From da84c0b4fe5f96c76b6a594f642b0e806be884de Mon Sep 17 00:00:00 2001 From: Timothy Stiles Date: Sat, 6 Aug 2022 20:10:28 -0700 Subject: [PATCH] got portable devcontainer working for vscode and resolved unlisted dependencies. --- .devcontainer/Dockerfile | 30 ++++++++++++++ .devcontainer/devcontainer.json | 73 +++++++++++++++++++++++++++++++++ requirements.txt | 18 ++++++++ 3 files changed, 121 insertions(+) create mode 100644 .devcontainer/Dockerfile create mode 100644 .devcontainer/devcontainer.json create mode 100644 requirements.txt diff --git a/.devcontainer/Dockerfile b/.devcontainer/Dockerfile new file mode 100644 index 0000000..3718e7c --- /dev/null +++ b/.devcontainer/Dockerfile @@ -0,0 +1,30 @@ +# See here for image contents: https://github.com/microsoft/vscode-dev-containers/blob/v0.202.3/containers/python-3/.devcontainer/base.Dockerfile +# [Choice] Python version (use -bullseye variants on local arm64/Apple Silicon): 3, 3.9, 3.8, 3.7, 3.6, 3-bullseye, 3.9-bullseye, 3.8-bullseye, 3.7-bullseye, 3.6-bullseye, 3-buster, 3.9-buster, 3.8-buster, 3.7-buster, 3.6-buster +ARG VARIANT=3-bullseye +FROM mcr.microsoft.com/vscode/devcontainers/python:0-${VARIANT} + +# [Optional] Allow the vscode user to pip install globally w/o sudo +ENV PIP_TARGET=/usr/local/pip-global +ENV PYTHONPATH=${PIP_TARGET}:${PYTHONPATH} +ENV PATH=${PIP_TARGET}/bin:${PATH} +RUN if ! cat /etc/group | grep -e "^pip-global:" > /dev/null 2>&1; then groupadd -r pip-global; fi \ + && usermod -a -G pip-global vscode \ + && umask 0002 && mkdir -p ${PIP_TARGET} \ + && chown :pip-global ${PIP_TARGET} \ + && ( [ ! -f "/etc/profile.d/00-restore-env.sh" ] || sed -i -e "s/export PATH=/export PATH=\/usr\/local\/pip-global:/" /etc/profile.d/00-restore-env.sh ) + +# [Choice] Node.js version: none, lts/*, 16, 14, 12, 10 +ARG NODE_VERSION="none" +RUN if [ "${NODE_VERSION}" != "none" ]; then su vscode -c "umask 0002 && . /usr/local/share/nvm/nvm.sh && nvm install ${NODE_VERSION} 2>&1"; fi + +# [Optional] If your pip requirements rarely change, uncomment this section to add them to the image. +# COPY requirements.txt /tmp/pip-tmp/ +# RUN pip3 --disable-pip-version-check --no-cache-dir install -r /tmp/pip-tmp/requirements.txt \ +# && rm -rf /tmp/pip-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 + +# [Optional] Uncomment this line to install global node packages. +# RUN su vscode -c "source /usr/local/share/nvm/nvm.sh && npm install -g " 2>&1 diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json new file mode 100644 index 0000000..417995c --- /dev/null +++ b/.devcontainer/devcontainer.json @@ -0,0 +1,73 @@ +// For format details, see https://aka.ms/vscode-remote/devcontainer.json or this file's README at: +// https://github.com/microsoft/vscode-dev-containers/tree/v0.202.3/containers/python-3 +{ + "name": "Python 3", + "build": { + "dockerfile": "Dockerfile", + "context": "..", + "args": { + // Update 'VARIANT' to pick a Python version: 3, 3.9, 3.8, 3.7, 3.6. + // Append -bullseye or -buster to pin to an OS version. + // Use -bullseye variants on local on arm64/Apple Silicon. + "VARIANT": "3.9-bullseye", + // Options + "NODE_VERSION": "lts/*" + } + }, + + // Configure tool-specific properties. + "customizations": { + // Configure properties specific to VS Code. + "vscode": { + // Set *default* container specific settings.json values on container create. + "settings": { + "terminal.integrated.profiles.linux": { + "bash": { + "path": "/bin/bash" + } + }, + "python.defaultInterpreterPath": "/usr/local/bin/python", + "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" + ] + } + }, + + // 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. + "remoteUser": "vscode" +} diff --git a/requirements.txt b/requirements.txt new file mode 100644 index 0000000..0076c57 --- /dev/null +++ b/requirements.txt @@ -0,0 +1,18 @@ +biopython==1.79 +cycler==0.11.0 +fonttools==4.34.4 +joblib==1.1.0 +kiwisolver==1.4.4 +matplotlib==3.5.2 +numpy==1.23.1 +packaging==21.3 +pandas==1.4.3 +Pillow==9.2.0 +pyparsing==3.0.9 +python-dateutil==2.8.2 +pytz==2022.1 +scikit-learn==1.1.2 +scipy==1.9.0 +seaborn==0.11.2 +six==1.16.0 +threadpoolctl==3.1.0