initial commit

.devcontainer/Dockerfile

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+FROM continuumio/miniconda3 as upstream
+
+# Temporary: Upgrade python packages due to mentioned CVEs
+# They are installed by the base image (continuumio/miniconda3) which does not have the patch.
+# RUN conda install \ 
+# https://github.com/advisories/<CVE_ID>
+# <package_name> = <version>
+
+RUN python3 -m pip install --upgrade \
+    # https://github.com/advisories/GHSA-6vqw-3v5j-54x4
+    cryptography==42.0.4 \
+    # installed for compatibility with cryptography v42.0.4
+    pyopenssl==24.0.0 
+
+# Reset and copy updated files with updated privs to keep image size down
+FROM mcr.microsoft.com/devcontainers/base:ubuntu
+
+ARG USERNAME=vscode
+
+# Create the conda group and add remote user to the group
+RUN groupadd -r conda --gid 900 \ 
+    && usermod -aG conda ${USERNAME}
+
+# Copy opt folder, set ownership and group permissions
+COPY --chown=:conda --chmod=775 --from=upstream /opt/conda /opt/conda
+RUN chmod =2775 /opt/conda
+
+USER root
+
+
+# Setup conda to mirror contents from https://github.com/ContinuumIO/docker-images/blob/main/miniconda3/debian/Dockerfile
+ENV LANG=C.UTF-8 \
+    LC_ALL=C.UTF-8 \
+    PATH=/opt/conda/bin:$PATH
+ARG USERNAME=vscode
+RUN apt-get update && export DEBIAN_FRONTEND=noninteractive \
+    && apt-get install -y --no-install-recommends \
+    bzip2 \
+    ca-certificates \
+    libglib2.0-0 \
+    libsm6 \
+    libxext6 \
+    libxrender1 \
+    mercurial \
+    openssh-client \
+    procps \
+    subversion \
+    tmux \
+    wget \    
+    && apt-get upgrade -y \
+    # && mv -f "/tmp/library-scripts/meta.env" /usr/local/etc/vscode-dev-containers/meta.env \
+    && ln -s /opt/conda/etc/profile.d/conda.sh /etc/profile.d/conda.sh \
+    && apt-get clean -y && rm -rf /var/lib/apt/lists/*
+
+COPY env.yml /tmp/conda-tmp/
+RUN conda env create -f /tmp/conda-tmp/env.yml && rm -rf /tmp/conda-tmp
+
+
+# [Optional] Uncomment this section to install additional OS packages.
+# RUN apt-get update && export DEBIAN_FRONTEND=noninteractive \
+#     && apt-get -y install --no-install-recommends <your-package-list-here>

.devcontainer/devcontainer.json

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+{
+    "name": "ae4353",
+    "build": {
+        "dockerfile": "./Dockerfile",
+        "context": ".."
+    },
+    "mounts": [
+        // Bind mount data here if necessary e.g.
+        //"source=<your-external-data-directory>,target=${containerWorkspaceFolder}/data,type=bind"
+    ],
+    "features": {
+        "ghcr.io/devcontainers/features/common-utils:2": {
+            "installZsh": "true",
+            "username": "vscode",
+            "userUid": "1000",
+            "userGid": "1000",
+            "upgradePackages": "true"
+        },
+        "ghcr.io/devcontainers/features/git:1": {
+            "version": "latest",
+            "ppa": "false"
+        }
+    },
+    "customizations": {
+        // Configure properties specific to VS Code.
+        "vscode": {
+            "settings": {
+                // TODO: change to specific conda env python bin
+                "python.defaultInterpreterPath": "/opt/conda/envs/AE4353/bin/python",
+                "python.linting.enabled": true,
+                "notebook.defaultFormatter": "ms-python.black-formatter",
+                "notebook.formatOnSave.enabled": true,
+                "[python]": {
+                    "editor.defaultFormatter": "ms-python.black-formatter",
+                    "editor.formatOnSave": true
+                }
+            },
+            "extensions": [
+                "ms-python.python",
+                "ms-python.vscode-pylance",
+                "ms-python.black-formatter",
+                "ms-toolsai.jupyter",
+                "github.copilot",
+                "github.copilot-chat"
+            ]
+        }
+    },
+    "hostRequirements": {
+        "gpu": "optional"
+    },
+    "postCreateCommand": "./.devcontainer/postCreateCommand.sh",
+    // Use 'forwardPorts' to make a list of ports inside the container available locally.
+    // "forwardPorts": [],
+    // Use 'postCreateCommand' to run commands after the container is created.
+    // "postCreateCommand": "uname -a",
+    // Set `remoteUser` to `root` to connect as root instead. More info: https://aka.ms/vscode-remote/containers/non-root.
+    "remoteUser": "vscode",
+    "remoteEnv": {
+        "SERVICE_HOST": "host.docker.internal",
+        "SERVICE_PORT": "9876"
+    }
+}

.devcontainer/noop.txt

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+This file is copied into the container along with environment.yml* from the
+parent folder. This is done to prevent the Dockerfile COPY instruction from 
+failing if no environment.yml is found.

.devcontainer/postCreateCommand.sh

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+#!/bin/bash
+/opt/conda/envs/AE4353/bin/pip install -e .

.gitattributes

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+*.ipynb filter=nbstripout
+*.zpln filter=nbstripout
+*.ipynb diff=ipynb

.gitignore

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+# data folder
+data/*
+!data/.gitkeep
+*/data/
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# 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/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/

LICENSE

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+MIT License
+
+Copyright (c) 2024 TU Delft
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.