Merge pull request #416 from CLARIAH/dev

Preparing for 1.3.8 release

.github/dependabot.yml

@@ -0,0 +1,12 @@
+version: 2
+
+updates:
+  - package-ecosystem: "pip"
+    directory: "/"
+    schedule:
+      interval: "monthly"
+    target-branch: "dev"
+    # Add reviewers
+    reviewers:
+      - "albertmeronyo"
+      - "c-martinez"

.github/workflows/publish_pypi.yml

@@ -0,0 +1,26 @@
+name: Publish
+# Publish to PyPI when a new release is published
+on:
+  release:
+    types:
+      - published
+jobs:
+  publish:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python
+      uses: actions/setup-python@v1
+      with:
+        python-version: 3.7
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install setuptools wheel twine
+        python setup.py sdist bdist_wheel
+    - name: Publish package
+      uses: pypa/[email protected]
+      with:
+        user: __token__
+        password: ${{ secrets.PYPI_API_TOKEN }}
+        # repository_url: https://test.pypi.org/legacy/

.github/workflows/testing.yml

@@ -0,0 +1,23 @@
+name: Testing
+on: [push]
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        python-version: [3.7, 3.8, 3.9]
+    steps:
+    - uses: actions/checkout@master
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install .
+        pip install -r requirements-test.txt
+    - name: Test with pytest
+      run: |
+        pytest ./tests

CITATION.cff

@@ -7,12 +7,16 @@ authors:
     family-names: Meroño-Peñuela
     given-names: Albert
     orcid: "https://orcid.org/0000-0003-4646-5842"
+  -
+    family-names: Hoekstra
+    given-names: Rinke
   -
     affiliation: "Netherlands eScience Center"
     family-names: Martinez
     given-names: Carlos
     orcid: "https://orcid.org/0000-0001-5565-7577"
 cff-version: "1.0.3"
+date-released: 2023-07-30
 doi: 10.5281/zenodo.1064391
 license: MIT
 message: "If you use this software, please cite it as below."
@@ -25,5 +29,4 @@ keywords:
   - "linked-data"
   - "semantic-web"
   - "linked-data-api"
-version: "1.3.7"
-date-released: 2021-11-03
+version: "1.3.8"

CONTRIBUTORS.md

@@ -18,4 +18,8 @@ This is a list of all people who have contributed to grlc. Big thanks to everyon
 [jspaaks](https://github.com/jspaaks)  
 [ecow](https://github.com/ecow)
 [rapw3k](https://github.com/rapw3k)
+[jaw111](https://github.com/jaw111)
+[tkuhn](https://github.com/tkuhn)
+[GenEars](https://github.com/GenEars)
+[nichtich](https://github.com/nichtich)
 [jblom](https://github.com/jblom)

Dockerfile

@@ -2,7 +2,7 @@
 #
 # SPDX-License-Identifier: MIT
 
-FROM python:3.6.8
+FROM python:3.8.16
 MAINTAINER [email protected]
 
 # Default values for env variables
@@ -26,14 +26,14 @@ ENV GRLC_INSTALL_DIR="${GRLC_HOME}/grlc" \
     GRLC_RUNTIME_DIR="${GRLC_CACHE_DIR}/runtime"
 
 RUN apt-get update \
- && DEBIAN_FRONTEND=noninteractive apt-get install -y nginx git-core logrotate python-pip locales gettext-base sudo build-essential apt-utils \
+ && DEBIAN_FRONTEND=noninteractive apt-get install -y nginx git-core logrotate python3-pip locales gettext-base sudo build-essential apt-utils \
  && update-locale LANG=C.UTF-8 LC_MESSAGES=POSIX \
  && locale-gen en_US.UTF-8 \
  && DEBIAN_FRONTEND=noninteractive dpkg-reconfigure locales \
  && rm -rf /var/lib/apt/lists/*
 
-RUN curl -sL https://deb.nodesource.com/setup_10.x | sudo -E bash -
-RUN apt-get update && apt-get install -y nodejs
+# RUN curl -sL https://deb.nodesource.com/setup_10.x | sudo -E bash -
+RUN apt-get update && apt-get install -y nodejs npm
 
 COPY ./ ${GRLC_INSTALL_DIR}
 

README.md

@@ -8,7 +8,7 @@ SPDX-License-Identifier: MIT
 
 [![PyPI version](https://badge.fury.io/py/grlc.svg)](https://badge.fury.io/py/grlc)
 [![DOI](https://zenodo.org/badge/46131212.svg)](https://zenodo.org/badge/latestdoi/46131212)
-[![Build Status](https://travis-ci.org/CLARIAH/grlc.svg?branch=master)](https://travis-ci.org/CLARIAH/grlc)
+![Build Status](https://github.com/CLARIAH/grlc/actions/workflows/testing.yml/badge.svg?branch=master)
 [![status](https://joss.theoj.org/papers/437074e2d77df8c6cbf3bc4e407b3b17/status.svg)](https://joss.theoj.org/papers/437074e2d77df8c6cbf3bc4e407b3b17)
 
 
@@ -90,7 +90,7 @@ A grlc API specification file is a YAML file which includes the necessary inform
  - `description`: API description
  - `contact`: Contact details of the API owner. This should include the `name` and `url` properties.
  - `licence`: A URL pointing to the licence file for the API.
- - `queries`: A list of URLs of SPARQL queries (with header decorators).
+ - `queries`: A list of URLs of SPARQL queries (with header decorators). Alternatively a query can be defined as a dictionary with a `name` and a `url`.
 
 For example:
 ```YAML
@@ -104,6 +104,8 @@ queries:
   - https://www.mywebsite.org/query1.rq
   - https://www.mywebsite.org/query2.rq
   - https://www.otherwebsite.org/query3.rq
+  - name: QueryFour
+    url: https://www.mywebsite.org/query4.rq
 ```
 
 ### grlc generated API
@@ -395,6 +397,8 @@ Quotes from grlc users:
 
 ## Academic publications
 
+- Albert Meroño-Peñuela, Carlos Martinez-Ortiz. “grlc: the git repository linked data API constructor.“ Journal of Open Source Software, 6(67), 2731 (2021), <https://doi.org/10.21105/joss.02731>
+- Albert Meroño-Peñuela, Pasquale Lisena, Carlos Martínez-Ortiz. “Web Data APIs for Knowledge Graphs: Easing Access to Semantic Data for Application Developers”. Synthesis Lectures on Data, Semantics, and Knowledge, 12(1), pp.1-118 (2021) (Morgan & Claypool) <https://doi.org/10.2200/S01114ED1V01Y202107DSK021>
 - Albert Meroño-Peñuela, Rinke Hoekstra. “grlc Makes GitHub Taste Like Linked Data APIs”. The Semantic Web – ESWC 2016 Satellite Events, Heraklion, Crete, Greece, May 29 – June 2, 2016, Revised Selected Papers. LNCS 9989, pp. 342-353 (2016). ([PDF](https://link.springer.com/content/pdf/10.1007%2F978-3-319-47602-5_48.pdf))
 - Albert Meroño-Peñuela, Rinke Hoekstra. “SPARQL2Git: Transparent SPARQL and Linked Data API Curation via Git”. In: Proceedings of the 14th Extended Semantic Web Conference (ESWC 2017), Poster and Demo Track. Portoroz, Slovenia, May 28th – June 1st, 2017 (2017). ([PDF](https://www.albertmeronyo.org/wp-content/uploads/2017/04/sparql2git-transparent-sparql-4.pdf))
 - Albert Meroño-Peñuela, Rinke Hoekstra. “Automatic Query-centric API for Routine Access to Linked Data”. In: The Semantic Web – ISWC 2017, 16th International Semantic Web Conference. Lecture Notes in Computer Science, vol 10587, pp. 334-339 (2017). ([PDF](https://www.albertmeronyo.org/wp-content/uploads/2017/07/ISWC2017_paper_430.pdf))

config.default.ini

@@ -16,4 +16,7 @@ server_name = grlc.io
 user = none
 password = none
 # Logging level
-debug = False
+debug = True
+
+[api_gitlab]
+gitlab_url=https://gitlab

requirements-test.txt

@@ -1,2 +1,3 @@
 mock==2.0.0
 pytest==5.2.1
+flake8==3.9.2

requirements.txt

@@ -1,25 +1,28 @@
 docopt==0.6.2
 docutils==0.17.1
 Flask==1.0.2
-Flask-Cors==3.0.6
-gevent==1.4.0
-greenlet==0.4.15
+Flask-Cors==3.0.9
+gevent==1.4.0; python_version <= '3.8'
+gevent==22.10.2; python_version > '3.8'
+greenlet==0.4.15; python_version <= '3.8'
+greenlet==2.0.0; python_version > '3.8'
 html5lib==1.0.1
-isodate==0.5.4
-keepalive==0.5
+isodate==0.6.1
+itsdangerous==2.0.1
 MarkupSafe==0.23
 pyaml==18.11.0
 pyparsing==2.0.7
+python-gitlab==2.10.1
 PyYAML==5.4
 rdflib==5.0.0
-rdflib-jsonld==0.4.0
-requests==2.20.0
+rdflib-jsonld==0.6.2
+requests==2.31.0
 six==1.12.0
 simplejson==3.16.0
 setuptools>=38.6.0
 SPARQLTransformer==2.1.1
 SPARQLWrapper==1.8.2
-werkzeug>=0.16.0
-PyGithub==1.43.5
+werkzeug==0.16.0
+PyGithub==1.57
 gunicorn==19.6.0; sys_platform!="win32"
 waitress>=1.4.2; sys_platform=="win32"

setup.py

@@ -53,12 +53,11 @@
         # dependency for `python setup.py test`
         'pytest-runner',
         # dependencies for `python setup.py build_sphinx`
-        'sphinx',
-        'recommonmark'
+        # 'sphinx',
+        # 'recommonmark'
     ],
     tests_require=tests_require,
     package_data = { 'grlc': grlc_data },
     include_package_data=True,
     data_files=[('citation/grlc', ['CITATION.cff'])],
-    python_requires='>=3.7, <=3.8',
 )