From c26f49e6a7505c777bbbd0ad6ecb05d74ec946e8 Mon Sep 17 00:00:00 2001
From: Adam Taranto <adam.p.taranto@gmail.com>
Date: Thu, 26 Dec 2024 09:32:09 +1100
Subject: [PATCH 1/2] Update README.md

Remove Gitpod button
---
 README.md | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

diff --git a/README.md b/README.md
index 8b4f095..acd3eb4 100644
--- a/README.md
+++ b/README.md
@@ -2,10 +2,6 @@
   <img src="https://img.shields.io/badge/License-BSD_3--Clause-blue.svg" align="left" height="20"/>
 </a> 
 
-<a href="https://gitpod.io/#https://github.com/oxli-bio/oxli">
-  <img src="https://gitpod.io/button/open-in-gitpod.svg" align="right" height="35"/>
-</a>
-
 <br>
 
 # oxli
@@ -130,4 +126,4 @@ And, voila! oxli was born.
 ## Authors
 
 * C. Titus Brown (@ctb), ctbrown@ucdavis.edu  
-* Adam Taranto (@Adamtaranto)
\ No newline at end of file
+* Adam Taranto (@Adamtaranto)

From c2a045b0550bfc6e3bbdcacb0b40ade106b8df0f Mon Sep 17 00:00:00 2001
From: Adam Taranto <adam.p.taranto@gmail.com>
Date: Thu, 26 Dec 2024 09:37:47 +1100
Subject: [PATCH 2/2] rm gitpod configs

---
 .gitpod.Dockerfile | 34 ----------------------------------
 .gitpod.yml        | 25 -------------------------
 2 files changed, 59 deletions(-)
 delete mode 100644 .gitpod.Dockerfile
 delete mode 100644 .gitpod.yml

diff --git a/.gitpod.Dockerfile b/.gitpod.Dockerfile
deleted file mode 100644
index aea795e..0000000
--- a/.gitpod.Dockerfile
+++ /dev/null
@@ -1,34 +0,0 @@
-# Image source code: https://github.com/axonasif/workspace-images/tree/tmp
-# Also see https://github.com/gitpod-io/workspace-images/issues/1071
-FROM axonasif/workspace-base@sha256:8c057b1d13bdfe8c279c68aef8242d32110c8d5310f9a393f9c0417bc61367d9
-
-# Set user
-USER gitpod
-
-# Install Miniconda
-RUN wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-py311_24.1.2-0-Linux-x86_64.sh -O ~/miniconda.sh && \
-    /bin/bash ~/miniconda.sh -b -p $HOME/miniconda && \
-    rm ~/miniconda.sh
-
-# Add Miniconda to PATH
-ENV PATH="$HOME/miniconda/bin:$PATH"
-
-# Initialize conda in bash config files:
-RUN conda init bash
-
-# Set up Conda channels
-RUN conda config --add channels conda-forge && \
-    conda config --add channels bioconda && \
-    conda config --set channel_priority strict
-
-# Set libmamba as solver
-RUN conda config --set solver libmamba
-
-# Persist ~/ (HOME) and lib
-RUN echo 'create-overlay $HOME /lib' > "$HOME/.runonce/1-home-lib_persist"
-
-# Referenced in `.vscode/settings.json`
-ENV PYTHON_INTERPRETER="$HOME/miniconda/bin/python"
-
-# Pycharm recognizes this variables
-ENV PYCHARM_PYTHON_PATH="${PYTHON_INTERPRETER}"
\ No newline at end of file
diff --git a/.gitpod.yml b/.gitpod.yml
deleted file mode 100644
index 5f4f419..0000000
--- a/.gitpod.yml
+++ /dev/null
@@ -1,25 +0,0 @@
-image:
-  file: .gitpod.Dockerfile
-
-tasks:
-  - name: Init Gitpod Workspace
-    init: |
-      conda install --yes --solver=libmamba -c conda-forge -c bioconda "compilers" "maturin>=1,<2" "pytest" "rust" "scipy" "toml"
-      conda clean --all --yes
-    command: |
-      echo "Running: $GITPOD_WORKSPACE_URL"
-
-ports:
-  - name: Jupyter Notebook
-    port: 8888
-    onOpen: open-browser
-
-vscode:
-  extensions:
-    - eamodio.gitlens
-    - github.vscode-pull-request-github
-    - janisdd.vscode-edit-csv
-    - mechatroner.rainbow-csv
-    - ms-python.debugpy
-    - ms-python.python
-