Merge pull request #769 from simphony/dev

 Merge release 3.8.0

.gitattributes

@@ -1,3 +1,3 @@
 * text=auto eol=lf
 *.{cmd,[cC][mM][dD]} text eol=crlf
-*.{bat,[bB][aA][tT]} text eol=crlf
+*.{bat,[bB][aA][tT]} text eol=crlf

.github/workflows/benchmarks.yml

@@ -11,7 +11,7 @@ jobs:
     name: Performance check
     runs-on: self-hosted
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       # - uses: actions/setup-python@v1  # (not needed for self-hosted runner)
       #   with:
       #     python-version: '3.8'
@@ -38,4 +38,4 @@ jobs:
           alert-threshold: '150%'
           comment-on-alert: true
           alert-comment-cc-users: '@yoavnash,@pablo-de-andres,@kysrpex'
-          fail-on-alert: true
+          fail-on-alert: true

.github/workflows/ci.yml

@@ -3,26 +3,39 @@ name: CI
 on: pull_request
 
 jobs:
-  code_analysis:
+  PEP8:
     runs-on: self-hosted
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - name: Flake8
-        run: flake8 . --exclude=*/__init__.py,osp/core/ontology/docs/EMMO/* --ignore=W503 --docstring-convention=google
+        run: flake8 . --exclude=*/__init__.py,osp/core/ontology/docs/EMMO/* --ignore=E203,W503 --docstring-convention=google
+
+      # Includes isort, black and other checks, see `.pre-commit.config.yaml`.
+      - name: pre-commit
+        run: pre-commit run --all-files
+
+  complexity:
+    runs-on: self-hosted
+    steps:
+      - uses: actions/checkout@v3
 
       - name: Radon
         run: |
           radon cc -s -a .,
           radon mi -s .
-        
-      - name: bandit
+
+  security:
+    runs-on: self-hosted
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Bandit
         run: bandit -r osp --skip B101
-  
-  test:
+
+  testing:
     runs-on: self-hosted
     steps:
-      - uses: actions/checkout@v2
-      - name: unittesting
+      - uses: actions/checkout@v3
+      - name: tox
         run: tox
-

.gitignore

@@ -22,4 +22,4 @@ osp/core/java/target
 osp/core/packageinfo.py
 *.jar
 *.so
-osp/core/java/lib/so/FaCT++
+osp/core/java/lib/so/FaCT++

.pre-commit-config.yaml

@@ -0,0 +1,23 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.1.0
+    hooks:
+      - id: check-json
+      - id: check-yaml
+      - id: pretty-format-json
+        args:
+        - --autofix
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+
+  - repo: https://github.com/pycqa/isort
+    rev: 5.10.1
+    hooks:
+      - id: isort
+        args: [--profile, black, --filter-files, --line-length, "79"]
+
+  - repo: https://github.com/psf/black
+    rev: 22.3.0
+    hooks:
+      - id: black
+        args: [--line-length, "79"]

Dockerfile

@@ -9,4 +9,4 @@ RUN update-alternatives --install /usr/bin/python python /usr/bin/python3 1
 RUN python -m pip install --upgrade pip
 
 ADD . /simphony/osp-core
-RUN pip install /simphony/osp-core
+RUN pip install /simphony/osp-core

LICENSE.md

@@ -10,4 +10,4 @@ Redistribution and use in source and binary forms, with or without modification,
 
 3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
 
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

MANIFEST.in

@@ -2,4 +2,4 @@ include packageinfo.py
 include osp/core/ontology/docs/*.yml
 include osp/core/ontology/docs/*.xml
 include osp/core/ontology/docs/*.ttl
-include osp/core/ontology/docs/EMMO/emmo-inferred.owl
+include osp/core/ontology/docs/EMMO/emmo-inferred.owl

README.md

@@ -86,4 +86,4 @@ From our experience, this will not happen if you use the virtual environements o
 
 ## Acknowledgements
 
-The OSP-core Python package originates from the European Project [SimPhoNy](https://www.simphony-project.eu/) (Project Nr. 604005). We would like to acknowledge and thank our project partners, especially [Enthought, Inc](https://www.enthought.com/), [Centre Internacional de Mètodes Numèrics a l'Enginyeria (CIMNE)](https://cimne.com/) and the [University of Jyväskylä](https://www.jyu.fi/en), for their important contributions to some of the core concepts of OSP-core, which were originally demonstrated under the project https://github.com/simphony/simphony-common.
+The OSP-core Python package originates from the European Project [SimPhoNy](https://www.simphony-project.eu/) (Project Nr. 604005). We would like to acknowledge and thank our project partners, especially [Enthought, Inc](https://www.enthought.com/), [Centre Internacional de Mètodes Numèrics a l'Enginyeria (CIMNE)](https://cimne.com/) and the [University of Jyväskylä](https://www.jyu.fi/en), for their important contributions to some of the core concepts of OSP-core, which were originally demonstrated under the project https://github.com/simphony/simphony-common.

examples/api_example.py

@@ -62,9 +62,8 @@
 print("\nAdding neighborhoods to Cuds object in a loop:")
 for i in range(6):
     print("Added neighborhood %s" % i)
-    c.add(city.Neighborhood(
-        name="neighborhood %s" % i))
+    c.add(city.Neighborhood(name="neighborhood %s" % i))
 print("internal dict of c:", c._neighbors, "\n")
 
-print('Trying out the `is_a` method trivially with the new neighborhoods.')
+print("Trying out the `is_a` method trivially with the new neighborhoods.")
 print(all(n.is_a(city.Neighborhood) for n in c.get(oclass=city.Neighborhood)))

examples/example_rdf_import_export.py

@@ -9,25 +9,33 @@
 # p = Parser()
 # p.parse("city")
 
-import uuid
-import re
 import os
+import re
+import uuid
+
 from rdflib import URIRef
-from osp.wrappers.sqlite import SqliteSession
+
 from osp.core.namespaces import city
-from osp.core.utils import import_cuds, export_cuds, branch, pretty_print
+from osp.core.utils import branch, export_cuds, import_cuds, pretty_print
+from osp.wrappers.sqlite import SqliteSession
 
-uuid_re = re.compile(r".*(http://www\.osp-core\.com/cuds#"
-                     r"([a-z0-9]{8}-[a-z0-9]{4}-[a-z0-9]{4}"
-                     r"-[a-z0-9]{4}-[a-z0-9]{12})).*")
+uuid_re = re.compile(
+    r".*(http://www\.osp-core\.com/cuds#"
+    r"([a-z0-9]{8}-[a-z0-9]{4}-[a-z0-9]{4}"
+    r"-[a-z0-9]{4}-[a-z0-9]{12})).*"
+)
 
 # Create CUDS structure
-c = branch(branch(city.City(name="Freiburg"),
-                  city.City(name="Pablo"),
-                  city.City(name="Yoav"),
-                  rel=city.hasInhabitant),
-           city.Neighborhood(name="Stühlinger"),
-           city.Neighborhood(name="Herdern"))
+c = branch(
+    branch(
+        city.City(name="Freiburg"),
+        city.City(name="Pablo"),
+        city.City(name="Yoav"),
+        rel=city.hasInhabitant,
+    ),
+    city.Neighborhood(name="Stühlinger"),
+    city.Neighborhood(name="Herdern"),
+)
 
 # Export from Core Session
 export_cuds(path="test.rdf", format="ttl")
@@ -64,8 +72,10 @@
                 match = uuid_re.match(line)
                 if match:
                     uid = uuid.UUID(match[2])
-                    line = line.replace(match[1], "http://city.com/"
-                                        + session._registry.get(uid).name)
+                    line = line.replace(
+                        match[1],
+                        "http://city.com/" + session._registry.get(uid).name,
+                    )
                 print("\t", line, end="")
                 print(line, end="", file=f2)
 

examples/example_sqlite_wrapper_city.py

@@ -3,10 +3,10 @@
 # Please install the city ontology: $pico install city
 
 import os
+
 from osp.core.namespaces import city
 from osp.core.utils import pretty_print
-from osp.wrappers.sqlite_wrapper_session import \
-    SqliteWrapperSession
+from osp.wrappers.sqlite_wrapper_session import SqliteWrapperSession
 
 try:
     # Construct the Datastructure.
@@ -17,7 +17,7 @@
     n = city.Neighborhood(name="Zähringen")
     s = city.Street(name="Le street")
     b = city.Building(name="Theater")
-    a = city.Address(postalCode=79123, name='Le street', number=12)
+    a = city.Address(postalCode=79123, name="Le street", number=12)
     c.add(p1, p2, p3, rel=city.hasInhabitant)
     c.add(n).add(s).add(b).add(a)
 

examples/file_upload.py

@@ -1,18 +1,20 @@
 """An example explaining how to upload files using the transport layer."""
 
-import sys
 import logging
-from osp.wrappers.sqlite import SqliteSession
-from osp.core.session import TransportSessionServer
+import sys
+
 from osp.core.namespaces import cuba
+from osp.core.session import TransportSessionServer
 from osp.wrappers.dataspace import DataspaceSession
+from osp.wrappers.sqlite import SqliteSession
 
 logging.getLogger("osp.core.session.transport").setLevel(logging.DEBUG)
 
 if sys.argv[-1] == "client":
     print("Please specify where you want to cache the files on the client:")
-    with DataspaceSession("ws://127.0.0.1:4587",
-                          input("file destination: > ")) as session:
+    with DataspaceSession(
+        "ws://127.0.0.1:4587", input("file destination: > ")
+    ) as session:
         wrapper = cuba.Wrapper(session=session)
         file = cuba.File(path=input("file to upload: > "))
         wrapper.add(file, rel=cuba.activeRelationship)
@@ -24,7 +26,9 @@
     print("Starting server now.")
     print("Please call 'python %s client' to connect" % __file__)
     TransportSessionServer(
-        SqliteSession, "localhost", 4587,
+        SqliteSession,
+        "localhost",
+        4587,
         session_kwargs={"path": "test.db"},
-        file_destination=file_destination
+        file_destination=file_destination,
     ).startListening()

examples/multiple_wrappers_example.py

@@ -2,16 +2,20 @@
 
 # Please install the city ontology: $pico install city
 
+from getpass import getpass
+
 from osp.core.namespaces import city
 from osp.core.utils import pretty_print
-from getpass import getpass
 from osp.wrappers.simdummy import SimDummySession
+
 try:
-    from osp.wrappers.sqlalchemy_wrapper_session import \
-        SqlAlchemyWrapperSession
+    from osp.wrappers.sqlalchemy_wrapper_session import (
+        SqlAlchemyWrapperSession,
+    )
 except ImportError as e:
-    raise ImportError("For this example, the SQLAlchemy "
-                      "wrapper for SimPhoNy is required!") from e
+    raise ImportError(
+        "For this example, the SQLAlchemy " "wrapper for SimPhoNy is required!"
+    ) from e
 
 # import logging
 # logger = logging.getLogger("osp.core")
@@ -23,18 +27,20 @@
 db_name = input("Database name: ")
 host = input("Host: ")
 port = int(input("Port [5432]: ") or 5432)
-postgres_url = 'postgresql://%s:%s@%s:%s/%s' % (user, pwd, host, port, db_name)
+postgres_url = "postgresql://%s:%s@%s:%s/%s" % (user, pwd, host, port, db_name)
 
 # Let's build an EMMO compatible city!
-emmo_town = city.City(name='EMMO town')
+emmo_town = city.City(name="EMMO town")
 
-emmo_town.add(city.Citizen(name='Emanuele Ghedini'), rel=city.hasInhabitant)
-emmo_town.add(city.Citizen(name='Adham Hashibon'), rel=city.hasInhabitant)
-emmo_town.add(city.Citizen(name='Jesper Friis'),
-              city.Citizen(name='Gerhard Goldbeck'),
-              city.Citizen(name='Georg Schmitz'),
-              city.Citizen(name='Anne de Baas'),
-              rel=city.hasInhabitant)
+emmo_town.add(city.Citizen(name="Emanuele Ghedini"), rel=city.hasInhabitant)
+emmo_town.add(city.Citizen(name="Adham Hashibon"), rel=city.hasInhabitant)
+emmo_town.add(
+    city.Citizen(name="Jesper Friis"),
+    city.Citizen(name="Gerhard Goldbeck"),
+    city.Citizen(name="Georg Schmitz"),
+    city.Citizen(name="Anne de Baas"),
+    rel=city.hasInhabitant,
+)
 
 emmo_town.add(city.Neighborhood(name="Ontology"))
 emmo_town.add(city.Neighborhood(name="User cases"))
@@ -49,7 +55,7 @@
 onto = emmo_town.get(ontology_uid)
 
 # We can go through inverse relationships
-print(onto.get(rel=city.isPartOf)[0].name + ' is my city!')
+print(onto.get(rel=city.isPartOf)[0].name + " is my city!")
 
 # Working with a DB-wrapper: Store in the DB.
 with SqlAlchemyWrapperSession(postgres_url) as session:
@@ -66,8 +72,7 @@
 
     # Working with a Simulation wrapper
     with SimDummySession() as sim_session:
-        sim_wrapper = city.CitySimWrapper(numSteps=1,
-                                          session=sim_session)
+        sim_wrapper = city.CitySimWrapper(numSteps=1, session=sim_session)
         new_inhabitant = city.Person(age=31, name="Peter")
         sim_emmo_town, _ = sim_wrapper.add(db_emmo_town, new_inhabitant)
         sim_session.run()