diff --git a/.devcontainer/Dockerfile b/.devcontainer/Dockerfile new file mode 100644 index 0000000..591f94b --- /dev/null +++ b/.devcontainer/Dockerfile @@ -0,0 +1,12 @@ +FROM FROM mcr.microsoft.com/devcontainers/universal:2 + +# Copy environment.yml (if found) to a temp location so we update the environment. Also +# copy "noop.txt" so the COPY instruction does not fail if no environment.yml exists. +COPY environment.yml* .devcontainer/noop.txt /tmp/conda-tmp/ + +RUN if [ -f "/tmp/conda-tmp/environment.yml" ]; then umask 0002 && /opt/conda/bin/conda env update -n base -f /tmp/conda-tmp/environment.yml; fi \ + && 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 diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json new file mode 100644 index 0000000..76ef979 --- /dev/null +++ b/.devcontainer/devcontainer.json @@ -0,0 +1,40 @@ +// For format details, see https://aka.ms/devcontainer.json. For config options, see the +// README at: https://github.com/devcontainers/templates/tree/main/src/anaconda +{ + "name": "Anaconda (Python 3)", + "build": { + "context": "..", + "dockerfile": "Dockerfile" + }, + + "customizations": { + "vscode": { + "extensions": [ + "ms-python.python", + "ms-toolsai.jupyter" + ], + + "settings": { + "python.defaultInterpreterPath": "/opt/conda/bin/python", + "python.languageServer": "Pylance" + } + } + } + + + + // Features to add to the dev container. More info: https://containers.dev/features. + // "features": {}, + + // 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": "python --version", + + // Configure tool-specific properties. + // "customizations": {}, + + // Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root. + // "remoteUser": "root" +} diff --git a/.devcontainer/noop.txt b/.devcontainer/noop.txt new file mode 100644 index 0000000..dde8dc3 --- /dev/null +++ b/.devcontainer/noop.txt @@ -0,0 +1,3 @@ +This file copied into the container along with environment.yml* from the parent +folder. This file is included to prevents the Dockerfile COPY instruction from +failing if no environment.yml is found. \ No newline at end of file diff --git a/environment.yml b/environment.yml index 4a4dde1..147efe3 100644 --- a/environment.yml +++ b/environment.yml @@ -1,15 +1,23 @@ -name: sermacs-workshop +name: sermacs-2024 channels: - conda-forge - defaults dependencies: - python=3.11 + - pip - pandas - - plotly - matplotlib - numpy - - scipy - jupyterlab + - plotly + - nglview - rdkit - - scikit-learn - - pip + - openbabel + - mdanalysis + - vina + - ipywidgets>8 + - prolif + - pip: + - pdb2pqr + - meeko + - py3Dmol \ No newline at end of file