http:// → https://

README.md

@@ -1,7 +1,7 @@
 ## About
 nipy.org is built with a custom theme created for Jekyll.
 
-- [site](http://www.nipy.org)
+- [site](https://www.nipy.org)
 - preview changes with [continuous integration](https://circleci.com/gh/nipy/nipy.github.com/tree/master)
 
 [![Circle CI](https://circleci.com/gh/nipy/nipy.github.com.svg?style=svg)](https://circleci.com/gh/nipy/nipy.github.com)
@@ -10,12 +10,12 @@ nipy.org is built with a custom theme created for Jekyll.
 ###### Install Jekyll and RubyGems
 
 Here are [complete instructions](https://help.github.com/articles/using-jekyll-with-pages/#installing-jekyll)
-Refer to the [Jekyll documentation](http://jekyllrb.com) for further help.
+Refer to the [Jekyll documentation](https://jekyllrb.com) for further help.
 
 
 #### Quick Start
 
-To see more detailed instructions for adding a new project ("data") please refer to the [Contribute section](http://nipy.org/contribute.html) on the site.
+To see more detailed instructions for adding a new project ("data") please refer to the [Contribute section](https://nipy.org/contribute.html) on the site.
 
 ###### Add a new project
 

_data/contribute.yml

@@ -5,22 +5,22 @@
       questions:
         - tag: "add-a-package"
           question: "How do I add a package?"
-          answer: "<h3>Venue</h3><p>Contributors are welcome to propose and discuss their ideas to develop Python packages for neuroimaging in the <a href='https://github.com/orgs/nipy/discussions' target='_blank'>Nipy GitHub Discussionss</a>.</p><h3>Infrastructure and workflow</h3><p>Let's first look at the infrastructure and workflow of the site</p><p><ul class='list-group'><li class='list-group-item'><strong>Github</strong>:The site is a repo under the nipy organization on<a href='https://github.com/nipy/nipy.github.com' target='_blank'> github</a>.This means that contribution to it goes by way of forking the repo and doing a pull request (PR).</li><li class='list-group-item'><strong>Github pages</strong>: We also use hosting on github pages, which only means that the site lives on a branch called gh-pages that gets rendered at nipy.github.io.</li><li class='list-group-item'><strong>CI</strong>: We use continuous integration to preview all PRs by way of viewing <a href='https://circle-artifacts.com/gh/vsoch/nipy-jekyll/63/artifacts/0/home/ubuntu/nipy-jekyll/_site/index.html' target='_blank'>artifacts</a>.</li></ul></p><h3>Your Workflow</h3><p>You should do the following:</p><ul><li>Fork the nipy jekyll repo</li><li>Make your changes</li><li>Submit a PR</li><li>We will review the PR, and push to master and ghpages branches.</li></ul></p><h3>Details</h3><ol><li>Add your package info to the data file, in the same format. This will have it rendered automatically in the navigation, and added to the animated brain on all pages.</li><li>Add a base page for your package in the base directory of the site repo. It should be named [packagetag].html where [packagetag] corresponds with the tag variable in the data file. We have a page template for packages, and the easiest thing to do is copy another package's page to start.</li><li>Static site content can be put in the js,css,img folders in the base directory. Any static content can be linked to like '{{ '/img/myimage.png' | prepend: site.baseurl }}'. Keep it organized.</li><li>To contribute an svg image, put it in the '_includes/svg' folder and include like {% include svg/mysvg.svg %}</li><li>Subpages should be contributed as posts to <a href='http://neuroimaging.tumblr.com'>blog content</a>.</li></ol>"
+          answer: "<h3>Venue</h3><p>Contributors are welcome to propose and discuss their ideas to develop Python packages for neuroimaging in the <a href='https://github.com/orgs/nipy/discussions' target='_blank'>Nipy GitHub Discussionss</a>.</p><h3>Infrastructure and workflow</h3><p>Let's first look at the infrastructure and workflow of the site</p><p><ul class='list-group'><li class='list-group-item'><strong>Github</strong>:The site is a repo under the nipy organization on<a href='https://github.com/nipy/nipy.github.com' target='_blank'> github</a>.This means that contribution to it goes by way of forking the repo and doing a pull request (PR).</li><li class='list-group-item'><strong>Github pages</strong>: We also use hosting on github pages, which only means that the site lives on a branch called gh-pages that gets rendered at nipy.github.io.</li><li class='list-group-item'><strong>CI</strong>: We use continuous integration to preview all PRs by way of viewing <a href='https://circle-artifacts.com/gh/vsoch/nipy-jekyll/63/artifacts/0/home/ubuntu/nipy-jekyll/_site/index.html' target='_blank'>artifacts</a>.</li></ul></p><h3>Your Workflow</h3><p>You should do the following:</p><ul><li>Fork the nipy jekyll repo</li><li>Make your changes</li><li>Submit a PR</li><li>We will review the PR, and push to master and ghpages branches.</li></ul></p><h3>Details</h3><ol><li>Add your package info to the data file, in the same format. This will have it rendered automatically in the navigation, and added to the animated brain on all pages.</li><li>Add a base page for your package in the base directory of the site repo. It should be named [packagetag].html where [packagetag] corresponds with the tag variable in the data file. We have a page template for packages, and the easiest thing to do is copy another package's page to start.</li><li>Static site content can be put in the js,css,img folders in the base directory. Any static content can be linked to like '{{ '/img/myimage.png' | prepend: site.baseurl }}'. Keep it organized.</li><li>To contribute an svg image, put it in the '_includes/svg' folder and include like {% include svg/mysvg.svg %}</li><li>Subpages should be contributed as posts to <a href='https://neuroimaging.tumblr.com'>blog content</a>.</li></ol>"
         - tag: "write-a-post"
           question: "How do I write a post?"
-          answer: "<h3>Quick and Easy</h3><p>The fastest way to contribute is to <a href='http://neuroimaging.tumblr.com/submit'> submit </a> an idea, link, or video right away. If you have questions, to maximize their visibility, you can ask them on <a href='https://neurostars.org/' target='_blank'>Neurostars</a>, or you can reach us <a href='mailto:[email protected]'>by email</a>. These resources should be preferred over using the <a href='http://neuroimaging.tumblr.com/ask'>neuroimaging tumblr ask space</a>. Your submission will be reviewed and immediately available on the site and for social media integration.</p><h3>Contribute Regularly</h3><p>If you like writing tutorials, or regularly write about your research, we encourage you to <a href='https://www.tumblr.com/docs/en/posting' target='_blank'> read more about posting</a> and <a href='mailto:[email protected]'>contact us</a> with your email or tumblr username, and you will be added as a contributor to the blog. As an official contributor you can write posts in several formats, receive notifications, integrate apps, and contribute via email. Contributors are subject to the same standards of conduct as non-affiliated posters.</p><h3>Package Specific</h3><p>To contribute content, or a 'blogroll' for your package, we encourage you to become a tumblr contributor, tag your posts with your package, and <a href='https://www.tumblr.com/docs/en/using_tags#specific' target='_blank'>link to the tagged posts</a> from your package page.</p>"
+          answer: "<h3>Quick and Easy</h3><p>The fastest way to contribute is to <a href='https://neuroimaging.tumblr.com/submit'> submit </a> an idea, link, or video right away. If you have questions, to maximize their visibility, you can ask them on <a href='https://neurostars.org/' target='_blank'>Neurostars</a>, or you can reach us <a href='mailto:[email protected]'>by email</a>. These resources should be preferred over using the <a href='https://neuroimaging.tumblr.com/ask'>neuroimaging tumblr ask space</a>. Your submission will be reviewed and immediately available on the site and for social media integration.</p><h3>Contribute Regularly</h3><p>If you like writing tutorials, or regularly write about your research, we encourage you to <a href='https://www.tumblr.com/docs/en/posting' target='_blank'> read more about posting</a> and <a href='mailto:[email protected]'>contact us</a> with your email or tumblr username, and you will be added as a contributor to the blog. As an official contributor you can write posts in several formats, receive notifications, integrate apps, and contribute via email. Contributors are subject to the same standards of conduct as non-affiliated posters.</p><h3>Package Specific</h3><p>To contribute content, or a 'blogroll' for your package, we encourage you to become a tumblr contributor, tag your posts with your package, and <a href='https://www.tumblr.com/docs/en/using_tags#specific' target='_blank'>link to the tagged posts</a> from your package page.</p>"
         - tag: "contribute-to-site"
           question: "How do I contribute (otherwise) to the site?"
-          answer: "<h3>New site pages</h3><p>New sites pages that are not packages, and not blog content, can be plopped into the base directory, and they will be automatically rendered by jekyll. You will need to add a link to your page in the '_includes/links.html' or from within some other page.</p><h3>New questions on this page</h3><p>The data on this page is rendered from contribute.yml in the _data folder, and so you can add new questions there.</p><h3>Design</h3><p>None of us are 'real' web-developers, and always appreciate fixes to the site theme or look. If you are familiar with <a href='http://jekyllrb.com/' target='_blank'>Jekyll</a> then you can fork the repo, make your changes, and submit a PR.</p>"
+          answer: "<h3>New site pages</h3><p>New sites pages that are not packages, and not blog content, can be plopped into the base directory, and they will be automatically rendered by jekyll. You will need to add a link to your page in the '_includes/links.html' or from within some other page.</p><h3>New questions on this page</h3><p>The data on this page is rendered from contribute.yml in the _data folder, and so you can add new questions there.</p><h3>Design</h3><p>None of us are 'real' web-developers, and always appreciate fixes to the site theme or look. If you are familiar with <a href='https://jekyllrb.com/' target='_blank'>Jekyll</a> then you can fork the repo, make your changes, and submit a PR.</p>"
     - subtitle: "Neuroimaging Scientist"
       tag: "neuroimaging-scientist"
       questions:
         - tag: "ask-a-question"
           question: "How do I ask a question?"
-          answer: "<p>For general questions about methods, analysis, and code, the best place to maximize the number of eyes on your issue is by way of <a href='https://neurostars.org/' target='_blank'>Neurostars</a>. Questions about specific packages are best to post as issues on the repository itself, a link to which you can find on any of the package pages. To be added as a contributor or ask a question about the site, you can reach us <a href='mailto:[email protected]'>by email</a>. Although you can ask your question through the <a href='http://neuroimaging.tumblr.com/ask'>neuroimaging tumblr ask space</a> note that it gets less attention than the previous resources.</p>"
+          answer: "<p>For general questions about methods, analysis, and code, the best place to maximize the number of eyes on your issue is by way of <a href='https://neurostars.org/' target='_blank'>Neurostars</a>. Questions about specific packages are best to post as issues on the repository itself, a link to which you can find on any of the package pages. To be added as a contributor or ask a question about the site, you can reach us <a href='mailto:[email protected]'>by email</a>. Although you can ask your question through the <a href='https://neuroimaging.tumblr.com/ask'>neuroimaging tumblr ask space</a> note that it gets less attention than the previous resources.</p>"
         - tag: "learn-about-nipy"
           question: "Where can I learn more about nipy?"
-          answer: "<p>Right on this site! Or look at our <a href='http://www.github.com/nipy' target='_blank'>organization on Github</a>.</p>"
+          answer: "<p>Right on this site! Or look at our <a href='https://www.github.com/nipy' target='_blank'>organization on Github</a>.</p>"
         - tag: "research-opportunities"
           question: "Where can I find opportunities for collaboration?"
           answer: "<p>Contribute a package, go to conferences, (someone else please write this) :)</p>"

_includes/footer.html

@@ -1,4 +1,4 @@
-<footer><span>&copy; 2015-2021 nipy</span><br/><a rel="license" href="http://creativecommons.org/licenses/by/4.0/"><img alt="Creative Commons License" style="border-width:0" src="https://i.creativecommons.org/l/by/4.0/88x31.png" /></a><br />This work is licensed under a <a rel="license" href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution 4.0 International License</a>.</footer>
+<footer><span>&copy; 2015-2021 nipy</span><br/><a rel="license" href="https://creativecommons.org/licenses/by/4.0/ "><img alt="Creative Commons License" style="border-width:0" src="https://i.creativecommons.org/l/by/4.0/88x31.png" /></a><br />This work is licensed under a <a rel="license" href="https://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution 4.0 International License</a>.</footer>
 
 <script>
   (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){

_includes/link.html

@@ -1,4 +1,4 @@
-<a href="http://neuroimaging.tumblr.com">Blog</a>
+<a href="https://neuroimaging.tumblr.com">Blog</a>
 <a href="{{ '/help.html' | prepend: site.baseurl }}">Help</a>
 <a href="{{ '/conduct.html' | prepend: site.baseurl }}">Conduct</a>
 <a href="{{ '/workshops' | prepend: site.baseurl }}">Workshops</a>

_packages/dipy.html

@@ -2,7 +2,7 @@
 layout: package
 name: "dipy"
 tag: "dipy"
-doc: "http://dipy.org/"
+doc: "https://dipy.org/"
 github: "https://github.com/dipy/dipy"
 one-liner: "Focuses on diffusion magnetic resonance imaging (dMRI) analysis."
 description: "Dipy is a free and open source software project focusing on diffusion magnetic resonance imaging (dMRI) analysis."

_packages/mindboggle.html

@@ -2,7 +2,7 @@
 layout: package
 name: "mindboggle"
 tag: "mindboggle"
-doc: "http://mindboggle.info/"
+doc: "https://mindboggle.info/"
 github: "https://github.com/nipy/mindboggle"
 one-liner: "Improves the accuracy, precision, and consistency of labeling & morphometry of brain imaging data."
 description: "Mindboggle improves the accuracy, precision, and consistency of labeling and morphometry of brain imaging data."

_packages/mne.html

@@ -2,7 +2,7 @@
 layout: package
 name: "MNE"
 tag: "mne"
-doc: "http://martinos.org/mne/stable/index.html"
+doc: "https://mne.tools/stable/index.html"
 github: "https://github.com/mne-tools/mne-python"
 one-liner: "Processes magnetoencephalography (MEG) and electroencephalography (EEG) data."
 description: "MNE is a software package for processing magnetoencephalography (MEG) and electroencephalography (EEG) data."

_packages/nibabel.html

@@ -2,7 +2,7 @@
 layout: package
 name: "nibabel"
 tag: "nibabel"
-doc: "http://nipy.org/nibabel/"
+doc: "https://nipy.org/nibabel/"
 github: "https://github.com/nipy/nibabel"
 one-liner: "Read / write common neuroimaging file formats."
 description: "Nibabel aims to provide read/write access to some common neuroimaging file formats."

_packages/nilearn.html

@@ -2,7 +2,7 @@
 layout: package
 name: "Nilearn"
 tag: "nilearn"
-doc: "http://nilearn.github.io"
+doc: "https://nilearn.github.io"
 github: "https://github.com/nilearn/nilearn"
 one-liner: "Fast and easy statistical learning on neuroimaging data."
 description: "Nilearn is a Python module for fast and easy statistical learning on neuroimaging data."

_packages/nipy.html

@@ -2,7 +2,7 @@
 layout: package
 name: "Nipy"
 tag: "nipy"
-doc: "http://nipy.org/nipy/"
+doc: "https://nipy.org/nipy/"
 github: "https://github.com/nipy"
 one-liner: "Analysis of structural and functional neuroimaging data."
 description: "NIPY is not only the name of the Neuroimaging in Python community, but also a python project for analysis of structural and functional neuroimaging data."

_packages/nitime.html

@@ -2,7 +2,7 @@
 layout: package
 name: "Nitime"
 tag: "nitime"
-doc: "http://nipy.org/nitime/"
+doc: "https://nipy.org/nitime/"
 github: "https://github.com/nipy/nitime"
 one-liner: "Time-series analysis of neuroscience data."
 description: "Nitime is a library for time-series analysis of neuroscience data."

_packages/niwidgets.html

@@ -2,7 +2,7 @@
 layout: package
 name: "niwidgets"
 tag: "niwidgets"
-doc: "http://www.nipy.org/niwidgets/"
+doc: "https://www.nipy.org/niwidgets/"
 github: "https://github.com/nipy/niwidgets"
 one-liner: "Provides interactive plots for volumetric images."
 description: "niwidgets provides you with interactive widgets for jupyter notebooks to plot neuroimaging data."

_packages/popeye.html

@@ -2,7 +2,7 @@
 layout: package
 name: "popeye"
 tag: "popeye"
-doc: "http://kdesimone.github.io/popeye/"
+doc: "https://kdesimone.github.io/popeye/"
 github: "https://github.com/kdesimone/popeye"
 one-liner: "Population receptive field estimation"
 description: "Popeye is a library for estimation of population receptive fields (pRF), accelerated with Cython and multiprocessing"

index.html

@@ -14,7 +14,7 @@
 <h2 style="margin-top:20px; margin-bottom:20px">{{ site.url }}</h2>
 
 <p>
-Welcome to NIPY. We are a <a href="https://en.wikipedia.org/wiki/Community_of_practice" target="_blank">community of practice</a> devoted to the use of the Python programming language in the analysis of neuroimaging data. You can find us on <a href="https://github.com/nipy" target="_blank">github</a>, as well as social media <a href="http://neuroimaging.tumblr.com" target="_blank">[blog]</a> <a href="https://twitter.com/nipyorg" target="_blank">[twitter]</a>. We welcome <a href="{{ '/contribute.html' | prepend: site.baseurl }}" target="_blank">contributions</a> and ask that you read about our <a href="{{ '/conduct.html' | prepend: site.baseurl }}" target="_blank">standards of conduct</a>. You are also invited to <a href="{{ '/help.html' | prepend: site.baseurl }}" target="_blank">ask for help.</a>
+Welcome to NIPY. We are a <a href="https://en.wikipedia.org/wiki/Community_of_practice" target="_blank">community of practice</a> devoted to the use of the Python programming language in the analysis of neuroimaging data. You can find us on <a href="https://github.com/nipy" target="_blank">github</a>, as well as social media <a href="https://neuroimaging.tumblr.com" target="_blank">[blog]</a> <a href="https://twitter.com/nipyorg" target="_blank">[twitter]</a>. We welcome <a href="{{ '/contribute.html' | prepend: site.baseurl }}" target="_blank">contributions</a> and ask that you read about our <a href="{{ '/conduct.html' | prepend: site.baseurl }}" target="_blank">standards of conduct</a>. You are also invited to <a href="{{ '/help.html' | prepend: site.baseurl }}" target="_blank">ask for help.</a>
 </p>
 
 <p>