From 62c1788b656b504b4c7922656abc36cee82b70ff Mon Sep 17 00:00:00 2001 From: Claude Date: Thu, 24 Sep 2026 20:33:03 +0000 Subject: [PATCH] Fix Colab setup: install git-annex from PyPI instead of NeuroDebian The NeuroDebian apt repository no longer works on Colab (Ubuntu noble): its signing key uses dsa1024, which apt now rejects, and the sources list was pinned to jammy, so git-annex-standalone had no install candidate. Install git-annex from PyPI instead. The wheel ships a standalone git-annex build, so it does not depend on the Ubuntu release, apt keys, or third-party repositories. Inkscape is still installed from the stock Ubuntu repositories. Fixes #59 Co-Authored-By: Claude Opus 5.5 Claude-Session: https://claude.ai/code/session_01JSD3PGSWRD4oZi4Z9zPe7W --- README.rst | 3 ++- .../notebooks/shortclips/01_setup_colab.ipynb | 14 ++++++-------- .../vem_tutorials_merged_for_colab.ipynb | 14 ++++++-------- ..._tutorials_merged_for_colab_model_fitting.ipynb | 14 ++++++-------- 4 files changed, 20 insertions(+), 25 deletions(-) diff --git a/README.rst b/README.rst index e61ee8e..a18b7ff 100644 --- a/README.rst +++ b/README.rst @@ -88,7 +88,8 @@ in the provided Docker containers. `git-annex `_ is required to download the data sets. Please follow the instructions in the `git-annex documentation `_ 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. diff --git a/tutorials/notebooks/shortclips/01_setup_colab.ipynb b/tutorials/notebooks/shortclips/01_setup_colab.ipynb index 25fb2f1..b7e44eb 100644 --- a/tutorials/notebooks/shortclips/01_setup_colab.ipynb +++ b/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" ] }, { diff --git a/tutorials/notebooks/shortclips/vem_tutorials_merged_for_colab.ipynb b/tutorials/notebooks/shortclips/vem_tutorials_merged_for_colab.ipynb index a47672d..c54758e 100644 --- a/tutorials/notebooks/shortclips/vem_tutorials_merged_for_colab.ipynb +++ b/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" ] }, { diff --git a/tutorials/notebooks/shortclips/vem_tutorials_merged_for_colab_model_fitting.ipynb b/tutorials/notebooks/shortclips/vem_tutorials_merged_for_colab_model_fitting.ipynb index 85656f2..55d2ac9 100644 --- a/tutorials/notebooks/shortclips/vem_tutorials_merged_for_colab_model_fitting.ipynb +++ b/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" ] }, {