# ICCS ReproHack March 2024 - Collaborative HackPad

###### tags: `Reprohack` `hackpad`

:::info
- :earth_africa: **LOCATION** [Online!](https://cam-ac-uk.zoom.us/j/86422585096?pwd=eGVPQU9CbEs1am1KQ04zbmw0MW90UT09)
- :calendar: **DATE** 12.03.2024
- :watch: **13:00 - 18:00 UTC**
- :arrow_forward: **Slides:** [https://hackmd.io/@MarionBWeinzierl/ByJhqYyjT](https://hackmd.io/@MarionBWeinzierl/ByJhqYyjT)
- :scroll: **Participant Guidelines:** https://reprohack.org/participant_guidelines
- :purple_heart: **Code of Conduct:** https://reprohack.org/code-of-conduct
- :left_speech_bubble: Chat to us on Slack: https://reprohack-autoinvite.herokuapp.com/
- :Bird: **Twitter/X:** #ReproHackHub @ReproHack
- **hackmd docs:** https://hackmd.io/s/features
:::

***

## Participants:
**Please sign in below:**
- ***Jane Doe (pronouns/ Affiliation / twitter / etc)***
- Marion Weinzierl (she/her / University of Cambridge, ICCS / [LinkedIn](https://www.linkedin.com/in/marion-weinzierl-547279191/), [Mastodon](https://mast.hpc.social/@MarionBWeinzierl))
- Paul Richmond (he/him / University of Cambridge, ICCS, [GitHub](https://github.com/mondus))
- Surbhi Goel (she/her / University of Cambridge, ICCS / [Github](https://github.com/surbhigoel77) / [LinkedIn](https://www.linkedin.com/in/surbhi-goel)
- Alejandro Coca-Castro (he/him / The Alan Turing Institute), [Github](https://github.com/acocac)
- Ellie Fisher (she/her / Centre for Environmental Data Analysis, STFC / [Github](https://github.com/efisher008) / [LinkedIn](https://www.linkedin.com/in/ellie-fisher-b3a6b7139?))
- Tom Meltzer (he/him / University of Cambridge, ICCS / [GitHub](https://github.com/tommelt), [Linkedin](https://www.linkedin.com/in/tommelt/))
- Karan Jakhar (he/him / Rice University / University of Chicago / [Github](https://github.com/jakharkaran) / [Linkedin](https://www.linkedin.com/in/karan-jakhar-a95435106/))
- Jack Atkinson [Website](https://jackatkinson.net/), [GitHub](https://github.com/jatkinson1000), [GitLab](https://gitlab.com/jatkinson1000), [Mastodon](https://fosstodon.org/@jatkinson1000)
- Tianzhang Cai (he/him / University of Cambridge ICCS / [Github](https://github.com/jatkinson1000))
- Romain Caneill (he/him / IGE, Grenoble, France), [website](https://romaincaneill.fr), [Mastodon](https://fediscience.org/@rcaneill), [GitHub](https://github.com/rcaneill), [GitLab](https://gitlab.com/rcaneill)
- Joe Wallwork (he/him, University of Cambridge, ICCS, [GitHub](https://github.com/jwallwork23), [GitLab](https://gitlab.com/jwallwork23))
- Dominic Orchard (he/him, University of Cambridge / University of Kent, [website](http://dorchard.github.io))

**Photo Consent - please write your name here if you do NOT agree to be on photos used on social media, our newsletter or other promotional material relating to the ReproHack event:**
- ***Jane Doe***
- Romain Caneill: I do not agree to be on twitter, facebook, or linkedin. Other websites, mastodon, etc are ok
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## Agenda

<!-- The following agenda is for a remote event from 10am to 5pm which includes 2 talks. Customise as required -->

| Time (UTC) | Event |
|--- |--- |
| 13:00 | Welcome and Orientation |
| 13:10 | Ice breaker session |
| 13:40 | **Talk: Alejandro Coca-Castro: The Turing Way** |
| 14:00 | Tips and Tricks for Reproducing and Reviewing. |
| 14:10 | Select papers, chat and coffee |
| 14:30 | Round I of ReproHacking (break-out rooms) |
| 15:30 | Re-group and sharing of experiences |
| 15:50 | Coffee break | |
| 16:15 | Round II of ReproHacking (break-out rooms) - Complete Feedback Form |
| 17:15 | Re-group and sharing of experiences |
| 17:45 | Feedback and Closing |
| 18:00 | End |

---

## Instructions for the day
### **Team formation**

We’ll start with a brief review of the **available papers** and then form into teams. Feel free to work on your own if you prefer but we highly recommend you discuss your experiences with fellow participants as you work.

### **Select and register a paper**

#### Climate Papers:

1. [Spatial modelling of rice yield losses in Tanzania due to bacterial leaf blight and leaf blast in a changing climate](https://www.reprohack.org/paper/1/)
1. [Climate change may have limited effect on global risk of potato late blight](https://www.reprohack.org/paper/2/)
1. [Statistical analysis of coverage error in simple global temperature estimators](https://www.reprohack.org/paper/31/)
1. [Optimizing the Use of Carbonate Standards to Minimize Uncertainties in Clumped Isotope Data](https://www.reprohack.org/paper/52/)
1. [Planning Support Systems for Long-Term Climate Resilience: A Critical Review](https://www.reprohack.org/paper/85/)
1. [The Polar Transition from Alpha to Beta Regions Set by a Surface Buoyancy Flux Inversion](https://www.reprohack.org/paper/87/)
1. [Revisiting the zonally asymmetric extratropical circulation of the Southern Hemisphere spring using complex empirical orthogonal functions](https://www.reprohack.org/paper/88/)
1. [Southern Ocean deep mixing band emerges from a competition between winter buoyancy loss and upper stratification strength](https://www.reprohack.org/paper/89/)

#### What to do

- Add your details in the **participants** section of the **hackpad** so we have a complete list of participants (e.g name, affiliation, social links, pronouns etc).
- In your teams, (or individually if you prefer) **decide which paper** you wish to work on.
- **[Create user accounts](https://www.reprohack.org/accounts/signup/)** on the Hub for all reviewers that want to be associated with the review.
- **Register your team and paper** by logging the title of the selected paper and the name(s) of the reviewer(s) below.

### **Work on your paper!**

Follow any instructions/documentation associated with the papers and try and reproduce the work. As you work through your paper, keep in mind the main points on which feedback to the authors will provided, **Access**, **Reproducibility**, **Documentation** and **Reusability** (see our [participant guidelines](https://www.reprohack.org/participant_guidelines) for more information). It might help to have a look at the **[Review form](https://www.reprohack.org/review/new)** before you begin and keep notes during your review. Feel free to use the event hackpad to record general findings you wish to share with the group.

We’ll **come together during the day** to discuss progress and troubleshoot any sticking points.

Should you finish reproducing your paper quickly, feel free to explore the work more deeply. For example, you could try and run additional analyses, create new plots or even combine materials with your own or other open materials available on the web!

Should you produce any additional materials relating to your reproduction during the session (e.g. a markdown report, jupyter notebook, issue or pull requests in authors repository), feel free to **share it publicly** and **add any links to such materials to the hackpad**.

### **Complete your review with feedback for the authors**

The most important part of the day is recording our experiences as feedback to the authors. Please make sure to complete a **[Review feedback form](https://www.reprohack.org/review/new)** for the paper you've selected, ideally, by the end of the day. Please also remember to be kind and constructive. Reproducibilty is hard and all authors submitting their papers have been incredibly brave. Feel free to browse any public feedback submissions to get inspiration.

### **Feedback to the group on your experiences**

You can use the hackpad to take notes and summarise your experiences.

-----

# Collaborative Notes

## Paper Registration

_Use the following template and register your review below._

### **Paper:** <Title of the paper reproduced>
**Reviewers:** Reviewer 1, Reviewer 2 etc.
***

<!-- Please register your paper in the space below using the template provided -->

***

**Paper:** The Polar Transition from Alpha to Beta Regions Set by a Surface Buoyancy Flux Inversion
**Reviewers:** Ellie Fisher, Paul Richmond, Surbhi Goel, Tianzhang Cai, Tom Meltzer

#### Notes:
Hardware tested: Windows 11 enterprise
* tried using anaconda prompt
* switched to Mobaxterm

* no explicit mention of supported OS's or recommend terminals
* We tried windows following build instructions but had to change `pip3 install --user pipenv` to `pip3 install pipenv`
* when running `pipenv install` we got error `python 3.8 was not found` -- `pipfile` forces version `3.8` but we could potentially use newer versions. Perhaps they could add `>=3.8`
* repo requires installing `apptainer` which is not accessible on a mac system (would require a virtual machine), the only option remains is to install the container specified by the primary author as the secondary option (author has put a word of caution)
* extraction of output data has terminal command but could use gui instead?
* Failed to build `datrie`
* error message: ```error: Microsoft Visual C++ 14.0 or greater is required. Get it with "Microsoft C++ Build Tools": https://visualstudio.microsoft.com/visual-cpp-build-tools/```
* we need to install visual cpp build tools
* :green_heart: they have a `Pipfile` and `Pipfile.lock` for reproducibility
* :green_heart: apptainer image
* :green_heart: bash script for downloading data from zenodo
* `download_and_extract_data_from_zenodo.sh` uses `data2/raw` but `README.md` suggests using `data`
* (Note from author) this bug should be corrected in the last version of the repository
***

**Paper:** Southern Ocean Deep Mixing Band Emerges From A Competition Between Winter Buoyancy Loss And Upper Stratification Strength
**Reviewers:** Jack Atkinson, Karan Jakhar, Joe Wallwork, Dominic Orchard

* Machines used by the group:
* Dominic: arm 64 (Mac)
* Karan: arm 64 (Mac)
* Joe: intel 64 (Ubuntu 22.04 LTS)
* Jack: arm 64 (Mac)?

* Joe wasn't able to install pyproj, so used alternative installation approach 1: install apptainer using a PPA.
* With this, figures 1, 2, 5-10 could be reproduced, all identical 'in the eyeball norm' (except figure 10, whose legend was differently positioned but the plot itself was the same).
* Figures 3, 4, 11, A1 and B1 couldn't be reproduced, but this was because of lack of time for downloading and lack of access to two of the data sets.

* Karan failed to install depedencies in his system and reproduce the results.
* The primary challenge was installing poetry. Poetry uses a depreciated version of pyproj - which in turn needs specific version of python installed. Could not manage to get these working.
***

**Paper:** Revisiting the zonally asymmetric extratropical circulation of the Southern Hemisphere spring using complex empirical orthogonal functions
**Reviewers:** Alejandro Coca-Castro, Romain Caneill

Docker

- Target (paper) file: [shceof.Rmd](https://github.com/eliocamp/shceof/blob/2eeadfbe67e4fdb9d6fe47f7d4871e89da1f6f0c/analysis/paper/shceof.Rmd)
- Installation via docker:
- Launch a RStudio session
- Missing instructions how to set the directory
- setwd('shceof')
- remotes::install_local(), option 3 (None)
- README suggests using Knit it to compile de PDF
- Knit route
- Missing R packages: ` Installing R Packages: 'bookdown', 'ggnewscale', 'ggpattern', 'ggperiodic', 'ggrepel', 'ppcor', 'shadowtext', 'widyr'`
- Missing R package: `tagger`
- Not available in R 4.1.3
- devtools::install_github("eliocamp/tagger") > requires devtools
- Download data from Zenodo (script for this??)
- Manually create folder raw_data in `analysis/data`

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## Questions for Speaker(s)
<!-- Please add any questions for our speaker below -->
- https://hidden-ref.org/
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## Discussion topics

<!-- Feel free to use this space to add topics for discussion and make notes on those discussions. You can remove if you don't plan to have any guided discussion sessions -->
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***

## Regroup notes
<!-- Any other notes you'd like to add. -->

### Group 8
- Going through installation
- trouble with installation and getting data
- group 8 to chat with author
- great README
- good troubleshooting
- some difficulty with `pyproj`
- is it related to mac M2? what platforms / hardware?
- using apptainer gets further
### Group 7
- using R for the first time
- either install R or use docker image
- installing deps
- some comments for installation process
- path issues? related to docker?
- still trying to run analysis
- docker image only contains Rstudio but without deps
- RMarkdown file

### Group 6
- trying venv instructions
- windows OS
- some windows specific problems
- dependency conflicts (python 3.8 is forced but we had 3.11)
- create venv and downloaded data, but we havent installed the program yet
- we need Microsoft cpp build tools
***

## Feedback (to organisers)

### One thing you enjoyed:

- Problem solving as a group.
- Opportunity to use new packages and command line tools.
- Troubleshooting tips from paper authors and ICCS "admins".
- As participant: meet you all
- As author: get feedback and see what points are unclear in the doc / instructions

### One thing that could be improved:

- Event could be longer, i.e. one full day, to hopefully permit some groups to move past dependency issues and get to reproducing something!
- Follow up on previous comment: maybe split the event into 2 days (e.g. 2 hours each day) to get the time to download the data
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