From ec36c79c9079aa9c76cfe5252686d3f78fd7da95 Mon Sep 17 00:00:00 2001 From: Ryan Lovett Date: Mon, 28 Oct 2024 23:13:29 -0700 Subject: [PATCH 1/6] Move TOC into myst.yml. Reorganize pages. --- _toc.yml | 97 --------- images/jupyterlab-memory.png | Bin 6648 -> 5246 bytes myst.yml | 87 +++++++- reference/terms-and-abbreviations.md | 35 ---- students/troubleshooting.md | 31 --- support/{contact-us.md => communication.md} | 0 {reference => support}/contributors.md | 0 support/troubleshoot.md | 198 ------------------ support/troubleshooting/jupyter.md | 108 ++++++++++ .../nbgitpuller.md} | 10 +- support/troubleshooting/otter-grader.md | 23 ++ .../python.md} | 10 +- support/troubleshooting/rstudio.md | 23 ++ 13 files changed, 250 insertions(+), 372 deletions(-) delete mode 100644 _toc.yml delete mode 100644 reference/terms-and-abbreviations.md delete mode 100644 students/troubleshooting.md rename support/{contact-us.md => communication.md} (100%) rename {reference => support}/contributors.md (100%) delete mode 100644 support/troubleshoot.md create mode 100644 support/troubleshooting/jupyter.md rename support/{troubleshoot-nbgitpuller.md => troubleshooting/nbgitpuller.md} (95%) create mode 100644 support/troubleshooting/otter-grader.md rename support/{python-errors.md => troubleshooting/python.md} (91%) create mode 100644 support/troubleshooting/rstudio.md diff --git a/_toc.yml b/_toc.yml deleted file mode 100644 index 5cec757..0000000 --- a/_toc.yml +++ /dev/null @@ -1,97 +0,0 @@ -# Each entry has the following schema: -# -# - file: /myurl # URL of section relative to the /content/ folder. -# sections: # Contains a list of more entries that make up the chapter's sections -# not_numbered: true # if the section shouldn't have a number in the sidebar -# (e.g. Introduction or appendices) -# expand_sections: true # if you'd like the sections of this chapter to always -# be expanded in the sidebar. -# external: true # Whether the URL is an external link or points to content in the book -# -# Below are some special values that trigger specific behavior: -# - search: true # Will provide a link to a search page -# - divider: true # Will insert a divider in the sidebar -# - header: My Header # Will insert a header with no link in the sidebar -# -# See the links below for an example. - -format: jb-book -root: intro -title: Home -parts: -- caption: DataHub Technology - chapters: - - file: technology/introduction-to-jupyter - - file: technology/jupyterlab - - file: technology/rstudio - - file: technology/shiny - - file: technology/quarto - - file: technology/remote-desktop - - file: technology/vscode.md - - file: technology/real-time-collaboration - - file: technology/syncthing - - file: technology/jupyter-ai -- caption: DataHub Workflows - chapters: - - file: workflows/logging-in - - file: workflows/creating-notebooks - - file: workflows/notebook-zero - - file: workflows/distributing-files - - file: workflows/pushing-to-github - - file: workflows/securely-push-github - - file: workflows/nbgitpuller-link - - file: workflows/install-packages - - file: workflows/elevated-privileges - - file: workflows/accessibility - - file: workflows/collecting-grading-assignments - - file: workflows/save-files-as-pdf.md - - file: workflows/download-archive.md - - file: workflows/performance-issue.md - - file: workflows/calculate-compute-cost.ipynb - - file: workflows/storing-datasets - - file: workflows/bestpractices - - file: workflows/external-technology - # FIXME: r-datahub has very little to do with using R on DataHub - - file: workflows/r-datahub -- caption: Support - chapters: - - file: support/contact-us - - file: support/common-requests - - file: support/onboarding - - file: support/memory-cpu - - file: support/troubleshoot - - file: support/troubleshoot-nbgitpuller - - file: support/python-errors - - file: support/workshop-research - - file: support/new-hub - - file: support/learn-more -- caption: Resources for Students - chapters: - - file: students/before-semester - - file: students/during-semester - - file: students/troubleshooting - - file: students/after-semester - - file: students/equipment-lending -- caption: Modules and Connectors - chapters: - - file: connector/general/what-is-a-connector - sections: - - file: connector/general/previous-connectors - - file: module/general/what-is-a-module - - file: dec/general/what-is-a-data-enabled-course -- caption: Creating a Connector - chapters: - - file: connector/instructor/logistics - - file: connector/instructor/syllabus-design - - file: connector/instructor/student-help - - file: connector/instructor/communication-channels - - file: connector/instructor/checklist -- caption: Creating a Module - chapters: - - file: module/instructor/preplanning - - file: module/instructor/develop - - file: module/instructor/deploy-help -- caption: Reference - chapters: - - file: reference/contributors - - file: reference/terms-and-abbreviations diff --git a/images/jupyterlab-memory.png b/images/jupyterlab-memory.png index b5f1397774cc0bf6e26c88d1d9a34596bf76d1eb..ced3e325e8902fa3355f5a970475fab8094958e9 100644 GIT binary patch literal 5246 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Repeat these steps as necessary. diff --git a/support/contact-us.md b/support/communication.md similarity index 100% rename from support/contact-us.md rename to support/communication.md diff --git a/reference/contributors.md b/support/contributors.md similarity index 100% rename from reference/contributors.md rename to support/contributors.md diff --git a/support/troubleshoot.md b/support/troubleshoot.md deleted file mode 100644 index 4a89b8c..0000000 --- a/support/troubleshoot.md +++ /dev/null @@ -1,198 +0,0 @@ -# Troubleshooting issues in the Hub - -```{note} -Facing issues with your hub and want to do some basic troubleshooting before escalating issues to us? If yes, read below! -``` - -One common error is a Jupyter notebook becoming unresponsive. You will know that a notebook is unresponsive. Another type of error is a user not being able to access some part of their JupyterHub account. - -We have outlined two methods below that you should try for each error type. For errors related to execution of code, such as the notebook not running properly, you should try restarting the kernel. For errors related to access, you should try restarting the server. - -### Restarting the Kernel - -If your notebook becomes unresponsive, you can try to restart the kernel. - -![](../assets/restart-kernel.png) - -### Restarting Servers - -There are different methods for restarting your own and restarting another user's server. - -##### Restarting Your Own Server - -All users can restart their own servers. To do so, start by going to the control panel. - -![](../assets/control-link.png)Click the `Stop My Server` button. - -![](../assets/stop-my-server.png)Once the server has stopped and the `Stop My Server` button is no longer visible, click the `My Server` button to restart the server. - -![](../assets/start-my-server.png) - -##### Restarting Student Servers - -Users with admin privileges on DataHub can restart other users' servers. To restart a student's server, first go to the control panel. - -![](../assets/control-link.png) - -Click on the `Admin` button at the top of the page. If you do not see this button, you do not have admin rights. To request admin rights, please [post on Piazza](http://piazza.com/berkeley/other/cs97). - -![](../assets/admin-link.png) - -After clicking the `Admin` button, you will see the admin panel. Usernames have been obfuscated here. To search for a user, you can use find \(type Control+F or Command+F\). An individual's username is the same as their CalNet ID. When you have found the desired user, click the `stop server` button in the user's row. - -![](../assets/admin-panel.png) - -After clicking the `stop server` button, you can click the `start server` button in the user's row. - -#### Troubleshoot issues with Hub/Server/Code running slow - -**What should I do if my hub is running slow?** - -Try these recommended options, - -- Restart your kernel. - -- Check whether there are lot of open tabs? If yes, close the tabs that are not required. - -If you still face the issue, raise a [bug](https://github.com/berkeley-dsep-infra/datahub/issues/new?assignees=&labels=bug&template=bug_report.yml)! - -**What should I do if my code is running slow?** - -In general, this issue could be attributed to the varied programming practices adopted that might have slowed the operation of the hub. Check whether your code does any of the following, - -- You are running an infinite loop -- Your computation/calculation is big -- You are joining tables that are too large -- You have too many notebooks open at the same time -- You are trying to show a table which is too large and as a result are crashing the browser - -If they are relevant, try fixing these issues by improving the programming practices or by reducing the size of the dataset. If none of the highlighted points seem relevant in your scenario, Please raise a [bug request](https://github.com/berkeley-dsep-infra/datahub/issues/new?assignees=&labels=bug&template=bug_report.yml)! - -#### Troubleshoot 4xx and 5xx errors - -**What should I do if a user's environment is unusable?** - -A user's Lab workspace might become unusable (e.g. it opens a notebook or workspace that is impossible to get out of). You have couple of options before you escalate this issue to us: - -- Start the user's server by visiting `{hub-url}/user/{username}/lab/workspaces/lab?reset` to reset the workspace.(Refer to this [documentation](https://jupyterlab.readthedocs.io/en/stable/user/urls.html#resetting-a-workspace) to reset the workspace for the users. -- Limit the environment to the user's file browser by visiting `{hub-url}/user/{username}/tree` in Jupyter Notebook. -- Launch a terminal by visiting `{hub-url}/user/{username}/terminals/N` (where `N` is any integer) in Jupyter Notebook. A terminal is useful if one needs to recover from an nbgitpuller issue or run other troubleshooting commands. -- If none of the above options work, Log into the [admin panel](https://datahub.berkeley.edu/hub/admin#/). Search for the calnet id of the user you want to troubleshoot. Click "Edit User" option and cLick on "Delete User" button which results in user getting deleted from the chosen hub. Now, Select the option "back" to go back to admin dashboard. Select "Add Users" option, Add the username (calnet id) and click on the "Add Users" button. Users will be added back to the admin interface. You can either check their instance or ask them to check their instance manually to confirm that the hack worked. - -**What if restarting the kernel is not solving spawn pending error message?** - -You can check if the output files are causing the ipynb files (in the case of python notebooks) to be bloated. If that be the case then you can run the following command to clear the output files which is causing this issue. - -```python -jupyter nbconvert --clear-output --inplace filename.ipynb -``` - -**What should I do if I get "503 service unavailable error" regularly?** - -Sorry, that you had to face this error! This error could be due to some of our stability improvements. Try restarting your server and wait for few minutes to see whether the issue still persists. If yes, raise a github [issue](https://github.com/berkeley-dsep-infra/datahub/issues/new/choose). - -**What should I do if I get "403 errors: Blocking request from unknown origin" regularly?** - -Sorry, that you had to face this error! This error could be due to multiple reasons outlined below, - -- You are using email id with a different domain other than berkeley.edu to authenticate with DataHub which could have potentially raised this error. Raise a github [issue](https://github.com/berkeley-dsep-infra/datahub/issues/new?assignees=&labels=bug&template=bug_report.yml), so that we can authorize your domain. - -- Large number of your students are trying to use the service resulting in failure of certain nodes. We are working on improving how we scale the hub with large volume of users. - -Raise a github [issue](https://github.com/berkeley-dsep-infra/datahub/issues/new?assignees=&labels=bug&template=bug_report.yml)! - -**What should I do if I get an “An unknown error occurred while loading this notebook” as part of the datahub service?** - -Try opening a new terminal from your instance and run the following command, - -```python -rm -f ~/.local/share/jupyter/nbsignatures.db -``` - -If the error still persists, raise a github [issue](https://github.com/berkeley-dsep-infra/datahub/issues/new?assignees=&labels=bug&template=bug_report.yml). - -#### Other hub issues - -**What should I do if there is a package conflict?** - -[Get inputs from the team] -Try moving to the previous version of the package and check if there are package conflicts. If it still exists, Raise a github [issue](https://github.com/berkeley-dsep-infra/datahub/issues/new?assignees=&labels=bug&template=bug_report.yml) - -**What should I do if my kernel dies?** - -As a rule of thumb, restart the kernel whenever it dies. This should work for most scenarios. - -```{note} -Kernel deaths are a common cause for your server running out of memory. As soon as you exceed your memory allocation, your kernel most probably will die because of the lack of availability of virtual memory or swap space. It is most likely due to a bug in your code. -``` - -**What should I do if I am getting RStudio Initialization Error: Error occurred during transmission error?** - -Please follow this workaround until a fix can be identified and implemented. Workaround involves renaming or removing ~/.rstudio via the terminal. To do so while bypassing the typical rstudio session startup: - -1. Go to this [link](https://r.datahub.berkeley.edu/user-redirect/tree) -2. Click New -> Terminal -3. In the terminal, type: ```mv .rstudio .rstudio.$(date +%s)``` and press return -4. Try to launch rstudio as you normally would and it should now work. - -**What should I do if R Studio times out and kicks me out every 5 minutes or so?** - -- Check if this is a browser or network issue - -- If that doesn't solve the issue, raise a request using this [template](https://github.com/berkeley-dsep-infra/datahub/issues/new?assignees=&labels=bug&template=bug_report.yml) - -```{note} -As a general note, These issues are challenging to reproduce. It will be helpful if you can be as specific as you can with regards to the steps required to reproduce the issue. We generally observe that the back and forth communication required to reproduce the issue for a request **that is not specific** increases the time needed to fix the issue exponentially. -``` - -**What should I do if I am not able to view the images annotated in my notebook when I download them as PDF?** - -Yes - this is an open issue we are aware of and don't have a direct solution. However, we have raised this issue to the developers of nbconvert which is a package responsible for the notebook to PDF conversion. -In the short term, the way to circumvent this issue is to copy-paste the required image in the notebook instead of saving them as a relative URL. Saving the image as a relative URL results in the image not getting added to the generated PDF. - -```{note} -On Windows and Linux, you can copy/paste by pressing Ctrl + Shift + C / Ctrl + Shift + V. On Mac, you can do it by pressing Cmd + C / Cmd + V. -``` - -#### nbgitpuller Issues - -**What should I do if I have issues with my nbgitpuller set up** - -Try the following steps from scratch again, - -- Enter the details for your hub. - -- Re-name the folder where you need to pull from to do a fresh pull request. - -- Check whether you should have followed good practices for setting up your repo. Check if there are files that should not be present. - -```{note} -Check this [documentation](https://jupyterhub.github.io/nbgitpuller/topic/repo-best-practices.html) for some tips to ensure that you don't get into git related issues. - -Check this [documentation](https://jupyterhub.github.io/nbgitpuller/) if you have issues setting up nbgitpuller! -``` - -#### Otter Issues - -**I am running into issues otter grader in datahub.berkeley.edu. It used to working with the same notebook files previously and I did not make any changes to the notebook. How do I fix this issue?** - -An upgrade to otter grader version 4.2.0 was made on 1/10/2022. If otter-grader was running smoothly in your notebooks previously then the updated version might have caused incompatibility with test cases. You can revert to otter version 3.1.0 by running the following command in the short term. - -```python -!pip install otter-grader==3.1.4 -``` - -**I am having issues with generating the zip file after running my code in the hub. What should I do?** - -If you got this error after running this command mentioned below, this is most likely an issue that the Otter team can debug. You can either access their [slack channel](https://join.slack.com/t/otter-grader/shared_invite/zt-bzfqbl82-C1s~YUBkbzvTcPCK60OOgg) or raise a [github issue](https://github.com/ucbds-infra/otter-grader) to seek their inputs directly. - -```python -grader.export(pdf=False, force_save=True) -``` - -In the long term, you should plan to rewrite your existing test cases to suit the new format and then run the latest version of otter grader in your notebooks. If you need further support with rewriting test cases then please [reach out to the otter team](https://github.com/ucbds-infra/otter-grader/issues/new?assignees=&labels=question&template=information-request.md&title=). - - -**What should I do if I have an issue that has not been documented in the FAQ?** - -Raise a github [issue](https://github.com/berkeley-dsep-infra/datahub/issues/new/choose) or reach out to Balaji Alwar(balajialwar@berkeley.edu)! We will keep adding common issues to this FAQ document! diff --git a/support/troubleshooting/jupyter.md b/support/troubleshooting/jupyter.md new file mode 100644 index 0000000..8323a70 --- /dev/null +++ b/support/troubleshooting/jupyter.md @@ -0,0 +1,108 @@ +--- +title: Jupyter +--- + +## Unresponsive Notebook + +Try restarting the kernel if you have errors related to execution of code, such as the notebook not running properly. + +### Restarting the Kernel + +If your notebook becomes unresponsive, you can try to restart the kernel. + +![](../../assets/restart-kernel.png) + +### Restarting Your Own Server + +All users can restart their own servers. To do so, start by going to the control panel. + +![](../../assets/control-link.png)Click the `Stop My Server` button. + +![](../../assets/stop-my-server.png)Once the server has stopped and the `Stop My Server` button is no longer visible, click the `My Server` button to restart the server. + +![](../../assets/start-my-server.png) + +### Restarting Student Servers + +Users with admin privileges on DataHub can restart other users' servers. To restart a student's server, first go to the control panel. + +![](../../assets/control-link.png) + +Click on the `Admin` button at the top of the page. If you do not see this button, you do not have admin rights. To request admin rights, please [post on Piazza](http://piazza.com/berkeley/other/cs97). + +![](../../assets/admin-link.png) + +After clicking the `Admin` button, you will see the admin panel. Usernames have been obfuscated here. To search for a user, you can use find \(type Control+F or Command+F\). An individual's username is the same as their CalNet ID. When you have found the desired user, click the `stop server` button in the user's row. + +![](../../assets/admin-panel.png) + +After clicking the `stop server` button, you can click the `start server` button in the user's row. + +#### Troubleshoot issues with Hub/Server/Code running slow + +**What should I do if my hub is running slow?** + +Try these recommended options, + +- Restart your kernel. + +- Check whether there are lot of open tabs? If yes, close the tabs that are not required. + +If you still face the issue, raise a [bug](https://github.com/berkeley-dsep-infra/datahub/issues/new?assignees=&labels=bug&template=bug_report.yml)! + +**What should I do if my code is running slow?** + +In general, this issue could be attributed to the varied programming practices adopted that might have slowed the operation of the hub. Check whether your code does any of the following, + +- You are running an infinite loop +- Your computation/calculation is big +- You are joining tables that are too large +- You have too many notebooks open at the same time +- You are trying to show a table which is too large and as a result are crashing the browser + +If they are relevant, try fixing these issues by improving the programming practices or by reducing the size of the dataset. If none of the highlighted points seem relevant in your scenario, Please raise a [bug request](https://github.com/berkeley-dsep-infra/datahub/issues/new?assignees=&labels=bug&template=bug_report.yml)! + +### 4xx and 5xx errors + +A user's Lab workspace might become unusable (e.g. it opens a notebook or workspace that is impossible to get out of). You have couple of options before you escalate this issue to us: + +- Start the user's server by visiting `{hub-url}/user/{username}/lab/workspaces/lab?reset` to reset the workspace.(Refer to this [documentation](https://jupyterlab.readthedocs.io/en/stable/user/urls.html#resetting-a-workspace) to reset the workspace for the users. +- Limit the environment to the user's file browser by visiting `{hub-url}/user/{username}/tree` in Jupyter Notebook. +- Launch a terminal by visiting `{hub-url}/user/{username}/terminals/N` (where `N` is any integer) in Jupyter Notebook. A terminal is useful if one needs to recover from an nbgitpuller issue or run other troubleshooting commands. +- If none of the above options work, Log into the [admin panel](https://datahub.berkeley.edu/hub/admin#/). Search for the calnet id of the user you want to troubleshoot. Click "Edit User" option and cLick on "Delete User" button which results in user getting deleted from the chosen hub. Now, Select the option "back" to go back to admin dashboard. Select "Add Users" option, Add the username (calnet id) and click on the "Add Users" button. Users will be added back to the admin interface. You can either check their instance or ask them to check their instance manually to confirm that the hack worked. + +**What if restarting the kernel is not solving spawn pending error message?** + +You can check if the output files are causing the ipynb files (in the case of python notebooks) to be bloated. If that be the case then you can run the following command to clear the output files which is causing this issue. + +```python +jupyter nbconvert --clear-output --inplace filename.ipynb +``` + +**What should I do if I get "503 service unavailable error" regularly?** + +Sorry, that you had to face this error! This error could be due to some of our stability improvements. Try restarting your server and wait for few minutes to see whether the issue still persists. If yes, raise a github [issue](https://github.com/berkeley-dsep-infra/datahub/issues/new/choose). + +**What should I do if I get "403 errors: Blocking request from unknown origin" regularly?** + +Sorry, that you had to face this error! This error could be due to multiple reasons outlined below, + +- You are using email id with a different domain other than berkeley.edu to authenticate with DataHub which could have potentially raised this error. Raise a github [issue](https://github.com/berkeley-dsep-infra/datahub/issues/new?assignees=&labels=bug&template=bug_report.yml), so that we can authorize your domain. + +- Large number of your students are trying to use the service resulting in failure of certain nodes. We are working on improving how we scale the hub with large volume of users. + +Raise a github [issue](https://github.com/berkeley-dsep-infra/datahub/issues/new?assignees=&labels=bug&template=bug_report.yml)! + +**What should I do if I get an “An unknown error occurred while loading this notebook” as part of the datahub service?** + +Try opening a new terminal from your instance and run the following command, + +```python +rm -f ~/.local/share/jupyter/nbsignatures.db +``` + +If the error still persists, raise a github [issue](https://github.com/berkeley-dsep-infra/datahub/issues/new?assignees=&labels=bug&template=bug_report.yml). + +### Kernels Dying + +Kernel deaths are a common result of your server running out of memory. As soon as you exceed your memory allocation, your kernel most probably will die because of the lack of availability of virtual memory or swap space. It is most likely due to a bug in your code. diff --git a/support/troubleshoot-nbgitpuller.md b/support/troubleshooting/nbgitpuller.md similarity index 95% rename from support/troubleshoot-nbgitpuller.md rename to support/troubleshooting/nbgitpuller.md index 6faf62d..945b24d 100644 --- a/support/troubleshoot-nbgitpuller.md +++ b/support/troubleshooting/nbgitpuller.md @@ -18,7 +18,7 @@ Open nbgitpuller links in Chrome, Firefox, or Safari. If the nbgitpuller link was not generated correctly, you'll see a red loading bar with an error message that says "Error: Command '['git', 'fetch']' returned non-zero exit status 128." An example screenshot is below: -```{image} ../assets/broken-nbgitpuller-link.png +```{image} ../../assets/broken-nbgitpuller-link.png :alt: Example error output from nbgitpuller ``` @@ -39,7 +39,7 @@ If you make changes to an assignment on GitHub after students have started worki The easiest and most conservative solution is to rename the file or folder that contains the incompatible changes, then click the nbgitpuller link again. If the file or folder is renamed to anything else (e.g. "SOC-5-old"), nbgitpuller will clone a fresh copy of the problematic files to the student's Jupyterhub. They can then copy over any work from the old version of the file. When you face an error like below, do the following steps -```{figure} ../images/mergeconflict.png +```{figure} ../../images/mergeconflict.png :align: center :name: DataHub Admin @@ -47,7 +47,7 @@ Here is how the admin dashboard looks like! ``` - Rename the existing folder where the merge conflict error arose -```{figure} ../images/tshoot.PNG +```{figure} ../../images/tshoot.PNG :align: center :name: Folder Rename! @@ -63,7 +63,7 @@ If you have command line experience then you can use "git stash" command in term - If you are using https://datahub.berkeley.edu then navigate to your file manager which acts as your home page. If you are using other hubs then you can access your file manager by navigating to "Hub URL/user/`Your-Username`/tree" which will take you to the home directory. For eg: If my user name is Julia and I want to access my home directory in R hub then the URL to access my home directory will be https://r.datahub.berkeley.edu/user/julia/tree. - On the upper right of the page, click the dropdown menu that says “New” and select “Terminal”. -```{figure} ../assets/terminal.png +```{figure} ../../assets/terminal.png :align: center :name: Launch Terminal @@ -73,7 +73,7 @@ Launch a terminal - Navigate to the folder where a) your files are stored and b) you have merge conflict issues - Run `git stash` command in the terminal and you will see the following output -```{figure} ../assets/gitstash_output.png +```{figure} ../../assets/gitstash_output.png :align: center :name: git stash output diff --git a/support/troubleshooting/otter-grader.md b/support/troubleshooting/otter-grader.md new file mode 100644 index 0000000..d486f20 --- /dev/null +++ b/support/troubleshooting/otter-grader.md @@ -0,0 +1,23 @@ +--- +title: Otter Grader +--- + +## Downgrading + +Otter Grader is periodically upgraded. If it was running smoothly previously, then it is possible the new version is incompatible with your test cases. You can revert to an older version temporarily with `pip`: + +```python +!pip install otter-grader==x.y.z +``` + +Where `x.y.z` is the desired version. + +In the long term, you should plan to rewrite your existing test cases to suit new formats and then run the latest version of otter grader in your notebooks. If you need further support with rewriting test cases then please [reach out to the otter team](https://github.com/ucbds-infra/otter-grader/issues/new?assignees=&labels=question&template=information-request.md&title=). + +## Zip File Generation + +If you got this error after running this command mentioned below, this is most likely an issue that the Otter team can debug. You can either access their [slack channel](https://join.slack.com/t/otter-grader/shared_invite/zt-bzfqbl82-C1s~YUBkbzvTcPCK60OOgg) or raise a [github issue](https://github.com/ucbds-infra/otter-grader) to seek their inputs directly. + +```python +grader.export(pdf=False, force_save=True) +``` diff --git a/support/python-errors.md b/support/troubleshooting/python.md similarity index 91% rename from support/python-errors.md rename to support/troubleshooting/python.md index 3e934f8..723cac2 100644 --- a/support/python-errors.md +++ b/support/troubleshooting/python.md @@ -7,7 +7,7 @@ This category describes errors that occur when running code cells. This list is ## NameError By far the most common errors that new students encounter are NameErrors. An example screenshot is below: -![](../assets/name-error.png) NameErrors occur when a code cell refers to a name that has not yet been defined. This usually happens when: +![](../../assets/name-error.png) NameErrors occur when a code cell refers to a name that has not yet been defined. This usually happens when: * a student forgets to run a cell, runs cells out of order, or restarts work on another day * a student misspells a variable name @@ -21,7 +21,7 @@ Solutions: ## ValueError Common when dealing with table data, ValueErrors arise when misspelled column labels are used. An example screenshot is below: -![](../assets/column-name-error.png) +![](../../assets/column-name-error.png) Solution: * The most likely solution is to review the column headers and ensure that the correct value is selected for. Python is case-sensitive, so it's important to check the spelling and capitalization of your strings/variable names. @@ -29,10 +29,10 @@ Solution: When using a function, e.g for table manipulation, it is possible to use the incorrect kind of value. In the example below, the column relabeling function is misused, causing errors in two different ways. In this error, the function was given too many values: -![](../assets/many-args-error.png) +![](../../assets/many-args-error.png) In this example, the function was given a boolean (in this case, the value True) rather than a string: -![](../assets/wrong-args-error.png) +![](../../assets/wrong-args-error.png) Solutions: * If you see an error relating to the *number* of arguments, check that you are using the correct number. If you aren't sure, refer to prior uses of the function for reference, or ask a friend. @@ -40,7 +40,7 @@ Solutions: ## Cells never stop running Sometimes, cells can get "stuck" running: -![](../assets/kernel-busy.png) +![](../../assets/kernel-busy.png) When this issue occurs, the square brackets to the left of the cell contain an asterisk for several minutes, the open circle next to kernel type at the top right will stay solid grey, and the expected output never appears. This may happen when: * the kernel isn't working properly diff --git a/support/troubleshooting/rstudio.md b/support/troubleshooting/rstudio.md new file mode 100644 index 0000000..2b967cc --- /dev/null +++ b/support/troubleshooting/rstudio.md @@ -0,0 +1,23 @@ +--- +title: RStudio +--- + +## Initialization Error + +If you are seeing the error "Error occurred during transmission error", follow +this workaround until a fix can be identified and implemented. Workaround +involves renaming or removing ~/.rstudio via the terminal. To do so while +bypassing the typical rstudio session startup: + +1. Go to https://{hub_url}/user-redirect/tree) +2. Click New > Terminal +3. In the terminal, run `mv .rstudio .rstudio.$(date +%s)`. +4. Try to launch rstudio as you normally would. + +## Timeouts + +Check if this is a browser or network issue. + +If that doesn't solve the issue, raise a request using this [template](https://github.com/berkeley-dsep-infra/datahub/issues/new?assignees=&labels=bug&template=bug_report.yml) + +As a general note, These issues are challenging to reproduce. It will be helpful if you can be as specific as you can with regards to the steps required to reproduce the issue. We generally observe that the back and forth communication required to reproduce the issue for a request **that is not specific** increases the time needed to fix the issue exponentially. From d0f62831c3ac815c507294b4825f14af3a0328df Mon Sep 17 00:00:00 2001 From: Ryan Lovett Date: Mon, 28 Oct 2024 23:14:10 -0700 Subject: [PATCH 2/6] Add abbreviations. --- connector/general/previous-connectors.md | 18 +++++++++++++++++- 1 file changed, 17 insertions(+), 1 deletion(-) diff --git a/connector/general/previous-connectors.md b/connector/general/previous-connectors.md index 3a550e6..a1d1b97 100644 --- a/connector/general/previous-connectors.md +++ b/connector/general/previous-connectors.md @@ -1,4 +1,20 @@ -# Previous Connector Courses +--- +title: Previous Connector Courses +abbreviations: + CIVENG: Civil Engineering + COGSCI: Cognitive Science + COMPSCI: Computer Science + DEMOG: Demography + EPS: Earth & Planetary Science + ESPM: Environmental Science, Policy, and Management + GEOG: Geography + HIST: History + INFO: School of Information + MCB: Moleculrar and Cell Biology + POLSCI: Political Science + SOCIOL: Sociology + STAT: Statistics +--- The links below point either to a PDF syllabus or to a course website that contains the syllabus. From 30d2cb663306bdd73af533a64fb0daab6486f2b3 Mon Sep 17 00:00:00 2001 From: Ryan Lovett Date: Mon, 28 Oct 2024 23:14:30 -0700 Subject: [PATCH 3/6] Add egress communication. --- .../instructor/communication-channels.md | 19 ++++--------------- 1 file changed, 4 insertions(+), 15 deletions(-) diff --git a/connector/instructor/communication-channels.md b/connector/instructor/communication-channels.md index 0fbb89f..eac9e48 100644 --- a/connector/instructor/communication-channels.md +++ b/connector/instructor/communication-channels.md @@ -1,18 +1,7 @@ -# Communication Channels +--- +title: Communication Channels +--- - - -### Biweekly Instructor Meetings +## Biweekly Instructor Meetings We will be holding connector instructor meetings every two weeks. These meetings are announced through the mailing list. We will post notes for those who are not able to attend. These meetings will focus on topics that are of interest to the connector instructors. - -### Mailing List - -You should have been added to the connector instructor mailing list/google group. If you are not sure whether you have been added, you can view all your memberships at [groups.google.com](/groups.google.com). To email all instructors on the mailing list, you can send an email to [ds-connector-instructors@lists.berkeley.edu](mailto:ds-connector-instructors@lists.berkeley.edu). - From 8e1e695b8ca50a7694d71db029bcca0b3b0196bc Mon Sep 17 00:00:00 2001 From: Ryan Lovett Date: Mon, 28 Oct 2024 23:15:14 -0700 Subject: [PATCH 4/6] Add egress communication. --- support/communication.md | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/support/communication.md b/support/communication.md index 7635b95..140981a 100644 --- a/support/communication.md +++ b/support/communication.md @@ -1,5 +1,5 @@ --- -title: Contact Us +title: Communication --- ## GitHub Issues @@ -21,3 +21,7 @@ We are trying to build a cadence by sending public announcements about feature r ```{tip} You can track our current priorities for this project on our [sprint board](https://github.com/berkeley-dsep-infra/datahub/projects). ``` + +## Mailing Lists + +Instructors will be added to the [ds-connector-instructors@lists.berkeley.edu](mailto:ds-connector-instructors@lists.berkeley.edu). If you are not sure whether you have been added, you can view all your memberships at [groups.google.com](https://groups.google.com). From 7494703d5aead6ab4f4baeda21ff81b3f36368c0 Mon Sep 17 00:00:00 2001 From: Ryan Lovett Date: Mon, 28 Oct 2024 23:15:32 -0700 Subject: [PATCH 5/6] Alphabetize. --- support/contributors.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/support/contributors.md b/support/contributors.md index de56b52..71ba8e5 100644 --- a/support/contributors.md +++ b/support/contributors.md @@ -6,12 +6,12 @@ Here are the people in involved with DataHub Infrastructure and Modules team | Name | Role | | :--- | :--- | -| [Eric Van Dusen](mailto:ericvd@berkeley.edu) | Tech and Outreach Lead at DSUS | -| [Shane Knapp](mailto:sknapp@berkeley.edu) | Technical Lead, DataHub Infrastructure | | [Balaji Alwar](mailto:balajialwar@berkeley.edu) | Service Lead for JupyterHub Infrastructure -| [Ryan Lovett](mailto:rylo@berkeley.edu) | Manages JupyterHub Infrastructure | | [Jonathan Felder](mailto:felder@berkeley.edu) | Manages JupyterHub Infrastructure | +| [Shane Knapp](mailto:sknapp@berkeley.edu) | Technical Lead, DataHub Infrastructure | +| [Ryan Lovett](mailto:rylo@berkeley.edu) | Manages JupyterHub Infrastructure | | [Greg Meritt](mailto:gmeritt@berkeley.edu) | Manages JupyterHub Infrastructure | +| [Eric Van Dusen](mailto:ericvd@berkeley.edu) | Tech and Outreach Lead at DSUS | Previous Contributors: Gunjan Baid, Yuvi Panda, Chris Pyles, Anthony Suen, Keeley Takimoto From c450e6d6603b833967442ae1684b23a41530c196 Mon Sep 17 00:00:00 2001 From: Ryan Lovett Date: Mon, 28 Oct 2024 23:15:58 -0700 Subject: [PATCH 6/6] Make small content changes. --- support/troubleshooting/jupyter.md | 5 +++++ support/troubleshooting/nbgitpuller.md | 6 +++--- support/troubleshooting/python.md | 2 +- 3 files changed, 9 insertions(+), 4 deletions(-) diff --git a/support/troubleshooting/jupyter.md b/support/troubleshooting/jupyter.md index 8323a70..3ddb38f 100644 --- a/support/troubleshooting/jupyter.md +++ b/support/troubleshooting/jupyter.md @@ -106,3 +106,8 @@ If the error still persists, raise a github [issue](https://github.com/berkeley- ### Kernels Dying Kernel deaths are a common result of your server running out of memory. As soon as you exceed your memory allocation, your kernel most probably will die because of the lack of availability of virtual memory or swap space. It is most likely due to a bug in your code. + +## Close JupyterLab Features + +. In Jupyter Lab, click the icon at the far left depicting a square within a circle. It displays open tabs, running kernels and language servers, and open terminals. Hover your mouse over any entry and a close icon (X) will appear. Click on the close icon to shut down that entry. + diff --git a/support/troubleshooting/nbgitpuller.md b/support/troubleshooting/nbgitpuller.md index 945b24d..2b07ec9 100644 --- a/support/troubleshooting/nbgitpuller.md +++ b/support/troubleshooting/nbgitpuller.md @@ -1,12 +1,12 @@ --- -title: Troubleshooting nbgitpuller +title: nbgitpuller --- You may run into different types of errors when you are using the JupyterHub or Jupyter notebooks. The majority of errors come from a few common causes and can be solved using the following methods. -## nbgitpuller Link Errors +## Link Errors -nbgitpuller link errors are usually due to one of three issues: +nbgitpuller link errors are usually due to one of three issues. ### Incompatible Browser diff --git a/support/troubleshooting/python.md b/support/troubleshooting/python.md index 723cac2..e1a67d5 100644 --- a/support/troubleshooting/python.md +++ b/support/troubleshooting/python.md @@ -1,5 +1,5 @@ --- -title: Troubleshooting Code Cell Errors +title: Python --- This category describes errors that occur when running code cells. This list is not exhaustive, but it details some of themost frequent errors that new Notebook users encounter.