# Creating a Code Ocean capsule synced to GitHub repo (create-repo)= ## GitHub: Create a new repository using one of the templates - Find the templates here: https://github.com/AllenSWDB/ SDK template: https://github.com/AllenSWDB/swdb2025_allensdk_environment PyNWB template: https://github.com/AllenSWDB/swdb2025_pynwb_environment - Use a template to make a new repository. Click the `Use this template` button in the top right corner: :::{figure} ../resources/GH_CO_1.png --- align: center --- ::: - Make yourself the owner of the new repository - Give the repository a name. - Select public or private - Click the `create repository` button. You have made a new repository!! In order to sync between your GitHub account and your Code Ocean account, you need to add a token from GitHub to your Code Ocean account. ## GitHub: Create a token: - Navigate to your profile picture in the top right corner. :::{figure} ../resources/GH_profile.png --- align: center width: 300 --- ::: - When you hover over this, a list of options will appear. Select `Settings` :::{figure} ../resources/GH_settings.png --- align: center width: 200 --- ::: - On the left-hand side, select the option for `Developer Settings` near the bottom of the list. :::{figure} ../resources/GH_developer.png --- align: center width: 200 --- ::: - On the left, select `Personal access tokens` and then select `Tokens (classic)` from the dropdown that appears. :::{figure} ../resources/GH_token.png --- align: center width: 200 --- ::: - On the top right, click on `Generate new token` and then select `Generate new token (classic)` from the drop down :::{figure} ../resources/GH_token_2.png --- align: center --- ::: - Add a note for what the token is for and set the expiration (you can choose no expiration if you want), and select the box next to `repo` under scopes :::{figure} ../resources/GH_token_3.png --- align: center width: 300 --- ::: - At the bottom of the page, select `Generate token` :::{figure} ../resources/GH_token_4.png --- align: center width: 300 --- ::: - You now have a token - something that looks like this: :::{figure} ../resources/GH_token_5.png --- align: center --- ::: - Copy this immediately! It is sometimes helpful to paste it into a text file to save as you won't be able to access it again. ## Add your GitHub token to your Code Ocean account - In Code Ocean, navigate to your account by clicking on the the icon with your initials on the bottom left. This gives you list of options. Choose `Account` :::{figure} ../resources/CO_account.png --- align: center width: 200 --- ::: - On the top right, click on `Add Credentials` and select `GitHub Credentials` :::{figure} ../resources/CO_credentials.png --- align: center --- ::: - You will be prompted to enter your GitHub account name and the GitHub token that you copied above. At this point, your GitHub and Code Ocean accounts are linked! (capsule-clone)= ## Code Ocean: Create a capsule from your GitHub repository - Create a new capsule. Click on the plus icon on the left near the top to Create New. Select the `Clone from Git` option under the "Capsule" header. It's the one with the GitHub icon. :::{figure} ../resources/CO_clone.png --- align: center width: 300 --- ::: - Paste the URL of your GitHub repository into the box. You have made a capule! ## Configuring your capsule - Change the name of your capsule so that it's clear what it is. Update the ReadMe as well - The environment is already set up according to the template. If you need to add more packages: Click on the `environment` tab on the left to add packages. :::{figure} ../resources/CO_environment.png --- align: center --- ::: - You might also need to increase the compute resources. This is also in the environment tab in the top right. :::{figure} ../resources/CO_compute.png --- align: center --- ::: - Attach data assets. Click on `Manage` next to the `data` tab on the left. Search for the data assets you need. (Look at the capsules we've used in the past week if you need help identifying the data you need). When you find the asset, click the `+` to the left of the asset name :::{figure} ../resources/CO_data.png --- align: center width: 300 --- ::: - Now you have a capsule with an environment set and data attached. It's up to you to add the code! Click on the `JupyterLab` icon on the right to launch Jupyter. :::{figure} ../resources/CO_jupyterlab.png --- align: center width: 200 --- ::: - Once it has launched, navigate into the Code folder. To open a blank notebook, click on the `Python3` option under Notebook in the Launcher. :::{figure} ../resources/CO_launch.png --- align: center --- ::: - Work in your notebook! Save your work! - To shut down the capsule when you, click the big red button on the top left. You can leave it on `Hold` to preserve any packages you've installed within jupyterlab, or shut down fully if you need to add new packages to the environment. (sync-github)= ## Sync with GitHub - When you've made changes and have shut down the capsule, you can commit your code to your GitHub repository. You can follow the steps you've learned using the Terminal, or you can use the panel on the right. Include a brief description and click `Commit Changes` :::{figure} ../resources/CO_commit.png --- align: center width: 300 --- ::: - Push changes to GitHub using the `Sync with GitHub` button on the panel on the right after your changes are committed. This button only appears when all changes are either committed or reverted. :::{figure} ../resources/CO_sync.png --- align: center width: 200 --- ::: - This sync button will also pull changes that have previously been merged into the GitHub repository. - This method of syncing with GitHub does not handle merge conflicts well, which is where using the Terminal will likely be preferred.