Merge branch 'gh-pages' of https://github.com/swcarpentry/git-novice …

…into gh-pages

.mailmap

@@ -1,108 +1,51 @@
-Aron Ahmadia <[email protected]>
-James Allen <[email protected]>
-Alison Appling <[email protected]>
-Sean Aubin <[email protected]>
-Pete Bachant <[email protected]>
-Piotr Banaszkiewicz <[email protected]>
-Pauline Barmby <[email protected]>
-Berenice Batut <[email protected]> <[email protected]>
-Trevor Bekolay <[email protected]>
-John Blischak <[email protected]>
-Madeleine Bonsma <[email protected]>
-Jon Borrelli <[email protected]>
-Andy Boughton <[email protected]> <[email protected]>
-Daina Bouquin <[email protected]>
-Rudi Brauning <[email protected]>
-Matthew Brett <[email protected]>
-Amy Brown <[email protected]>
+Abigail Cabunoc Mayes <[email protected]>
 Abigail Cabunoc Mayes <[email protected]> <[email protected]>
-Jane Charlesworth <[email protected]>
-Billy Charlton <[email protected]>
-Daniel Chen <[email protected]>
-Garret Christensen <[email protected]>
-Ruth Collings <[email protected]>
-Marianne Corvellec <[email protected]>
-Matt Davis <[email protected]>
-Emily Dolson <[email protected]>
-Laurent Duchesne <[email protected]>
-Jonah Duckles <[email protected]>
-Rémi Emonet <[email protected]> <[email protected]>
-Loïc Estève <[email protected]>
-Sean Farley <[email protected]>
-Emmanouil Farsarakis <[email protected]> <[email protected]>
-Bennet Fauber <[email protected]>
-Anne Fouilloux <[email protected]>
-Konrad Förstner <[email protected]>
-Stuart Geiger <[email protected]>
-Ivan Gonzalez <[email protected]>
-Marisa Guarinello <[email protected]>
-Jamie Hadwin <[email protected]>
-Nicholas Hannah <[email protected]>
-Michael Hansen <[email protected]>
-Martin Heroux <[email protected]>
-Kate Hertweck <[email protected]> <[email protected]>
-Konrad Hinsen <[email protected]>
-Daisie Huang <[email protected]>
-Daisie Huang_local <[email protected]>
-Yuandra Ismiraldi <[email protected]>
-Mike Jackson <[email protected]>
-Christian Jacobs <[email protected]>
-Dorota Jarecka <[email protected]>
-Dorota Jarecka <[email protected]>
-David Jones <[email protected]>
-Zbigniew Jędrzejewski-Szmek <[email protected]>
-Thomas Kluyver <[email protected]>
+Alois Heilmaier <[email protected]>
+Andrew Rohl <[email protected]>
+Andy Boughton <[email protected]> <[email protected]>
+Ariel Rokem <[email protected]>
+Bennet Fauber <[email protected]>
+Bérénice Batut <[email protected]>
+Bérénice Batut <[email protected]> <[email protected]>
 Bernhard Konrad <[email protected]>
-Mateusz Kuzak <[email protected]>
-Kathleen Labrie <[email protected]>
-Hilmar Lapp <[email protected]>
-Doug Latornell <[email protected]>
-Mark Laufersweiler <[email protected]>
-David LeBauer <[email protected]>
-Kate Lee <[email protected]>
-Matthias Liffers <[email protected]>
-Catrina Loucks <[email protected]>
-Keith Ma <[email protected]>
-Kunal Marwaha <[email protected]>
-François Michonneau <[email protected]>
 Bill Mills <[email protected]>
-Andreas Mueller <[email protected]>
-VP Nagraj <[email protected]>
-Lex Nederbragt <[email protected]>
-Juan Nunez-Iglesias <[email protected]>
 Brenna O'Brien <[email protected]>
-Aaron O'Leary <[email protected]>
-Catherine Olsson <[email protected]>
 Chris Pawsey <[email protected]>
-Stefan Pfenninger <[email protected]>
-Jon Pipitone <[email protected]>
-Timothée Poisot <[email protected]>
-Paul Preney <[email protected]>
-Timothy Rice <[email protected]>
-Kristina Riemer <[email protected]>
-David Rio Deiros <[email protected]>
-Natalie Robinson <[email protected]>
-Andrew Rohl <[email protected]>
-Andrew Rohl <[email protected]>
-Ariel Rokem <[email protected]>
-Michael Sarahan <[email protected]>
-Sebastian Schmeier <[email protected]>
-Hartmut Schmider <[email protected]>
-Raniere Silva <[email protected]> <[email protected]> <[email protected]>
-Brendan Smithyman <[email protected]>
-Nicola Soranzo <[email protected]>
-Peter Steinbach <[email protected]>
-Sarah Stevens <[email protected]>
-Tiffany Timbers <[email protected]>
+Daisie Huang <[email protected]>
 Danielle Traphagen <[email protected]>
-W. Trevor King <[email protected]>
-Tim Tröndle <[email protected]>
-Steve Vandervalk <[email protected]>
+Dorota Jarecka <[email protected]>
+Emily Dolson <[email protected]>
+Emmanouil Farsarakis <[email protected]> <[email protected]>
+Evan P. Williamson <[email protected]>
+François Michonneau <[email protected]>
+François Michonneau <[email protected]> <[email protected]>
+Greg Watson <[email protected]>
+Greg Wilson <[email protected]> <[email protected]>
+Ivan Gonzalez <[email protected]> <[email protected]>
+James Allen <[email protected]> <[email protected]>
+Jane Charlesworth <[email protected]>
+Kate Hertweck <[email protected]>
+Kate Lee <[email protected]>
 Luke W. Johnston <[email protected]>
-Belinda Weaver <[email protected]>
+Marisa Guarinello <[email protected]>
 Mark Wheelhouse <[email protected]>
-Ethan White <[email protected]>
-Greg Wilson <[email protected]> <[email protected]>
-Steven Wu <[email protected]>
-Qingpeng Zhang <[email protected]>
-Anelda van der Walt <[email protected]>
+Mateusz Kuzak <[email protected]>
+Matthias Haeni <[email protected]>
+Michael Panitz <[email protected]>
+Mike Jackson <[email protected]> <[email protected]>
+Natalie Robinson <[email protected]>
+Nicholas Hannah <[email protected]> <[email protected]>
+Nicola Soranzo <[email protected]> <[email protected]>
+Patrick C. Shriwise <[email protected]>
+Pauline Barmby <[email protected]>
+Peter Steinbach <[email protected]> <[email protected]>
+Raniere Silva <[email protected]> <[email protected]>
+Raniere Silva <[email protected]> <[email protected]>
+Rémi Emonet <[email protected]> <[email protected]>
+Rémi Emonet <[email protected]> <[email protected]>
+Sean Aubin <[email protected]>
+Steve Vandervalk <[email protected]> <[email protected]>
+Tiffany Timbers <[email protected]>
+Timothée Poisot <[email protected]> <[email protected]>
+Tom Kelly <[email protected]>
+Yuandra Ismiraldi <[email protected]>

AUTHORS

@@ -3,11 +3,14 @@ James Allen
 Alison Appling
 Sean Aubin
 Pete Bachant
+Daniel Baird
 Piotr Banaszkiewicz
 Pauline Barmby
-Berenice Batut
+Bérénice Batut
 Trevor Bekolay
+Maxim Belkin
 John Blischak
+Stephen Bond
 Madeleine Bonsma
 Jon Borrelli
 Andy Boughton
@@ -23,6 +26,7 @@ Garret Christensen
 Ruth Collings
 Marianne Corvellec
 Matt Davis
+Gabriel A. Devenyi
 Emily Dolson
 Laurent Duchesne
 Jonah Duckles
@@ -35,11 +39,17 @@ Konrad Förstner
 Stuart Geiger
 Ivan Gonzalez
 Marisa Guarinello
+Stéphane Guillou
 Jamie Hadwin
+Matthias Haeni
+Pierre Haessig
 Nicholas Hannah
 Michael Hansen
+Sumana Harihareswara
+Alois Heilmaier
 Martin Heroux
 Kate Hertweck
+Andreas Hilboll
 Konrad Hinsen
 Daisie Huang
 Yuandra Ismiraldi
@@ -49,29 +59,35 @@ Dorota Jarecka
 Luke W. Johnston
 David Jones
 Zbigniew Jędrzejewski-Szmek
+Tom Kelly
 W. Trevor King
 Thomas Kluyver
 Bernhard Konrad
 Mateusz Kuzak
+Arne Küderle
 Kathleen Labrie
 Hilmar Lapp
 Doug Latornell
 Mark Laufersweiler
 David LeBauer
 Kate Lee
 Matthias Liffers
+Clara Llebot
 Catrina Loucks
 Keith Ma
 Kunal Marwaha
+Ryan May
 François Michonneau
 Bill Mills
 Andreas Mueller
+Madicken Munk
 VP Nagraj
 Lex Nederbragt
 Juan Nunez-Iglesias
 Brenna O'Brien
 Aaron O'Leary
 Catherine Olsson
+Michael Panitz
 Chris Pawsey
 Stefan Pfenninger
 Jon Pipitone
@@ -81,24 +97,32 @@ Timothy Rice
 Kristina Riemer
 David Rio Deiros
 Natalie Robinson
+Annika Rockenberger
 Andrew Rohl
 Ariel Rokem
+Bill Sacks
 Michael Sarahan
 Sebastian Schmeier
 Hartmut Schmider
+Peter Shellito
+Patrick C. Shriwise
 Raniere Silva
 Brendan Smithyman
 Nicola Soranzo
 Peter Steinbach
 Sarah Stevens
+Oliver Stueker
+Benjamin Stuermer
 Tiffany Timbers
 Danielle Traphagen
 Tim Tröndle
 Anelda van der Walt
 Steve Vandervalk
+Greg Watson
 Belinda Weaver
 Mark Wheelhouse
 Ethan White
+Evan P. Williamson
 Greg Wilson
 Steven Wu
 Qingpeng Zhang

LICENSE.md

@@ -73,7 +73,7 @@ WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 
 ## Trademark
 
-"Software Carpentry" an "Data Carpentry" and their respective logos
+"Software Carpentry" and "Data Carpentry" and their respective logos
 are registered trademarks of [NumFOCUS][numfocus].
 
 [cc-by-human]: https://creativecommons.org/licenses/by/4.0/

Makefile

@@ -9,18 +9,19 @@ DST=_site
 
 # Controls
 .PHONY : commands clean files
+.NOTPARALLEL:
 all : commands
 
 ## commands         : show all commands.
 commands :
 	@grep -h -E '^##' ${MAKEFILES} | sed -e 's/## //g'
 
 ## serve            : run a local server.
-serve : lesson-rmd
+serve : lesson-md
 	${JEKYLL} serve
 
 ## site             : build files but do not run a server.
-site : lesson-rmd
+site : lesson-md
 	${JEKYLL} build
 
 # repo-check        : check repository settings.
@@ -53,7 +54,7 @@ workshop-check :
 ## ----------------------------------------
 ## Commands specific to lesson websites.
 
-.PHONY : lesson-check lesson-rmd lesson-files lesson-fixme
+.PHONY : lesson-check lesson-md lesson-files lesson-fixme
 
 # RMarkdown files
 RMD_SRC = $(wildcard _episodes_rmd/??-*.Rmd)
@@ -79,13 +80,16 @@ HTML_DST = \
   $(patsubst _extras/%.md,${DST}/%/index.html,$(wildcard _extras/*.md)) \
   ${DST}/license/index.html
 
-## lesson-rmd       : convert Rmarkdown files to markdown
-lesson-rmd: $(RMD_SRC)
-	@bin/knit_lessons.sh $(RMD_SRC)
+## lesson-md        : convert Rmarkdown files to markdown
+lesson-md : ${RMD_DST}
+
+# Use of .NOTPARALLEL makes rule execute only once
+${RMD_DST} : ${RMD_SRC}
+	@bin/knit_lessons.sh ${RMD_SRC}
 
 ## lesson-check     : validate lesson Markdown.
 lesson-check :
-	@bin/lesson_check.py -s . -p ${PARSER}
+	@bin/lesson_check.py -s . -p ${PARSER} -r _includes/links.md
 
 ## lesson-check-all : validate lesson Markdown, checking line lengths and trailing whitespace.
 lesson-check-all :

_episodes/01-basics.md

@@ -24,7 +24,7 @@ automated version control is much better than this situation:
 We've all been in this situation before: it seems ridiculous to have
 multiple nearly-identical versions of the same document. Some word
 processors let us deal with this a little better, such as Microsoft
-Word's "Track Changes" or Google Docs' [version
+Word's [Track Changes](https://support.office.com/en-us/article/Track-changes-in-Word-197ba630-0f5f-4a8e-9a77-3712475e806a) or Google Docs' [version
 history](https://support.google.com/docs/answer/190843?hl=en).
 
 Version control systems start with a base version of the document and

_episodes/02-setup.md

@@ -54,7 +54,7 @@ He also has to set his favorite text editor, following this table:
 | Notepad++ (Win, 32-bit install)    | `$ git config --global core.editor "'c:/program files (x86)/Notepad++/notepad++.exe' -multiInst -notabbar -nosession -noPlugin"`|
 | Notepad++ (Win, 64-bit install)    | `$ git config --global core.editor "'c:/program files/Notepad++/notepad++.exe' -multiInst -notabbar -nosession -noPlugin"`|
 | Kate (Linux)       | `$ git config --global core.editor "kate"`       |
-| Gedit (Linux)      | `$ git config --global core.editor "gedit -s -w"`   |
+| Gedit (Linux)      | `$ git config --global core.editor "gedit --wait --new-window"`   |
 | Scratch (Linux)       | `$ git config --global core.editor "scratch-text-editor"`  |
 | emacs              | `$ git config --global core.editor "emacs"`   |
 | vim                | `$ git config --global core.editor "vim"`   |

_episodes/04-changes.md

@@ -477,6 +477,39 @@ Date:   Thu Aug 22 09:51:46 2013 -0400
 ~~~
 {: .output}
 
+> ## Directories
+>
+> Two important facts you should know about directories in Git.
+>
+> 1. Git does not track directories on their own, only files within them.
+> Try it for yourself:
+>
+> ~~~
+> $ mkdir directory
+> $ git status
+> $ git add directory
+> $ git status
+> ~~~
+> {: .bash}
+> 
+> Note, our newly created empty directory `directory` does not appear in
+> the list of untracked files even if we explicitly add it (_via_ `git add`) to our
+> repository. This is the reason why you will sometimes see `.gitkeep` files
+> in otherwise empty directories. Unlike `.gitignore`, these files are not special
+> and their sole purpose is to populate a directory so that Git adds it to
+> the repository. In fact, you can name such files anything you like.
+>
+> {:start="2"}
+> 2. If you create a directory in your Git repository and populate it with files,
+> you can add all files in the directory at once by:
+>
+> ~~~
+> git add <directory-with-files>
+> ~~~
+> {: .bash}
+>
+{: .callout}
+
 To recap, when we want to add changes to our repository,
 we first need to add the changed files to the staging area
 (`git add`) and then commit the staged changes to the
@@ -607,4 +640,4 @@ repository (`git commit`):
 > {: .solution}
 {: .challenge}
 
-[commit-messages]: http://tbaggery.com/2008/04/19/a-note-about-git-commit-messages.html
+[commit-messages]: http://chris.beams.io/posts/git-commit/

_episodes/06-ignore.md

@@ -168,6 +168,9 @@ nothing to commit, working directory clean
 > > and create an exception for the `results/data/` folder.
 > > The next challenge will cover this type of solution.
 > >
+> > Sometimes the `**` pattern comes in handy, too, which matches
+> > multiple directory levels. E.g. `**/results/plots/*` would make git ignore
+> > the `results/plots` directory in any root directory.
 > {: .solution}
 {: .challenge}