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DEV: make dockerfile setup dev environment #131

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Dec 12, 2024
Merged

DEV: make dockerfile setup dev environment #131

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33 changes: 16 additions & 17 deletions .devcontainer/DockerFile
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Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,7 @@ FROM continuumio/miniconda3
# Install dependencies
RUN apt-get update && apt-get install -y \
build-essential \
btop \
cmake \
gdb \
gh \
Expand Down Expand Up @@ -33,29 +34,27 @@ RUN git clone https://github.com/zsh-users/zsh-syntax-highlighting.git ${ZSH_CUS
# Configure zsh
RUN sed -i 's/plugins=(git)/plugins=(git zsh-autosuggestions zsh-syntax-highlighting)/' ~/.zshrc

# Create a new conda environment with Python 3.12 and fix the bug with VS-code terminal showing 2 conda env prompts
# Create a new conda environment with Python 3.12 (dev+docs) and fix the bug with VS-code terminal showing 2 conda env prompts
RUN . /opt/conda/etc/profile.d/conda.sh && \
conda config --set auto_activate_base False && \
/opt/conda/bin/conda create -n c312 python=3.12 -y && \
conda activate c312
/opt/conda/bin/conda create -n piqtree python=3.12 -y && \
conda activate piqtree

# Initialize conda for zsh shell
RUN echo ". /opt/conda/etc/profile.d/conda.sh" >> ~/.zshrc
# Initialise conda for zsh shell
RUN echo ". /opt/conda/etc/profile.d/conda.sh" >> ~/.zshrc && \
echo 'alias sac="conda activate"' >> ~/.zshrc && \
echo 'alias sde="conda deactivate"' >> ~/.zshrc

# Clone cogent3 using SSH
WORKDIR /home/user/repos
RUN git clone --branch develop https://github.com/cogent3/cogent3.git /home/user/repos/cogent3
# Setup submodule
RUN git submodule update --init --recursive

# Install pybind11 in the conda environment
RUN . /opt/conda/etc/profile.d/conda.sh && \
conda activate c312 && \
pip install pybind11

# Install the cogent3 repository
# Build piqtree
RUN ./build_tools/build_iqtree.sh

# Set up conda environments
RUN . /opt/conda/etc/profile.d/conda.sh && \
conda activate c312 && \
cd /home/user/repos/cogent3 && \
pip install -e .
conda activate piqtree && \
pip install -e ".[dev]"

# Set up zsh as the default shell
SHELL ["/bin/zsh", "-c"]
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2 changes: 1 addition & 1 deletion pyproject.toml
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Expand Up @@ -41,7 +41,7 @@ Documentation = "https://piqtree2.readthedocs.io"


[project.optional-dependencies]
dev = ["cibuildwheel", "pybind11", "scriv", "piqtree2[test]", "piqtree2[lint]", "piqtree2[typing]"]
dev = ["cibuildwheel", "pybind11", "scriv", "piqtree2[doc]", "piqtree2[test]", "piqtree2[lint]", "piqtree2[typing]"]
test = ["pytest", "pytest-cov", "nox"]
lint = ["ruff==0.8.2"]
typing = ["mypy==1.13.0", "piqtree2[stubs]", "piqtree2[test]"]
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