6 files changed, 0 insertions, 221 deletions
diff --git a/topics/notebooks/binderlite-cli.gmi b/topics/notebooks/binderlite-cli.gmi
deleted file mode 100644
index 81e6db8..0000000
--- a/topics/notebooks/binderlite-cli.gmi
+++ /dev/null
@@ -1,19 +0,0 @@
-# CLI Features
-
-## Tags
-
-* assigned: jgart
-* priority: low
-* status: unclear
-* type: feature-request
-* keywords: bindelite, notebooks
-
-## Admin
-
-* Clear Database
-
-## User
-
-* Upload Notebooks
-* List Notebooks
-* Download Notebooks
diff --git a/topics/notebooks/guix-containers.gmi b/topics/notebooks/guix-containers.gmi
deleted file mode 100644
index 134acc1..0000000
--- a/topics/notebooks/guix-containers.gmi
+++ /dev/null
@@ -1,18 +0,0 @@
-# Guix Containers
-
-## Tags
-
-* type: bug
-* assigned: jgart
-* status: unclear
-* priority: medium
-* keywords: notebooks, guix, containers
-
-## Bugs
-
-guix container exec command does not currently work: 
-
-http://issues.guix.gnu.org/50916
-
-Good to know in case we think we might need it for something container related 
-in the future.
diff --git a/topics/notebooks/pluto.gmi b/topics/notebooks/pluto.gmi
deleted file mode 100644
index b924020..0000000
--- a/topics/notebooks/pluto.gmi
+++ /dev/null
@@ -1,22 +0,0 @@
-# Julia Pluto
-
-## Tags
-
-* type: documentation
-* status: unclear
-
-## Pluto in a Guix container
-
-We run Pluto in a container. It allows for self-install of Julia packages:
-
-```
-guix environment -L ~/guix-past/modules/ -L ~/guix-bioinformatics/ julia-visuals -C --ad-hoc vim bash wget openssl nss  --network
-```
-
-To prevent complaints of SSL set the path correctly, or simply (not ideal)
-
-```
-echo "check_certificate = off" >> ~/.wgetrc
-
-bash runpluto.sh 4343
-```
diff --git a/topics/notebooks/port-map.gmi b/topics/notebooks/port-map.gmi
deleted file mode 100644
index 4a7d680..0000000
--- a/topics/notebooks/port-map.gmi
+++ /dev/null
@@ -1,14 +0,0 @@
-# port map
-
-|-----|-----------|
-|port |service    |
-|-----|-----------|
-|80   |nginx      |
-|8989 |binderlite |
-|xxxx |jupyter(s) |
-
-
-## Tags
-
-* type: documentation
-* keywords: documentation, port map
diff --git a/topics/notebooks/reproducibility.gmi b/topics/notebooks/reproducibility.gmi
deleted file mode 100644
index 7219539..0000000
--- a/topics/notebooks/reproducibility.gmi
+++ /dev/null
@@ -1,22 +0,0 @@
-# Reproducibility
-
-## How Guix manages reproducibility
-
-=> https://hpc.guix.info/blog/2021/09/whats-in-a-package/ whats in a package
-
-=> https://lists.gnu.org/archive/html/emacs-bug-tracker/2019-11/msg00569.html
-
-=> https://guix.gnu.org/cookbook/en/html_node/Basic-setup-with-manifests.html
-
-## Notes on how others are managing or thinking about reproducibility
-
-https://github.com/fonsp/Pluto.jl#built-in-package-manager
-
-https://mybinder.readthedocs.io/en/latest/tutorials/reproducibility.html#pin-dependencies
-
-## Tags
-
-* type: documentation
-* priority: medium
-* assigned: jgart
-* keywords: documentation, notebooks, reproducibility, guix
diff --git a/topics/notebooks/user-stories.gmi b/topics/notebooks/user-stories.gmi
deleted file mode 100644
index 013ee48..0000000
--- a/topics/notebooks/user-stories.gmi
+++ /dev/null
@@ -1,126 +0,0 @@
-# Next Steps
-
-## Tags
-
-* assigned: jgart
-* type: enhancement
-* keywords: notebooks, jupyter
-* status: unclear
-
-## Description
-Whenever we start a notebook let's generate an id (put the id in a db or in memory start) and then accept the id as
-part of the route to get to the notebook.
-
-The server has to look that id up and route the user to that particular jupyter notebook instance.
-
-Currently, users are directed to a jupyter notebook instance via parsing the output of `list_running_servers`:
-
-=> https://git.genenetwork.org/jgart/binderlite/src/branch/master/app.py#L37 list_running_servers in binderlite src
-
-This has its issues because we cannot uniquely identify the last launched notebook.
-
-## Optimizations
-
-### Shutdown notebook and save to memory
-
-If we are shutting down the notebook to save memory then we want
-to remember it's location in order to return to it.
-
-The jupyter notebook API has a function for listing currently running notebooks (mentioned above):
-
-```
-def list_running_servers(runtime_dir=None):
-    """Iterate over the server info files of running notebook servers.
-
-    Given a runtime directory, find nbserver-* files in the security directory,
-    and yield dicts of their information, each one pertaining to
-    a currently running notebook server instance.
-    """
-```
-
-There is also a function for getting a timestamp of the last time the notebook server did something:
-
-```
- def last_activity(self):
-        """Get a UTC timestamp for when the server last did something.
-
-        Includes: API activity, kernel activity, kernel shutdown, and terminal
-        activity.
-        """
-```
-
-I need to decide on a way to uniquely identify the last built jupyter notebook.
-
-### Shutdown kernels gracefully
-
-* shutdown jupyter gracefully
-
-Find a way to shutdown jupyter kernels gracefully. Jupyter kernels are currently shutdown by sending a kill signal
-(SIGINT, Ctrl+c) via the terminal.
-
-This currently produces the following error:
-
-```
-Exception in thread Thread-1:
-Traceback (most recent call last):
-  File "/gnu/store/sd2ic7bpv8fx3imy1j8xcjclx71sv6q0-python-3.8.2/lib/python3.8/threading.py", line 932, in _bootstrap_inner
-      self.run()
-        File "/gnu/store/sd2ic7bpv8fx3imy1j8xcjclx71sv6q0-python-3.8.2/lib/python3.8/threading.py", line 870, in run
-            self._target(*self._args, **self._kwargs)
-              File "/gnu/store/w9bgs701xg1gbhxb6a4fsrjkj10c4sxc-python-notebook-6.3.0/lib/python3.8/site-packages/notebook/notebookapp.py", line 1961, in _confirm_exit
-                  line = sys.stdin.readline()
-                  OSError: [Errno 5] Input/output error
-```
-
-## guix-kernel runs by default in a container
-
-guix-kernel (AKA guix-jupyter) runs by default in a container.
-
-See here:
-
-=> https://gitlab.inria.fr/guix-hpc/guix-kernel/-/blob/master/guix/jupyter/kernel.scm#L181 eval/container*
-
-The reason I bring this up is because I currently run binderlite without the `--container` flag.
-
-If I try to run it with the `--container` flag then I run into permission issues due to running a container
-
-inside another container.
-
-## Question(s)
-
-###
-
-What is the idiomatic way in nginx to forward everything beyond some prefix.
-
-Currently using the $rest arg but that might not be a good way to do it:
-
-=> https://git.genenetwork.org/jgart/binderlite/src/branch/master/nginx.conf#L36
-
-###
-
-Do we want to avoid hard coding guix-kernel to run inside a container and instead be able to explicitly
-specify a container environment from the binderlite app or should this be left to guix-kernel?
-
-See above section on guix-kernel running by default in a container.
-
-Suggestion: we will create our own derived kernels and dependencies.
-
-###
-
-I currently cannot kill running jupyter instances on penguin2:
-
-```
-kill-jupyter
-kill: (1251): Operation not permitted
-kill: (34495): No such process
-kill: (52689): Operation not permitted
-kill: (52720): Operation not permitted
-kill: (52956): Operation not permitted
-Killed
-```
-
-=> https://git.genenetwork.org/jgart/binderlite/src/branch/master/bin/kill-jupyter kill-jupyter
-
-How should I get around this?
-
-Suggestion: try killing a container rather then the jupyter process. Use the pid of the container.