<: *only_releases
-  <<: *patch_version
+  <<: *check_version
 
   stage: build
-  image: python:3.5
+  image: python:3.10
 
   tags:
     - docker
 
   script:
-   - pip install wheel
-   - python setup.py sdist
-   - python setup.py bdist_wheel
+   - bash ./.ci/build_pypi_dist.sh
 
   artifacts:
     expire_in: 1 day
@@ -405,36 +261,35 @@ build-dist:
 ##############
 
 
-deploy-doc:
-  <<: *only_upstream
+deploy-pypi:
+  <<: *only_releases
   <<: *setup_ssh
   stage: deploy
   when:  manual
-  image: python:3.5
+  image: python:3.10
 
   tags:
     - docker
 
   dependencies:
-    - build-doc
+    - build-pypi-dist
 
   script:
-    - rsync -rv doc/"$CI_COMMIT_REF_NAME" "docdeploy:"
+    - bash ./.ci/deploy_pypi.sh
 
 
-deploy-pypi:
+deploy-zenodo:
   <<: *only_releases
   <<: *setup_ssh
   stage: deploy
   when:  manual
-  image: python:3.5
+  image: python:3.10
 
   tags:
     - docker
 
   dependencies:
-    - build-dist
+    - build-pypi-dist
 
   script:
-    - pip install setuptools wheel twine
-    - twine upload dist/*
+    - bash ./.ci/zenodo_deposit.sh "$ZENODO_URL" "$ZENODO_TOKEN" "$ZENODO_DEPOSIT_ID"

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           requirements.txt
-include           pytest.ini
-recursive-include doc      *
-recursive-exclude doc/html *
-recursive-include tests    *
+include           LICENSE
+include           README.rst
+include           conftest.py
+recursive-include doc       *
+recursive-include fsl/tests *

README.rst

 fslpy
 =====
 
+.. image:: https://img.shields.io/pypi/v/fslpy.svg
+   :target: https://pypi.python.org/pypi/fslpy/
 
-.. image:: https://git.fmrib.ox.ac.uk/fsl/fslpy/badges/master/build.svg
-   :target: https://git.fmrib.ox.ac.uk/fsl/fslpy/commits/master/
+.. 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/
 
-.. image:: https://img.shields.io/pypi/v/fslpy.svg
-   :target: https://pypi.python.org/pypi/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/>`_.
+<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 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 or higher.
+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::
 
-    python setup.py doc
+    pip install ".[doc]"
+    sphinx-build doc html
 
-The HTML documentation will be generated and saved in the ``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>`_.
 
 
-Tests
------
+Credits
+-------
 
-Run the test suite via::
 
-    python setup.py test
+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.
+
 
-A test report will be generated at ``report.html``, and a code coverage report
-will be generated in ``htmlcov/``.
+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;
+}

doc/conf.py

@@ -12,12 +12,70 @@
 # All configuration values have a default; values that are commented out
 # serve to show the default.
 
+import glob
+import itertools as it
 import os
+import os.path as op
 import sys
 import datetime
 
 date = datetime.date.today()
 
+
+def check_for_missing_stubs():
+
+    docdir  = op.dirname(__file__)
+    basedir = op.join(docdir, '..')
+    modules = []
+
+    def tomodname(f):
+        if f.endswith('.py'):
+            f = f[:-3]
+        return op.relpath(op.join(dirpath, f), basedir).replace(op.sep, '.')
+
+    for dirpath, dirnames, filenames in os.walk(op.join(basedir, 'fsl')):
+        for d in dirnames:
+            if d == '__pycache__':
+                continue
+            if len(glob.glob(op.join(dirpath, d, '**', '*.py'), recursive=True)) == 0:
+                continue
+            modules.append(tomodname(d))
+
+        for f in filenames:
+            if not f.endswith('.py'):
+                continue
+            if f in ('__init__.py', '__main__.py'):
+                continue
+            modules.append(tomodname(f))
+
+    modules = [m for m in modules if not m.startswith('fsl.tests')]
+
+    # import fsl
+    # modules = recurse(fsl)
+    # modules = [m.name for m in modules]
+
+    # print()
+    # print()
+    # print()
+
+    for mod in modules:
+
+        docfile = op.join(docdir, f'{mod}.rst')
+
+        if not op.exists(docfile):
+            print(f'No doc file found for module: {mod}')
+
+    for docfile in glob.glob(op.join(docdir, '*.rst')):
+        docfile = op.relpath(docfile, basedir)
+        mod     = op.splitext(op.basename(docfile))[0]
+        if mod not in modules:
+            print(f'No module found for doc file: {docfile}')
+
+
+if __name__ == '__main__':
+    check_for_missing_stubs()
+
+
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
@@ -33,7 +91,8 @@ date = datetime.date.today()
 # ones.
 extensions = [
     'sphinx.ext.autodoc',
-    'sphinx.ext.autosummary', 
+    'sphinx.ext.viewcode',
+    'sphinx.ext.autosummary',
     'sphinx.ext.mathjax',
     'sphinx.ext.graphviz',
     'sphinx.ext.todo',
@@ -55,13 +114,13 @@ master_doc = 'index'
 
 # General information about the project.
 project = u'fslpy'
-copyright = u'{}, Paul McCarthy, University of Oxford, Oxford, UK'.format(
+copyright = u'{}, FMRIB Centre, University of Oxford, Oxford, UK'.format(
     date.year)
 
 # Links to other things
 rst_epilog = """
 .. |fsleyes_apidoc| replace:: FSLeyes
-.. _fsleyes_apidoc: http://users.fmrib.ox.ac.uk/~paulmc/fsleyes_apidoc/index.html
+.. _fsleyes_apidoc: http://users.fmrib.ox.ac.uk/~paulmc/fsleyes/userdoc/latest/index.html
 """
 
 
@@ -121,6 +180,7 @@ pygments_style = 'sphinx'
 # a list of builtin themes.
 html_theme = 'sphinx_rtd_theme'
 
+
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
 # documentation.
@@ -148,7 +208,11 @@ html_theme = 'sphinx_rtd_theme'
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = []
+html_static_path = ['_static']
+
+html_css_files = [
+    'theme_overrides.css',  # overrides for wide tables in RTD theme
+]
 
 # Add any extra paths that contain custom files (such as robots.txt or
 # .htaccess) here, relative to this directory. These files are copied
@@ -353,26 +417,12 @@ epub_exclude_files = ['search.html']
 # special-members flag)
 autoclass_content = 'class'
 
-# Document private members and special members (e.g. __init__)
-autodocsourc_default_flags = ['private-members', 'special-members']
-
-# Documentation for python modules is in the same order
-# as the source code.
-autodoc_member_order = 'bysource'
-
-def autodoc_skip_member(app, what, name, obj, skip, options):
 
-    # Do not document the _sync_* properties
-    # that are added by the props package to
-    # all SyncableHasProperties classes.
-    if what == 'class':
-        attName = name.split('.')[-1]
-        return skip or attName.startswith('_sync_')
-    
-    return skip or False
-
-
-def setup(app):
-    app.connect('autodoc-skip-member', autodoc_skip_member)
+autodoc_default_options = {
+    'special-members' : True,
+    'private-members' : True,
+    'undoc-members'   : True,
+    'member-order'    : 'bysource',
+}
 
 graphviz_output_format = 'svg'

doc/contributing.rst

@@ -9,10 +9,10 @@ Development model
 -----------------
 
 
-- The master branch should always be stable and ready to release. All
-  development occurs on the master branch.
+- The main branch should always be stable and ready to release. All
+  development occurs on the main branch.
 
-- All changes to the master branch occur via merge requests. Individual
+- All changes to the main branch occur via merge requests. Individual
   developers are free to choose their own development workflow in their own
   repositories.
 
@@ -24,6 +24,27 @@ Development model
  - Coding conventions are adhered to (unless there is good reason not to).
 
 
+Commit messages
+---------------
+
+
+To aid readability, all commit messages should be prefixed with one or more of
+the following labels (this convention has been inherited from `nibabel
+<https://github.com/nipy/nibabel>`_):
+
+  * *BF*  : bug fix
+  * *RF*  : refactoring
+  * *ENH*:  enhancement/new feature
+  * *BW*  : addresses backward-compatibility
+  * *OPT* : optimization
+  * *BK*  : breaks something and/or tests fail
+  * *PL*  : making pylint happier
+  * *DOC* : for all kinds of documentation related commits
+  * *TEST*: for adding or changing tests
+  * *MNT* : for administrative/maintenance changes
+  * *CI*  : for continuous-integration changes
+
+
 Version number
 --------------
 
@@ -45,10 +66,10 @@ numbers::
   backwards-incompatible changes.
 
 
-The version number in the ``master`` branch should be of the form
-``major.minor.patch.dev``, to indicate that any releases made from this branch
-are development releases (although development releases are not part of the
-release model).
+The version number in the ``main`` branch should be of the form
+``major.minor.patch.dev0``, to indicate that any releases made from this
+branch are development releases (although development releases are not part of
+the release model).
 
 
 Releases
@@ -62,7 +83,7 @@ name for minor release ``1.0`` would be ``v1.0``.
 
 
 Patches and bugfixes may be added to these release branches as ``patch``
-releases.  These changes should be made on the master branch like any other
+releases.  These changes should be made on the main branch like any other
 change (i.e. via merge requests), and then cherry-picked onto the relevant
 release branch(es).
 
@@ -73,6 +94,44 @@ example, the first release off the ``v1.0`` branch would be tagged with
 ``1.0.1``, ``1.0.2``, etc.
 
 
+Major/minor releases
+^^^^^^^^^^^^^^^^^^^^
+
+
+Follow this process for major and minor releases. Steps 1 and 2 should be
+performed via a merge request onto the main branch, and step 4 via a merge
+request onto the relevant minor branch.
+
+
+1. Update the changelog on the main branch to include the new version number
+   and release date.
+2. On the main branch, update the version number in ``fsl/version.py`` to
+   a development version of **the next** minor release number. For example,
+   if you are about to release version ``1.3.0``, the version in the main
+   branch should be ``1.4.0.dev0``.
+3. Create the new minor release branch off the main branch.
+4. Update the version number on the release branch. If CI tests fail on the
+   release branch, postpone the release until they are fixed.
+5. Tag the new release on the minor release branch.
+
+
+Bugfix/patch releases
+^^^^^^^^^^^^^^^^^^^^^
+
+
+Follow this process for patch releases. Step 1 should be performed via
+a merge request onto the main branch, and step 2 via a merge request onto
+the relevant minor branch.
+
+
+1. Add the fix to the main branch, along with an updated changelog including
+   the version number and date for the bugfix release.
+2. Cherry-pick the relevant commit(s) from the main branch onto the minor
+   release branch, and update the version number on the minor release branch.
+   If CI tests fail on the release branch, go back to step 1.
+3. Tag the new release on the minor release branch.
+
+
 Testing
 -------
 
@@ -81,7 +140,7 @@ Unit and integration tests are currently run with ``py.test`` and
 ``coverage``.
 
 - Aim for 100% code coverage.
-- Tests must pass on python 2.7, 3.4, 3.5, and 3.6
+- Tests must pass on python 3.5, 3.6, and 3.7.
 
 
 Coding conventions
@@ -123,6 +182,7 @@ for a list of error codes):
 - E302: expected 2 blank lines, found 0
 - E303: too many blank lines (3)
 - E701: multiple statements on one line (colon)
+- W504: line break after binary operator
 
 
 The ``pylint`` tool can be *very* opinionated about how you write your code,
@@ -141,7 +201,7 @@ refactoring and convention messages, and a few select warnings (type ``pylint
 To check code with ``flake8`` and ``pylint``, I use the following commands::
 
 
-  flake8 --ignore=E127,E201,E203,E221,E222,E241,E271,E272,E301,E302,E303,E701 fsl
+  flake8 --ignore=E127,E201,E203,E221,E222,E241,E271,E272,E301,E302,E303,E701,W504 fsl
   pylint --extension-pkg-whitelist=numpy,wx \
          --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 \
          --disable=R,C,W0511,W0703,W1202 fsl