feat: python 3.8 compatibility (#861)

* chore: update library and ci config for python 3.8 compatibility
* fix: python3.8 deps update and rdflib patch
* chore: set pipenv default to version 3.7

Author: lorenzo-cavazzi

.github/workflows/integration_tests.yml

@@ -11,7 +11,7 @@ jobs:
     strategy:
       max-parallel: 4
       matrix:
-        python-version: [3.6, 3.7]
+        python-version: [3.6, 3.7, 3.8]
     steps:
     - uses: actions/checkout@master
     - name: Set up Python ${{ matrix.python-version }}
@@ -32,7 +32,7 @@ jobs:
     strategy:
       max-parallel: 4
       matrix:
-        python-version: [3.6, 3.7]
+        python-version: [3.6, 3.7, 3.8]
     steps:
     - uses: actions/checkout@master
     - name: Set up Python ${{ matrix.python-version }}

.github/workflows/test.yml

@@ -8,7 +8,7 @@ jobs:
     strategy:
       max-parallel: 4
       matrix:
-        python-version: [3.6, 3.7]
+        python-version: [3.6, 3.7, 3.8]
     steps:
     - uses: actions/checkout@master
     - name: Set up Python ${{ matrix.python-version }}
@@ -28,7 +28,7 @@ jobs:
     strategy:
       max-parallel: 4
       matrix:
-        python-version: [3.6, 3.7]
+        python-version: [3.6, 3.7, 3.8]
     steps:
     - uses: actions/checkout@master
     - name: Set up Python ${{ matrix.python-version }}
@@ -49,7 +49,7 @@ jobs:
     strategy:
       max-parallel: 4
       matrix:
-        python-version: [3.6, 3.7]
+        python-version: [3.6, 3.7, 3.8]
     steps:
     - uses: actions/checkout@master
     - name: Set up Python ${{ matrix.python-version }}

Pipfile.lock

@@ -91,7 +91,7 @@
     option_use_external_storage
 from renku.core.commands.version import check_version, print_version
 from renku.core.management.client import LocalClient
-from renku.core.management.config import ConfigManagerMixin, RENKU_HOME
+from renku.core.management.config import RENKU_HOME, ConfigManagerMixin
 from renku.core.management.repository import default_path
 
 #: Monkeypatch Click application.

renku/cli/__init__.py

@@ -20,7 +20,7 @@
 from .githooks import check_git_hooks_installed
 from .migration import check_dataset_metadata, check_missing_files
 from .references import check_missing_references
-from .validate_shacl import check_project_structure, check_datasets_structure
+from .validate_shacl import check_datasets_structure, check_project_structure
 
 # Checks will be executed in the order as they are listed in __all__.
 # They are mostly used in ``doctor`` command to inspect broken things.

renku/core/commands/checks/__init__.py

@@ -199,9 +199,8 @@ def _rdf2dot_reduced(g, stream):
     Adapted from original source:
     https://rdflib.readthedocs.io/en/stable/_modules/rdflib/tools/rdf2dot.html
     """
-    import cgi
+    import html
     import collections
-
     import rdflib
 
     from rdflib.tools.rdf2dot import LABEL_PROPERTIES, NODECOLOR
@@ -228,7 +227,7 @@ def label(x, g):
 
     def formatliteral(l, g):
         """Format and escape literal."""
-        v = cgi.escape(l)
+        v = html.escape(l)
         if l.datatype:
             return '"%s"^^%s' % (v, qname(l.datatype, g))
         elif l.language:
@@ -268,11 +267,11 @@ def color(p):
             continue
         # inject the type predicate into the node itself
         if p == rdflib.RDF.type:
-            types[sn].add((qname(p, g), cgi.escape(o)))
+            types[sn].add((qname(p, g), html.escape(o)))
             continue
         # add the project membership to the node
         if p == rdflib.term.URIRef('schema:isPartOf'):
-            fields[sn].add((qname(p, g), cgi.escape(o)))
+            fields[sn].add((qname(p, g), html.escape(o)))
             continue
 
         if isinstance(o, (rdflib.URIRef, rdflib.BNode)):

renku/core/commands/format/graph.py

@@ -17,7 +17,9 @@
 # limitations under the License.
 """Compatibility layer for different Python versions."""
 
+import cgi
 import contextlib
+import html
 import json
 import os
 import sys
@@ -87,4 +89,12 @@ def set(self, active_ctx, local_ctx, result):
 
 pyld.jsonld._cache = {'activeCtx': PatchedActiveContextCache()}
 
-__all__ = ('FileNotFoundError', 'Path', 'contextlib', 'pyld')
+cgi.escape = html.escape
+
+__all__ = (
+    'FileNotFoundError',
+    'Path',
+    'contextlib',
+    'pyld',
+    'cgi',
+)

renku/core/compat.py

@@ -77,7 +77,7 @@
     'click-completion>=0.5.0',
     'click>=7.0',
     'cryptography>=2.7',
-    'cwltool==1.0.20181012180214',
+    'cwltool==1.0.20191206125148',
     'environ_config>=18.2.0',
     'filelock>=3.0.0',
     'gitpython==3.0.3',
@@ -90,6 +90,7 @@
     'pyshacl>=0.11.3.post1',
     'python-dateutil>=2.6.1',
     'python-editor>=1.0.4',
+    'rdflib==4.2.2',
     'rdflib-jsonld>=0.4.0',
     'requests>=2.21.0',
     'ndg-httpsclient>=0.5.1',
@@ -172,6 +173,7 @@ def _get_disribution_url():
     classifiers=[
         'Environment :: Web Environment',
         'Intended Audience :: Developers',
+        'Intended Audience :: Science/Research',
         'License :: OSI Approved :: Apache Software License',
         'Operating System :: OS Independent',
         'Programming Language :: Python',
@@ -180,6 +182,8 @@ def _get_disribution_url():
         'Programming Language :: Python :: 3',
         'Programming Language :: Python :: 3.5',
         'Programming Language :: Python :: 3.6',
-        'Development Status :: 1 - Planning',
+        'Programming Language :: Python :: 3.7',
+        'Programming Language :: Python :: 3.8',
+        'Development Status :: 4 - Beta',
     ],
 )