Merge pull request #1 from TGSAI/main

Update to TGSAI

.devcontainer/Dockerfile

@@ -0,0 +1,36 @@
+ARG PYTHON_VERSION=3.11
+ARG LINUX_DISTRO=bookworm
+
+FROM mcr.microsoft.com/devcontainers/python:1-${PYTHON_VERSION}-${LINUX_DISTRO}
+
+# Install git for nox pre-commit
+RUN apt-get update \
+ && apt-get install -y --no-install-recommends \
+ git \
+ && rm -rf /var/lib/apt/lists/*
+
+# Poetry
+ARG POETRY_VERSION="1.6.1"
+RUN if [ "${POETRY_VERSION}" != "none" ]; then bash -c "umask 0002 && pip3 install poetry==${POETRY_VERSION}"; fi
+
+# Nox
+ARG NOX_VERSION="2023.4.22"
+RUN if [ "${NOX_VERSION}" != "none" ]; then bash -c "umask 0002 && pip3 install nox-poetry nox==${NOX_VERSION}"; fi
+
+# Nox poetry
+ARG NOX_POETRY_VERSION="1.0.3"
+RUN if [ "${NOX_POETRY_VERSION}" != "none" ]; then bash -c "umask 0002 && pip3 install nox-poetry nox-poetry==${NOX_POETRY_VERSION}"; fi
+
+# Extra python packages for dev
+RUN bash -c "umask 0002 && pip3 install msgpack ipykernel"
+
+# Create venv
+RUN python -m venv /opt/venv
+RUN poetry config virtualenvs.create false
+ENV PATH="/opt/venv/bin:$PATH"
+
+# Extra python packages for dev
+RUN bash -c "umask 0002 && pip3 install msgpack ipykernel"
+
+# Allow users to update venv
+RUN chmod -R 777 /opt/venv

.devcontainer/devcontainer.json

@@ -0,0 +1,43 @@
+// For format details, see https://aka.ms/devcontainer.json. For config options, see the
+// README at: https:/devcontainers/templates/tree/main/src/python
+{
+ "build": {
+ "dockerfile": "Dockerfile",
+ "context": ".."
+ },
+ // Use 'postCreateCommand' to run commands after the container is created.
+ "postCreateCommand": {
+ "post_create_script": "bash ./.devcontainer/post-install.sh"
+ },
+ // Forward 8787 to enable us to view dask dashboard
+ "forwardPorts": [8787],
+ // Configure tool-specific properties.
+ "customizations": {
+ // Configure properties specific to VS Code.
+ "vscode": {
+ "settings": {
+ "python.terminal.activateEnvInCurrentTerminal": true,
+ "python.defaultInterpreterPath": "/opt/venv/bin/python"
+ },
+ "extensions": [
+ "ms-python.python",
+ "ms-python.vscode-pylance",
+ "ms-toolsai.jupyter",
+ "ms-toolsai.jupyter-keymap",
+ "ms-toolsai.jupyter-renderers",
+ "vscode-icons-team.vscode-icons",
+ "wayou.vscode-todo-highlight",
+ "streetsidesoftware.code-spell-checker"
+ ]
+ }
+ },
+ // Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root.
+ // "remoteUser": "root",
+ "updateRemoteUserUID": true,
+ "mounts": [
+ // Re-use local Git configuration
+ "source=${localEnv:HOME}/.gitconfig,target=/home/vscode/.gitconfig_tmp,type=bind,consistency=cached",
+ "source=${localEnv:HOME}/.gitconfig,target=/root/.gitconfig_tmp,type=bind,consistency=cached",
+ "source=${localEnv:SCRATCH_DIR}/${localEnv:USER},target=/scratch/,type=bind,consistency=cached"
+ ]
+}

.devcontainer/post-install.sh

@@ -0,0 +1,13 @@
+cp -f /root/.gitconfig_tmp /root/.gitconfig
+cp -f /home/vscode/.gitconfig_tmp /home/vscode/.gitconfig
+chmod 777 /home/vscode/.gitconfig
+git config --global --add safe.directory `pwd`
+
+# Enable ssh with github for git push
+ssh-keygen -f "/root/.ssh/known_hosts" -R "github.com"
+
+# Setup venv
+source /opt/venv/bin/activate
+
+# Poetry cmds
+poetry config virtualenvs.create false

.dockerignore

@@ -0,0 +1,151 @@
+# 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
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+debugging/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# ruff
+.ruff_cache/
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# IDE settings
+.vscode/
+.idea/
+
+# tests
+mdio1/*
+*/mdio1/*
+pytest-of-*

.github/workflows/constraints.txt

@@ -1,4 +1,4 @@
-pip==23.2.1
+pip==23.3.1
 nox==2023.4.22
 nox-poetry==1.0.3
-virtualenv==20.24.5
+virtualenv==20.24.6

.github/workflows/release.yml

@@ -71,7 +71,7 @@ jobs:
  repository_url: https://test.pypi.org/legacy/
 
  - name: Publish the release notes
- uses: release-drafter/release-drafter@v5.24.0
+ uses: release-drafter/release-drafter@v5.25.0
  with:
  publish: ${{ steps.check-version.outputs.tag != '' }}
  tag: ${{ steps.check-version.outputs.tag }}

.gitignore

@@ -70,6 +70,7 @@ instance/
 
 # Sphinx documentation
 docs/_build/
+docs/jupyter_execute/
 
 # PyBuilder
 .pybuilder/
@@ -112,6 +113,7 @@ venv/
 ENV/
 env.bak/
 venv.bak/
+venv*/
 
 # Spyder project settings
 .spyderproject
@@ -143,3 +145,9 @@ cython_debug/
 # IDE settings
 .vscode/
 .idea/
+
+# tests
+mdio1/*
+*/mdio1/*
+pytest-of-*
+tmp/

CONTRIBUTING.md

@@ -37,12 +37,24 @@ Request features on the [Issue Tracker].
 
 ## How to set up your development environment
 
-You need Python 3.7+ and the following tools:
+You need Python 3.9+ and the following tools:
 
 - [Poetry]
 - [Nox]
 - [nox-poetry]
 
+Another alternative is to use a [Development Container] has been setup to provide
+an environment with the required dependencies. This facilitates development on
+different systems.
+
+This should seamlessly enable development for users of [VS Code] on systems with docker installed.
+
+### Known Issues:
+
+- `git config --global --add safe.directory $(pwd)` might be needed inside the container.
+
+## How to Install and Run MDIO
+
 Install the package with development requirements:
 
 ```console
@@ -60,6 +72,8 @@ $ poetry run mdio
 [poetry]: https://python-poetry.org/
 [nox]: https://nox.thea.codes/
 [nox-poetry]: https://nox-poetry.readthedocs.io/
+[development container]: https://containers.dev/
+[vs code]: https://code.visualstudio.com/docs/devcontainers/containers/
 
 ## How to test the project