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  • paulmc/fslpy
  • ndcn0236/fslpy
  • seanf/fslpy
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.ci/build_doc.sh
View file @ 3b2a186e
...@@ -2,6 +2,6 @@ ...@@ -2,6 +2,6 @@
set -e set -e
pip install -r requirements-dev.txt source /test.venv/bin/activate
python setup.py doc pip install ".[doc]"
mv doc/html doc/"$CI_COMMIT_REF_NAME" sphinx-build doc public
.ci/build_pypi_dist.sh
View file @ 3b2a186e
...@@ -2,27 +2,15 @@ ...@@ -2,27 +2,15 @@
set -e set -e
pip install wheel pip install --upgrade pip wheel setuptools twine build
python setup.py sdist
python setup.py bdist_wheel python -m build
twine check dist/*
# do a test install from both source and wheel # do a test install from both source and wheel
sdist=`find dist -maxdepth 1 -name *.tar.gz` sdist=`find dist -maxdepth 1 -name *.tar.gz`
wheel=`find dist -maxdepth 1 -name *.whl` 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 for target in $sdist $wheel; do
python -m venv test.venv python -m venv test.venv
. test.venv/bin/activate . test.venv/bin/activate
......
.ci/check_version.sh 0 → 100644
View file @ 3b2a186e
#!/usr/bin/env bash
set -e
cat fsl/version.py | egrep "^__version__ += +'$CI_COMMIT_REF_NAME' *$"
.ci/deploy_doc.sh deleted 100644 → 0
View file @ bad9585c
#!/usr/bin/env bash
set -e
rsync -rv doc/"$CI_COMMIT_REF_NAME" "docdeploy:"
.ci/patch_version.sh deleted 100644 → 0
View file @ bad9585c
#!/usr/bin/env bash
set -e
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
.ci/setup_ssh.sh
View file @ 3b2a186e
...@@ -21,43 +21,39 @@ set -e ...@@ -21,43 +21,39 @@ set -e
if [[ -f /.dockerenv ]]; then 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 update -y || yum -y check-update || true;
apt-get install -y openssh-client rsync git || yum install -y openssh-client rsync git || true; apt-get install -y openssh-client rsync git || yum install -y openssh-client rsync git || true;
eval $(ssh-agent -s); eval $(ssh-agent -s);
mkdir -p $HOME/.ssh; mkdir -p $HOME/.ssh;
echo "$SSH_PRIVATE_KEY_GIT" > $HOME/.ssh/id_git; # for downloading FSL atlases/standards
echo "$SSH_PRIVATE_KEY_FSL_DOWNLOAD" > $HOME/.ssh/id_fsl_download; echo "$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_*; chmod go-rwx $HOME/.ssh/id_*;
ssh-add $HOME/.ssh/id_git;
ssh-add $HOME/.ssh/id_fsl_download; ssh-add $HOME/.ssh/id_fsl_download;
if [[ "$CI_PROJECT_PATH" == "$UPSTREAM_PROJECT" ]]; then ssh-keyscan ${FSL_HOST##*@} >> $HOME/.ssh/known_hosts;
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;
touch $HOME/.ssh/config; 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 "Host fsldownload" >> $HOME/.ssh/config;
echo " HostName ${FSL_HOST##*@}" >> $HOME/.ssh/config; echo " HostName ${FSL_HOST##*@}" >> $HOME/.ssh/config;
echo " User ${FSL_HOST%@*}" >> $HOME/.ssh/config; echo " User ${FSL_HOST%@*}" >> $HOME/.ssh/config;
......
.ci/test_template.sh
View file @ 3b2a186e
...@@ -2,43 +2,36 @@ ...@@ -2,43 +2,36 @@
set -e set -e
# If running on a fork repository, we merge in the
# upstream/master branch. This is done so that merge
# requests from fork to the parent repository will
# have unit tests run on the merged code, something
# which gitlab CE does not currently do for us.
if [[ "$CI_PROJECT_PATH" != "$UPSTREAM_PROJECT" ]]; then
git fetch upstream;
git merge --no-commit --no-ff upstream/master;
fi;
source /test.venv/bin/activate source /test.venv/bin/activate
pip install --retries 10 -r requirements.txt pip install ".[extra,test,style]"
pip install --retries 10 -r requirements-extra.txt
pip install --retries 10 -r requirements-dev.txt
# style stage # style stage
if [ "$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 flake8 fsl || true; fi;
if [ "$TEST_STYLE"x != "x" ]; then pylint --output-format=colorized fsl || true; fi; if [ "$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 # We need the FSL atlases for the atlas
# tests, and need $FSLDIR to be defined # tests, and need $FSLDIR to be defined
export FSLDIR=/fsl/ export FSLDIR=/fsl/
mkdir -p $FSLDIR/data/ mkdir -p $FSLDIR/data/
rsync -rv "fsldownload:data/atlases/" "$FSLDIR/data/atlases/" 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" 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 # We run some tests under xvfb-run
# because they invoke wx. Sleep in # because they invoke wx. Sleep in
# between, otherwise xvfb gets upset. # between, otherwise xvfb gets upset.
xvfb-run python setup.py test --addopts="$TEST_OPTS tests/test_idle.py" xvfb-run -a pytest $TEST_OPTS fsl/tests/test_idle.py
sleep 5 sleep 5
xvfb-run python setup.py test --addopts="$TEST_OPTS tests/test_platform.py" xvfb-run -a pytest $TEST_OPTS fsl/tests/test_platform.py
# We run the immv/imcp tests as the nobody # We run the immv/imcp tests as the nobody
# user because some tests expect permission # user because some tests expect permission
...@@ -47,16 +40,20 @@ xvfb-run python setup.py test --addopts="$TEST_OPTS tests/test_platform.py" ...@@ -47,16 +40,20 @@ xvfb-run python setup.py test --addopts="$TEST_OPTS tests/test_platform.py"
# this directory writable by anybody (which, # this directory writable by anybody (which,
# unintuitively, includes nobody) # unintuitively, includes nobody)
chmod -R a+w `pwd` chmod -R a+w `pwd`
cmd="source /test.venv/bin/activate && python setup.py test" cmd="source /test.venv/bin/activate && pytest"
cmd="$cmd --addopts='$TEST_OPTS tests/test_immv_imcp.py'" cmd="$cmd $TEST_OPTS fsl/tests/test_scripts/test_immv_imcp.py fsl/tests/test_immv_imcp.py"
su -s /bin/bash -c "$cmd" nobody su -s /bin/bash -c "$cmd" nobody
# All other tests can be run as normal. # All other tests can be run as normal.
python setup.py test --addopts="$TEST_OPTS -m 'not longtest' --ignore=tests/test_idle.py --ignore=tests/test_platform.py --ignore=tests/test_immv_imcp.py" 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 # Long tests are only run on release branches
if [[ $CI_COMMIT_REF_NAME == v* ]]; then if [[ $CI_COMMIT_REF_NAME == v* ]]; then
python setup.py test --addopts="$TEST_OPTS -m 'longtest'" pytest $TEST_OPTS -m 'longtest'
fi fi
python -m coverage report python -m coverage report -i
.ci/zenodo.py 0 → 100644
View file @ 3b2a186e
#!/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 0 → 100644
View file @ 3b2a186e
#!/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 0 → 100644
View file @ 3b2a186e
{
"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
View file @ 3b2a186e
...@@ -9,12 +9,12 @@ ...@@ -9,12 +9,12 @@
# #
# 2. style: Check coding style # 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 # 4. build: Building source and wheel distributions
# #
# 5. deploy: Uploading the build outputs to pypi/hosting servers, and the # 5. deploy: Uploading the build outputs to pypi/hosting servers.
# documentation to a hosting server. #
# #
# Custom docker images are used for several jobs - these images are # Custom docker images are used for several jobs - these images are
# available at: # available at:
...@@ -24,13 +24,10 @@ ...@@ -24,13 +24,10 @@
# The test and style stages are executed on all branches of upstream and fork # The test and style stages are executed on all branches of upstream and fork
# repositories. # repositories.
# #
# The doc stage, and the deploy-doc job, is executed on all branches of the # The doc stage is executed on release branches of the upstream repository.
# 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 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 # Most of the logic for each job is defined in shell scripts in the .ci
# sub-directory. # sub-directory.
...@@ -61,22 +58,25 @@ stages: ...@@ -61,22 +58,25 @@ stages:
# - SSH_PRIVATE_KEY_FSL_DOWNLOAD - private key for downloading some FSL # - SSH_PRIVATE_KEY_FSL_DOWNLOAD - private key for downloading some FSL
# files from a remote server (FSL_HOST) # 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 # - 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 # - 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 # - TWINE_USERNAME: - Username to use when uploading to pypi
# #
# - TWINE_PASSWORD: - Password to use when uploading to pypi # - TWINE_PASSWORD: - Password to use when uploading to pypi
# #
# - TWINE_REPOSITORY_URL: - Pypi repository to upload to # - 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.
############################################################################### ###############################################################################
...@@ -91,14 +91,9 @@ variables: ...@@ -91,14 +91,9 @@ variables:
#################################### ####################################
.only_upstream: &only_upstream .only_release_branches: &only_release_branches
only: only:
- branches@fsl/fslpy - /^v.+$/@fsl/fslpy
.only_master: &only_master
only:
- master@fsl/fslpy
.only_releases: &only_releases .only_releases: &only_releases
...@@ -106,40 +101,53 @@ variables: ...@@ -106,40 +101,53 @@ variables:
- tags@fsl/fslpy - tags@fsl/fslpy
.except_releases: &except_releases
except:
- tags
.setup_ssh: &setup_ssh .setup_ssh: &setup_ssh
before_script: before_script:
- bash ./.ci/setup_ssh.sh - 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 # section which is run on release builds, and makes
# sure that the version in the code is up to date # sure that the version in the code is up to date
# (i.e. equal to the tag name). # (i.e. equal to the tag name).
################################################### ###################################################
.patch_version: &patch_version .check_version: &check_version
before_script: before_script:
- bash ./.ci/patch_version.sh - bash ./.ci/check_version.sh
############ ############
# Test stage # 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 .test: &test_template
<<: *setup_ssh <<: *setup_ssh
<<: *test_rules
# Releases are just tags on a release
# branch, so we don't need to test them.
<<: *except_releases
tags: tags:
- docker - docker
...@@ -148,24 +156,42 @@ variables: ...@@ -148,24 +156,42 @@ variables:
- bash ./.ci/test_template.sh - bash ./.ci/test_template.sh
test:3.5: test:3.10:
stage: test
image: pauldmccarthy/fsleyes-py310-wxpy4-gtk3
<<: *test_template
test:3.11:
stage: test stage: test
image: pauldmccarthy/fsleyes-py35-wxpy4-gtk2 image: pauldmccarthy/fsleyes-py311-wxpy4-gtk3
<<: *test_template <<: *test_template
test:3.6: test:3.12:
stage: test stage: test
image: pauldmccarthy/fsleyes-py36-wxpy4-gtk2 image: pauldmccarthy/fsleyes-py312-wxpy4-gtk3
<<: *test_template <<: *test_template
test:3.7: test:3.13:
stage: test stage: test
image: pauldmccarthy/fsleyes-py37-wxpy4-gtk2 image: pauldmccarthy/fsleyes-py313-wxpy4-gtk3
<<: *test_template <<: *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
############# #############
...@@ -173,33 +199,37 @@ test:3.7: ...@@ -173,33 +199,37 @@ test:3.7:
style: style:
stage: style stage: style
image: pauldmccarthy/fsleyes-py35-wxpy4-gtk2 image: pauldmccarthy/fsleyes-py310-wxpy4-gtk3
<<: *test_template <<: *test_template
variables: variables:
TEST_STYLE: "true" 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: pages:
<<: *only_upstream <<: *only_release_branches
<<: *patch_version
tags: tags:
- docker - docker
stage: doc stage: doc
image: python:3.6 image: pauldmccarthy/fsleyes-py310-wxpy4-gtk3
script: script:
- bash ./.ci/build_doc.sh - bash ./.ci/build_doc.sh
artifacts: artifacts:
expire_in: 1 day
paths: paths:
- doc/$CI_COMMIT_REF_NAME - public
############# #############
...@@ -209,10 +239,10 @@ build-doc: ...@@ -209,10 +239,10 @@ build-doc:
build-pypi-dist: build-pypi-dist:
<<: *only_releases <<: *only_releases
<<: *patch_version <<: *check_version
stage: build stage: build
image: python:3.6 image: python:3.10
tags: tags:
- docker - docker
...@@ -231,29 +261,29 @@ build-pypi-dist: ...@@ -231,29 +261,29 @@ build-pypi-dist:
############## ##############
deploy-doc: deploy-pypi:
<<: *only_upstream <<: *only_releases
<<: *setup_ssh <<: *setup_ssh
stage: deploy stage: deploy
when: manual when: manual
image: python:3.6 image: python:3.10
tags: tags:
- docker - docker
dependencies: dependencies:
- build-doc - build-pypi-dist
script: script:
- bash ./.ci/deploy_doc.sh - bash ./.ci/deploy_pypi.sh
deploy-pypi: deploy-zenodo:
<<: *only_releases <<: *only_releases
<<: *setup_ssh <<: *setup_ssh
stage: deploy stage: deploy
when: manual when: manual
image: python:3.6 image: python:3.10
tags: tags:
- docker - docker
...@@ -262,4 +292,4 @@ deploy-pypi: ...@@ -262,4 +292,4 @@ deploy-pypi:
- build-pypi-dist - build-pypi-dist
script: script:
- bash ./.ci/deploy_pypi.sh - bash ./.ci/zenodo_deposit.sh "$ZENODO_URL" "$ZENODO_TOKEN" "$ZENODO_DEPOSIT_ID"
AUTHOR
View file @ 3b2a186e
...@@ -2,4 +2,8 @@ Paul McCarthy <pauldmccarthy@gmail.com> ...@@ -2,4 +2,8 @@ Paul McCarthy <pauldmccarthy@gmail.com>
Michiel Cottaar <michiel.cottaar@ndcn.ox.ac.uk> Michiel Cottaar <michiel.cottaar@ndcn.ox.ac.uk>
Matthew Webster <matthew.webster@ndcn.ox.ac.uk> Matthew Webster <matthew.webster@ndcn.ox.ac.uk>
Sean Fitzgibbon <sean.fitzgibbon@ndcn.ox.ac.uk> Sean Fitzgibbon <sean.fitzgibbon@ndcn.ox.ac.uk>
Martin Craig <martin.craig@eng.ox.ac.uk> Martin Craig <martin.craig@eng.ox.ac.uk>
\ No newline at end of file Taylor Hanayik <taylor.hanayik@ndcn.ox.ac.uk>
Evan Edmond <evan.edmond@ndcn.ox.ac.uk>
Christoph Arthofer <christoph.arthofer@ndcn.oxc.ac.uk>
Fidel Alfaro Almagro <fidel.alfaroalmagro@ndcn.ox.ac.uk>
\ No newline at end of file
CHANGELOG.rst
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COPYRIGHT
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Copyright 2016-2018 University of Oxford, Oxford, UK Copyright 2016-2023 University of Oxford, Oxford, UK
LICENSE
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The fslpy library 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"); Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License. you may not use this file except in compliance with the License.
......
MANIFEST.in
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include LICENSE include AUTHOR
include CHANGELOG.rst
include COPYRIGHT include COPYRIGHT
include requirements.txt include LICENSE
include requirements-dev.txt include README.rst
include requirements-extra.txt include conftest.py
include pytest.ini recursive-include doc *
recursive-include doc * recursive-include fsl/tests *
recursive-exclude doc/html *
recursive-include tests *
README.rst
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fslpy 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://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 .. image:: https://img.shields.io/pypi/v/fslpy.svg
:target: https://pypi.python.org/pypi/fslpy/ :target: https://pypi.python.org/pypi/fslpy/
.. image:: https://anaconda.org/conda-forge/fslpy/badges/version.svg .. image:: https://anaconda.org/conda-forge/fslpy/badges/version.svg
:target: https://anaconda.org/conda-forge/fslpy :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/>`_ The ``fslpy`` project is a `FSL <http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/>`_
programming library written in Python. It is used by `FSLeyes programming library written in Python. It is used by `FSLeyes
<https://git.fmrib.ox.ac.uk/fsl/fsleyes/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 Installation
...@@ -41,11 +40,11 @@ Dependencies ...@@ -41,11 +40,11 @@ Dependencies
------------ ------------
All of the core dependencies of ``fslpy`` are listed in the `requirements.txt All of the core dependencies of ``fslpy`` are listed in the
<requirements.txt>`_ file. `pyproject.toml <pyproject.toml>`_ file.
Some extra dependencies are listed in `requirements.txt Some optional dependencies (labelled ``extra`` in ``pyproject.toml``) provide
<requirements-extra.txt>`_ which provide addditional functionality: addditional functionality:
- ``wxPython``: The `fsl.utils.idle <fsl/utils/idle.py>`_ module has - ``wxPython``: The `fsl.utils.idle <fsl/utils/idle.py>`_ module has
functionality to schedule functions on the ``wx`` idle loop. functionality to schedule functions on the ``wx`` idle loop.
...@@ -58,45 +57,56 @@ Some extra dependencies are listed in `requirements.txt ...@@ -58,45 +57,56 @@ Some extra dependencies are listed in `requirements.txt
class has some methods which use ``trimesh`` to perform geometric queries class has some methods which use ``trimesh`` to perform geometric queries
on the mesh. 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 If you are using Linux, you need to install wxPython first, as binaries are
not available on PyPI. Change the URL for your specific platform:: 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 pip install -f https://extras.wxpython.org/wxPython4/extras/linux/gtk2/ubuntu-16.04/ wxpython
The ``rtree`` library also assumes that ``libspatialindex`` is installed on Once wxPython has been installed, you can type the following to install the
your system. remaining optional dependencies::
Once wxPython has been installed, you can simply type the following to install
the rest of the extra dependencies::
pip install fslpy[extras] pip install "fslpy[extra]"
Dependencies for testing and documentation are listed in the Dependencies for testing and documentation are also listed in ``pyproject.toml``,
`requirements-dev.txt <requirements-dev.txt>`_ file. and are respectively labelled as ``test`` and ``doc``.
Non-Python dependencies Non-Python dependencies
^^^^^^^^^^^^^^^^^^^^^^^ ^^^^^^^^^^^^^^^^^^^^^^^
The ``fsl.data.dicom`` module requires the presence of Chris Rorden's The `fsl.data.dicom <fsl/data/dicom.py>`_ module requires the presence of
`dcm2niix <https://github.com/rordenlab/dcm2niix>`_ program. 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 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 ``fslpy`` is documented using `sphinx <http://http://sphinx-doc.org/>`_. You
can build the API documentation by running:: can build the API documentation by running::
pip install -r requirements-dev.txt pip install ".[doc]"
python setup.py 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. directory.
...@@ -105,11 +115,15 @@ Tests ...@@ -105,11 +115,15 @@ Tests
Run the test suite via:: Run the test suite via::
pip install -r requirements-dev.txt pip install ".[test]"
python setup.py test pytest
A test report will be generated at ``report.html``, and a code coverage report Some tests will only pass if the test environment meets certain criteria -
will be generated in ``htmlcov/``. 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 Contributing
......
tests/conftest.py → conftest.py
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...@@ -14,12 +14,6 @@ import numpy as np ...@@ -14,12 +14,6 @@ import numpy as np
def pytest_addoption(parser): def pytest_addoption(parser):
parser.addoption('--niters',
type=int,
action='store',
default=50,
help='Number of test iterations for imagewrapper')
parser.addoption('--testdir', parser.addoption('--testdir',
action='store', action='store',
help='FSLeyes test data directory') help='FSLeyes test data directory')
...@@ -29,11 +23,6 @@ def pytest_addoption(parser): ...@@ -29,11 +23,6 @@ def pytest_addoption(parser):
help='Seed for random number generator') help='Seed for random number generator')
@pytest.fixture
def niters(request):
"""Number of test iterations."""
return request.config.getoption('--niters')
@pytest.fixture @pytest.fixture
def seed(request): def seed(request):
......
doc/_static/theme_overrides.css 0 → 100644
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/* 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
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...@@ -12,12 +12,70 @@ ...@@ -12,12 +12,70 @@
# All configuration values have a default; values that are commented out # All configuration values have a default; values that are commented out
# serve to show the default. # serve to show the default.
import glob
import itertools as it
import os import os
import os.path as op
import sys import sys
import datetime import datetime
date = datetime.date.today() 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, # 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 # 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. # documentation root, use os.path.abspath to make it absolute, like shown here.
...@@ -33,7 +91,8 @@ date = datetime.date.today() ...@@ -33,7 +91,8 @@ date = datetime.date.today()
# ones. # ones.
extensions = [ extensions = [
'sphinx.ext.autodoc', 'sphinx.ext.autodoc',
'sphinx.ext.autosummary', 'sphinx.ext.viewcode',
'sphinx.ext.autosummary',
'sphinx.ext.mathjax', 'sphinx.ext.mathjax',
'sphinx.ext.graphviz', 'sphinx.ext.graphviz',
'sphinx.ext.todo', 'sphinx.ext.todo',
...@@ -55,13 +114,13 @@ master_doc = 'index' ...@@ -55,13 +114,13 @@ master_doc = 'index'
# General information about the project. # General information about the project.
project = u'fslpy' 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) date.year)
# Links to other things # Links to other things
rst_epilog = """ rst_epilog = """
.. |fsleyes_apidoc| replace:: FSLeyes .. |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' ...@@ -121,6 +180,7 @@ pygments_style = 'sphinx'
# a list of builtin themes. # a list of builtin themes.
html_theme = 'sphinx_rtd_theme' html_theme = 'sphinx_rtd_theme'
# Theme options are theme-specific and customize the look and feel of a 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 # further. For a list of options available for each theme, see the
# documentation. # documentation.
...@@ -148,7 +208,11 @@ html_theme = 'sphinx_rtd_theme' ...@@ -148,7 +208,11 @@ html_theme = 'sphinx_rtd_theme'
# Add any paths that contain custom static files (such as style sheets) here, # 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, # relative to this directory. They are copied after the builtin static files,
# so a file named "default.css" will overwrite the builtin "default.css". # 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 # Add any extra paths that contain custom files (such as robots.txt or
# .htaccess) here, relative to this directory. These files are copied # .htaccess) here, relative to this directory. These files are copied
...@@ -353,26 +417,12 @@ epub_exclude_files = ['search.html'] ...@@ -353,26 +417,12 @@ epub_exclude_files = ['search.html']
# special-members flag) # special-members flag)
autoclass_content = 'class' 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 autodoc_default_options = {
# that are added by the props package to 'special-members' : True,
# all SyncableHasProperties classes. 'private-members' : True,
if what == 'class': 'undoc-members' : True,
attName = name.split('.')[-1] 'member-order' : 'bysource',
return skip or attName.startswith('_sync_') }
return skip or False
def setup(app):
app.connect('autodoc-skip-member', autodoc_skip_member)
graphviz_output_format = 'svg' graphviz_output_format = 'svg'