first rebuild with pyscaffold

.circleci/config.yml

@@ -0,0 +1,45 @@
+version: 2
+jobs:
+  build:
+    machine: true
+    steps:
+      - checkout
+      - run:
+          name: Build and start container
+          command: docker-compose -f docker-compose.yml -f docker-compose.test.yml up -d
+
+      - run:
+          name: Install test environment
+          command: |
+            docker exec -it openclsim bash -c "pip install -r test-requirements.txt"
+            docker exec -it openclsim bash -c "pip install coverage coverage-badge"
+      
+      - run:
+          name: Run tests
+          command: |
+            docker exec -it openclsim bash -c "python setup.py test"
+            docker cp openclsim:/openclsim/htmlcov /tmp/artifacts
+      - run:
+          name: Build docs
+          command: |
+            docker exec -it openclsim bash -c "pip install sphinx"
+            docker exec -it openclsim bash -c "python setup.py docs"
+            docker cp openclsim:/OpenCLSim/docs/_build/html /tmp/artifacts/docs
+          
+      - run:
+          name: Generate coverage badge
+          command: |
+            docker exec -it openclsim bash -c "coverage-badge -o coverage.svg"
+            docker cp openclsim:/OpenCLSim/coverage.svg /tmp/artifacts/
+          
+      - store_artifacts:
+          path: /tmp/artifacts
+
+workflows:
+  version: 2
+  build:
+    jobs:
+      - build:
+          filters:
+            tags:
+              only: /.*/

.coveragerc

@@ -0,0 +1,3 @@
+[run]
+source = openclsim
+omit = openclsim/tests*

.devcontainer/devcontainer.json

@@ -0,0 +1,22 @@
+// See https://aka.ms/vscode-remote/devcontainer.json for format details.
+{
+    "dockerComposeFile": [
+        "../docker-compose.yml",
+        "docker-compose.dev.yml"
+    ],
+    "service": "main",
+    "workspaceFolder": "/openclsim",
+    "extensions": [
+        "ms-python.python"
+    ],
+    "settings": {
+        "python.pythonPath": "/opt/conda/bin/python",
+        "python.linting.pylintEnabled": false,
+        "python.linting.enabled": true,
+        "python.testing.unittestEnabled": false,
+        "python.testing.nosetestsEnabled": false,
+        "python.testing.pytestEnabled": true,
+        "python.linting.pylamaEnabled": true,
+        "python.formatting.provider": "black"
+    },
+}

.devcontainer/docker-compose.dev.yml

@@ -0,0 +1,8 @@
+# docker-compose -f docker-compose.yml -f .devcontainer/docker-compose.dev.yml up -d
+version: '3.2'
+
+services:
+  main:
+    command: bash -c "tail -f /dev/null"
+    volumes:
+      - .:/

.dockerignore

@@ -0,0 +1,10 @@
+# Ignore
+.pytest_cache
+.htmlcov
+.eggs
+.docs
+.v**/scode
+**/__pycache__
+*.egg-info
+app/frontend
+Notebooks/*

.gitignore

@@ -0,0 +1,121 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+coverage.svg
+.cache
+nosetests.xml
+coverage.xml
+*,cover
+.hypothesis/
+.mypy_cache
+.pytest_cache
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# IPython Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# virtualenv
+venv/
+ENV/
+
+# Spyder project settings
+.spyderproject
+
+# Rope project settings
+.ropeproject
+
+.vscode/settings.json
+
+.pylint.d/
+faux_data
+
+# vue app
+.DS_Store
+node_modules
+
+# local env files
+.env.local
+.env.*.local
+
+# Log files
+npm-debug.log*
+yarn-debug.log*
+yarn-error.log*
+
+# Editor directories and files
+.idea
+.vscode
+*.suo
+*.ntvs*
+*.njsproj
+*.sln
+*.sw*
+
+
+# data Files
+*.csv
+*.pkl

AUTHORS.rst

@@ -0,0 +1,36 @@
+=======
+Credits
+=======
+
+Development Lead
+----------------
+* `Mark van Koningsveld`_
+* `Joris den Uijl`_
+* `Fedor Baart`_
+* `Anne Hommelberg`_
+
+.. _Mark van Koningsveld: https://www.tudelft.nl/citg/over-faculteit/afdelingen/hydraulic-engineering/sections/rivers-ports-waterways-and-dredging-engineering/staff/prof-dr-ir-m-mark-van-koningsveld/
+.. _Joris den Uijl: https://github.com/uijl
+.. _Fedor Baart: https://github.com/SiggyF
+.. _Anne Hommelberg: https://github.com/AnneHommelberg
+
+Contributors
+------------
+
+Various MSc projects
+
+* `Joris den Uijl,`_ 2018. **Integrating engineering knowledge in logistical optimisation: development of a concept evaluation tool.** MSc thesis. Delft University of Technology, Civil Engineering and Geosciences, Hydraulic Engineering. Delft, the Netherlands.
+* `Vibeke van der Bilt`_, 2019. **Assessing emission performance of dredging projects.** MSc thesis. Delft University of Technology, Civil Engineering and Geosciences, Hydraulic Engineering - Ports and Waterways. Delft, the Netherlands.
+* `Pieter van Halem`_, 2019. **Route optimization in dynamic currents. Navigation system for the North Sea and Wadden Sea.** MSc thesis. Delft University of Technology, Civil Engineering and Geosciences, Environmental Fluid Mechanics. Delft, the Netherlands.
+* `Servaas Kievits`_, 2019. **A framework for the impact assessment of low discharges on the performance of inland waterway transport.** MSc thesis. Delft University of Technology, Civil Engineering and Geosciences, Hydraulic Engineering - Ports and Waterways. Delft, the Netherlands.
+
+.. _Joris den Uijl,: http://resolver.tudelft.nl/uuid:8d82b44c-59e3-4307-a0af-03a20f1a931e
+.. _Vibeke van der Bilt: http://resolver.tudelft.nl/uuid:ab6d12ea-34fe-4577-b72c-6aa688e0d1bf
+.. _Pieter van Halem: http://resolver.tudelft.nl/uuid:5d34d333-34fe-4181-95b6-d8d82f72d979
+.. _Servaas Kievits: http://resolver.tudelft.nl/uuid:b457c9c3-922e-4016-9580-f79a2549128d
+
+Ongoing PhD work
+
+* `Frederik Vinke`_, 2019. **Climate proofing the inland water transport system in the Netherlands.** PhD thesis. Delft University of Technology, Civil Engineering and Geosciences, Hydraulic Engineering - Ports and Waterways. Delft, the Netherlands.
+
+.. _Frederik Vinke: https://repository.tudelft.nl