Merge branch 'markus-link-pyarpes-with-north' into 'develop'

Pyarpes container final touches

See merge request !40

docker/pyarpes/01-chown-dir

-#!/usr/bin/with-contentenv bash
-
-chown -R abc:abc /pyarpes
\ No newline at end of file

docker/pyarpes/02-exec-cmd

 #!/usr/bin/with-contentenv bash
 
 # Add the command to run an app on startup
-echo "/pyarpes/miniconda3/bin/conda run -n arpes jupyter lab $CWD" > /config/.config/openbox/autostart
\ No newline at end of file
+echo "/pyarpes/miniconda3/bin/conda run -n arpes jupyter lab $RUNDIR" > /config/.config/openbox/autostart

docker/pyarpes/Dockerfile

 FROM linuxserver/webtop:amd64-ubuntu-openbox-version-e1079163
 
 RUN apt update \
-    && apt install git:amd64=1:2.25.1-1ubuntu3 -y
-
-# Helps install miniconda in the directory we have ownership over
-ENV HOME=/pyarpes
-# Install Miniconda
-RUN curl https://repo.anaconda.com/miniconda/Miniconda3-py38_4.10.3-Linux-x86_64.sh --output miniconda-install.sh \
+    && apt install git:amd64=1:2.25.1-1ubuntu3 -y \
+    && export HOME=/pyarpes \
+    && curl https://repo.anaconda.com/miniconda/Miniconda3-py38_4.10.3-Linux-x86_64.sh --output miniconda-install.sh \
     && chmod +x miniconda-install.sh \
-    && bash ./miniconda-install.sh -b
-
-# Needed to be set to run conda in the Dockerfile
-ENV PATH=/pyarpes/miniconda3/bin:$PATH
-
-RUN git clone https://github.com/Tommaso-Pincelli/arpes /pyarpes/arpes
-WORKDIR /pyarpes/arpes
-RUN git checkout 792a26dc0f335e2e310968d59750311b91209218
-
-RUN conda env create -f environment.yml
-
-# Make RUN commands use the new environment:
-SHELL ["conda", "run", "--no-capture-output", "-n", "arpes", "/bin/bash", "-c"]
-
-RUN pip install .
-
-RUN conda install -c conda-forge jupyterlab
-
-COPY 01-chown-dir /config/custom-cont-init.d/01-chown-dir
+    && bash ./miniconda-install.sh -b \
+    && chown -R 1000:1000 /pyarpes/miniconda3/bin \
+    && export PATH=/pyarpes/miniconda3/bin:$PATH \
+    && git clone https://github.com/Tommaso-Pincelli/arpes /pyarpes/arpes \
+    && cd /pyarpes/arpes \
+    && git checkout be27050716f9e306b99f6e6b416f82bfb071c8b4 \
+    && conda env create -f environment.yml \
+    && conda run --no-capture-output -n arpes pip install . \
+    && conda run --no-capture-output -n arpes conda install -c conda-forge jupyterlab \
+    && chown -R 1000:1000 /pyarpes
+
+ENV PUID=1000 PGID=1000
 COPY 02-exec-cmd /config/custom-cont-init.d/02-exec-cmd
-COPY pyARPES_download_and_visualize.ipynb /pyarpes/example/pyARPES_download_and_visualize.ipynb
-WORKDIR /pyarpes/example
\ No newline at end of file

north/app/models.py

@@ -59,6 +59,11 @@ all_tools: List[ToolModel] = [
         description='Run paraprobe on atom probe data',
         docker_image='TODO'
     ),
+    ToolModel(
+        name='pyarpes',
+        description='Run pyARPES to analyze data',
+        docker_image='TODO'
+    ),
     ToolModel(
         name='pyarpes',
         description='Run pyARPES to analyze data',

north/app/routes/instances.py

@@ -58,7 +58,7 @@ def get_docker_client() -> DockerClient:
 
 # Placeholder code for something that retains information of what container channel are available
 # Todo: Add channel number tag to the docker container created and use that as a store
-available_channel = deque(['0', '1', '2', '3', '4', '5', '6'])
+available_channel = deque(['0', '1', '2', '3', '4', '5', '6', '7', '8', '9'])
 
 
 def get_available_channel() -> str:
@@ -161,7 +161,7 @@ async def post_instances(request: Request, instance: InstanceModel, token=Depend
             ports={"3000": int(f'1000{channel}')},
             detach=True,
             name=container_name,
-            environment={"SUBFOLDER": str(path), "PUID": 1000, "PGID": 1000},
+            environment={"SUBFOLDER": str(path), "PUID": 1000, "PGID": 1000, "RUNDIR": "/home/jovyan/work/raw"},
             labels={"path": path, "channel_token": channel_token},
             mounts=get_docker_mounts_from_paths(instance.paths)
         )