Merge branch 'mnt/zenodo' into 'master'

Mnt/zenodo

See merge request fsl/fslpy!80

.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=$3
+
+version=`python setup.py -V`
+upfile=`pwd`/dist/fslpy-"$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

@@ -77,6 +77,12 @@ stages:
 #   - TWINE_PASSWORD:                - Password to use when uploading to pypi
 #
 #   - TWINE_REPOSITORY_URL:          - Pypi repository to upload to
+#
+#   - ZENODO_URL:                    - Zenodo URL to deposit release file to.
+#
+#   - ZENODO_TOKEN:                  - Zenodo access token.
+#
+#   - ZENODO_DEPOSIT_ID:             - Deposit ID of previous Zenodo deposit.
 ###############################################################################
 
 
@@ -263,3 +269,20 @@ deploy-pypi:
 
   script:
     - bash ./.ci/deploy_pypi.sh
+
+
+deploy-zenodo:
+  <<: *only_releases
+  <<: *setup_ssh
+  stage: deploy
+  when:  manual
+  image: python3.6
+
+  tags:
+    - docker
+
+  dependencies:
+    - build-pypi-dist
+
+  script:
+    - bash ./.ci/zenodo_deposit.sh "$ZENODO_URL" "$ZENODO_TOKEN" "$ZENODO_DEPOSIT_ID"

README.rst

@@ -5,6 +5,9 @@ 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://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/