DEV: revert docker editting

.devcontainer/DockerFile

@@ -3,7 +3,6 @@ FROM continuumio/miniconda3
 # Install dependencies
 RUN apt-get update && apt-get install -y \
     build-essential \
-    btop \
     cmake \
     gdb \
     gh \
@@ -34,21 +33,29 @@ 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 (dev+docs) and fix the bug with VS-code terminal showing 2 conda env prompts 
+# Create a new conda environment with Python 3.12 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 piqtree python=3.12 -y && \
-    conda activate piqtree
+    /opt/conda/bin/conda create -n c312 python=3.12 -y && \
+    conda activate c312
 
-# 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
+# Initialize conda for zsh shell
+RUN echo ". /opt/conda/etc/profile.d/conda.sh" >> ~/.zshrc
 
-# Set up conda environments
+# Clone cogent3 using SSH
+WORKDIR /home/user/repos
+RUN git clone --branch develop https://github.com/cogent3/cogent3.git /home/user/repos/cogent3 
+
+# Install pybind11 in the conda environment
 RUN . /opt/conda/etc/profile.d/conda.sh && \
-    conda activate piqtree && \
+    conda activate c312 && \
     pip install pybind11
+
+# Install the cogent3 repository
+RUN . /opt/conda/etc/profile.d/conda.sh && \
+    conda activate c312 && \
+    cd /home/user/repos/cogent3 && \
+    pip install -e . 
 
 # Set up zsh as the default shell
 SHELL ["/bin/zsh", "-c"]

.github/workflows/build_container.yml

@@ -16,11 +16,11 @@ jobs:
         uses: actions/checkout@v4
 
       - name: Log in to GitHub Container Registry
-        run: echo "${{ secrets.GITHUB_TOKEN }}" | docker login ghcr.io -u ${{ github.actor }} --password-stdin
+        run: echo "${{ secrets.GHCR_PAT }}" | docker login ghcr.io -u cogent3 --password-stdin
 
       - name: Build and Push Base Docker image
         run: |
           docker build -f .devcontainer/DockerFile . \
-            -t ghcr.io/iqtree/piqtree2:latest
-          docker push ghcr.io/iqtree/piqtree2:latest
+            -t ghcr.io/cogent3/piqtree2:latest
+          docker push ghcr.io/cogent3/piqtree2:latest
 

pyproject.toml

@@ -41,7 +41,7 @@ Documentation = "https://piqtree2.readthedocs.io"
 
 
 [project.optional-dependencies]
-dev = ["cibuildwheel", "pybind11", "scriv", "piqtree2[doc]", "piqtree2[test]", "piqtree2[lint]", "piqtree2[typing]"]
+dev = ["cibuildwheel", "pybind11", "scriv", "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]"]