diff --git a/codemeta.json b/codemeta.json
index bc9bdc885a7935946fa87d45e5d3313726b0bb64..385c35c8b4035dcef8fa3889039759d68824763b 100644
--- a/codemeta.json
+++ b/codemeta.json
@@ -1,115 +1,117 @@
- {
- "@context": "https://doi.org/10.5063/schema/codemeta-2.0",
- "@type": "SoftwareSourceCode",
- "name": "eossr",
- "description": "ESCAPE OSSR library",
- "license": "https://spdx.org/licenses/MIT",
- "softwareVersion": "v0.3.3",
- "codeRepository": "https://gitlab.in2p3.fr/escape2020/wp3/eossr",
- "developmentStatus": "active",
- "isAccessibleForFree": true,
- "isPartOf": [
- "https://gitlab.in2p3.fr/escape2020",
- "https://projectescape.eu/"
- ],
- "contIntegration": "https://gitlab.in2p3.fr/escape2020/wp3/eossr/-/pipelines",
- "buildInstructions": "https://gitlab.in2p3.fr/escape2020/wp3/eossr/-/blob/master/README.md",
- "issueTracker": "https://gitlab.in2p3.fr/escape2020/wp3/eossr/-/issues",
- "readme": "https://gitlab.in2p3.fr/escape2020/wp3/eossr/-/blob/master/README.md",
- "programmingLanguage": [
- {
- "@type": "ComputerLanguage",
- "name": "Python",
- "url": "https://www.python.org/"
- }
- ],
- "softwareRequirements": [
- {
- "@type": "SoftwareApplication",
- "identifier": "requests",
- "name": "requests",
- "softwareVersion": ">=3.6"
+{
+ "@context": "https://doi.org/10.5063/schema/codemeta-2.0",
+ "@type": "SoftwareSourceCode",
+ "name": "eossr",
+ "description": "<p><img alt=\"eOSSR\" src=\"docs/images/eossr_logo.png\" /></p><h2>The ESCAPE OSSR library</h2><p>The eOSSR Python library gathers all the developments made for the OSSR. In particular, it includes:- an API to programmatically access the OSSR, retrieve records and publish content- functions to map and crosswalk metadata between the CodeMeta schema adopted for the OSSR and Zenodo internal schema- functions to help developers automatically contribute to the OSSR, in particular using their continuous integration (see also code snippets)</p><p>Code: <a href=\"https://gitlab.in2p3.fr/escape2020/wp3/eossr\">https://gitlab.in2p3.fr/escape2020/wp3/eossr</a> <br />Documentation: <a href=\"https://escape2020.pages.in2p3.fr/wp3/eossr/\">https://escape2020.pages.in2p3.fr/wp3/eossr/</a></p><p><a href=\"https://gitlab.in2p3.fr/escape2020/wp3/eossr/-/commits/master\"><img alt=\"pipeline status\" src=\"https://gitlab.in2p3.fr/escape2020/wp3/eossr/badges/master/pipeline.svg\" /></a><a href=\"https://opensource.org/licenses/MIT\"><img alt=\"License: MIT\" src=\"https://img.shields.io/badge/License-MIT-blue.svg\" /></a><a href=\"https://gitlab.in2p3.fr/escape2020/wp3/eossr/-/commits/master\"><img alt=\"coverage report\" src=\"https://gitlab.in2p3.fr/escape2020/wp3/eossr/badges/master/coverage.svg\" /></a><a href=\"https://doi.org/10.5281/zenodo.5524912\"><img alt=\"DOI\" src=\"https://zenodo.org/badge/DOI/10.5281/zenodo.5524912.svg\" /></a><a href=\"https://mybinder.org/v2/git/https%3A%2F%2Fgitlab.in2p3.fr%2Fescape2020%2Fwp3%2Feossr/HEAD\"><img alt=\"Binder\" src=\"https://mybinder.org/badge_logo.svg\" /></a></p><h2>Stable versions</h2><ul><li>v0.3.3: <a href=\"https://doi.org/10.5281/zenodo.5592584\"><img alt=\"DOI\" src=\"https://zenodo.org/badge/DOI/10.5281/zenodo.5592584.svg\" /></a></li><li>v0.2 : <a href=\"https://doi.org/10.5281/zenodo.5524913\"><img alt=\"DOI\" src=\"https://zenodo.org/badge/DOI/10.5281/zenodo.5524913.svg\" /></a></li></ul><h2>Install</h2><p>Commands to be run in your terminal.</p><h3>For users</h3><pre><code>pip install eossr</code></pre><p>You can also run it with docker:</p><pre><code>docker run -it gitlab-registry.in2p3.fr/escape2020/wp3/eossr:latest</code></pre><p><a href=\"https://gitlab.in2p3.fr/escape2020/wp3/eossr/container_registry\">Visit our registry</a> to see the available docker containers.</p><p>Note that <code>latest</code> tag always point to the latest stable released container.</p><h3>For developers</h3><pre><code>git clone https://gitlab.in2p3.fr/escape2020/wp3/eossr.gitpip install -e eossr</code></pre><h4>Running tests</h4><p>To run tests locally, run:</p><pre><code>pip install pytestpytest eossr</code></pre><p>Some tests will be skiped if <code>SANDBOX_ZENODO_TOKEN</code> is not defined in your environment variables.If you want to run these tests, you will need to create a <a href=\"https://sandbox.zenodo.org/account/settings/applications/tokens/new/\">sandbox zenodo token</a> and add it to your env:</p><pre><code>export SANDBOX_ZENODO_TOKEN="your_sandbox_token"</code></pre><h2>Cite</h2><p>To cite this library, use the cite module in <a href=\"https://zenodo.org/record/5524913#.YWBq79kzZB0\">the Zenodo page</a>.</p>",
+ "license": "https://spdx.org/licenses/MIT",
+ "softwareVersion": "v0.3.3",
+ "codeRepository": "https://gitlab.in2p3.fr/escape2020/wp3/eossr",
+ "developmentStatus": "active",
+ "isAccessibleForFree": true,
+ "isPartOf": [
+ "https://gitlab.in2p3.fr/escape2020",
+ "https://projectescape.eu/"
+ ],
+ "contIntegration": "https://gitlab.in2p3.fr/escape2020/wp3/eossr/-/pipelines",
+ "buildInstructions": "https://gitlab.in2p3.fr/escape2020/wp3/eossr/-/blob/master/README.md",
+ "issueTracker": "https://gitlab.in2p3.fr/escape2020/wp3/eossr/-/issues",
+ "readme": "https://gitlab.in2p3.fr/escape2020/wp3/eossr/-/blob/master/README.md",
+ "programmingLanguage": [
+ {
+ "@type": "ComputerLanguage",
+ "name": "Python",
+ "url": "https://www.python.org/"
+ }
+ ],
+ "softwareRequirements": [
+ {
+ "@type": "SoftwareApplication",
+ "identifier": "requests",
+ "name": "requests",
+ "softwareVersion": ">=3.6"
+ },
+ {
+ "@type": "SoftwareApplication",
+ "identifier": "pytest",
+ "name": "pytest",
+ "softwareVersion": ">=5.4.2"
+ }
+ ],
+ "keywords": [
+ "jupyter-notebook"
+ ],
+ "runtimePlatform": "",
+ "downloadUrl": "",
+ "installUrl": "",
+ "releaseNotes": "Bug fix in the CI and much lighter docker container",
+ "dateCreated": "2021-08-31",
+ "datePublished": "2021-12-02",
+ "dateModified": "2021-12-02",
+ "operatingSystem": "",
+ "maintainer": {
+ "@type": "Person",
+ "@id": "https://orcid.org/0000-0003-2224-4594",
+ "givenName": "Enrique",
+ "familyName": "Garcia",
+ "email": "garcia@lapp.in2p3.fr",
+ "affiliation": {
+ "@type": "Organization",
+ "name": "Univ. Savoie Mont Blanc, CNRS, LAPP"
+ }
},
- {
- "@type": "SoftwareApplication",
- "identifier": "pytest",
- "name": "pytest",
- "softwareVersion": ">=5.4.2"
- }
- ],
- "keywords": ["jupyter-notebook"],
- "runtimePlatform": "",
- "downloadUrl": "",
- "installUrl": "",
- "releaseNotes": "Bug fix in the CI and much lighter docker container",
- "dateCreated": "2021-08-31",
- "datePublished": "2021-10-22",
- "dateModified": "2021-10-22",
- "operatingSystem": "",
- "maintainer": {
- "@type": "Person",
- "@id": "https://orcid.org/0000-0003-2224-4594",
- "givenName": "Enrique",
- "familyName": "Garcia",
- "email": "garcia@lapp.in2p3.fr",
- "affiliation": {
- "@type": "Organization",
- "name": "Univ. Savoie Mont Blanc, CNRS, LAPP"
- }
- },
- "author": [
- {
- "@type": "Person",
- "@id": "https://orcid.org/0000-0002-5686-2078",
- "givenName": "Thomas",
- "familyName": "Vuillaume",
- "email": "vuillaume@lapp.in2p3.fr",
- "affiliation": {
- "@type": "Organization",
- "name": "Univ. Savoie Mont Blanc, CNRS, LAPP"
- }
- },
- {
- "@type": "Person",
- "@id": "https://orcid.org/0000-0003-2224-4594",
- "givenName": "Enrique",
- "familyName": "Garcia",
- "email": "garcia@lapp.in2p3.fr",
- "affiliation": {
- "@type": "Organization",
- "name": "Univ. Savoie Mont Blanc, CNRS, LAPP"
- }
- }
- ],
- "contributor": [
- {
- "@type": "Person",
- "@id": "https://orcid.org/0000-0002-5321-8404",
- "givenName": "Christian",
- "familyName": "Tacke",
- "affiliation": {
- "@type": "Organization",
- "name": "GSI"
- }
- },
- {
- "@type": "Person",
- "@id": "https://orcid.org/0000-0001-7821-8673",
- "givenName": "Tamás",
- "familyName": "Gál",
- "email": "tamas.gal@fau.de",
- "affiliation": {
- "@type": "Organization",
- "name": "ECAP, FAU (Nuremberg, Germany)"
- }
- }
- ],
- "funder":[
- {
- "@type": "Organization",
- "name": "European Commission",
- "@id": "https://doi.org/10.13039/501100000780"
- }
- ],
- "funding": "824064"
-}
+ "author": [
+ {
+ "@type": "Person",
+ "@id": "https://orcid.org/0000-0002-5686-2078",
+ "givenName": "Thomas",
+ "familyName": "Vuillaume",
+ "email": "vuillaume@lapp.in2p3.fr",
+ "affiliation": {
+ "@type": "Organization",
+ "name": "Univ. Savoie Mont Blanc, CNRS, LAPP"
+ }
+ },
+ {
+ "@type": "Person",
+ "@id": "https://orcid.org/0000-0003-2224-4594",
+ "givenName": "Enrique",
+ "familyName": "Garcia",
+ "email": "garcia@lapp.in2p3.fr",
+ "affiliation": {
+ "@type": "Organization",
+ "name": "Univ. Savoie Mont Blanc, CNRS, LAPP"
+ }
+ }
+ ],
+ "contributor": [
+ {
+ "@type": "Person",
+ "@id": "https://orcid.org/0000-0002-5321-8404",
+ "givenName": "Christian",
+ "familyName": "Tacke",
+ "affiliation": {
+ "@type": "Organization",
+ "name": "GSI"
+ }
+ },
+ {
+ "@type": "Person",
+ "@id": "https://orcid.org/0000-0001-7821-8673",
+ "givenName": "Tam\u00e1s",
+ "familyName": "G\u00e1l",
+ "email": "tamas.gal@fau.de",
+ "affiliation": {
+ "@type": "Organization",
+ "name": "ECAP, FAU (Nuremberg, Germany)"
+ }
+ }
+ ],
+ "funder": [
+ {
+ "@type": "Organization",
+ "name": "European Commission",
+ "@id": "https://doi.org/10.13039/501100000780"
+ }
+ ],
+ "funding": "824064"
+}
\ No newline at end of file
diff --git a/eossr/scripts/update_codemeta.py b/eossr/scripts/update_codemeta.py
new file mode 100644
index 0000000000000000000000000000000000000000..8ca2162a52faf7d43dc6000629626b123f32dc6d
--- /dev/null
+++ b/eossr/scripts/update_codemeta.py
@@ -0,0 +1,21 @@
+import argparse
+from pathlib import Path
+from eossr.utils import update_codemeta
+from eossr import ROOT_DIR
+
+
+
+
+if __name__ == '__main__':
+
+ parser = argparse.ArgumentParser(description="Update Codemeta")
+
+ parser.add_argument('--codemeta_path', '-c', type=str,
+ dest='codemeta_path',
+ help='Path to codemeta.json',
+ default=Path(ROOT_DIR).joinpath('codemeta.json'),
+ required=False)
+
+ args = parser.parse_args()
+ html = update_codemeta(codemeta_path=args.codemeta_path)
+
diff --git a/eossr/tests/test_utils.py b/eossr/tests/test_utils.py
index c8b414c3f67a0c22bca136a5364e90f5e39c3022..927dbcdd9ccfa1847366b98f90343d66916f4a70 100644
--- a/eossr/tests/test_utils.py
+++ b/eossr/tests/test_utils.py
@@ -43,3 +43,13 @@ def test_zip_repository():
assert 'test_zip_repo.zip' not in [Path(f).name for f in zo.namelist()]
assert os.path.join(os.path.join(os.path.basename(tmpdir), os.path.basename(subtmpdir)),
os.path.basename(tmpfile)) in zo.namelist()
+
+
+def test_readme_to_html():
+ from eossr.utils import readme_to_html
+ readme_to_html()
+
+
+def test_update_codemeta():
+ from eossr.utils import update_codemeta
+ update_codemeta(overwrite=False)
\ No newline at end of file
diff --git a/eossr/utils.py b/eossr/utils.py
index 55cf49aea3b4c8362cc4a864c2317edc02620694..de75eefb92c5513f04dfd7ae2ffbb67e3e8af92d 100644
--- a/eossr/utils.py
+++ b/eossr/utils.py
@@ -4,6 +4,9 @@ import shutil
from io import BytesIO
from zipfile import ZipFile
from pathlib import Path
+from markdown import markdown
+from datetime import date
+from . import ROOT_DIR
__all__ = [
'ZipUrl',
@@ -95,3 +98,41 @@ def zip_repository(directory, zip_filename=None):
print(f"Zipping done: {zip_filename}.zip")
return zip_filename + '.zip'
+
+
+def readme_to_html(readme_path=Path(ROOT_DIR).joinpath('README.md').as_posix()):
+ """
+ Read README.md and return html transcript
+ :param readme_path: str
+ :return: str
+ text in readme converted to html
+ """
+ html = markdown(open(readme_path).read(), extensions=['fenced_code'])
+ html = html.replace('\n', '')
+ return html
+
+
+def update_codemeta(codemeta_path=Path(ROOT_DIR).joinpath('codemeta.json').as_posix(), published=True, overwrite=True):
+ """
+ Update codemeta.json file for dates and description based on README.md
+
+ :param codemeta_path: Path
+ :param published: boolean
+ if True, datePublished is updated.
+ :param overwrite: boolean
+ overwrite codemeta file
+ :return:
+ """
+ with open(codemeta_path) as file:
+ metadata = json.load(file)
+ metadata['description'] = readme_to_html()
+ metadata['dateModified'] = f'{date.today()}'
+
+ if published:
+ metadata['datePublished'] = f'{date.today()}'
+
+ if overwrite:
+ with open(codemeta_path, 'w') as file:
+ json.dump(metadata, file, indent=4)
+ return metadata
+
diff --git a/setup.py b/setup.py
index e9733a5cc6ecbb733c8d0ab8b6d70992a12cdcd2..7749532b7d36a1e69f0bc691f80979f609c6f5ae 100644
--- a/setup.py
+++ b/setup.py
@@ -33,6 +33,7 @@ setup(
install_requires=[
"requests",
"bs4",
+ "markdown"
],
packages=find_packages(),
scripts=['eossr/scripts/gitlab_prepare_upload_zenodo.sh'],