Merge pull request #75 from ScilifelabDataCentre/SS-1241_Include_git-…

…lfs_in_our_standard_jupyterlab_image

SS-1241 Include git-lfs in our standard jupyterlab image

Include git-lfs in our standard jupyterlab image

Source: https://scilifelab.atlassian.net/browse/SS-1241

serve-jupyterlab/Dockerfile

@@ -9,6 +9,7 @@ COPY requirements.txt /tmp
 USER root
 RUN apt-get update && apt-get install curl -y --no-install-recommends \
     && apt-get clean \
+    && apt-get install git-lfs  -y --no-install-recommends \
     && rm -rf /var/lib/apt/lists/*
 
 USER $NB_UID

serve-jupyterlab/Dockerfile.test

@@ -10,6 +10,7 @@ COPY tests/notebooks/basic.ipynb tests/basic.ipynb
 USER root
 RUN apt-get update && apt-get install curl -y --no-install-recommends \
     && apt-get clean \
+    && apt-get install git-lfs -y --no-install-recommends \
     && rm -rf /var/lib/apt/lists/*
 
 USER $NB_UID

serve-jupyterlab/tests/notebooks/basic.ipynb

@@ -14,28 +14,38 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "9\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "x = 4\n",
     "y = 5\n",
     "z = x + y\n",
     "print(z)"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "!git lfs install"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "!git lfs version"
+   ]
   }
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "venv",
    "language": "python",
    "name": "python3"
   },
@@ -49,14 +59,9 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.10"
+   "version": "3.12.7"
   },
-  "orig_nbformat": 4,
-  "vscode": {
-   "interpreter": {
-    "hash": "916dbcbb3f70747c44a77c7bcd40155683ae19c65e1c03b4aa3499c5328201f1"
-   }
-  }
+  "orig_nbformat": 4
  },
  "nbformat": 4,
  "nbformat_minor": 2

serve-jupyterlab/tests/requirements.txt

@@ -2,4 +2,5 @@ black
 requests
 docker
 pytest
-nbval
+nbval
+websocket-client

serve-jupyterlab/tests/test_api.py

@@ -73,11 +73,27 @@ def test_notebook():
     cell_outputs = _get_notebook_cell_outputs(
         headers, HOST, NOTEBOOK_PATH, TIMEOUT_CALL
     )
-    assert len(cell_outputs) == 1, len(cell_outputs)
+    assert len(cell_outputs) == 3, len(cell_outputs)
 
     val = cell_outputs[0]
     assert type(val) == str
     assert val == "9", val
+    # check lfs installation
+    lfs_init_val = cell_outputs[1]
+    assert isinstance(lfs_init_val, str)
+    assert lfs_init_val == "Git LFS initialized.", lfs_init_val
+    lfs_ver_val = cell_outputs[2]
+    assert isinstance(lfs_ver_val, str)
+    # Ensure the latest version here
+    error_message = f"""
+        Check the version here. 
+        If it is different from expected, update the assert. 
+        Current version to check:
+        "{lfs_ver_val}"
+        """
+    assert (
+        lfs_ver_val == "git-lfs/3.0.2 (GitHub; linux amd64; go 1.18.1)"
+    ), error_message
 
 
 def test_shutdown():