Merge pull request #39 from swelborn/housekeeping

Housekeeping

.gitignore

@@ -120,4 +120,6 @@ dmypy.json
 *.sublime-workspace
 
 # Data folder
-data/
+.vscode/
+.devcontainer/
+.trunk/

docker/Dockerfile

@@ -0,0 +1,41 @@
+# Use an official NVIDIA CUDA  image
+FROM nvidia/cuda:11.8.0-runtime-ubuntu22.04   
+
+# Install some basic utilities, Python, and necessary libraries for Conda
+RUN apt-get update && apt-get install -y \
+    python3-pip python3-dev wget bzip2 git \
+    && rm -rf /var/lib/apt/lists/*
+
+# Determine platform (x86_64 vs. ARM) and fetch the appropriate Miniconda installer
+RUN case $(uname -m) in \
+    x86_64)     ARCH="x86_64";; \
+    aarch64)    ARCH="aarch64";; \
+    *)          echo "Unsupported architecture"; exit 1 ;; \
+    esac && \
+    wget "https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-${ARCH}.sh" -O miniconda.sh && \
+    bash miniconda.sh -b -p /miniconda && \
+    rm miniconda.sh
+
+
+# Update PATH so that pip and conda are available
+ENV PATH="/miniconda/bin:$PATH"
+
+# Create a Conda environment from environment.yml. Assuming environment.yml is at the Docker build context root
+ARG ENV_FILE=environment.yml
+COPY ./${ENV_FILE} ./environment.yml
+RUN conda env create -f environment.yml
+
+# Activate the Conda environment. Any command run in this layer or subsequent layers will use the Conda environment by default
+SHELL ["conda", "run", "-n", "tomopyui", "/bin/bash", "-c"]
+
+# Set working directory
+WORKDIR /src
+COPY . /src
+RUN pip install -e .
+
+
+# Expose the port JupyterLab will run on
+EXPOSE 8888
+
+# Command to run JupyterLab within the Conda environment
+CMD ["conda", "run", "-n", "tomopyui", "jupyter", "lab", "--ip=0.0.0.0", "--port=8888", "--no-browser", "--allow-root", "--NotebookApp.token=''"]

environment-docs.yml

@@ -0,0 +1,34 @@
+name: tomopyui
+channels:
+  - astra-toolbox
+  - conda-forge
+  - defaults
+dependencies:
+  - python=3.11
+  - matplotlib
+  - ffmpeg
+  - dask
+  - dask-image
+  - olefile
+  - git
+  - pip
+  - tomopy
+  - dxchange
+  - jupyterlab
+  - astropy
+  - ipyfilechooser
+  - ipywidgets
+  - astra-toolbox
+  - bqplot
+  - sphinx
+  - jupyter_sphinx
+  - numpydoc
+  - sphinx-copybutton
+  - sphinx-panels
+  - sphinx-thebe
+  - sphinx-togglebutton
+  - sphinx-book-theme
+  - sphinx-gallery
+  - myst-nb
+  - pip:
+      - bqplot-image-gl

environment-nocuda.yml

@@ -1,13 +1,10 @@
-name: tomopyui-nocuda
+name: tomopyui
 channels:
-  - conda-forge/label/widgetsnbextension_dev
-  - conda-forge/label/jupyterlab_widgets_rc
-  - conda-forge/label/ipywidgets_dev
   - astra-toolbox
   - conda-forge
   - defaults
 dependencies:
-  - python=3.9
+  - python=3.11
   - matplotlib
   - ffmpeg
   - dask
@@ -20,26 +17,8 @@ dependencies:
   - jupyterlab
   - astropy
   - ipyfilechooser
-  - ipywidgets=8
-  - widgetsnbextension
-  - jupyterlab_widgets
-  - ca-certificates
-  - certifi
-  - openssl
+  - ipywidgets
   - astra-toolbox
-  - joblib
-  - ipympl [--no-deps]
   - bqplot
-  - sphinx
-  - jupyter_sphinx
-  - numpydoc
-  - sphinx-copybutton
-  - sphinx-panels
-  - sphinx-thebe
-  - sphinx-togglebutton
-  - sphinx-book-theme
-  - sphinx-gallery
-  - myst-nb [--no-deps]
   - pip:
-    - bqplot-image-gl
-    - tomopyui
+      - bqplot-image-gl

environment.yml

@@ -1,13 +1,10 @@
 name: tomopyui
 channels:
-  - conda-forge/label/widgetsnbextension_rc
-  - conda-forge/label/jupyterlab_widgets_rc
-  - conda-forge/label/ipywidgets_rc
   - astra-toolbox
   - conda-forge
   - defaults
 dependencies:
-  - python=3.9
+  - python=3.11
   - matplotlib
   - ffmpeg
   - dask
@@ -20,28 +17,10 @@ dependencies:
   - jupyterlab
   - astropy
   - ipyfilechooser
-  - ipywidgets=8
-  - widgetsnbextension
-  - jupyterlab_widgets
-  - ca-certificates
-  - certifi
-  - openssl
+  - ipywidgets
   - astra-toolbox
   - cudatoolkit
   - cupy
-  - joblib
-  - ipympl [--no-deps]
   - bqplot
-  - sphinx
-  - jupyter_sphinx
-  - numpydoc
-  - sphinx-copybutton
-  - sphinx-panels
-  - sphinx-thebe
-  - sphinx-togglebutton
-  - sphinx-book-theme
-  - sphinx-gallery
-  - myst-nb [--no-deps]
   - pip:
-    - bqplot-image-gl
-    - tomopyui
+      - bqplot-image-gl