From 7fcc6a62b1762fda0494285d42f39d7ddcb88e5d Mon Sep 17 00:00:00 2001
From: Carlos Paniagua <cpaniaguam@gmail.com>
Date: Sat, 17 Feb 2024 02:19:10 -0500
Subject: [PATCH 1/3] Update Dockerfile to use Python 3.11 image and install
 required packages

---
 Dockerfile | 60 ++++++++++++++++--------------------------------------
 1 file changed, 17 insertions(+), 43 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index dd0de0d7..466445eb 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,48 +1,22 @@
-# Using the ubuntu:20.04 base image for compatibility with the ICESat-2 SlideRule software
-# Some code to add conda from https://github.com/conda-forge/miniforge-images/blob/master/ubuntu/Dockerfile
-# This file builds the docker image for the ICESat-2 tracks project. Includes the ICESat-2 SlideRule tool, conda, and the python3.11 environment for the project with dependencies provided in the environment_small.yml file.
-FROM ubuntu:20.04
-ARG DEBIAN_FRONTEND=noninteractive
-ARG MINIFORGE_NAME=Miniforge3
-ARG MINIFORGE_VERSION=23.3.1-0
-ARG TARGETPLATFORM
+# Use the official Python 3.11 image from the Docker Hub
+FROM python:3.11
 
-ENV CONDA_DIR=/opt/conda
-ENV LANG=C.UTF-8 LC_ALL=C.UTF-8
-ENV PATH=${CONDA_DIR}/bin:${PATH}
-ENV ENVNAME=2021-icesat2-tracks
-RUN apt-get update && \
-    apt-get install -y git curl wget
+# Update the system and install the packages
+RUN apt-get update && apt-get install -y \
+    openmpi-bin \
+    openmpi-doc \
+    libopenmpi-dev
 
-# Install sliderule dependencies
-RUN apt-get install -y build-essential libreadline-dev liblua5.3-dev zlib1g-dev cmake
-RUN git clone https://github.com/ICESat2-SlideRule/sliderule.git
-WORKDIR /sliderule/
-RUN make config && \
-    make && \
-    make install
+# Set the working directory to /app
+WORKDIR /app
 
-# Install conda
-RUN apt-get update > /dev/null && \
-    apt-get install --no-install-recommends --yes \
-    bzip2 ca-certificates \
-    tini \
-    > /dev/null && \
-    apt-get clean && \
-    rm -rf /var/lib/apt/lists/* && \
-    wget --no-hsts --quiet https://github.com/conda-forge/miniforge/releases/download/${MINIFORGE_VERSION}/${MINIFORGE_NAME}-${MINIFORGE_VERSION}-Linux-$(uname -m).sh -O /tmp/miniforge.sh && \
-    /bin/bash /tmp/miniforge.sh -b -p ${CONDA_DIR} && \
-    rm /tmp/miniforge.sh && \
-    conda clean --tarballs --index-cache --packages --yes && \
-    find ${CONDA_DIR} -follow -type f -name '*.a' -delete && \
-    find ${CONDA_DIR} -follow -type f -name '*.pyc' -delete && \
-    conda clean --force-pkgs-dirs --all --yes && \
-    echo ". ${CONDA_DIR}/etc/profile.d/conda.sh && conda activate base" >> /etc/skel/.bashrc && \
-    echo ". ${CONDA_DIR}/etc/profile.d/conda.sh && conda activate base" >> ~/.bashrc
+# Copy the current directory contents into the container at /app
+COPY . /app
 
-# Install conda environment
-COPY environment_small.yml /tmp/environment.yml
-RUN mamba env create -f /tmp/environment.yml
+# Create the output directory
+RUN mkdir -p /app/output
 
-ENTRYPOINT ["tini", "--"]
-CMD ["/bin/bash"]
+# Install any needed packages specified in pyproject.toml
+RUN pip install .
+
+CMD ["/bin/bash"]
\ No newline at end of file

From 99fdc59be80320439137a06f9b76d7ead99c108d Mon Sep 17 00:00:00 2001
From: John Gerrard Holland <john_holland1@brown.edu>
Date: Mon, 4 Mar 2024 22:12:06 +0000
Subject: [PATCH 2/3] add Dockerfile and devcontainer.json arguments to make
 install work

---
 .devcontainer/devcontainer.json | 26 ++++++++++++++++++++++++++
 Dockerfile                      | 10 +++++++---
 2 files changed, 33 insertions(+), 3 deletions(-)
 create mode 100644 .devcontainer/devcontainer.json

diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
new file mode 100644
index 00000000..8d96444e
--- /dev/null
+++ b/.devcontainer/devcontainer.json
@@ -0,0 +1,26 @@
+// For format details, see https://aka.ms/devcontainer.json. For config options, see the
+// README at: https://github.com/devcontainers/templates/tree/main/src/docker-existing-dockerfile
+{
+	"name": "Existing Dockerfile",
+	"build": {
+		// Sets the run context to one level up instead of the .devcontainer folder.
+		"context": "..",
+		// Update the 'dockerFile' property if you aren't using the standard 'Dockerfile' filename.
+		"dockerfile": "../Dockerfile"
+	}
+
+	// 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": [],
+
+	// Uncomment the next line to run commands after the container is created.
+	// "postCreateCommand": "cat /etc/os-release",
+
+	// Configure tool-specific properties.
+	// "customizations": {},
+
+	// Uncomment to connect as an existing user other than the container default. More info: https://aka.ms/dev-containers-non-root.
+	// "remoteUser": "devcontainer"
+}
diff --git a/Dockerfile b/Dockerfile
index 466445eb..ef57b371 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,11 +1,15 @@
 # Use the official Python 3.11 image from the Docker Hub
-FROM python:3.11
+FROM python:3.9
 
 # Update the system and install the packages
 RUN apt-get update && apt-get install -y \
+    git-lfs \
     openmpi-bin \
     openmpi-doc \
-    libopenmpi-dev
+    libopenmpi-dev \
+    gdal-bin \
+    libgdal-dev
+
 
 # Set the working directory to /app
 WORKDIR /app
@@ -17,6 +21,6 @@ COPY . /app
 RUN mkdir -p /app/output
 
 # Install any needed packages specified in pyproject.toml
-RUN pip install .
+RUN pip install --editable ".[dev]"
 
 CMD ["/bin/bash"]
\ No newline at end of file

From 268377c698c5e5f1662991bc3de9032e9eaa4063 Mon Sep 17 00:00:00 2001
From: John Gerrard Holland <john_holland1@brown.edu>
Date: Mon, 4 Mar 2024 22:44:45 +0000
Subject: [PATCH 3/3] =?UTF-8?q?add=20GDAL=20and=20LFS=20=E2=80=93=20make?=
 =?UTF-8?q?=20docker=20work?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 Dockerfile => .devcontainer/Dockerfile | 2 +-
 .devcontainer/devcontainer.json        | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)
 rename Dockerfile => .devcontainer/Dockerfile (96%)

diff --git a/Dockerfile b/.devcontainer/Dockerfile
similarity index 96%
rename from Dockerfile
rename to .devcontainer/Dockerfile
index ef57b371..ccff69f5 100644
--- a/Dockerfile
+++ b/.devcontainer/Dockerfile
@@ -1,5 +1,5 @@
 # Use the official Python 3.11 image from the Docker Hub
-FROM python:3.9
+FROM python:3.11
 
 # Update the system and install the packages
 RUN apt-get update && apt-get install -y \
diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index 8d96444e..43a4a24b 100644
--- a/.devcontainer/devcontainer.json
+++ b/.devcontainer/devcontainer.json
@@ -6,7 +6,7 @@
 		// Sets the run context to one level up instead of the .devcontainer folder.
 		"context": "..",
 		// Update the 'dockerFile' property if you aren't using the standard 'Dockerfile' filename.
-		"dockerfile": "../Dockerfile"
+		"dockerfile": "Dockerfile"
 	}
 
 	// Features to add to the dev container. More info: https://containers.dev/features.