publish v3.0.0 (#213)

* Add Shubhangi as contributor on Zenodo, bump Zenodo version

* Fix vulnerability to CVE-2023-25399

* Bump ConFlowGen version as it is used by setup.py / pip, add Shubhangi as contributor in the docstring

* Fix qodana issues

* add installation of parameterized to CI

.github/workflows/installation-from-remote.yaml

@@ -32,7 +32,7 @@ jobs:
         conda info
         conda update conda
         conda info
-        conda create -n test-install-conflowgen -c conda-forge conflowgen pytest
+        conda create -n test-install-conflowgen -c conda-forge conflowgen pytest parameterized
 
     - name: Prepare tests
       run: |
@@ -71,7 +71,7 @@ jobs:
         conda update conda
         conda info
         conda activate base
-        conda create -n test-install-conflowgen -c conda-forge conflowgen pytest
+        conda create -n test-install-conflowgen -c conda-forge conflowgen pytest parameterized
 
     - name: Run tests
       run: |
@@ -102,7 +102,7 @@ jobs:
 
     - name: Install ConFlowGen
       run: |
-        python -m pip install conflowgen pytest
+        python -m pip install conflowgen pytest parameterized
         python -m pip show --verbose conflowgen
 
     - name: Run tests

CITATION.cff

@@ -24,7 +24,12 @@ authors:
     email: ole.grasse@tuhh.de
     affiliation: Hamburg University of Technology (TUHH), Institute of Maritime Logistics
     orcid: 'https://orcid.org/0000-0003-1982-9436'
-version: 2.1.1
+  - given-names: Shubhangi
+    family-names: Gupta
+    email: shubhangi.gupta@tuhh.de
+    affiliation: Hamburg University of Technology (TUHH), Institute of Maritime Logistics
+    orcid: 'https://orcid.org/0009-0003-3574-2899'
+version: 3.0.0
 repository-code: "https://github.com/1kastner/conflowgen"
 keywords:
   - logistics

conflowgen/analyses/abstract_analysis.py

@@ -119,7 +119,7 @@ def _restrict_container_picked_up_by_vehicle_type(
         if container_picked_up_by_vehicle_type == "scheduled vehicles":
             container_picked_up_by_vehicle_type = ModeOfTransport.get_scheduled_vehicles()
             list_of_vehicle_types = container_picked_up_by_vehicle_type
-        if hashable(container_picked_up_by_vehicle_type) \
+        elif hashable(container_picked_up_by_vehicle_type) \
                 and container_picked_up_by_vehicle_type in set(ModeOfTransport):
             selected_containers = selected_containers.where(
                 Container.picked_up_by == container_picked_up_by_vehicle_type

conflowgen/analyses/container_flow_by_vehicle_instance_analysis_report.py

@@ -1,7 +1,6 @@
 from __future__ import annotations
 
 import logging
-import typing
 
 import matplotlib.figure
 import matplotlib.pyplot as plt
@@ -36,7 +35,6 @@ def __init__(self):
 
     def get_report_as_text(
             self,
-            vehicle_types: ModeOfTransport | str | typing.Collection = "scheduled vehicles",
             **kwargs
     ) -> str:
         """
@@ -99,7 +97,10 @@ def _get_analysis(self, kwargs: dict) -> (list, list):
 
         return plain_table, vehicle_types
 
-    def get_report_as_graph(self, **kwargs) -> matplotlib.figure.Figure:
+    def get_report_as_graph(
+            self,
+            **kwargs
+    ) -> matplotlib.figure.Figure:
         """
         Keyword Args:
             vehicle_types (typing.Collection[ModeOfTransport]): A collection of vehicle types, e.g., passed as a

conflowgen/application/services/export_container_flow_service.py

@@ -149,7 +149,7 @@ def _convert_table_to_pandas_dataframe(
         # extract data from sql database
         data = list(model.select().dicts())
 
-        if type(model) == ModelSelect:  # pylint: disable=unidiomatic-typecheck  # TODO: check if isinstance works
+        if isinstance(model, ModelSelect):
             model = model.model
 
         foreign_keys_to_resolve = {}

conflowgen/metadata.py

@@ -1,9 +1,9 @@
-__version__ = "2.1.1"
+__version__ = "3.0.0"
 __license__ = "MIT"
 __description__ = """
 A generator for synthetic container flows at maritime container terminals with a focus on yard operations
 """
 
-__author__ = "Marvin Kastner and Ole Grasse"
+__author__ = "Marvin Kastner, Ole Grasse, and Shubhangi Gupta"
 __maintainer__ = "Marvin Kastner"
 __email__ = "marvin.kastner@tuhh.de"

docs/conf.py

@@ -193,7 +193,7 @@
     database_names = ["demo_continental_gateway", "demo_deham_cta", "demo_poc"]  # List of database names to download
     sqlite_databases_directory = "notebooks/data/prepared_dbs/"
     os.system("echo 'Current directory:'")
-    os.system("pwd") # Print current directory; we expect to be in the docs folder
+    os.system("pwd")  # Print current directory; we expect to be in the docs folder
     os.makedirs(sqlite_databases_directory, exist_ok=True)  # Create the destination folder if it doesn't exist
     for database_name in database_names:
         os.system(f'echo "Fetching {database_name}"')

qodana.yaml

@@ -0,0 +1,29 @@
+#-------------------------------------------------------------------------------#
+#               Qodana analysis is configured by qodana.yaml file               #
+#             https://www.jetbrains.com/help/qodana/qodana-yaml.html            #
+#-------------------------------------------------------------------------------#
+version: "1.0"
+
+#Specify inspection profile for code analysis
+profile:
+  name: qodana.starter
+
+#Enable inspections
+#include:
+#  - name: <SomeEnabledInspectionId>
+
+#Disable inspections
+#exclude:
+#  - name: <SomeDisabledInspectionId>
+#    paths:
+#      - <path/where/not/run/inspection>
+
+#Execute shell command before Qodana execution (Applied in CI/CD pipeline)
+#bootstrap: sh ./prepare-qodana.sh
+
+#Install IDE plugins before Qodana execution (Applied in CI/CD pipeline)
+#plugins:
+#  - id: <plugin.id> #(plugin id can be found at https://plugins.jetbrains.com)
+
+#Specify Qodana linter for analysis (Applied in CI/CD pipeline)
+linter: jetbrains/qodana-<linter>:latest

setup.py

@@ -24,7 +24,7 @@
     python_requires='>=3.8',
     install_requires=[
         # working with distributions and statistics
-        'scipy',  # used for, e.g., the lognorm distribution
+        "scipy >=1.10.0-rc1",  # used for, e.g., the lognorm distribution, version fixed due to CVE-2023-25399
 
         # data export
         'numpy',  # used in combination with pandas for column types
@@ -53,6 +53,7 @@
             'parameterized',  # for parameterized testing
             'seaborn',  # some visuals in unittests are generated by seaborn
             'nbconvert',  # used to run tests in Jupyter notebooks, see ./test/notebooks/test_run_notebooks.py
+            'nbformat',  # used to run tests in Jupyter notebooks
 
             # build documentation
             'sphinx >=6.2',  # build the documentation - restrict version to improve pip version resolution