[custom] fix lesson contents

datacarpentry · Sep 18, 2023 · 4a18147 · 4a18147
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diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md
@@ -8,6 +8,8 @@ we pledge to follow the [The Carpentries Code of Conduct][coc].
 Instances of abusive, harassing, or otherwise unacceptable behavior
 may be reported by following our [reporting guidelines][coc-reporting].
 
-
-[coc-reporting]: https://docs.carpentries.org/topic_folders/policies/incident-reporting.html
 [coc]: https://docs.carpentries.org/topic_folders/policies/code-of-conduct.html
+[coc-reporting]: https://docs.carpentries.org/topic_folders/policies/incident-reporting.html
+
+
+
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -21,18 +21,18 @@ mistake, some awkward wording, or a factual error. This is a good way to
 introduce yourself and to meet some of our community members.
 
 1. If you do not have a [GitHub][github] account, you can [send us comments by
-   email][contact]. However, we will be able to respond more quickly if you use
-   one of the other methods described below.
+  email][contact]. However, we will be able to respond more quickly if you use
+  one of the other methods described below.
 
 2. If you have a [GitHub][github] account, or are willing to [create
-   one][github-join], but do not know how to use Git, you can report problems
-   or suggest improvements by [creating an issue][repo-issues]. This allows us
-   to assign the item to someone and to respond to it in a threaded discussion.
+  one][github-join], but do not know how to use Git, you can report problems
+  or suggest improvements by [creating an issue][repo-issues]. This allows us
+  to assign the item to someone and to respond to it in a threaded discussion.
 
 3. If you are comfortable with Git, and would like to add or change material,
-   you can submit a pull request (PR). Instructions for doing this are
-   [included below](#using-github). For inspiration about changes that need to
-   be made, check out the [list of open issues][issues] across the Carpentries.
+  you can submit a pull request (PR). Instructions for doing this are
+  [included below](#using-github). For inspiration about changes that need to
+  be made, check out the [list of open issues][issues] across the Carpentries.
 
 Note: if you want to build the website locally, please refer to [The Workbench
 documentation][template-doc].
@@ -41,8 +41,7 @@ documentation][template-doc].
 
 1. If you wish to change this lesson, add issues and pull requests here.
 2. If you wish to change the template used for workshop websites, please refer
-   to [The Workbench documentation][template-doc].
-
+  to [The Workbench documentation][template-doc].
 
 ### What to Contribute
 
@@ -80,12 +79,12 @@ Contribute to an Open Source Project on GitHub][how-contribute]. In brief, we
 use [GitHub flow][github-flow] to manage changes:
 
 1. Create a new branch in your desktop copy of this repository for each
-   significant change.
+  significant change.
 2. Commit the change in that branch.
 3. Push that branch to your fork of this repository on GitHub.
 4. Submit a pull request from that branch to the [upstream repository][repo].
 5. If you receive feedback, make changes on your desktop and push to your
-   branch on GitHub: the pull request will update automatically.
+  branch on GitHub: the pull request will update automatically.
 
 NB: The published copy of the lesson is usually in the `main` branch.
 
@@ -98,26 +97,26 @@ final say over what gets merged into the lesson.
 The Carpentries is a global organisation with volunteers and learners all over
 the world. We share values of inclusivity and a passion for sharing knowledge,
 teaching and learning. There are several ways to connect with The Carpentries
-community listed at <https://carpentries.org/connect/> including via social
+community listed at [https://carpentries.org/connect/](https://carpentries.org/connect/) including via social
 media, slack, newsletters, and email lists. You can also [reach us by
 email][contact].
 
-[repo]: https://example.com/FIXME
-[repo-issues]: https://example.com/FIXME/issues
-[contact]: mailto:[email protected]
 [cp-site]: https://carpentries.org/
-[dc-issues]: https://github.com/issues?q=user%3Adatacarpentry
-[dc-lessons]: https://datacarpentry.org/lessons/
+[swc-site]: https://software-carpentry.org/
 [dc-site]: https://datacarpentry.org/
-[discuss-list]: https://carpentries.topicbox.com/groups/discuss
+[lc-site]: https://librarycarpentry.org/
 [github]: https://github.com
-[github-flow]: https://guides.github.com/introduction/flow/
+[contact]: mailto:[email protected]
 [github-join]: https://github.com/join
-[how-contribute]: https://egghead.io/courses/how-to-contribute-to-an-open-source-project-on-github
+[repo-issues]: https://github.com/datacarpentry/geospatial-workshop/issues
 [issues]: https://carpentries.org/help-wanted-issues/
+[template-doc]: https://carpentries.github.io/workbench/
+[dc-issues]: https://github.com/issues?q=user%3Adatacarpentry
 [lc-issues]: https://github.com/issues?q=user%3ALibraryCarpentry
 [swc-issues]: https://github.com/issues?q=user%3Aswcarpentry
-[swc-lessons]: https://software-carpentry.org/lessons/
-[swc-site]: https://software-carpentry.org/
-[lc-site]: https://librarycarpentry.org/
-[template-doc]: https://carpentries.github.io/workbench/
+[how-contribute]: https://egghead.io/courses/how-to-contribute-to-an-open-source-project-on-github
+[github-flow]: https://guides.github.com/introduction/flow/
+[repo]: https://github.com/datacarpentry/geospatial-workshop
+
+
+
diff --git a/LICENSE.md b/LICENSE.md
@@ -12,8 +12,8 @@ license][cc-by-legal].
 
 You are free:
 
-- to **Share**---copy and redistribute the material in any medium or format
-- to **Adapt**---remix, transform, and build upon the material
+- to **Share**\---copy and redistribute the material in any medium or format
+- to **Adapt**\---remix, transform, and build upon the material
 
 for any purpose, even commercially.
 
@@ -22,30 +22,30 @@ terms.
 
 Under the following terms:
 
-- **Attribution**---You must give appropriate credit (mentioning that your work
+- **Attribution**\---You must give appropriate credit (mentioning that your work
   is derived from work that is Copyright (c) The Carpentries and, where
-  practical, linking to <https://carpentries.org/>), provide a [link to the
+  practical, linking to [https://carpentries.org/](https://carpentries.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.
 
-- **No additional restrictions**---You may not apply legal terms or
+- **No additional restrictions**\---You may not apply legal terms or
   technological measures that legally restrict others from doing anything the
   license permits.  With the understanding that:
 
 Notices:
 
-* You do not have to comply with the license for elements of the material in
+- You do not have to comply with the license for elements of the material in
   the public domain or where your use is permitted by an applicable exception
   or limitation.
-* No warranties are given. The license may not give you all of the permissions
+- No warranties are given. The license may not give you all of the permissions
   necessary for your intended use. For example, other rights such as publicity,
   privacy, or moral rights may limit how you use the material.
 
 ## Software
 
 Except where otherwise noted, the example programs and other software provided
-by The Carpentries are made available under the [OSI][osi]-approved [MIT
+by The Carpentries are made available under the [OSI][osi]\-approved [MIT
 license][mit-license].
 
 Permission is hereby granted, free of charge, to any person obtaining a copy of
@@ -74,6 +74,9 @@ Initiatives][ci].
 
 [cc-by-human]: https://creativecommons.org/licenses/by/4.0/
 [cc-by-legal]: https://creativecommons.org/licenses/by/4.0/legalcode
+[osi]: https://opensource.org
 [mit-license]: https://opensource.org/licenses/mit-license.html
 [ci]: https://communityin.org/
-[osi]: https://opensource.org
+
+
+
diff --git a/config.yaml b/config.yaml
@@ -14,7 +14,7 @@ carpentry: 'dc'
 title: 'Geospatial Workshop Overview'
 
 # Date the lesson was created (YYYY-MM-DD, this is empty by default)
-created: ~ # FIXME
+created: '2018-03-06'
 
 # Comma-separated list of keywords for the lesson
 keywords: 'software, data, lesson, The Carpentries' # FIXME

diff --git a/index.md b/index.md
@@ -26,7 +26,6 @@ Similarly, learners who have prior experience with the `R` programming language
 To get started, follow the directions in the [Setup](learners/setup.md) tab to
 get access to the required software and data for this workshop.
 
-
 ::::::::::::::::::::::::::::::::::::::::::::::::::
 
 ::::::::::::::::::::::::::::::::::::::::::  prereq
@@ -53,7 +52,7 @@ These data files represent the teaching version of the data, with sufficient com
 management, but with many complexities removed to allow students to focus on the core ideas and skills being taught.
 
 | Dataset                      | File name                                                                                  | Description                                                                                                                                                                                                                                             | 
-| ---------------------------- | ------------------------------------------------------------------------------------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| ------------------------------------------------------------------------------------------------------------------------- | ----------------------------------------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
 | Site layout shapefiles       | NEON-DS-Site-Layout-Files.zip                                                              | A set of shapefiles for the NEON's Harvard Forest field site and US and (some) state boundary layers.                                                                                                                                                   | 
 | Meteorological data          | NEON-DS-Met-Time-Series.zip                                                                | Precipitation, temperature and other variables collected from a flux tower at the NEON Harvard Forest site                                                                                                                                              | 
 | Airborne remote sensing data | NEON-DS-Airborne-RemoteSensing.zip                                                         | LiDAR data collected by the NEON Airborne Observation Platform (AOP) and processed at NEON including a canopy height model, digital elevation model and digital surface model for NEON's Harvard Forest and San Joaquin Experimental Range field sites. | 
@@ -66,7 +65,7 @@ management, but with many complexities removed to allow students to focus on the
 # Workshop Overview
 
 | Lesson                       | Overview                                                                                   | 
-| ---------------------------- | ------------------------------------------------------------------------------------------ |
+| ---------------------------------------------------------- | ------------------------------------------------------------ |
 | [Introduction to Geospatial Concepts](https://www.datacarpentry.org/organization-geospatial/)                             | Understand data structures and common storage and transfer formats for spatial data.       | 
 | [Introduction to R for Geospatial Data](https://www.datacarpentry.org/r-intro-geospatial)                             | Import data into R, calculate summary statistics, and create publication-quality graphics. | 
 | [Introduction to Geospatial Raster and Vector Data with R](https://www.datacarpentry.org/r-raster-vector-geospatial)                             | Open, work with, and plot vector and raster-format spatial data in R.                      | 

diff --git a/instructors/instructor-notes.md b/instructors/instructor-notes.md
@@ -10,9 +10,9 @@ The following table provides the structure for the Geospatial Workshop and *esti
 
 | Lesson | Length                             | Include if:                                       | 
 | ------ | ---------------------------------- | ------------------------------------------------- |
-| [Introduction to Geospatial Concepts](https://datacarpentry.org/organization-geospatial/) ([instructor notes](https://datacarpentry.org/organization-geospatial/guide/index.html))     | **75 minutes** - estimated, will not be accurate | Learners have no experience with geospatial data. | 
-| [Introduction to R for Geospatial Data](https://datacarpentry.org/r-intro-geospatial/) ([instructor notes](https://datacarpentry.org/r-intro-geospatial/guide/index.html))     | **4 hours** - estimated, will not be accurate | Learners have no experience with R.               | 
-| [Introduction to Geospatial Raster and Vector Data with R](https://datacarpentry.org/r-raster-vector-geospatial/) ([instructor notes](https://datacarpentry.org/r-raster-vector-geospatial/guide/index.html))     | **7 hours** - estimated, will not be accurate | Always.                                           | 
+| [Introduction to Geospatial Concepts](https://datacarpentry.org/organization-geospatial/) ([instructor notes](https://datacarpentry.org/organization-geospatialinstructor/instructor-notes.html))     | **75 minutes** - estimated, will not be accurate | Learners have no experience with geospatial data. | 
+| [Introduction to R for Geospatial Data](https://datacarpentry.org/r-intro-geospatial/) ([instructor notes](https://datacarpentry.org/r-intro-geospatialinstructor/instructor-notes.html))     | **4 hours** - estimated, will not be accurate | Learners have no experience with R.               | 
+| [Introduction to Geospatial Raster and Vector Data with R](https://datacarpentry.org/r-raster-vector-geospatial/) ([instructor notes](https://datacarpentry.org/r-raster-vector-geospatialinstructor/instructor-notes.html))     | **7 hours** - estimated, will not be accurate | Always.                                           | 
 
 If the workshop audience is experienced in both R and geospatial concepts, this workshop could theoretically be taught in one day. However, note that these timings are estimates and we are relying on feedback from pilot workshop Instructors to add accurate timing information.
 
@@ -23,7 +23,7 @@ If the workshop audience is experienced in both R and geospatial concepts, this
 #### Installation
 
 - For the [Introduction to Geospatial Raster and Vector Data with R](https://datacarpentry.org/r-raster-vector-geospatial/) lesson, learners MUST download the data and install the software before the workshop. The data set is large (>150 Mb) and there are numerous software packages and R libraries to install. **Remind your learners multiple times!**
-  - Instructions to download data and set up a machine to analyze and process geospatial data: [http://datacarpentry.org/geospatial-workshop/setup.html](https://datacarpentry.org/geospatial-workshop/setup.html)
+  - Instructions to download data and set up a machine to analyze and process geospatial data: [http://datacarpentry.org/geospatial-workshop/setup.html](https://datacarpentry.org/geospatial-workshop/index.html#setup)
 - You may find it helpful to host an "install party" prior to your workshop where you and your co-instructors help learners install the necessary software for the workshop. If this is unfeasible, leave time at the beginning of your workshop to ensure that learners have necessary geospatial software (GDAL, GEOS, PROJ.4) installed prior to teaching the course.
 
 [Instructors: add information about supporting learners with installation here]

diff --git a/learners/setup.md b/learners/setup.md
@@ -36,15 +36,15 @@ We provide quick instructions below for installing the various software needed f
 
 The installation of the geospatial libraries GDAL, GEOS, and PROJ.4 varies significantly based on operating system. These are all dependencies for `sf`, the `R` package that we will be using for spatial data operations throughout this workshop.
 
-:::::::::::::::  solution
+:::::::::::::::: spoiler
 
 ## Windows
 
 To install the geospatial libraries, install the latest version [RTools](https://cran.r-project.org/bin/windows/Rtools/)
 
 :::::::::::::::::::::::::
 
-:::::::::::::::  solution
+:::::::::::::::: spoiler
 
 ## macOS - Install with Packages (Beginner)
 
@@ -54,7 +54,7 @@ After downloading the package in the link above, you will need to double-click t
 
 :::::::::::::::::::::::::
 
-:::::::::::::::  solution
+:::::::::::::::: spoiler
 
 ## macOS - Install with Homebrew (Advanced)
 
@@ -69,7 +69,7 @@ $ brew install gdal2
 
 :::::::::::::::::::::::::
 
-:::::::::::::::  solution
+:::::::::::::::: spoiler
 
 ## Linux
 
@@ -103,7 +103,7 @@ For **Debian**: The [rocker geospatial](https://github.com/rocker-org/geospatial
 
 Linux users will have to install UDUNITS separately. Like the geospatial libraries discussed above, this is a dependency for the `R` package `sf`. Due to conflicts, it does not install properly on Linux machines when installed as part of the `sf` installation process. It is therefore necessary to install it using the command line ahead of time.
 
-:::::::::::::::  solution
+:::::::::::::::: spoiler
 
 ## Linux
 
@@ -139,23 +139,23 @@ $ sudo apt-get install -y libudunits2-dev
 
 Participants who do not already have `R` installed should download and install it.
 
-:::::::::::::::  solution
+:::::::::::::::: spoiler
 
 ## Windows
 
 To install `R`, Windows users should select "Download R for Windows" from RStudio and CRAN's [cloud download page](https://cloud.r-project.org), which will automatically detect a CRAN mirror for you to use. Select the `base` subdirectory after choosing the Windows download page. A `.exe` executable file containing the necessary components of base R can be downloaded by clicking on "Download R 3.x.x for Windows".
 
 :::::::::::::::::::::::::
 
-:::::::::::::::  solution
+:::::::::::::::: spoiler
 
 ## macOS
 
 To install `R`, macOS users should select "Download R for (Mac) OS X" from RStudio and CRAN's [cloud download page](https://cloud.r-project.org), which will automatically detect a CRAN mirror for you to use. A `.pkg` file containing the necessary components of base R can be downloaded by clicking on the first available link (this will be the most recent), which will read `R-3.x.x.pkg`.
 
 :::::::::::::::::::::::::
 
-:::::::::::::::  solution
+:::::::::::::::: spoiler
 
 ## Linux
 
@@ -226,7 +226,7 @@ Once up and running - you'll have full access to RStudio right from your browser
 
 Please be aware that the `R` package `rasterVis` is not included in the `rocker/geospatial` Docker image. If your instructor teaches with this package then you will need to install this `R` package yourself. All other `R` packages will already be installed for you.
 
-:::::::::::::::  solution
+:::::::::::::::: spoiler
 
 ## Downloading and Installing Docker Community Edition
 
@@ -238,7 +238,7 @@ Additional installation notes are available in Docker's documentation for each o
 
 :::::::::::::::::::::::::
 
-:::::::::::::::  solution
+:::::::::::::::: spoiler
 
 ## Using the `rocker/geospatial` Docker Image via the Command Line
 
@@ -296,7 +296,7 @@ If you are returning to a session after stopping Docker itself, make sure Docker
 
 :::::::::::::::::::::::::
 
-:::::::::::::::  solution
+:::::::::::::::: spoiler
 
 ## Using the `rocker/geospatial` Docker Image via Kitematic
 
@@ -330,7 +330,7 @@ You can restart your container later by clicking the `Restart` button.
 
 :::::::::::::::::::::::::
 
-:::::::::::::::  solution
+:::::::::::::::: spoiler
 
 ## Managing Docker Containers and Images