markdown source builds

Auto-generated via {sandpaper}
Source  : b28eef5
Branch  : main
Author  : Neil Shephard <[email protected]>
Time    : 2024-01-26 11:34:37 +0000
Message : Merge pull request #9 from AFM-SPM/ns-rse/setup

index.md

@@ -2,8 +2,8 @@
 site: sandpaper::sandpaper_site
 ---
 
-This is a new lesson built with [The Carpentries Workbench][workbench]. 
+Welcome to the training material for the [TopoStats][topostats] Atomic Force Microscopy image processing software.
 
 
+[topostats]: https://afm-spm.github.io/TopoStats
 [workbench]: https://carpentries.github.io/sandpaper-docs
-

instructor-notes.md

@@ -2,4 +2,5 @@
 title: 'Instructor Notes'
 ---
 
-This is a placeholder file. Please add content here. 
+Instructors should be familiar with the material contained in this course prior to delivery. It might be useful to run
+through the exercises yourself at least once.

md5sum.txt

@@ -2,10 +2,10 @@
 "CODE_OF_CONDUCT.md" "c93c83c630db2fe2462240bf72552548" "site/built/CODE_OF_CONDUCT.md" "2024-01-08"
 "LICENSE.md" "b24ebbb41b14ca25cf6b8216dda83e5f" "site/built/LICENSE.md" "2024-01-08"
 "config.yaml" "8b5eb93fb1a6714e2dfbcf08e1686b5c" "site/built/config.yaml" "2024-01-12"
-"index.md" "a02c9c785ed98ddd84fe3d34ddb12fcd" "site/built/index.md" "2024-01-08"
+"index.md" "32ded82e3af3920844de9879f05cc873" "site/built/index.md" "2024-01-26"
 "links.md" "8184cf4149eafbf03ce8da8ff0778c14" "site/built/links.md" "2024-01-08"
 "episodes/introduction.md" "6c55d31b41d322729fb3276f8d4371fc" "site/built/introduction.md" "2024-01-08"
-"instructors/instructor-notes.md" "cae72b6712578d74a49fea7513099f8c" "site/built/instructor-notes.md" "2024-01-08"
+"instructors/instructor-notes.md" "69e9a8d25797039f14984f17abc80042" "site/built/instructor-notes.md" "2024-01-26"
 "learners/reference.md" "1c7cc4e229304d9806a13f69ca1b8ba4" "site/built/reference.md" "2024-01-08"
-"learners/setup.md" "61568b36c8b96363218c9736f6aee03a" "site/built/setup.md" "2024-01-08"
+"learners/setup.md" "8ae366f9ee33e5f83c28d7b4d4765aa8" "site/built/setup.md" "2024-01-26"
 "profiles/learner-profiles.md" "60b93493cf1da06dfd63255d73854461" "site/built/learner-profiles.md" "2024-01-08"

setup.md

@@ -2,8 +2,15 @@
 title: Setup
 ---
 
-FIXME: Setup instructions live in this document. Please specify the tools and
-the data sets the Learner needs to have installed.
+This course teaches you the basics of using [TopoStats][topostats] to process Atomic Force Microscopy images. TopoStats
+is software written in the [Python][python] programming language so you will need this installed on your system. Most
+GNU/Linux and OSX operating systems already have Python installed however in order to make a reproducible environment
+available we will guide you through how to use [Conda][conda] environments to setup and install an isolated environment
+for installing TopoStats and its dependencies.
+
+Because of the vast heterogeneity in AFM images we have created a sample data set for you to work through this tutorial
+with. If time permits at the end of the class you can try processing your own images and instructors may be able to help
+with any problems that you encounter.
 
 ## Data Sets
 
@@ -12,34 +19,43 @@ FIXME: place any data you want learners to use in `episodes/data` and then use
        a relative link ( [data zip file](data/lesson-data.zip) ) to provide a
        link to it, replacing the example.com link.
 -->
-Download the [data zip file](https://example.com/FIXME) and unzip it to your Desktop
+Download the [data zip file](data/topostats-data.zip) and unzip it to your Desktop
 
 ## Software Setup
 
 ::::::::::::::::::::::::::::::::::::::: discussion
 
-### Details
+### Conda
+
+[Conda][conda] is an open-source, cross-platform, language-agnostic package manager and environment
+management system for the popular programming and data science languages [Python][python] and [R][r]. For the purposes
+of this class we will only be using the support for Python.
+
+We ask that you install Conda on your laptops prior to the class so we can maximise the time available for covering the
+course material. You do _not_ need to worry about creating any Conda environments before the class starts, we cover that
+as part of the material.
+
+The official [installation instructions](https://docs.conda.io/projects/conda/en/stable/user-guide/install/index.html)
+are comprehensive and detailed and should get you setup.
 
-Setup for different systems can be presented in dropdown menus via a `solution`
-tag. They will join to this discussion block, so you can give a general overview
-of the software used in this lesson here and fill out the individual operating
-systems (and potentially add more, e.g. online setup) in the solutions blocks.
+If you find you are having problems installing the software please contact [the
+instructors](mailto:[email protected]) for assistance.
 
 :::::::::::::::::::::::::::::::::::::::::::::::::::
 
 :::::::::::::::: solution
 
 ### Windows
 
-Use PuTTY
+[Installing Conda on Windows](https://docs.conda.io/projects/conda/en/stable/user-guide/install/windows.html)
 
 :::::::::::::::::::::::::
 
 :::::::::::::::: solution
 
 ### MacOS
 
-Use Terminal.app
+[Installing Conda on macOS](https://docs.conda.io/projects/conda/en/stable/user-guide/install/macos.html)
 
 :::::::::::::::::::::::::
 
@@ -48,7 +64,11 @@ Use Terminal.app
 
 ### Linux
 
-Use Terminal
+[Installing Conda on Linux](https://docs.conda.io/projects/conda/en/stable/user-guide/install/linux.html)
 
 :::::::::::::::::::::::::
 
+[conda]: https://docs.conda.io/en/latest/
+[python]: https://www.python.org
+[r]: https://www.r-project.org/
+[topostats]: https://afm-spm.github.io/TopoStats