Dev

.devcontainer/devcontainer.json

@@ -0,0 +1,61 @@
+{
+	"name": "exsclaim-dev",
+	"build": {
+		"dockerfile": "../Dockerfile",
+		"context": "..",
+		"args": {},
+		"target": "dev"
+	},
+	// Set *default* container specific settings.json values on container create.
+	"settings": {
+		"terminal.integrated.profiles.linux": {
+			"bash": {
+				"path": "/bin/bash"
+			}
+		},
+		"python.defaultInterpreterPath": "/usr/local/bin/python3",
+		"python.languageServer": "Default",
+		"python.linting.enabled": true,
+		"python.linting.pylintEnabled": true,
+		"python.formatting.autopep8Path": "/usr/local/py-utils/bin/autopep8",
+		"python.formatting.blackPath": "/usr/local/py-utils/bin/black",
+		"python.formatting.yapfPath": "/usr/local/py-utils/bin/yapf",
+		"python.linting.banditPath": "/usr/local/py-utils/bin/bandit",
+		"python.linting.flake8Path": "/usr/local/py-utils/bin/flake8",
+		"python.linting.mypyPath": "/usr/local/py-utils/bin/mypy",
+		"python.linting.pycodestylePath": "/usr/local/py-utils/bin/pycodestyle",
+		"python.linting.pydocstylePath": "/usr/local/py-utils/bin/pydocstyle",
+		"python.linting.pylintPath": "/usr/local/py-utils/bin/pylint"
+	},
+	// Add the IDs of extensions you want installed when the container is created.
+	"extensions": [
+		"ms-python.python",
+		"ms-python.vscode-pylance",
+		"ms-vscode-remote.remote-containers",
+		"ms-toolsai.jupyter",
+	],
+	"features": {
+		"github-cli": "latest"
+	},
+	"runArgs": [
+		"--shm-size=16gb"
+	],
+	// Use 'forwardPorts' to make a list of ports inside the container available locally.
+	// "forwardPorts": [9000],
+	// Use 'portsAttributes' to set default properties for specific forwarded ports. More info: https://code.visualstudio.com/docs/remote/devcontainerjson-reference.
+	// "portsAttributes": {
+	//     "9000": {
+	//         "label": "Hello Remote World",
+	//         "onAutoForward": "notify"
+	//     }
+	// },
+	// Use 'otherPortsAttributes' to configure any ports that aren't configured using 'portsAttributes'.
+	// "otherPortsAttributes": {
+	// 		"onAutoForward": "silent"
+	// },
+	// Use 'postCreateCommand' to run commands after the container is created.
+	// "postCreateCommand": "pip3 install -r requirements.txt",
+	// Comment out to connect as root instead. More info: https://aka.ms/vscode-remote/containers/non-root.
+	"workspaceMount": "source=${localWorkspaceFolder},target=/src,type=bind",
+	"workspaceFolder": "/src"
+}

.devcontainer/docker-compose.yml

@@ -0,0 +1,37 @@
+version: '3.9'
+services:
+  # Update this to the name of the service you want to work with in your docker-compose.yml file
+  exsclaim:
+    # If you want add a non-root user to your Dockerfile, you can use the "remoteUser"
+    # property in devcontainer.json to cause VS Code its sub-processes (terminals, tasks,
+    # debugging) to execute as the user. Uncomment the next line if you want the entire
+    # container to run as this user instead. Note that, on Linux, you may need to
+    # ensure the UID and GID of the container user you create matches your local user.
+    # See https://aka.ms/vscode-remote/containers/non-root for details.
+    #
+    # user: vscode
+
+    # Uncomment if you want to override the service's Dockerfile to one in the .devcontainer
+    # folder. Note that the path of the Dockerfile and context is relative to the *primary*
+    # docker-compose.yml file (the first in the devcontainer.json "dockerComposeFile"
+    # array). The sample below assumes your primary file is in the root of your project.
+    #
+    # build:
+    #   context: .
+    #   dockerfile: .devcontainer/Dockerfile
+
+    volumes:
+      # Update this to wherever you want VS Code to mount the folder of your project
+      - .:/workspace:cached
+
+      # Uncomment the next line to use Docker from inside the container. See https://aka.ms/vscode-remote/samples/docker-from-docker-compose for details.
+      # - /var/run/docker.sock:/var/run/docker.sock
+
+    # Uncomment the next four lines if you will use a ptrace-based debugger like C++, Go, and Rust.
+    # cap_add:
+    #   - SYS_PTRACE
+    # security_opt:
+    #   - seccomp:unconfined
+
+    # Overrides default command so things don't shut down after the process ends.
+    command: /bin/sh -c "while sleep 1000; do :; done"

.dockerignore

@@ -0,0 +1,6 @@
+docs/
+*/tests
+build/
+dist/
+.ipynb_checkpoints/
+exsclaim.egg-info/

.github/ISSUE_TEMPLATE/bug_report.md

@@ -19,7 +19,7 @@ Steps to reproduce the behavior:
 A clear and concise description of what you expected to happen.
 
 **Outputs**
-If applicable, add screenshots to help explain your problem. For error messages, please copy and paste them here. 
+If applicable, add screenshots to help explain your problem. For error messages, please copy and paste them here.
 
 **Environment (please complete the following information):**
  - OS: [e.g. Ubuntu]

.github/workflows/main.workflow.yml

@@ -0,0 +1,28 @@
+name: Development Checks
+
+on:
+  # Trigger the workflow on push or pull request,
+  # but only for the main branch
+  pull_request:
+    branches:
+      - main
+      - master
+      - dev
+
+jobs:
+  linter:
+    runs-on: ubuntu-latest
+    steps:
+
+      - name: Checkout Code Repository
+        uses: actions/checkout@v3
+
+      - name: Set up Python
+        uses: actions/setup-python@v3
+        with:
+          python-version: "3.9"
+          cache: pip
+          cache-dependency-path: |
+            requirements.txt
+      - name: Run pre-commit
+        uses: pre-commit/[email protected]

.gitignore

@@ -30,4 +30,7 @@ cookie
 dist/
 build/
 *.sh
-*/results_dirs
+*/results_dirs
+.ipynb_checkpoints/
+**/local.ini
+docs/build/

.pre-commit-config.yaml

@@ -0,0 +1,34 @@
+exclude: "^docs/"
+default_stages: [commit]
+
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.1.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+
+  - repo: https://github.com/psf/black
+    rev: 22.1.0
+    hooks:
+      - id: black
+        additional_dependencies: ['click==8.0.4']
+
+  - repo: https://github.com/PyCQA/isort
+    rev: 5.10.1
+    hooks:
+      - id: isort
+
+  - repo: https://github.com/PyCQA/flake8
+    rev: 4.0.1
+    hooks:
+      - id: flake8
+        args: ["--config=setup.cfg"]
+        additional_dependencies: [flake8-isort]
+
+# sets up .pre-commit-ci.yaml to ensure pre-commit dependencies stay up to date
+ci:
+  autoupdate_schedule: weekly
+  skip: []
+  submodules: false