From d670b761431c68fd9747ddb405ae8da8bddbcfd5 Mon Sep 17 00:00:00 2001
From: pikid <130920237+pikid@users.noreply.github.com>
Date: Wed, 12 Jun 2024 22:37:35 +0800
Subject: [PATCH 1/6] Update Dockerfile

fix bugs:
1.[ 9/28] RUN pip3 install neuron==8.0.1:
0.252 WARNING: The directory '/home/ow/.cache/pip' or its parent directory is not owned or is not writable by the current user. The cache has been disabled. Check the permissions and owner of that directory. If executing pip with sudo, you should use sudo's -H flag.
1.575 ERROR: Could not find a version that satisfies the requirement neuron==8.0.1 (from versions: 8.1a0, 8.1.0, 8.2, 8.2.1, 8.2.2, 8.2.3, 8.2.4)
1.576 ERROR: No matching distribution found for neuron==8.0.1
2.ERROR: Could not find a version that satisfies the requirement neuron==8.0.1 (from versions: 8.1a0, 8.1.0, 8.2, 8.2.1, 8.2.2, 8.2.3, 8.2.4)
---
 Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Dockerfile b/Dockerfile
index 1a4bf89..772fc93 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -52,7 +52,7 @@ RUN  sudo update-alternatives --install /usr/bin/pip pip /usr/bin/pip3 10
 ################################################################################
 ########     Install NEURON simulator
 
-RUN pip3 install neuron==8.0.1
+RUN sudo pip3 install neuron==8.1.0
 
 
 ################################################################################

From e29a7753988e116fc7567d7a6d4af4a1e68a009e Mon Sep 17 00:00:00 2001
From: Tijs Zwinkels <tijs@tinkertank.eu>
Date: Fri, 5 Jul 2024 11:54:04 +0200
Subject: [PATCH 2/6] auto-detect arm platform in build.sh

---
 build.sh | 14 ++++++++++++--
 1 file changed, 12 insertions(+), 2 deletions(-)

diff --git a/build.sh b/build.sh
index 4ab0e61..ccf6a7e 100755
--- a/build.sh
+++ b/build.sh
@@ -1,4 +1,14 @@
 #!/bin/bash
 
-version=$(<VERSION) # Read version of Dockerfile from file VERSION
-docker build "$@" -t "openworm/openworm:$version" .
+version=$(<VERSION)
+
+# Set the platform flag if we're on ARM
+arch=$(uname -m)
+if [[ "$arch" == "arm64" || "$arch" == "aarch64" ]]; then
+    platform_flag="--platform linux/amd64"
+else
+    platform_flag=""
+fi
+
+# Build the Docker image
+docker build $platform_flag "$@" -t "openworm/openworm:$version" .

From 0f68b03e5c0796195051fcfbc2cb78ea10b109da Mon Sep 17 00:00:00 2001
From: Padraig Gleeson <p.gleeson@gmail.com>
Date: Thu, 15 Aug 2024 15:20:39 +0100
Subject: [PATCH 3/6] Add exp branch

---
 .github/workflows/docker-image.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/docker-image.yml b/.github/workflows/docker-image.yml
index f5ea7d3..2faa0d2 100644
--- a/.github/workflows/docker-image.yml
+++ b/.github/workflows/docker-image.yml
@@ -2,9 +2,9 @@ name: Docker Image Build & Run
 
 on:
   push:
-    branches: [ master, dev*, test* ]
+    branches: [ master, dev*, experimental, test* ]
   pull_request:
-    branches: [ master, dev*, test* ]
+    branches: [ master, dev*, experimental, test* ]
 
 jobs:
 

From c11c5b13f79f5bb36753cca3714b225d94670947 Mon Sep 17 00:00:00 2001
From: Tomas Stary <tomas.stary@kit.edu>
Date: Sat, 21 Sep 2024 19:01:24 +0200
Subject: [PATCH 4/6] Add the jupyterlab for compatibility with binder

Inspired:
https://mybinder.readthedocs.io/en/latest/tutorials/dockerfile.html#preparing-your-dockerfile
---
 Dockerfile | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/Dockerfile b/Dockerfile
index 1a4bf89..a2aa43d 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -122,3 +122,5 @@ RUN echo '\n\nalias cd..="cd .."\nalias h=history\nalias ll="ls -alt"' >> ~/.bas
 RUN pip list
 
 RUN echo "Built the OpenWorm Docker image!"
+
+RUN python3 -m pip install --no-cache-dir notebook jupyterlab

From d36a9fea6e3869e70cf5a39b4f2ed2a58c2912cb Mon Sep 17 00:00:00 2001
From: pgleeson <p.gleeson@gmail.com>
Date: Sat, 5 Oct 2024 10:01:59 +0100
Subject: [PATCH 5/6] Arch check in rebuild also

---
 build.sh   |  2 +-
 rebuild.sh | 12 +++++++++++-
 2 files changed, 12 insertions(+), 2 deletions(-)

diff --git a/build.sh b/build.sh
index ccf6a7e..1481427 100755
--- a/build.sh
+++ b/build.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-version=$(<VERSION)
+version=$(<VERSION) # Read version of Dockerfile from file VERSION
 
 # Set the platform flag if we're on ARM
 arch=$(uname -m)
diff --git a/rebuild.sh b/rebuild.sh
index 48f2d68..5b38617 100755
--- a/rebuild.sh
+++ b/rebuild.sh
@@ -1,4 +1,14 @@
 #!/bin/bash
 
 version=$(<VERSION) # Read version of Dockerfile from file VERSION
-docker build "$@" -t "openworm/openworm:$version"  --no-cache .
+
+# Set the platform flag if we're on ARM
+arch=$(uname -m)
+if [[ "$arch" == "arm64" || "$arch" == "aarch64" ]]; then
+    platform_flag="--platform linux/amd64"
+else
+    platform_flag=""
+fi
+
+# Rebuild the Docker image
+docker build $platform_flag "$@" -t "openworm/openworm:$version"  --no-cache .

From 4e6e757bcbd971e903a63f131f81b202dd8710db Mon Sep 17 00:00:00 2001
From: pgleeson <p.gleeson@gmail.com>
Date: Sat, 5 Oct 2024 10:02:16 +0100
Subject: [PATCH 6/6] Initial jupyterlab run script

---
 run-jl.sh | 5 +++++
 1 file changed, 5 insertions(+)
 create mode 100755 run-jl.sh

diff --git a/run-jl.sh b/run-jl.sh
new file mode 100755
index 0000000..fb39de1
--- /dev/null
+++ b/run-jl.sh
@@ -0,0 +1,5 @@
+#!/bin/bash
+
+version=$(<VERSION) # Read version of Dockerfile from file VERSION
+
+docker run -it --rm -p 8888:8888 "openworm/openworm:$version" jupyter lab --NotebookApp.default_url=/lab/ --ip=0.0.0.0 --port=8888 --allow-root