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.devcontainer/Dockerfile

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+##########################################################################################
+#
+#   DESCRIPTION:  Development Docker Container.  Installs the following:
+#                 * miniconda
+#                 * Oh-My-Zsh
+#                 * awesome-vim
+#
+#   GPU SUPPORT:  In order to get GPU support the nvidia image's CUDA version must
+#                 match the version on the host computer.
+#
+#     RENDERING:  If rendering to the screen is required then execute the following
+#                 prior to starting the container:
+#
+#                 ```console
+#                 xhost +local:root
+#                 ```
+#
+#        AUTHOR:  W. Li
+#       VERSION:  1.0
+#       CREATED:  12/15/2023
+##########################################################################################
+
+# Source Image (this should match the CUDA version on the host)
+# FROM nvidia/cuda:11.4.1-base-ubuntu20.04
+FROM ubuntu:20.04
+
+# Labels
+LABEL version="1.0"
+LABEL description="Miniconda Dev Image"
+
+# Expose ports here
+# EXPOSE 8080
+
+# Install basic packages needed for development
+RUN yes Y | apt update
+RUN yes Y | apt-get update
+RUN yes Y | apt upgrade
+RUN yes Y | apt install vim
+RUN apt-get install -y --no-install-recommends \
+    git \
+    wget \
+    g++ \
+    gcc \
+    && rm -rf /var/lib/apt/lists/*
+
+# Setup shell
+RUN sh -c "$(wget -O- https://github.com/deluan/zsh-in-docker/releases/download/v1.1.1/zsh-in-docker.sh)" -- \
+    -t robbyrussell \
+    -p git -p ssh-agent -p 'history-substring-search' \
+    -a 'bindkey "\$terminfo[kcuu1]" history-substring-search-up' \
+    -a 'bindkey "\$terminfo[kcud1]" history-substring-search-down'
+
+# Setup Shell
+SHELL ["/bin/zsh", "-c"]
+
+# Miniconda requires that the path point to its python binary
+ENV PATH="/root/miniconda3/bin:${PATH}"
+ARG PATH="/root/miniconda3/bin:${PATH}"
+
+# Source python versions: https://repo.anaconda.com/miniconda/
+RUN wget \
+    https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh \
+    && mkdir /root/.conda \
+    && bash Miniconda3-latest-Linux-x86_64.sh -b \
+    && rm -f Miniconda3-latest-Linux-x86_64.sh
+
+RUN conda init zsh
+
+# Setup Vim-Awesome
+RUN git clone --depth=1 https://github.com/amix/vimrc.git ~/.vim_runtime \
+    && sh ~/.vim_runtime/install_basic_vimrc.sh
+
+# Setup working directory
+WORKDIR /projects
+
+# Copy folder/files into container (must be within context directory)
+# Process: local files -> artifact dir -> container dir
+# COPY <local_path> <container_path>
+
+# Environment
+ENV SHELL /bin/zsh

.devcontainer/README.md

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+# 📒 Description
+## 🐳 Docker
+* Primary method for building and maintaining **un-secure** containers.
+* Must have root access in order to work.
+* Deployable to any machine.
+* [Additional Information](#🐳-docker-notes)
+
+## 🦉 Apptainer
+* Primary method for building and maintaining **secure** containers.
+* Used primarily in settings where root access is not possible.
+* Deployable to any machine.
+* [Additional Information](#🦉-apptainer-notes)
+
+## 📦 Packages
+The default development containers will these packages by default.  Only the essentials are included.
+
+* [Miniconda](https://docs.conda.io/projects/miniconda/en/latest/)
+* [Oh My Bash](https://github.com/ohmybash/oh-my-bash)
+* [Oh My Zsh](https://ohmyz.sh)
+* [Precommit](https://pre-commit.com)
+
+# 🐳 Docker Notes
+
+## 🎼  Docker Compose
+* Allows you to create multiple different builds using different Docker files.
+* The context directory can be set from the `docker_compose.yml` file.
+* More options than a standard Docker file.
+
+## 👟 Running Commands
+* In Docker each `RUN` command is treated as a new shell instance.  This means that commands cannot persist across different RUN commands.
+
+```Docker
+RUN command1    # this command is run in its own shell!
+RUN command2    # this command is run in its own shell!
+```
+
+## 🗃️ Copying Folders/Files
+* If you need to copy files or directories into the Docker container, first put them in an **artifacts** directory that can be seen from the context directory.
+
+```Docker
+COPY <artifact_directory> <container_path>
+```
+## 📂 Context Directory
+
+* By default Dockerfiles are only aware of what is in their **context directory**.  A context directory is the directory where a Dockerfile is located in.  It cannot access any files outside of the context directory.
+
+* The context directory can be set from the command line or from a `docker_compose.yml` file.
+
+* It is recommended that all folders/files be copied be placed in an **artifacts** directory that is under the context directory.
+
+## 💾 Out of Memory
+* Occasionally you will need to clean your docker images and docker volumes in order to recover memory.
+
+```console
+docker volume prune
+docker image prune
+docker container prune
+```
+
+# 🦉 Apptainer Notes

.devcontainer/build.py

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+"""
+Run this script to build the Docker development image.
+"""
+import subprocess
+
+image_name = "development-base"
+
+# Build the image from the development Dockerfile
+subprocess.run(["docker", "build", "-t", image_name, "."])

.devcontainer/devcontainer.json

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+// For format details, see https://aka.ms/devcontainer.json. For config options, see the README at:
+// https://github.com/microsoft/vscode-dev-containers/tree/v0.191.0/containers/ubuntu
+{
+	"name": "dev-python",
+	"image": "development-base",
+	"build": {
+		"dockerfile": "Dockerfile",
+	},
+	// Add arguments that run with the container
+	// These are arguments needed for GPU support on a Linux machine
+	"runArgs": [
+		// "--net=host",
+		// "-m=10g",
+		// "--shm-size=10g",
+		// "--gpus=all",
+		// "-v",
+		// "/tmp/.X11-unix:/tmp/.X11-unix",
+		// "-e",
+		// "DISPLAY",
+		// "--device",
+		// "/dev/dri"
+	],
+	"customizations": {
+		"vscode": {
+			// Set *default* container specific settings.json values on container create.
+			"settings": {},
+			// Add the IDs of extensions you want installed when the container is created.
+			"extensions": [
+				"eamodio.gitlens",
+				"littlefoxteam.vscode-python-test-adapter",
+				"ms-python.python",
+				"mhutchie.git-graph",
+				"njpwerner.autodocstring",
+				"pkief.material-icon-theme",
+			]
+		}
+	},
+	// 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"
+	// Comment out connect as root instead. More info: https://aka.ms/vscode-remote/containers/non-root.
+	// "remoteUser": "vscode"
+}

.github/workflows/pre-commit.yml

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+##########################################################################################
+#   DESCRIPTION:  Run pre-commit on all files in repo.
+#        AUTHOR:  W. Li
+#       VERSION:  1.0
+#       CREATED:  1/6/2024
+#
+# References:
+# * https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-pythonCommon
+#
+##########################################################################################
+
+name: pre-commit
+
+on:
+  pull_request:
+  push:
+    branches: [main]
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v5
+    - uses: pre-commit/[email protected]

.github/workflows/pytest.yml

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+##########################################################################################
+#   DESCRIPTION:  Runs pytests with multiple versions of python.
+#        AUTHOR:  W. Li
+#       VERSION:  1.0
+#       CREATED:  1/6/2024
+#
+# References:
+# * https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-pythonCommon
+#
+##########################################################################################
+
+name: pytests
+
+on:
+  # Configure the branches you want Github actions to run on.
+  # Leave blank if you want to run on all branches.
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
+
+# Configure jobs
+jobs:
+  test:
+    # Set the OS and python versions
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.10", "3.11"]
+    # Checkout the repo
+    steps:
+    - uses: actions/checkout@v4
+    # Setup the python environments to use.
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+    # Install poetry and disable virtual environments.
+    - name: Install Poetry
+      uses: snok/install-poetry@v1
+      with:
+        virtualenvs-create: false
+        virtualenvs-in-project: false
+        installer-parallel: true
+    # Install dependencies.
+    - name: Install dependencies
+      run: |
+        poetry install --no-interaction --with=dev --no-root
+    # Run pytest with coverage.
+    - name: Test with pytest
+      run: >
+        pytest
+        --doctest-modules
+        --cov=./
+        --cov-report=xml
+        --cov-report=html:pytest-results-${{ matrix.python-version }}
+    # Save artifacts from pytests.
+    - name: Upload pytest test results
+      uses: actions/upload-artifact@v3
+      with:
+        name: pytest-results-${{ matrix.python-version }}
+        path: pytest-results-${{ matrix.python-version }}
+      # Use always() to always run this step to publish test results when there are test failures
+      if: ${{ always() }}

.gitignore

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+# Files to ignore
+*.pyc
+*.sif
+.coverage
+.DS_Store
+profile.html
+profile.json
+
+
+# Folders to ignore
+__pycache__
+.mypy_cache
+.nox
+.pytest_cache
+html
+save
+runs

.pre-commit-config.yaml

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+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
+    hooks:
+    -   id: check-ast
+    -   id: check-byte-order-marker
+    -   id: check-builtin-literals
+    -   id: check-case-conflict
+    -   id: check-docstring-first
+    -   id: check-merge-conflict
+    -   id: check-symlinks
+    -   id: check-toml
+    -   id: check-xml
+    -   id: check-yaml
+    -   id: debug-statements
+    -   id: detect-private-key
+    -   id: end-of-file-fixer
+    -   id: name-tests-test
+    -   id: requirements-txt-fixer
+    -   id: sort-simple-yaml
+    -   id: trailing-whitespace
+-   repo: https://github.com/pre-commit/pygrep-hooks
+    rev: v1.10.0  # Use the ref you want to point at
+    hooks:
+    -   id: python-check-blanket-noqa
+    -   id: python-check-mock-methods
+    -   id: python-no-eval
+    -   id: python-no-log-warn
+    -   id: python-use-type-annotations
+    -   id: text-unicode-replacement-char
+-   repo: https://github.com/asottile/pyupgrade
+    rev: v3.15.0
+    hooks:
+    -   id: pyupgrade
+-   repo: https://github.com/psf/black
+    rev: 23.12.1    # Replace by any tag/version: https://github.com/psf/black/tags
+    hooks:
+    -   id: black
+        language_version: python3 # Should be a command that runs python3.6+
+        args: ["--target-version", "py310"]
+-   repo: https://github.com/asottile/reorder_python_imports
+    rev: v3.12.0
+    hooks:
+    -   id: reorder-python-imports
+        args: [--py3-plus]
+-   repo: https://github.com/asottile/setup-cfg-fmt
+    rev: v2.5.0
+    hooks:
+    -   id: setup-cfg-fmt
+-   repo: https://github.com/pre-commit/mirrors-mypy
+    rev: 'v1.8.0'  # Use the sha / tag you want to point at
+    hooks:
+    -   id: mypy
+-   repo: https://gitlab.com/smop/pre-commit-hooks
+    rev: 'v1.0.0'
+    hooks:
+    -   id: check-gitlab-ci

.vscode/configs/.git-blame-ignore-revs

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+# Commits to ignore (enter revision numbers here)

.vscode/launch.json

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+{
+    "version": "0.2.0",
+    "configurations": [
+        {
+            "name": "Python: Current File",
+            "type": "python",
+            "request": "launch",
+            "program": "${file}",
+            "console": "integratedTerminal",
+            "cwd": "${workspaceFolder}",
+            "env": {
+                "PYTHONPATH": "${workspaceFolder}:${env:PYTHONPATH}"
+            }
+        },
+        {
+            "name": "Debug Unit Test",
+            "type": "python",
+            "request": "test",
+            "justMyCode": false,
+        }
+    ]
+}

.vscode/ltex.dictionary.en-US.txt

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+Mujoco
+SLURM
+Syndeo
+Apptainer