MAINT: ensure unix line endings (artefact from initial windows develo…

…pment)
YapengLang · Oct 21, 2024 · b6125a8 · b6125a8
1 parent 726353c
commit b6125a8
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Showing 11 changed files with 768 additions and 768 deletions.
diff --git a/.devcontainer/DockerFile b/.devcontainer/DockerFile
@@ -1,64 +1,64 @@
-FROM continuumio/miniconda3
-
-# Install dependencies
-RUN apt-get update && apt-get install -y \
-    build-essential \
-    cmake \
-    gdb \
-    gh \
-    git \
-    zsh \
-    sudo \
-    wget \
-    libeigen3-dev \  
-    libboost-all-dev \  
-    binutils \  
-    && rm -rf /var/lib/apt/lists/*
-
-# Set up a non-root user with sudo
-RUN useradd -ms /bin/zsh user && echo "user ALL=(ALL) NOPASSWD: ALL" > /etc/sudoers.d/user
-
-USER user
-WORKDIR /home/user/repos
-
-# Install Oh My Zsh
-RUN sh -c "$(wget https://raw.githubusercontent.com/ohmyzsh/ohmyzsh/master/tools/install.sh -O -)" "" --unattended
-
-# Install zsh autosuggestions
-RUN git clone https://github.com/zsh-users/zsh-autosuggestions ${ZSH_CUSTOM:-~/.oh-my-zsh/custom}/plugins/zsh-autosuggestions
-
-# Install zsh syntax highlighting
-RUN git clone https://github.com/zsh-users/zsh-syntax-highlighting.git ${ZSH_CUSTOM:-~/.oh-my-zsh/custom}/plugins/zsh-syntax-highlighting
-
-# Configure zsh
-RUN sed -i 's/plugins=(git)/plugins=(git zsh-autosuggestions zsh-syntax-highlighting)/' ~/.zshrc
-
-# Create a new conda environment with Python 3.12 and fix the bug with VS-code terminal showing 2 conda env prompts 
-RUN . /opt/conda/etc/profile.d/conda.sh && \
-    conda config --set auto_activate_base False && \
-    /opt/conda/bin/conda create -n c312 python=3.12 -y && \
-    conda activate c312
-
-# Initialize conda for zsh shell
-RUN echo ". /opt/conda/etc/profile.d/conda.sh" >> ~/.zshrc
-
-# Clone cogent3 using SSH
-WORKDIR /home/user/repos
-RUN git clone --branch develop https://github.com/cogent3/cogent3.git /home/user/repos/cogent3 
-
-# Install pybind11 in the conda environment
-RUN . /opt/conda/etc/profile.d/conda.sh && \
-    conda activate c312 && \
-    pip install pybind11
-    
-# Install the cogent3 repository
-RUN . /opt/conda/etc/profile.d/conda.sh && \
-    conda activate c312 && \
-    cd /home/user/repos/cogent3 && \
-    pip install -e . 
-
-# Set up zsh as the default shell
-SHELL ["/bin/zsh", "-c"]
-
-# Set zsh as the default shell for the container
+FROM continuumio/miniconda3
+
+# Install dependencies
+RUN apt-get update && apt-get install -y \
+    build-essential \
+    cmake \
+    gdb \
+    gh \
+    git \
+    zsh \
+    sudo \
+    wget \
+    libeigen3-dev \  
+    libboost-all-dev \  
+    binutils \  
+    && rm -rf /var/lib/apt/lists/*
+
+# Set up a non-root user with sudo
+RUN useradd -ms /bin/zsh user && echo "user ALL=(ALL) NOPASSWD: ALL" > /etc/sudoers.d/user
+
+USER user
+WORKDIR /home/user/repos
+
+# Install Oh My Zsh
+RUN sh -c "$(wget https://raw.githubusercontent.com/ohmyzsh/ohmyzsh/master/tools/install.sh -O -)" "" --unattended
+
+# Install zsh autosuggestions
+RUN git clone https://github.com/zsh-users/zsh-autosuggestions ${ZSH_CUSTOM:-~/.oh-my-zsh/custom}/plugins/zsh-autosuggestions
+
+# Install zsh syntax highlighting
+RUN git clone https://github.com/zsh-users/zsh-syntax-highlighting.git ${ZSH_CUSTOM:-~/.oh-my-zsh/custom}/plugins/zsh-syntax-highlighting
+
+# 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 
+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
+
+# Initialize conda for zsh shell
+RUN echo ". /opt/conda/etc/profile.d/conda.sh" >> ~/.zshrc
+
+# 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 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"]
+
+# Set zsh as the default shell for the container
 CMD [ "zsh" ]
diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
@@ -1,33 +1,33 @@
-{
-    "name": "piqtree2 devcontainer",
-    "image": "ghcr.io/cogent3/piqtree2:latest",
-    "customizations": {
-        "vscode": {
-            "settings": {
-                "terminal.integrated.shell.linux": "/bin/zsh",
-                "terminal.integrated.profiles.linux": {
-                    "zsh": {
-                        "path": "zsh"
-                    }
-                },
-                "python.defaultInterpreterPath": "/home/user/.conda/envs/c312/bin/python"
-            },
-            "extensions": [
-                "ms-python.python",
-                "ms-toolsai.jupyter",
-                "ms-vscode.cpptools",
-                "ms-vscode.cpptools-extension-pack",
-                "ms-vscode.makefile-tools",
-                "charliermarsh.ruff",
-                "njpwerner.autodocstring",
-                "github.vscode-github-actions",
-                "tamasfe.even-better-toml",
-                "DavidAnson.vscode-markdownlint",
-                "be5invis.toml",
-                "mhutchie.git-graph"
-            ]
-        }
-    },
-    "remoteUser": "user",
-    "postCreateCommand": "sudo chown -R user:user /home/user/.ssh && git config --global --add safe.directory ${containerWorkspaceFolder}"
+{
+    "name": "piqtree2 devcontainer",
+    "image": "ghcr.io/cogent3/piqtree2:latest",
+    "customizations": {
+        "vscode": {
+            "settings": {
+                "terminal.integrated.shell.linux": "/bin/zsh",
+                "terminal.integrated.profiles.linux": {
+                    "zsh": {
+                        "path": "zsh"
+                    }
+                },
+                "python.defaultInterpreterPath": "/home/user/.conda/envs/c312/bin/python"
+            },
+            "extensions": [
+                "ms-python.python",
+                "ms-toolsai.jupyter",
+                "ms-vscode.cpptools",
+                "ms-vscode.cpptools-extension-pack",
+                "ms-vscode.makefile-tools",
+                "charliermarsh.ruff",
+                "njpwerner.autodocstring",
+                "github.vscode-github-actions",
+                "tamasfe.even-better-toml",
+                "DavidAnson.vscode-markdownlint",
+                "be5invis.toml",
+                "mhutchie.git-graph"
+            ]
+        }
+    },
+    "remoteUser": "user",
+    "postCreateCommand": "sudo chown -R user:user /home/user/.ssh && git config --global --add safe.directory ${containerWorkspaceFolder}"
 }
diff --git a/.github/workflows/build_container.yml b/.github/workflows/build_container.yml
@@ -1,26 +1,26 @@
-name: Build and Push Docker Image to ghcr
-
-on:
-  workflow_dispatch:
-  push:
-    branches:
-      - main
-    paths:
-      - .devcontainer/DockerFile
-
-jobs:
-  build-and-push:
-    runs-on: ubuntu-latest
-    steps:
-      - name: Checkout repository
-        uses: actions/checkout@v4
-
-      - name: Log in to GitHub Container Registry
-        run: echo "${{ 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/cogent3/piqtree2:latest
-          docker push ghcr.io/cogent3/piqtree2:latest
-
+name: Build and Push Docker Image to ghcr
+
+on:
+  workflow_dispatch:
+  push:
+    branches:
+      - main
+    paths:
+      - .devcontainer/DockerFile
+
+jobs:
+  build-and-push:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Log in to GitHub Container Registry
+        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/cogent3/piqtree2:latest
+          docker push ghcr.io/cogent3/piqtree2:latest
+