fix: Fix paths and add codespaces instructions

README.md

@@ -10,7 +10,44 @@ There are two important directories:
 The configuration for GNATSS can be found in [`config.yaml`](./config.yaml) file.
 This file will be read automatically during a GNATSS run.
 
-## Setting up for the benchmark
+## Running on the Cloud (Github Codespaces)
+
+This repository is configured to work with Github Codespaces.
+To use Github Codespaces to run the benchmark, simply click on the button below:
+
+[![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://codespaces.new/seafloor-geodesy/gnatss-fortran-benchmark/tree/main)
+
+You'll be directed to a page that asks for various configurations for codespace.
+You can leave the default values and click on "Create Codespace".
+Github will then build the codespace for you, which may take a few minutes ☕.
+
+Once your codespace is launched, follow the instructions below:
+
+- [Visual Studio Code](https://code.visualstudio.com/) Interface will open up within your browser.
+- On the left hand side, you'll see a file explorer. Navigate to a file called `main.ipynb` and open it.
+- Once the notebook opens up, you need to select the kernel to run the notebook.
+  - Click on the "Select Kernel" button on the top right corner of the notebook.
+  - This will open up a drop down menu in the top center of the page.
+    Select "Python Environments...", and then
+    select "notebook (Python 3.10.13)" conda environment from the list.
+  - You'll know that the kernel is selected when you see
+    "notebook (Python 3.10.13)" in the top right corner of the notebook.
+- Now you can run the notebook by clicking on the "Run All" button on the top left corner of the notebook.
+  Or you can choose to run the cells one by one to see what's happening in each step.
+
+### What is Github Codespaces?
+
+A codespace is "a development environment that's hosted in the cloud".
+This particular codespace uses the [`environment.yml`](conda/environment.yml)
+to create a conda environment with all the dependencies needed to run the benchmark.
+
+GitHub currently gives every user [120 vCPU hours per month for free](https://docs.github.com/en/billing/managing-billing-for-github-codespaces/about-billing-for-github-codespaces#monthly-included-storage-and-core-hours-for-personal-accounts), beyond that you must pay. **So be sure to explicitly stop or shut down your codespace when you are done by going to this page (https://github.com/codespaces).**
+
+## Running Locally
+
+Below are instructions for running the benchmark locally in your own machine.
+
+### Setting up for the benchmark
 
 To run the benchmark, you will need to have GNATSS installed.
 We recommend using `conda` to install GNATSS for quick setup.
@@ -23,7 +60,7 @@ conda env create -f conda/environment.yml
 conda activate gnatss-benchmark
 ```
 
-## Running the benchmark
+### Running the benchmark
 
 Once the environment is setup, you can run the benchmark by spinning up
 a Jupyter lab server.

config.yaml

@@ -35,13 +35,13 @@ solver:
   harmonic_mean_start_depth: -4.0
   input_files:
     sound_speed:
-      path: ~/Repos/SSEC/gnatss-fortran-benchmark/data/NDP1_Ch_Mi_2022_fit
+      path: ./data/NDP1_Ch_Mi_2022_fit
     travel_times: # Glob path to pxp_tt
-      path: ~/Repos/SSEC/gnatss-fortran-benchmark/data/pxp_tt
+      path: ./data/pxp_tt
     gps_solution:  # Glob path to POS_FREED_TRANS_TWTT
-      path: ~/Repos/SSEC/gnatss-fortran-benchmark/data/POS_FREED_TRANS_TWTT
+      path: ./data/POS_FREED_TRANS_TWTT
     deletions: # Path to deletns.dat deletions file used by Chadwell code as well
-      path: ~/Repos/SSEC/gnatss-fortran-benchmark/data/deletns.dat
+      path: ./data/deletns.dat
 
 
 output: # Directory path to output directory