.ci/build_doc.sh

@@ -2,6 +2,6 @@
 
 set -e
 
-pip install -r requirements-dev.txt
-python setup.py doc
-mv doc/html doc/"$CI_COMMIT_REF_NAME"
+source /test.venv/bin/activate
+pip install ".[doc]"
+sphinx-build doc public

.ci/build_pypi_dist.sh

@@ -2,28 +2,15 @@
 
 set -e
 
-pip install wheel setuptools twine
-python setup.py sdist
-python setup.py bdist_wheel
+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`
 
-# pip < 10 will not install wheels
-# with an invalid name. So we can
-# generate builds from non-releases
-# (e.g. master master branch),
-# we hack the wheel file name here
-# so that pip will accept it.
-#
-# This will no longer be necessary
-# when pip 10 is available.
-nwheel=`echo -n $wheel | sed -e 's/fslpy-/fslpy-0/g'`
-mv $wheel $nwheel
-wheel=$nwheel
-
 for target in $sdist $wheel; do
     python -m venv test.venv
     . test.venv/bin/activate

.ci/deploy_doc.sh

-#!/usr/bin/env bash
-
-set -e
-
-rsync -rv doc/"$CI_COMMIT_REF_NAME" "docdeploy:"

.ci/setup_ssh.sh

@@ -43,37 +43,17 @@ if [[ -f /.dockerenv ]]; then
  eval $(ssh-agent -s);
  mkdir -p $HOME/.ssh;
 
- echo "$SSH_PRIVATE_KEY_GIT"          > $HOME/.ssh/id_git;
+ # for downloading FSL atlases/standards
  echo "$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
-
- ssh-keyscan ${UPSTREAM_URL##*@} >> $HOME/.ssh/known_hosts;
- ssh-keyscan ${DOC_HOST##*@}     >> $HOME/.ssh/known_hosts;
- ssh-keyscan ${FSL_HOST##*@}     >> $HOME/.ssh/known_hosts;
+ ssh-keyscan ${FSL_HOST##*@} >> $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;

.ci/test_template.sh

@@ -2,27 +2,14 @@
 
 set -e
 
-# 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 -s recursive -X ours upstream/master;
-fi;
-
 source /test.venv/bin/activate
 
-pip install --retries 10 -r requirements.txt
-pip install --retries 10 -r requirements-extra.txt
-pip install --retries 10 -r requirements-dev.txt
+pip install ".[extra,test,style]"
 
 # style stage
-if [ "$TEST_STYLE"x != "x" ]; then pip install --retries 10 pylint flake8; fi;
 if [ "$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
+if [ "$TEST_STYLE"x != "x" ]; then exit 0;                                       fi;
 
 # We need the FSL atlases for the atlas
 # tests, and need $FSLDIR to be defined
@@ -30,15 +17,21 @@ export FSLDIR=/fsl/
 mkdir -p $FSLDIR/data/
 rsync -rv "fsldownload:$FSL_ATLAS_DIR" "$FSLDIR/data/atlases/"
 
-# Finally, run the damned tests.
+# 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 python setup.py test --addopts="$TEST_OPTS tests/test_idle.py"
+xvfb-run -a pytest $TEST_OPTS fsl/tests/test_idle.py
 sleep 5
-xvfb-run -a python setup.py test --addopts="$TEST_OPTS tests/test_platform.py"
+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
@@ -47,16 +40,20 @@ xvfb-run -a python setup.py test --addopts="$TEST_OPTS tests/test_platform.py"
 # this directory writable by anybody (which,
 # unintuitively, includes nobody)
 chmod -R a+w `pwd`
-cmd="source /test.venv/bin/activate && python setup.py test"
-cmd="$cmd --addopts='$TEST_OPTS tests/test_scripts/test_immv_imcp.py tests/test_immv_imcp.py'"
+cmd="source /test.venv/bin/activate && pytest"
+cmd="$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.
-python setup.py test --addopts="$TEST_OPTS -m 'not longtest' --ignore=tests/test_idle.py --ignore=tests/test_platform.py --ignore=tests/test_immv_imcp.py --ignore=tests/test_scripts/test_immv_imcp.py"
+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 [[ $CI_COMMIT_REF_NAME == v* ]]; then
-    python setup.py test --addopts="$TEST_OPTS -m 'longtest'"
+    pytest $TEST_OPTS -m 'longtest'
 fi
 
-python -m coverage report
+python -m coverage report -i

.ci/zenodo_deposit.sh

@@ -9,10 +9,14 @@ zenodo_url=$1
 zenodo_tkn=$2
 zenodo_depid=$3
 
-version=`python setup.py -V`
-upfile=`pwd`/dist/fslpy-"$version".tar.gz
-metafile=`pwd`/.ci/zenodo_meta.json.jinja2
-date=`date +"%Y-%m-%d"`
+version=$(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
 

.gitlab-ci.yml

@@ -9,12 +9,12 @@
 #
 #    2. style:  Check coding style
 #
-#    3. doc:    Building API documentation
+#    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, 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:
@@ -24,13 +24,10 @@
 # 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 build stage, and the remaining jobs in the deploy stage, are only
-# executed on the upstream repository, and only for release tags.
+# The doc stage is executed on release branches of the upstream repository.
 #
-# The deploy stages are manually instantiated.
+# 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.
@@ -61,16 +58,10 @@ 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.
@@ -100,14 +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
@@ -115,11 +101,6 @@ variables:
     - tags@fsl/fslpy
 
 
-.except_releases: &except_releases
-  except:
-    - tags
-
-
 .setup_ssh: &setup_ssh
   before_script:
     - bash ./.ci/setup_ssh.sh
@@ -142,13 +123,31 @@ variables:
 # 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
@@ -157,34 +156,39 @@ variables:
     - bash ./.ci/test_template.sh
 
 
-test:3.6:
+test:3.10:
+  stage: test
+  image: pauldmccarthy/fsleyes-py310-wxpy4-gtk3
+  <<: *test_template
+
+
+test:3.11:
   stage: test
-  image: pauldmccarthy/fsleyes-py36-wxpy4-gtk3
+  image: pauldmccarthy/fsleyes-py311-wxpy4-gtk3
   <<: *test_template
 
 
-test:3.7:
+test:3.12:
   stage: test
-  image: pauldmccarthy/fsleyes-py37-wxpy4-gtk3
+  image: pauldmccarthy/fsleyes-py312-wxpy4-gtk3
   <<: *test_template
 
 
-test:3.8:
+test:3.13:
   stage: test
-  image: pauldmccarthy/fsleyes-py38-wxpy4-gtk3
+  image: pauldmccarthy/fsleyes-py313-wxpy4-gtk3
   <<: *test_template
 
 
 test:build-pypi-dist:
   stage: test
-  image: pauldmccarthy/fsleyes-py36-wxpy4-gtk3
-  <<: *except_releases
+  image: python:3.10
+  <<: *test_rules
 
   tags:
     - docker
 
   script:
-   - source /test.venv/bin/activate
    - bash ./.ci/build_pypi_dist.sh
 
 
@@ -195,32 +199,37 @@ test:build-pypi-dist:
 
 style:
   stage: style
-  image: pauldmccarthy/fsleyes-py36-wxpy4-gtk3
+  image: pauldmccarthy/fsleyes-py310-wxpy4-gtk3
   <<: *test_template
   variables:
     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
+pages:
+  <<: *only_release_branches
 
   tags:
    - docker
 
   stage: doc
-  image: python:3.6
+  image: pauldmccarthy/fsleyes-py310-wxpy4-gtk3
 
   script:
     - bash ./.ci/build_doc.sh
 
   artifacts:
-    expire_in: 1 day
     paths:
-      - doc/$CI_COMMIT_REF_NAME
+      - public
 
 
 #############
@@ -233,7 +242,7 @@ build-pypi-dist:
   <<: *check_version
 
   stage: build
-  image: python:3.6
+  image: python:3.10
 
   tags:
     - docker
@@ -252,29 +261,12 @@ build-pypi-dist:
 ##############
 
 
-deploy-doc:
-  <<: *only_upstream
-  <<: *setup_ssh
-  stage: deploy
-  when:  manual
-  image: python:3.6
-
-  tags:
-    - docker
-
-  dependencies:
-    - build-doc
-
-  script:
-    - bash ./.ci/deploy_doc.sh
-
-
 deploy-pypi:
   <<: *only_releases
   <<: *setup_ssh
   stage: deploy
   when:  manual
-  image: python:3.6
+  image: python:3.10
 
   tags:
     - docker
@@ -291,7 +283,7 @@ deploy-zenodo:
   <<: *setup_ssh
   stage: deploy
   when:  manual
-  image: python:3.6
+  image: python:3.10
 
   tags:
     - docker

AUTHOR

@@ -3,4 +3,7 @@ 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>
+Taylor Hanayik <taylor.hanayik@ndcn.ox.ac.uk>
\ No newline at end of file
+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 2016-2020 University of Oxford, Oxford, UK
+Copyright 2016-2023 University of Oxford, Oxford, UK

LICENSE

 The fslpy library
 
-Copyright 2016-2020 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           AUTHOR
-include           LICENSE
-include           COPYRIGHT
 include           CHANGELOG.rst
+include           COPYRIGHT
+include           LICENSE
 include           README.rst
-include           requirements.txt
-include           requirements-dev.txt
-include           requirements-extra.txt
-include           setup.cfg
-recursive-include doc      *
-recursive-exclude doc/html *
-recursive-include tests    *
+include           conftest.py
+recursive-include doc       *
+recursive-include fsl/tests *

README.rst

@@ -19,7 +19,7 @@ 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 3.5, 3.6 and 3.7.
+``fslpy`` is tested against Python versions 3.10, 3.11, 3.12, and 3.13.
 
 
 Installation
@@ -41,11 +41,10 @@ Dependencies
 
 
 All of the core dependencies of ``fslpy`` are listed in the
-`requirements.txt <requirements.txt>`_ file.
+`pyproject.toml <pyproject.toml>`_ file.
 
-Some extra dependencies are listed in
-`requirements-extra.txt <requirements-extra.txt>`_
-which provide addditional functionality:
+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.
@@ -70,13 +69,13 @@ specific platform::
 
 
 Once wxPython has been installed, you can type the following to install the
-rest of the extra dependencies::
+remaining optional dependencies::
 
-    pip install fslpy[extras]
+    pip install "fslpy[extra]"
 
 
-Dependencies for testing and documentation are listed in the
-`requirements-dev.txt <requirements-dev.txt>`_ file.
+Dependencies for testing and documentation are also listed in ``pyproject.toml``,
+and are respectively labelled as ``test`` and ``doc``.
 
 
 Non-Python dependencies
@@ -98,13 +97,16 @@ The `fsl.transform.x5 <fsl/transform/x5.py>`_ module uses `h5py
 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 -r requirements-dev.txt
-    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.
 
 
@@ -113,11 +115,15 @@ Tests
 
 Run the test suite via::
 
-    pip install -r requirements-dev.txt
-    python setup.py test
+    pip install ".[test]"
+    pytest
+
 
-A test report will be generated at ``report.html``, and a code coverage report
-will be generated in ``htmlcov/``.
+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

tests/conftest.py → conftest.py

@@ -14,12 +14,6 @@ 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')
@@ -29,11 +23,6 @@ def pytest_addoption(parser):
                      help='Seed for random number generator')
 
 
-@pytest.fixture
-def niters(request):
-    """Number of test iterations."""
-    return request.config.getoption('--niters')
-
 
 @pytest.fixture
 def seed(request):

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.
@@ -56,7 +114,7 @@ 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
@@ -152,11 +210,9 @@ html_theme = 'sphinx_rtd_theme'
 # so a file named "default.css" will overwrite the builtin "default.css".
 html_static_path = ['_static']
 
-html_context = {
-    'css_files': [
-        '_static/theme_overrides.css',  # overrides for wide tables in RTD theme
-        ],
-    }
+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
@@ -361,26 +417,12 @@ epub_exclude_files = ['search.html']
 # special-members flag)
 autoclass_content = 'class'
 
-# Document private members and special members (e.g. __init__)
-autodoc_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.
 
@@ -66,7 +66,7 @@ numbers::
   backwards-incompatible changes.
 
 
-The version number in the ``master`` branch should be of the form
+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).
@@ -83,7 +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).
 
@@ -99,17 +99,17 @@ Major/minor releases
 
 
 Follow this process for major and minor releases. Steps 1 and 2 should be
-performed via a merge request onto the master branch, and step 4 via a merge
+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 master branch to include the new version number
+1. Update the changelog on the main branch to include the new version number
    and release date.
-2. On the master branch, update the version number in ``fsl/version.py`` to
+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 master
+   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 master branch.
+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.
@@ -120,13 +120,13 @@ Bugfix/patch releases
 
 
 Follow this process for patch releases. Step 1 should be performed via
-a merge request onto the master branch, and step 2 via a merge request onto
+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 master branch, along with an updated changelog including
+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 master branch onto the minor
+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.

doc/fsl.data.cifti.rst

+``fsl.data.cifti``
+==================
+
+.. automodule:: fsl.data.cifti
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/fsl.data.rst

@@ -6,6 +6,7 @@
 
    fsl.data.atlases
    fsl.data.bitmap
+   fsl.data.cifti
    fsl.data.constants
    fsl.data.dicom
    fsl.data.dtifit

doc/fsl.rst

-``fsl``
-=======
-
-.. toctree::
-   :hidden:
-
-   fsl.data
-   fsl.scripts
-   fsl.utils
-   fsl.transform
-   fsl.version
-   fsl.wrappers
-
-.. automodule:: fsl
-    :members:
-    :undoc-members:
-    :show-inheritance:

doc/fsl.scripts.Text2Vest.rst

+``fsl.scripts.Text2Vest``
+=========================
+
+.. automodule:: fsl.scripts.Text2Vest
+    :members:
+    :undoc-members:
+    :show-inheritance: