diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index 9e04007..b3ad128 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -140,7 +140,7 @@ You can also [reach us by email][contact].
[dc-lessons]: http://datacarpentry.org/lessons/
[dc-site]: http://datacarpentry.org/
[discuss-list]: http://lists.software-carpentry.org/listinfo/discuss
-[github]: http://github.com
+[github]: https://github.com
[github-flow]: https://guides.github.com/introduction/flow/
[github-join]: https://github.com/join
[how-contribute]: https://egghead.io/series/how-to-contribute-to-an-open-source-project-on-github
@@ -148,5 +148,5 @@ You can also [reach us by email][contact].
[issues]: https://github.com/swcarpentry/git-novice/issues/
[repo]: https://github.com/swcarpentry/git-novice/
[swc-issues]: https://github.com/issues?q=user%3Aswcarpentry
-[swc-lessons]: http://software-carpentry.org/lessons/
-[swc-site]: http://software-carpentry.org/
+[swc-lessons]: https://software-carpentry.org/lessons/
+[swc-site]: https://software-carpentry.org/
diff --git a/LICENSE.md b/LICENSE.md
index 179758a..c265a58 100644
--- a/LICENSE.md
+++ b/LICENSE.md
@@ -26,7 +26,7 @@ Under the following terms:
* **Attribution**---You must give appropriate credit (mentioning that
your work is derived from work that is Copyright © Software
Carpentry and, where practical, linking to
- http://software-carpentry.org/), provide a [link to the
+ https://software-carpentry.org/), provide a [link to the
license][cc-by-human], and indicate if changes were made. You may do
so in any reasonable manner, but not in any way that suggests the
licensor endorses you or your use.
@@ -78,6 +78,6 @@ are registered trademarks of [NumFOCUS][numfocus].
[cc-by-human]: https://creativecommons.org/licenses/by/4.0/
[cc-by-legal]: https://creativecommons.org/licenses/by/4.0/legalcode
-[mit-license]: http://opensource.org/licenses/mit-license.html
-[numfocus]: http://numfocus.org/
-[osi]: http://opensource.org
+[mit-license]: https://opensource.org/licenses/mit-license.html
+[numfocus]: https://numfocus.org/
+[osi]: https://opensource.org
diff --git a/README.md b/README.md
index 6d7af3e..46583f0 100644
--- a/README.md
+++ b/README.md
@@ -12,6 +12,6 @@ Maintainers:
* [Ivan Gonzalez][gonzalez_ivan]
* [Daisie Huang][huang_daisie]
-[gonzalez_ivan]: http://software-carpentry.org/team/#gonzalez_ivan
-[huang_daisie]: http://software-carpentry.org/team/#huang_daisie
+[gonzalez_ivan]: https://software-carpentry.org/team/#gonzalez_ivan
+[huang_daisie]: https://software-carpentry.org/team/#huang_daisie
[lesson-example]: https://swcarpentry.github.io/lesson-example
diff --git a/_episodes/01-basics.md b/_episodes/01-basics.md
index 3a0d791..a4be677 100644
--- a/_episodes/01-basics.md
+++ b/_episodes/01-basics.md
@@ -60,7 +60,7 @@ across different computers facilitating collaboration among different people.
> Automated version control systems are nothing new.
> Tools like RCS, CVS, or Subversion have been around since the early 1980s and are used by many large companies.
> However, many of these are now becoming considered as legacy systems due to various limitations in their capabilities.
-> In particular, the more modern systems, such as Git and [Mercurial](http://swcarpentry.github.io/hg-novice/)
+> In particular, the more modern systems, such as Git and [Mercurial](https://swcarpentry.github.io/hg-novice/)
> are *distributed*, meaning that they do not need a centralized server to host the repository.
> These modern systems also include powerful merging tools that make it possible for multiple authors to work within
> the same files concurrently.
diff --git a/_episodes/02-setup.md b/_episodes/02-setup.md
index e6638c2..58bb376 100644
--- a/_episodes/02-setup.md
+++ b/_episodes/02-setup.md
@@ -33,9 +33,9 @@ $ git config --global color.ui "auto"
Please use your own name and email address instead of Dracula's. This user name and email will be associated with your subsequent Git activity,
which means that any changes pushed to
-[GitHub](http://github.com/),
-[BitBucket](http://bitbucket.org/),
-[GitLab](http://gitlab.com/) or
+[GitHub](https://github.com/),
+[BitBucket](https://bitbucket.org/),
+[GitLab](https://gitlab.com/) or
another Git host server
in a later lesson will include this information.
@@ -71,7 +71,7 @@ in a later lesson will include this information.
> [on this GitHub page](https://help.github.com/articles/dealing-with-line-endings/).
{: .callout}
-For these lessons, we will be interacting with [GitHub](http://github.com/) and so the email address used should be the same as the one used when setting up your GitHub account. If you are concerned about privacy, please review [GitHub's instructions for keeping your email address private][git-privacy].
+For these lessons, we will be interacting with [GitHub](https://github.com/) and so the email address used should be the same as the one used when setting up your GitHub account. If you are concerned about privacy, please review [GitHub's instructions for keeping your email address private][git-privacy].
If you elect to use a private email address with GitHub, then use that same email address for the `user.email` value, e.g. `username@users.noreply.github.com` replacing `username` with your GitHub one. You can change the email address later on by using the `git config` command again.
Dracula also has to set his favorite text editor, following this table:
diff --git a/_episodes/04-changes.md b/_episodes/04-changes.md
index 764f4c5..3e08b3b 100644
--- a/_episodes/04-changes.md
+++ b/_episodes/04-changes.md
@@ -8,7 +8,7 @@ questions:
- "How do I record notes about what changes I made and why?"
objectives:
- "Go through the modify-add-commit cycle for one or more files."
-- "Explain where information is stored at each stage of Git commit workflow."
+- "Explain where information is stored at each stage of that cycle."
- "Distinguish between descriptive and non-descriptive commit messages."
keypoints:
- "`git status` shows the status of a repository."
@@ -326,11 +326,10 @@ before actually committing anything. This allows us to commit our
changes in stages and capture changes in logical portions rather than
only large batches.
For example,
-suppose we're adding a few citations to our supervisor's work
-to our thesis.
+suppose we're adding a few citations to relevant research to our thesis.
We might want to commit those additions,
-and the corresponding addition to the bibliography,
-but *not* commit the work we're doing on the conclusion
+and the corresponding bibliography entries,
+but *not* commit some of our work drafting the conclusion
(which we haven't finished yet).
To allow for this,
@@ -754,4 +753,4 @@ repository (`git commit`):
> {: .solution}
{: .challenge}
-[commit-messages]: http://chris.beams.io/posts/git-commit/
+[commit-messages]: https://chris.beams.io/posts/git-commit/
diff --git a/_episodes/05-history.md b/_episodes/05-history.md
index c13d152..332e8ee 100644
--- a/_episodes/05-history.md
+++ b/_episodes/05-history.md
@@ -303,7 +303,7 @@ recent commit (`HEAD~1`), which is commit `f22b25e`:
So, to put it all together,
here's how Git works in cartoon form:
-
+
> ## Simplifying the Common Case
>
diff --git a/_episodes/07-github.md b/_episodes/07-github.md
index a0a7e0e..8e93f55 100644
--- a/_episodes/07-github.md
+++ b/_episodes/07-github.md
@@ -21,8 +21,8 @@ only thing missing is to copy changes from one repository to another.
Systems like Git allow us to move work between any two repositories. In
practice, though, it's easiest to use one copy as a central hub, and to keep it
on the web rather than on someone's laptop. Most programmers use hosting
-services like [GitHub](http://github.com), [BitBucket](http://bitbucket.org) or
-[GitLab](http://gitlab.com/) to hold those master copies; we'll explore the pros
+services like [GitHub](https://github.com), [BitBucket](https://bitbucket.org) or
+[GitLab](https://gitlab.com/) to hold those master copies; we'll explore the pros
and cons of this in the final section of this lesson.
Let's start by sharing the changes we've made to our current project with the
@@ -161,7 +161,7 @@ Branch master set up to track remote branch master from origin.
>
> in the terminal, before you run `git push`. Despite the name, [git uses
> `SSH_ASKPASS` for all credential
-> entry](http://git-scm.com/docs/gitcredentials#_requesting_credentials), so
+> entry](https://git-scm.com/docs/gitcredentials#_requesting_credentials), so
> you may want to unset `SSH_ASKPASS` whether you are using git via SSH or
> https.
>
diff --git a/_episodes/09-conflict.md b/_episodes/09-conflict.md
index 0274312..32e9120 100644
--- a/_episodes/09-conflict.md
+++ b/_episodes/09-conflict.md
@@ -12,8 +12,8 @@ keypoints:
- "The version control system does not allow people to overwrite each other's changes blindly, but highlights conflicts so that they can be resolved."
---
-As soon as people can work in parallel, it's likely someone's going to step on someone
-else's toes. This will even happen with a single person: if we are working on
+As soon as people can work in parallel, they'll likely step on each other's
+toes. This will even happen with a single person: if we are working on
a piece of software on both our laptop and a server in the lab, we could make
different changes to each copy. Version control helps us manage these
[conflicts]({{ page.root }}/reference/#conflicts) by giving us tools to
@@ -178,7 +178,7 @@ This line added to Wolfman's copy
~~~
{: .output}
-Our change—the one in `HEAD`—is preceded by `<<<<<<<`.
+Our change is preceded by `<<<<<<< HEAD`.
Git has then inserted `=======` as a separator between the conflicting changes
and marked the end of the content downloaded from GitHub with `>>>>>>>`.
(The string of letters and digits after that marker
diff --git a/_episodes/10-open.md b/_episodes/10-open.md
index 2ca95bb..016cf4b 100644
--- a/_episodes/10-open.md
+++ b/_episodes/10-open.md
@@ -46,12 +46,12 @@ though,
the process looks like this:
* The data that the scientist collects is stored in an open access repository
- like [figshare](http://figshare.com/) or
- [Zenodo](http://zenodo.org), possibly as soon as it's collected,
+ like [figshare](https://figshare.com/) or
+ [Zenodo](https://zenodo.org), possibly as soon as it's collected,
and given its own
[Digital Object Identifier](https://en.wikipedia.org/wiki/Digital_object_identifier) (DOI).
Or the data was already published and is stored in
- [Dryad](http://datadryad.org/).
+ [Dryad](https://datadryad.org/).
* The scientist creates a new repository on GitHub to hold her work.
* As she does her analysis,
she pushes changes to her scripts
@@ -60,7 +60,7 @@ the process looks like this:
She also uses the repository for her paper;
that repository is then the hub for collaboration with her colleagues.
* When she's happy with the state of her paper,
- she posts a version to [arXiv](http://arxiv.org/)
+ she posts a version to [arXiv](https://arxiv.org/)
or some other preprint server
to invite feedback from peers.
* Based on that feedback,
@@ -73,10 +73,10 @@ the process looks like this:
This open model accelerates discovery:
the more open work is,
-[the more widely it is cited and re-used](http://dx.doi.org/10.1371/journal.pone.0000308).
+[the more widely it is cited and re-used](https://doi.org/10.1371/journal.pone.0000308).
However,
people who want to work this way need to make some decisions
-about what exactly "open" means and how to do it. You can find more on the different aspects of Open Science in [this book](http://link.springer.com/book/10.1007/978-3-319-00026-8).
+about what exactly "open" means and how to do it. You can find more on the different aspects of Open Science in [this book](https://link.springer.com/book/10.1007/978-3-319-00026-8).
This is one of the (many) reasons we teach version control.
When used diligently,
@@ -96,10 +96,9 @@ by acting as a shareable electronic lab notebook for computational work:
> ## Making Code Citable
>
-> [This short guide](https://guides.github.com/activities/citable-code/) from GitHub
-> explains how to create a Digital Object Identifier (DOI) for your code,
-> your papers,
-> or anything else hosted in a version control repository.
+> Anything that is hosted in a version control repository (data, code, papers,
+> etc.) can be turned into a citable object. You'll learn how to do this in
+> [lesson 12: Citation]({{ page.root }}/12-citation/).
{: .callout}
> ## How Reproducible Is My Work?
@@ -113,21 +112,11 @@ by acting as a shareable electronic lab notebook for computational work:
> ## How to Find an Appropriate Data Repository?
>
> Surf the internet for a couple of minutes and check out the data repositories
-> mentioned above: [Figshare](http://figshare.com/), [Zenodo](http://zenodo.org),
-> [Dryad](http://datadryad.org/). Depending on your field of research, you might
+> mentioned above: [Figshare](https://figshare.com/), [Zenodo](https://zenodo.org),
+> [Dryad](https://datadryad.org/). Depending on your field of research, you might
> find community-recognized repositories that are well-known in your field.
> You might also find useful [these data repositories recommended by Nature](
-> http://www.nature.com/sdata/data-policies/repositories).
+> https://www.nature.com/sdata/data-policies/repositories).
> Discuss with your neighbor which data repository you might want to
> approach for your current project and explain why.
{: .challenge}
-
-> ## Can I Also Publish Code?
->
-> There are many new ways to publish code and to make it citable. One
-> way is described [on the homepage of GitHub itself](
-> https://guides.github.com/activities/citable-code/).
-> Basically it's a combination of GitHub (where the code is) and Zenodo (the
-> repository creating the DOI). Read through this page while being aware
-> that this is only one of many ways to making your code citable.
-{: .challenge}
diff --git a/_episodes/11-licensing.md b/_episodes/11-licensing.md
index c559bc3..4d09896 100644
--- a/_episodes/11-licensing.md
+++ b/_episodes/11-licensing.md
@@ -27,7 +27,7 @@ A license solves this problem by granting rights to others (the
licensees) that they would otherwise not have. What rights are being
granted under which conditions differs, often only slightly, from one
license to another. In practice, a few licenses are by far the most
-popular, and [choosealicense.com](http://choosealicense.com/) will
+popular, and [choosealicense.com](https://choosealicense.com/) will
help you find a common license that suits your needs. Important
considerations include:
@@ -41,8 +41,8 @@ Choosing a license that is in common use makes life easier for
contributors and users, because they are more likely to already be
familiar with the license and don't have to wade through a bunch of
jargon to decide if they're ok with it. The [Open Source
-Initiative](http://opensource.org/licenses) and [Free Software
-Foundation](http://www.gnu.org/licenses/license-list.html) both
+Initiative](https://opensource.org/licenses) and [Free Software
+Foundation](https://www.gnu.org/licenses/license-list.html) both
maintain lists of licenses which are good choices.
[This article][software-licensing] provides an excellent overview of
@@ -77,4 +77,4 @@ thus need to be asked for approval once a license is chosen.
> - [EtherPad](https://github.com/ether/etherpad-lite), a real-time collaborative editor
{: .challenge}
-[software-licensing]: http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002598
+[software-licensing]: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002598
diff --git a/_episodes/12-citation.md b/_episodes/12-citation.md
index 6060d86..4a340f8 100644
--- a/_episodes/12-citation.md
+++ b/_episodes/12-citation.md
@@ -44,3 +44,15 @@ July 2013.
}
~~~
{: .source}
+
+More detailed advice, and other ways to make your code citable can be found in
+[here](https://www.software.ac.uk/how-cite-and-describe-software) and in:
+
+> Smith AM, Katz DS, Niemeyer KE, FORCE11 Software Citation Working Group.
+> (2016) Software citation principles. [PeerJ Computer Science 2:e86](https://peerj.com/articles/cs-86/) https://doi.org/10.7717/peerj-cs.86
+
+There is also an [`@software{…`](https://www.google.de/search?q=git+citation+%22%40software%7B%22)
+[BibTeX](https://www.ctan.org/pkg/bibtex) entry type in case
+no "umbrella" citation like a paper or book exists for the project you want to
+make citable.
+
diff --git a/_episodes/13-hosting.md b/_episodes/13-hosting.md
index 07f4727..fe2f0b5 100644
--- a/_episodes/13-hosting.md
+++ b/_episodes/13-hosting.md
@@ -29,8 +29,8 @@ but requires more time and effort to set up than either the option above or the
option below.
The third option is to use a public hosting service like
-[GitHub](http://github.com), [GitLab](http://gitlab.com),
-[BitBucket](http://bitbucket.org), or [SourceForge](http://sourceforge.net).
+[GitHub](https://github.com), [GitLab](https://gitlab.com),
+[BitBucket](https://bitbucket.org), or [SourceForge](http://sourceforge.net).
Each of these services provides a web interface that enables people to create,
view, and edit their code repositories. These services also provide
communication and project management tools including issue tracking, wiki pages,
@@ -45,6 +45,11 @@ GitHub]({{ swc_github }}) where you can find the [source for this
page]({{page.root}}/_episodes/13-hosting.md).
Anyone with a GitHub account can suggest changes to this text.
+GitHub repositories can also be assigned DOIs, [by connecting its releases to
+Zenodo](https://guides.github.com/activities/citable-code/). For example,
+[`10.5281/zenodo.57467`](https://zenodo.org/record/57467) is the DOI that has
+been "minted" for this introduction to Git.
+
Using large, well-established services can also help you quickly take advantage
of powerful tools. One such tool, continuous integration (CI), can
automatically run software builds and tests whenever code is committed or pull
@@ -78,5 +83,5 @@ open source projects, and are also available for private repositories for a fee.
>
> Does your institution have a repository or repositories that you can
> use to share your papers, data and software? How do institutional repositories
-> differ from services like [arXiV](http://arxiv.org/), [figshare](http://figshare.com/) and [GitHub](http://github.com/)?
+> differ from services like [arXiV](https://arxiv.org/), [figshare](https://figshare.com/), [GitHub](https://github.com/) or [GitLab](https://about.gitlab.com/)?
{: .challenge}
diff --git a/_episodes/14-supplemental-rstudio.md b/_episodes/14-supplemental-rstudio.md
index 36ce344..34b5264 100644
--- a/_episodes/14-supplemental-rstudio.md
+++ b/_episodes/14-supplemental-rstudio.md
@@ -33,12 +33,12 @@ our computer, we'll choose "existing directory":
>
> Although we're not going to use it here, there should be a "version control"
> option on this menu. That is what you would click on if you wanted to
-> create a project on your computer by cloning a repository from github.
+> create a project on your computer by cloning a repository from GitHub.
> If that option is not present, it probably means that RStudio doesn't know
> where your Git executable is. See
> [this page](https://stat545-ubc.github.io/git03_rstudio-meet-git.html)
> for some debugging advice. Even if you have Git installed, you may need
-> to accept the XCode license if you are using MacOSX.
+> to accept the XCode license if you are using macOS.
{: .callout}
Next, RStudio will ask which existing directory we want to use. Click "browse"
@@ -91,8 +91,8 @@ If we click on "history", we can see a pretty graphical version of what
-RStudio creates some files that is uses to keep track of your project. You
-generally don't want to track these, so adding them to your .gitignore file
+RStudio creates some files that it uses to keep track of your project. You
+generally don't want to track these, so adding them to your `.gitignore` file
is a good idea:
diff --git a/_extras/guide.md b/_extras/guide.md
index 069c85d..22b88f5 100644
--- a/_extras/guide.md
+++ b/_extras/guide.md
@@ -288,7 +288,7 @@ web-hosted private repositories.
[git-it-electron]: https://github.com/jlord/git-it-electron
[git-parable]: http://tom.preston-werner.com/2009/05/19/the-git-parable.html
[github]: https://github.com/
-[github-gui]: http://git-scm.com/downloads/guis
+[github-gui]: https://git-scm.com/downloads/guis
[github-line-endings]: https://help.github.com/articles/dealing-with-line-endings/#platform-all
[github-privacy]: https://help.github.com/articles/keeping-your-email-address-private/
[repos-in-repos]: https://github.com/swcarpentry/git-novice/issues/272
diff --git a/_includes/all_figures.html b/_includes/all_figures.html
index 8162e1e..9f6254b 100644
--- a/_includes/all_figures.html
+++ b/_includes/all_figures.html
@@ -16,7 +16,7 @@
-
+
diff --git a/_includes/lc/syllabys.html b/_includes/lc/syllabys.html
index 4dc2077..e2c7012 100644
--- a/_includes/lc/syllabys.html
+++ b/_includes/lc/syllabys.html
@@ -8,7 +8,7 @@ Data Intro
Plain text formats
Naming files
Regular expressions
- Reference...
+ Reference...
@@ -19,7 +19,7 @@
The Unix Shell
Counting and sorting contents in files
Pipes and redirection
Mining or searching in files
-
Reference...
+
Reference...
Version Control with Git
Viewing state changes with status
Working on the web: clone, pull, push, ...
Where to host work, and why
- Reference...
+ Reference...
@@ -62,7 +62,7 @@ SQL Intro
Filtering with where
Combining values using aggregation
Combining information from multiple tables using join
- Reference...
+ Reference...
diff --git a/_includes/links.md b/_includes/links.md
index a163786..e2606eb 100644
--- a/_includes/links.md
+++ b/_includes/links.md
@@ -1,35 +1,35 @@
[cc-by-human]: https://creativecommons.org/licenses/by/4.0/
[cc-by-legal]: https://creativecommons.org/licenses/by/4.0/legalcode
-[concept-maps]: http://swcarpentry.github.io/instructor-training/08-memory/
+[concept-maps]: https://swcarpentry.github.io/instructor-training/08-memory/
[contact]: mailto:lessons@software-carpentry.org
-[contrib-covenant]: http://contributor-covenant.org/
+[contrib-covenant]: https://contributor-covenant.org/
[contributing]: {{ site.github.repository_url }}/blob/gh-pages/CONTRIBUTING.md
[cran-checkpoint]: https://cran.r-project.org/web/packages/checkpoint/index.html
[cran-knitr]: https://cran.r-project.org/web/packages/knitr/index.html
[cran-stringr]: https://cran.r-project.org/web/packages/stringr/index.html
[github-importer]: https://import.github.com/
-[importer]: http://import.github.com/new
+[importer]: https://import.github.com/new
[jekyll-collection]: https://jekyllrb.com/docs/collections/
[jekyll-install]: https://jekyllrb.com/docs/installation/
[jekyll-windows]: http://jekyll-windows.juthilo.com/
[jekyll]: https://jekyllrb.com/
[jupyter]: https://jupyter.org/
-[mit-license]: http://opensource.org/licenses/mit-license.html
+[mit-license]: https://opensource.org/licenses/mit-license.html
[morea]: https://morea-framework.github.io/
-[numfocus]: http://numfocus.org/
-[osi]: http://opensource.org
+[numfocus]: https://numfocus.org/
+[osi]: https://opensource.org
[pandoc]: https://pandoc.org/
[paper-now]: https://github.com/PeerJ/paper-now
[python-gapminder]: https://swcarpentry.github.io/python-novice-gapminder/
[pyyaml]: https://pypi.python.org/pypi/PyYAML
-[r-markdown]: http://rmarkdown.rstudio.com/
+[r-markdown]: https://rmarkdown.rstudio.com/
[rstudio]: https://www.rstudio.com/
[ruby-install-guide]: https://www.ruby-lang.org/en/downloads/
-[ruby-installer]: http://rubyinstaller.org/
+[ruby-installer]: https://rubyinstaller.org/
[rubygems]: https://rubygems.org/pages/download/
[styles]: https://github.com/swcarpentry/styles/
-[training]: http://swcarpentry.github.io/instructor-training/
+[training]: https://swcarpentry.github.io/instructor-training/
[workshop-repo]: {{ site.workshop_repo }}
[yaml]: http://yaml.org/
[coc]: https://software-carpentry.org/conduct/
-[coc-reporting]: https://software-carpentry.org/CoC-reporting/
\ No newline at end of file
+[coc-reporting]: https://software-carpentry.org/CoC-reporting/
diff --git a/bin/lesson_initialize.py b/bin/lesson_initialize.py
index fc7baf7..905adb9 100755
--- a/bin/lesson_initialize.py
+++ b/bin/lesson_initialize.py
@@ -158,15 +158,15 @@
[dc-lessons]: http://datacarpentry.org/lessons/
[dc-site]: http://datacarpentry.org/
[discuss-list]: http://lists.software-carpentry.org/listinfo/discuss
-[github]: http://github.com
+[github]: https://github.com
[github-flow]: https://guides.github.com/introduction/flow/
[github-join]: https://github.com/join
[how-contribute]: https://egghead.io/series/how-to-contribute-to-an-open-source-project-on-github
[issues]: https://github.com/swcarpentry/FIXME/issues/
[repo]: https://github.com/swcarpentry/FIXME/
[swc-issues]: https://github.com/issues?q=user%3Aswcarpentry
-[swc-lessons]: http://software-carpentry.org/lessons/
-[swc-site]: http://software-carpentry.org/
+[swc-lessons]: https://software-carpentry.org/lessons/
+[swc-site]: https://software-carpentry.org/
'''
ROOT_CONFIG_YML = '''\
diff --git a/reference.md b/reference.md
index 5899cb4..11e437d 100644
--- a/reference.md
+++ b/reference.md
@@ -62,7 +62,7 @@ revision
: A synonym for [commit](#commit).
SHA-1
-: [SHA-1 hashes](http://en.wikipedia.org/wiki/SHA-1) is what Git uses to compute identifiers, including for commits.
+: [SHA-1 hashes](https://en.wikipedia.org/wiki/SHA-1) is what Git uses to compute identifiers, including for commits.
To compute these, Git uses not only the actual change of a commit, but also its metadata (such as date, author,
message), including the identifiers of all commits of preceding changes. This makes Git commit IDs virtually unique.
I.e., the likelihood that two commits made independently, even of the same change, receive the same ID is exceedingly