From 56f1b6db3ea05b8682feb4bbb32e919e22c2a8a3 Mon Sep 17 00:00:00 2001
From: chun9l <97897047+chun9l@users.noreply.github.com>
Date: Sat, 18 May 2024 18:41:03 +0100
Subject: [PATCH 1/3] Revert achlys dockerfile and change venv

---
 models/achlys/Dockerfile | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/models/achlys/Dockerfile b/models/achlys/Dockerfile
index a70a90a..d85d177 100644
--- a/models/achlys/Dockerfile
+++ b/models/achlys/Dockerfile
@@ -1,9 +1,9 @@
-FROM achlys-ubuntu
+FROM linusseelinger/achlys-ubuntu
 
 RUN apt update && apt install -y inotify-tools && \
     rm -rf /var/lib/apt/lists/*
 
-RUN apt install -y python3-pip python3-venv && \
+RUN apt install -y python3-pip python3-virtualenv && \
     python3 -m venv venv && \
     . venv/bin/activate && \
     pip install umbridge

From f58e2de21d740c03c58bf57575157101131da165 Mon Sep 17 00:00:00 2001
From: chun9l <97897047+chun9l@users.noreply.github.com>
Date: Sat, 18 May 2024 19:14:58 +0100
Subject: [PATCH 2/3] Add command to start server

---
 models/gs2/Dockerfile | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/models/gs2/Dockerfile b/models/gs2/Dockerfile
index 1c33f07..6f27470 100644
--- a/models/gs2/Dockerfile
+++ b/models/gs2/Dockerfile
@@ -36,7 +36,8 @@ RUN echo 'alias pip=pip3' >> $HOME/.bashrc
 
 RUN echo 'export GK_SYSTEM=gnu_ubuntu' >> $HOME/.bashrc
 
-RUN pip install ford netCDF4==1.6.2
+RUN python -m venv venv && . venv/bin/activate && \
+    pip install ford netCDF4==1.6.2 umbridge pyrokinetics 
 
 RUN git clone https://whornsby@bitbucket.org/gyrokinetics/gs2.git /usr/gs2
 
@@ -51,5 +52,8 @@ RUN echo ${GK_SYSTEM}
 RUN make -IMakefiles depend
 
 RUN make -IMakefiles gs2
-
 #RUN make -IMakefiles tests
+
+COPY server.py fast.in .
+
+CMD . venv/bin/activate && python server.py

From f0b20e08eb011677b9aea8e087591656b0d587e8 Mon Sep 17 00:00:00 2001
From: chun9l <97897047+chun9l@users.noreply.github.com>
Date: Sat, 18 May 2024 19:15:29 +0100
Subject: [PATCH 3/3] only mkdir if didnt exist

---
 models/gs2/server.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/models/gs2/server.py b/models/gs2/server.py
index a3491f7..d2d392b 100644
--- a/models/gs2/server.py
+++ b/models/gs2/server.py
@@ -3,7 +3,6 @@
 import os
 import csv
 from pyrokinetics import Pyro
-import numpy as np
 from datetime import datetime
 from fileinput import FileInput
 
@@ -21,7 +20,7 @@ def get_output_sizes(self, config):
 
     def __call__(self, parameters, config):
         input_file = "fast.in" # Select input file
-        os.system("mkdir restart") # GS2 needs this folder otherwise will fail
+        os.system("mkdir -p restart") # GS2 needs this folder otherwise will fail
         with FileInput(files=input_file, inplace=True) as file:
             checkpoint = 0
             for line in file: