merged

.github/workflows/jekyll-gh-pages.yml

@@ -42,10 +42,10 @@ jobs:
       - name: Check html
         uses: chabad360/htmlproofer@master
         with:
-          directory: "./_site"
           # The directory to scan
-          arguments: --no-enforce-https --allow_hash_href --ignore-missing-alt --assume_extension - ./_site --ignore-urls '/http:\/\/www.hluce.org/' --ignore-files '/.+\/assets\/.+/'
-          # The arguments to pass to HTMLProofer
+          directory: "./_site"
+          # The arguments to pass to HTMLProofer. swap-urls is because of this issue: https://github.com/gjtorikian/html-proofer/issues/170 and basically turns all absolute links from our site that point to our site into relative
+          arguments: --no-enforce-https --allow_hash_href --ignore-missing-alt --assume_extension - ./_site --ignore-files '/.+\/assets\/.+/'  --swap-urls "https?\:\/\/(localhost\:4000|neurorse\.flatironinstitute\.org):"
       - name: Upload artifact
         uses: actions/upload-pages-artifact@v2
 

Gemfile

@@ -33,4 +33,6 @@ gem "webrick"
 gem "logger"
 gem "csv"
 gem "ostruct"
-gem "base64"
+gem "base64"
+
+gem "kramdown-parser-gfm"

README.md

@@ -6,15 +6,19 @@ Website for Flatiron CCN's NeuroRSE group
 
 - The "Posts" section contains all the files from `site/_posts` whose names must
   be of the form `YYYY-MM-DD-title.md` in order to be included in the built site.
+- If you write a post that you do not want rendered yet, save it in the
+  `site/_drafts` folder. Then, to render it when building locally, add `--drafts` to
+  the `jekyll serve` command below to see it. When you are ready to include it
+  on the site, move it to the `site/_posts` folder.
 
 ## Building locally
 
 - Install Jekyll's [requirements](https://jekyllrb.com/docs/installation/)
 - From the root directory, run `gem install jekyll bundler`, which will install
   jekyll and the other required packages.
 - Run `bundle install` to install all the missing gems listed in the `Gemfile`.
-- From the root directory, run `bundle exec jekyll serve -s ./site -d ./_site
-  --livereload`, then open `localhost:4000` in your browser
+- From the root directory, run `bundle exec jekyll serve --livereload`, then
+  open `localhost:4000` in your browser
 
 ## Helpful resources
 

_config.yml

@@ -22,7 +22,7 @@ source: site
 title: NeuroRSE
 description: >- # this means to ignore newlines until "baseurl:"
 baseurl: ""
-url: "https://neurorse.flatironinstitute.org/" # the base hostname & protocol for your site, e.g. http://example.com
+url: "https://neurorse.flatironinstitute.org" # the base hostname & protocol for your site, e.g. http://example.com
 
 # Build settings
 plugins:

site/_people/broderick.md

@@ -5,4 +5,4 @@ external_url: https://wfbroderick.com
 picture: /assets/billy.jpg
 job: Associate Research Scientist, CCN
 ---
-Billy Broderick received his Ph.D. from NYU's Center for Neural Science, where he was advised by Eero Simoncelli and Jon Winawer. During his Ph.D., he studied how vision changes across the visual field using fMRI, psychophysics, and computational models. Before that, he worked as a research assistant at Duke University, spent a year at South China Normal University in Guangzhou, China as a [Luce Scholar](http://www.hluce.org/lsprogram.aspx), and got his B.A. in neuroscience and mathematics at Oberlin College
+Billy Broderick received his Ph.D. from NYU's Center for Neural Science, where he was advised by Eero Simoncelli and Jon Winawer. During his Ph.D., he studied how vision changes across the visual field using fMRI, psychophysics, and computational models. Before that, he worked as a research assistant at Duke University, spent a year at South China Normal University in Guangzhou, China as a [Luce Scholar](https://lucescholars.org/), and got his B.A. in neuroscience and mathematics at Oberlin College

site/_posts/2023-11-17-summer-2024-internship.md

@@ -1,6 +1,6 @@
 ---
 layout: post
-title: "Neuroscience Software Summer Internship"
+title: "2024 Neuroscience Software Summer Internship"
 categories: events
 ---
 

site/_posts/2025-01-06-summer-2025-internship.md

@@ -0,0 +1,52 @@
+---
+layout: post
+title: "2025 Neuroscience Software Summer Internship"
+categories: events
+---
+
+Come work with us on an open source neuroscience software package in Manhattan for a summer! The  [NeuroRSE team](https://neurorse.flatironinstitute.org/) at the Flatiron Institute Center for Computational Neuroscience is looking for paid interns for Summer 2025. Interns will spend the summer living and working in New York City. 
+
+[Apply here by Jan 17!](https://apply.interfolio.com/159680)
+
+## What would you work on?
+The specific project you will work on will be determined in close consultation with your mentor, a member of the NeuroRSE team. This process will involve finding a good fit between your interests/background and the goals set out in the roadmap for the package you are working on. You can check out the GitHub repositories for each package below to get a sense of the range of possibilities. It is okay if you are not sure exactly what you want to work on before you start; we do not expect applicants to have experience with the packages before applying. 
+
+## Software packages
+The three software packages that are currently in development at CCN are: 
+
+![Nemos](/assets/nemos_logo.svg)
+
+[nemos](https://github.com/flatironinstitute/nemos) is a statistical modeling framework for neurophysiology data. 
+
+![plenoptic](/assets/plenoptic_logo.svg)
+
+[plenoptic](https://github.com/LabForComputationalVision/plenoptic) is a library for model-based visual and auditory stimulus synthesis. 
+
+![pynapple](/assets/pynapple_logo.svg) 
+{:style="width:50%"}
+
+[Pynapple](https://github.com/pynapple-org/pynapple) (Python Neural Analysis Package) is a library for neurophysiological time series data analysis and visualization. 
+
+## What types of background are we looking for?
+We are looking for interns who have experience in at least one of: 
+
+- Using Python packages for scientific computing (e.g., matplotlib, numpy, scikit-learn, etc.).
+- Open-source software development (e.g., git, pull request workflow, writing documentation, etc.).
+- The relevant neuroscience domain (e.g., calcium image analysis, fitting models to neuroscience data) with *some* programming background.
+
+We *do not* expect you to already be an expert in both neuroscience and software development! If the internship sounds exciting to you, and you are worried about your qualifications, we recommend that you apply. One of the goals of the internship is to help people learn to contribute to open-source projects. We don't expect you to already be an expert. 
+
+## Anything else I should know?
+- The application to work with the NeuroRSE team will be part of the broader CCN intern application. If you specifically want to work with us, **please mention** that in your application, as well as one or two packages from the above list that you would be interested in working on, and why.
+- If you have a GitHub, GitLab, or similar profile, please include a link to the profile in your application. If you have a specific project or two that is particularly relevant, please include a link to those as well.
+
+## Fine print
+Elibigle to current students at Bachelor's level or above. Applications will be accepted starting December 2, 2024. You will be paid $20 - $25 per hour, depending on whether you are an undergraduate or graduate student. Travel, housing, and meals will be provided for all interns. We especially encourage applications from underrepresented populations in the open-source community. 
+
+## To apply
+To submit an application, please visit [the Simons website](https://apply.interfolio.com/159680). Deadline for application is **January 17, 2025**. Applications are structured so that you need to put a PI at CCN as primary group and NeuroRSE as secondary group: the written part of the application will clarify your intentions to work on software development. While it is not essential, we recommend that if you are most interested in working on Nemos that you put Alex Williams as the primary group; those interested in Plenoptic or Pynapple should list Eero Simoncelli. 
+
+## Who are we?
+
+{% assign members = "balzani,broderick,venditto,viejo" | split: "," %}
+{% include people_list.html people=members %}