From 2a9483e52171404fe96d9818d97837be3baa2c11 Mon Sep 17 00:00:00 2001 From: bendichter Date: Thu, 7 Sep 2023 16:49:36 +0200 Subject: [PATCH 1/5] add submission instructions to README.md --- README.md | 29 +++++++++++++++++++++++++++-- 1 file changed, 27 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index baf1df7..cfe9b1e 100644 --- a/README.md +++ b/README.md @@ -2,10 +2,35 @@ This repository contains example notebooks associated with datasets, conference tools, or more generally notebooks that illustrate the use of data on DANDI. This repository is cloned into the [DANDI JupyterHub environment](https://hub.dandiarchive.org). Please note that you will need to visit https://dandiarchive.org and sign in once to get access to the JupyterHub. -To add a new notebook, please send a PR. For specific dandiset related analysis, place your notebooks or other code into: +## Submission instructions +To add new notebooks, please send a Pull Request. Submissions should use the following file structure: -`///` +``` +example-notebooks +└── / + └── / + └── / + ├── environment.yml + ├── README.md + ├── .ipynb + ├── .ipynb + ├── ... + └── .ipynb +``` For example, [000055/bruntonlab/peterson21](https://github.com/dandi/example-notebooks/tree/9b1fb88667595a3abcdefda46bbe08e538dcbf0f/000055/BruntonLab/peterson21) +The `README.md` file should explain the goal of the submission, provide links to relevant scientific publications, and explain the purpose of each notebook file. + +The `environment.yml` file should define the dependencies of the environment required for the notebooks to be executed. `environment.yml` files are like `requirements.txt` files, but are designed to work with `conda`. To create this file, follow these steps: + +1. Create a new environment: `conda create -n -python ` +2. Switch into that environment: `conda activate ` +3. Use `conda install ` and `pip install ` to install the necessary dependencies until the notebook runs through successfully. +4. Confirm that all the notebooks can be run without error. +5. Export the environment: `conda env export > environment.yml`. + +See detailed instructions for creating a `environment.yml` file [here](https://conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html#sharing-an-environment). + + Feel free to reach out on the [DANDI helpdesk](https://github.com/dandi/helpdesk/issues/new/choose) with any questions. From e496cafec3d18fb4ab3052182c3064280beafa45 Mon Sep 17 00:00:00 2001 From: Ben Dichter Date: Thu, 7 Sep 2023 12:19:07 -0400 Subject: [PATCH 2/5] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index cfe9b1e..8fd12d9 100644 --- a/README.md +++ b/README.md @@ -6,7 +6,7 @@ This repository contains example notebooks associated with datasets, conference To add new notebooks, please send a Pull Request. Submissions should use the following file structure: ``` -example-notebooks +example-notebooks/ └── / └── / └── / From 5261303f152029468077fbf222d6c2ead4aa0b9e Mon Sep 17 00:00:00 2001 From: Ben Dichter Date: Thu, 7 Sep 2023 12:19:43 -0400 Subject: [PATCH 3/5] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 8fd12d9..d7e6fd5 100644 --- a/README.md +++ b/README.md @@ -26,7 +26,7 @@ The `environment.yml` file should define the dependencies of the environment req 1. Create a new environment: `conda create -n -python ` 2. Switch into that environment: `conda activate ` -3. Use `conda install ` and `pip install ` to install the necessary dependencies until the notebook runs through successfully. +3. Use `conda install ` and `pip install ` to install the necessary dependencies until the notebook(s) run through successfully. 4. Confirm that all the notebooks can be run without error. 5. Export the environment: `conda env export > environment.yml`. From 1d1e650a1b963e7d3feab97d4767e53cb12503b9 Mon Sep 17 00:00:00 2001 From: Ben Dichter Date: Tue, 12 Sep 2023 15:51:56 -0400 Subject: [PATCH 4/5] Update README.md Co-authored-by: Yaroslav Halchenko --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index d7e6fd5..f6c7166 100644 --- a/README.md +++ b/README.md @@ -18,7 +18,7 @@ example-notebooks/ └── .ipynb ``` -For example, [000055/bruntonlab/peterson21](https://github.com/dandi/example-notebooks/tree/9b1fb88667595a3abcdefda46bbe08e538dcbf0f/000055/BruntonLab/peterson21) +For example, [000055/bruntonlab/peterson21](./000055/BruntonLab/peterson21) The `README.md` file should explain the goal of the submission, provide links to relevant scientific publications, and explain the purpose of each notebook file. From ff8b74a4ed60ed987dd49abfce9088316776856c Mon Sep 17 00:00:00 2001 From: Ben Dichter Date: Tue, 12 Sep 2023 15:52:06 -0400 Subject: [PATCH 5/5] Update README.md Co-authored-by: Yaroslav Halchenko --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index f6c7166..606e8c0 100644 --- a/README.md +++ b/README.md @@ -30,7 +30,7 @@ The `environment.yml` file should define the dependencies of the environment req 4. Confirm that all the notebooks can be run without error. 5. Export the environment: `conda env export > environment.yml`. -See detailed instructions for creating a `environment.yml` file [here](https://conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html#sharing-an-environment). +See [detailed instructions](https://conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html#sharing-an-environment) for creating a `environment.yml` file. Feel free to reach out on the [DANDI helpdesk](https://github.com/dandi/helpdesk/issues/new/choose) with any questions.