Fix Colab setup: install git-annex from PyPI instead of NeuroDebian

README.rst

@@ -88,7 +88,8 @@ in the provided Docker containers.
 `git-annex <https://git-annex.branchable.com/>`_ is required to download the
 data sets. Please follow the instructions in the
 `git-annex documentation <https://git-annex.branchable.com/install/>`_ to install
-it on your system.
+it on your system. On Linux, a standalone build can also be installed from PyPI
+with ``pip install git-annex``.
 
 The tutorials and the package ``voxelwise_tutorials`` require Python 3.9 or higher.
 

tutorials/notebooks/shortclips/01_setup_colab.ipynb

@@ -48,11 +48,9 @@
       "outputs": [],
       "source": [
         "#!git config --global user.email \"you@example.com\" && git config --global user.name \"Your Name\"\n",
-        "#!wget -O- http://neuro.debian.net/lists/jammy.us-ca.libre | sudo tee /etc/apt/sources.list.d/neurodebian.sources.list\n",
-        "#!apt-key adv --recv-keys --keyserver hkps://keyserver.ubuntu.com 0xA5D32F012649A5A9 > /dev/null\n",
         "#!apt-get -qq update > /dev/null\n",
-        "#!apt-get install -qq inkscape git-annex-standalone > /dev/null\n",
-        "#!pip install -q voxelwise_tutorials"
+        "#!apt-get install -qq inkscape > /dev/null\n",
+        "#!pip install -q git-annex voxelwise_tutorials"
       ]
     },
     {
@@ -72,11 +70,11 @@
       "outputs": [],
       "source": [
         "# - Set up an email and username to use git, git-annex, and datalad (required to download the data)\n",
-        "# - Add NeuroDebian to the package sources\n",
-        "# - Update the gpg keys to use NeuroDebian\n",
         "# - Update the list of available packages\n",
-        "# - Install Inkscape to use more features from Pycortex, and install git-annex to download the data\n",
-        "# - Install the tutorial helper package, and all the required dependencies"
+        "# - Install Inkscape to use more features from Pycortex\n",
+        "# - Install git-annex (required to download the data) from PyPI, which provides a\n",
+        "#   standalone build that does not depend on the Ubuntu version or on third-party apt\n",
+        "#   repositories, and install the tutorial helper package with all the required dependencies"
       ]
     },
     {

tutorials/notebooks/shortclips/vem_tutorials_merged_for_colab.ipynb

@@ -48,11 +48,9 @@
    "outputs": [],
    "source": [
     "#!git config --global user.email \"you@example.com\" && git config --global user.name \"Your Name\"\n",
-    "#!wget -O- http://neuro.debian.net/lists/jammy.us-ca.libre | sudo tee /etc/apt/sources.list.d/neurodebian.sources.list\n",
-    "#!apt-key adv --recv-keys --keyserver hkps://keyserver.ubuntu.com 0xA5D32F012649A5A9 > /dev/null\n",
     "#!apt-get -qq update > /dev/null\n",
-    "#!apt-get install -qq inkscape git-annex-standalone > /dev/null\n",
-    "#!pip install -q voxelwise_tutorials"
+    "#!apt-get install -qq inkscape > /dev/null\n",
+    "#!pip install -q git-annex voxelwise_tutorials"
    ]
   },
   {
@@ -72,11 +70,11 @@
    "outputs": [],
    "source": [
     "# - Set up an email and username to use git, git-annex, and datalad (required to download the data)\n",
-    "# - Add NeuroDebian to the package sources\n",
-    "# - Update the gpg keys to use NeuroDebian\n",
     "# - Update the list of available packages\n",
-    "# - Install Inkscape to use more features from Pycortex, and install git-annex to download the data\n",
-    "# - Install the tutorial helper package, and all the required dependencies"
+    "# - Install Inkscape to use more features from Pycortex\n",
+    "# - Install git-annex (required to download the data) from PyPI, which provides a\n",
+    "#   standalone build that does not depend on the Ubuntu version or on third-party apt\n",
+    "#   repositories, and install the tutorial helper package with all the required dependencies"
    ]
   },
   {

tutorials/notebooks/shortclips/vem_tutorials_merged_for_colab_model_fitting.ipynb

@@ -48,11 +48,9 @@
    "outputs": [],
    "source": [
     "#!git config --global user.email \"you@example.com\" && git config --global user.name \"Your Name\"\n",
-    "#!wget -O- http://neuro.debian.net/lists/jammy.us-ca.libre | sudo tee /etc/apt/sources.list.d/neurodebian.sources.list\n",
-    "#!apt-key adv --recv-keys --keyserver hkps://keyserver.ubuntu.com 0xA5D32F012649A5A9 > /dev/null\n",
     "#!apt-get -qq update > /dev/null\n",
-    "#!apt-get install -qq inkscape git-annex-standalone > /dev/null\n",
-    "#!pip install -q voxelwise_tutorials"
+    "#!apt-get install -qq inkscape > /dev/null\n",
+    "#!pip install -q git-annex voxelwise_tutorials"
    ]
   },
   {
@@ -72,11 +70,11 @@
    "outputs": [],
    "source": [
     "# - Set up an email and username to use git, git-annex, and datalad (required to download the data)\n",
-    "# - Add NeuroDebian to the package sources\n",
-    "# - Update the gpg keys to use NeuroDebian\n",
     "# - Update the list of available packages\n",
-    "# - Install Inkscape to use more features from Pycortex, and install git-annex to download the data\n",
-    "# - Install the tutorial helper package, and all the required dependencies"
+    "# - Install Inkscape to use more features from Pycortex\n",
+    "# - Install git-annex (required to download the data) from PyPI, which provides a\n",
+    "#   standalone build that does not depend on the Ubuntu version or on third-party apt\n",
+    "#   repositories, and install the tutorial helper package with all the required dependencies"
    ]
   },
   {