Integrate your bugfixes with nauralcodinglab/openscope_surround

[efharkin]

Hi Saskia, please consider merging this PR to bring your code up to date with what Kai Lun, Remi, and I are using. There are quite a few commits because this includes all of the work from Kai Lun and I since July 2020, but nothing before May 19, 2021 overlaps with your work. The commits from May 19 onwards clean up the repo but don't make any changes to how your code works, with three exceptions:

• I fixed a couple of scripts that were broken in your version due to merge conflicts (marked with <<<<<<<</>>>>>>>) by restoring your work.
• I ported a few scripts to python 3 using 2to3 which is an official python tool for migrating code; this mainly added brackets to print statements, but you can review the exact changes in commits that mention python in the commit message (eg 59b2ddf). Apparently Kai Lun had been running everything in python 3 already, so the affected code might be dead anyway.
• I moved files that were mainly meant to be imported into the oscopetools package; this won't affect you unless you don't have oscopetools installed. Run pip install -e path/to/openscope_surround (preceded by conda activate your_env_name if you use Anaconda, as described in the README) if you don't have it.

How to merge

1. Make a backup copy of your working copy of openscope_surround by right-clicking the openscope_surround folder and choosing "Compress openscope_surround"
2. Open a terminal and move to your openscope_surround folder by typing cd and then dragging the folder icon at the top of your Finder window into the terminal
3. Run the following command

git remote add efharkin https://github.com/efharkin/openscope_surround.git &&
git fetch efharkin &&
git checkout -b before_merge &&
git add -A &&
git commit -m "Current state of Saskia's working directory" &&
git diff --quiet HEAD b641ee640e08c034b77d842094d29b473301f5cf &&
echo "Working directory is identical to Emerson's copy. Ok to proceed with merge." ||
echo "Working directory has changed, don't proceed with merge. Send backup to Emerson and restore your copy from backup."

4. If the output is "Ok to proceed with merge", please run the following command to merge it into your working copy (the PR will be accepted automatically the next time you push)

git checkout HEAD^ &&
git merge --ff-only efharkin/cleanup &&
echo "Success!" ||
echo "Unexpected error. Please copy contents of terminal into TextEdit and send to Emerson."

6. git push
7. You can replace the before_merge branch with a tag (git tag -a before_merge before_merge && git branch -D before_merge) or just delete it.

Details about commits that touch your code

The commits from May 2021 are dedicated to merging scripts that were duplicated across analysis and oscopetools. I made sure that no work would be lost during the merge by carefully reviewing differences using git diff --no-index oscopetools/x.py analysis/x.py for each script. This was actually a pretty easy process because the files were mostly exact copies or close to it. I documented what I did in the commit messages, which you can read by clicking on them below, and in my PR on the nauralcodinglab page.

The commits from June 2021 are dedicated to merging work that you sent me over Slack on June 3. Basically I committed everything you sent me, cleaned it up a bit, and then merged the nauralcodinglab version. The cleanup basically consisted of removing more duplicated material and applying autoformatting. As with the May commits, I was careful not to lose any of your work.