First validation

Make sure you have followed the installation instructions. You will need Git, Python and the various Python libraries installed.

cd $HOME/Documents

Warning If you get The system cannot find the path specified, and you are on Windows, make sure you are running a Powershell shell, not the much older Windows cmd shell. If you get this message, and you are trying things on out a JupyterHub or other Linux system, check that the Documents directory exists in your home directory, and, if not, create it with mkdir $HOME/Documents.

Make a new directory to store your work, if you have not already done this in the installation instructions.

mkdir nipraxis-work

Change your shell to that directory:

cd nipraxis-work

Next go to this page : https://github.com/nipraxis/first-validation

Click on the "Fork" button on the mid-top-right.

Accept the defaults and click on "Create fork"

You will find yourself at the page for your new Fork. In my case that is https://github.com/matthew-brett/first-validation but the address will have your username in it, rather than matthew-brett.

Copy the URL.

Clone the repository from the command line, by typing git clone at the terminal and then copy-pasting the URL. For example, for me, that would be git clone https://github.com/matthew-brett/first-validation but you need to make sure you clone your own fork, with your own URL.

# Your git clone command here:
git clone https://github.com/your-github-username/first-validation

Next:

cd first-validation
# Show the files
ls

We are going to be working on some fixes, to be proposed to the upstream repository at https://github.com/nipraxis/first-validation. The upstream repository is the repository from which you created your fork above.

Whenever we work on a new set of changes we make a new branch.

We do that like this:

# Create the branch (bookmark).
git branch fix-validation

Warning Before you run the next command, bear in mind that Git displays information using a pager. This is a way of outputting text that takes into account there may be multiple pages. When you are in the pager, you can press the down and up arrow (cursor) keys to move around and press q to quit.

# Show the branches verbosely (-v).  Notice the asterisk on "main".
git branch -v

# Checkout the branch ready for work.
git checkout fix-validation

# Show the branches verbosely (-v).  Notice the asterisk on "fix-validation".
git branch -v

Now you are ready to do the work. First get the images you need.

python3 get_data.py

You should see something like this:

Saving files to "data" directory
Fetched mni_icbm152_t1_tal_nlin_asym_09a_masked_222.nii to /Users/mb312/Library/Caches/nipraxis/0.4/mni_icbm152_t1_tal_nlin_asym_09a_masked_222.nii
Copied /Users/mb312/Library/Caches/nipraxis/0.4/mni_icbm152_t1_tal_nlin_asym_09a_masked_222.nii to data/mni_icbm152_t1_tal_nlin_asym_09a_masked_222.nii
Fetched ds114_sub009_highres_brain_222.nii to /Users/mb312/Library/Caches/nipraxis/0.4/ds114_sub009_highres_brain_222.nii
Copied /Users/mb312/Library/Caches/nipraxis/0.4/ds114_sub009_highres_brain_222.nii to data/ds114_sub009_highres_brain_222.nii
Fetched 24719.f3_beh_CHYM.csv to /Users/mb312/Library/Caches/nipraxis/0.4/24719.f3_beh_CHYM.csv
Copied /Users/mb312/Library/Caches/nipraxis/0.4/24719.f3_beh_CHYM.csv to data/24719.f3_beh_CHYM.csv
Contents of "data" subdirectory:
   data/mni_icbm152_t1_tal_nlin_asym_09a_masked_222.nii
   data/24719.f3_beh_CHYM.csv
   data/ds114_sub009_highres_brain_222.nii

You will see a different cache directory in the printout above. My cache directory was /Users/mb312/Library/Caches/nipraxis/0.4/ but your directory will be specific to you, and the current version of the nipraxis module.

If there are any errors, let us know.

Check the files are in the data sub-directory with:

ls data

You will see an extra file in that directory, called data_hashes.txt.

Next run the as-yet-unfixed data validation script:

python3 first_validation.py

Notice the output. Notice too that you get an AssertionError. This is the error you are aiming to fix.

Open the script in a text editor. At a pinch you can open in Textedit (Mac) or Wordpad (Windows). On Unix you can use the Nano editor (use nano at the command line). At a pinch you can even use the Jupyter Notebook itself, opening the first_validation.py file from the notebook interface.

Look at the script. Edit the script to fix the assertion error. Run python first_validation.py again. You should see another, new AssertionError. If you have time, try fixing that error.

When you are ready, or you think you are going to run out of time, save your changes, and check that Git can see you have made changes with:

git status

You should first_validation.py in red, with changes that have not been staged ready for commit.

Now, put the changes into the Git staging area:

git add first_validation.py

Show the changes are now in the staging area with:

# Notice the filename should now be in green.
git status

Make a commit. For now (and only for now) use the -m flag to add a commit message:

git commit -m "Fixes to the validation script"

Finally, push the changes up to your fork:

git push origin fix-validation --set-upstream

You will see a message at the console telling you the link to go to, to make a pull request. In my case that link was "https://github.com/matthew-brett/first-validation/pull/new/fix-validation", but your link will be different, because it will contain your own Github user name.

Go to that URL in your browser.

Type something about your changes into the "Description".

Click on "Create pull request".

You should see a new page with your pull request.