Setup instructions; Customise README.md

Initial customisation of generic materials pointing people to instructions for installing Conda on their operating
system.

Rewrites the `README.md` for the particular lesson.

README.md

@@ -1,72 +1,39 @@
-# The Carpentries Workbench Template Markdown Lesson
+# TopoStats AFM Image Processing Tutorial
 
-This lesson is a template lesson that uses [The Carpentries Workbench][workbench]. 
+This lesson uses [The Carpentries Workbench][workbench] to develop training material for the [TopoStats][topostats]
+Atomic Force Microscopy batch image processing software.
 
-## Note about lesson life cycle stage
-Although the `config.yaml` states the life cycle stage as pre-alpha, **the template is stable and ready to use**. The life cycle stage is preset to `"pre-alpha"` as this setting is appropriate for new lessons initialised using the template.
+The course material is rendered and available [online][topostats-training].
 
-## Create a new repository from this template
+## Code of Conduct
 
-To use this template to start a new lesson repository, 
-make sure you're logged into Github.   
-Visit https://github.com/carpentries/workbench-template-md/generate
-and follow the instructions.
-Checking the 'Include all branches' option will save some time waiting for the first website build
-when your new repository is initialised.
+Please refer to the `CODE_OF_CONDUCT.md` at the top level of this repository.
 
-If you have any questions, contact [@tobyhodges](https://github.com/tobyhodges)
+## Contributing
 
-## Configure a new lesson
+Contributions are welcome, please see the `CONTRIBUTING.md` file at the top level of this repository.
 
-Follow the steps below to
-complete the initial configuration of a new lesson repository built from this template:
+### Building Locally
 
-1. **Make sure GitHub Pages is activated:**
-   navigate to _Settings_,
-   select _Pages_ from the left sidebar,
-   and make sure that `gh-pages` is selected as the branch to build from.
-   If no `gh-pages` branch is available, check _Actions_ to see if the first
-   website build workflows are still running.
-   The branch should become available when those have completed.
-1. **Adjust the `config.yaml` file:**
-   this file contains global parameters for your lesson site.
-   Individual fields within the file are documented with comments (beginning with `#`)
-   At minimum, you should adjust all the fields marked 'FIXME':
-   - `title`
-   - `created`
-   - `keywords`
-   - `life_cycle` (the default, _pre-alpha_, is the appropriate for brand new lessons)
-   - `contact`
-1. **Annotate the repository** with site URL and topic tags:
-   navigate back to the repository landing page and
-   click on the gear wheel/cog icon (similar to ⚙️) 
-   at the top-right of the _About_ box.
-   Check the "Use your GitHub Pages website" option,
-   and [add some keywords and other annotations to describe your lesson](https://cdh.carpentries.org/the-carpentries-incubator.html#topic-tags)
-   in the _Topics_ field.
-   At minimum, these should include:
-   - `lesson`
-   - the life cycle of the lesson (e.g. `pre-alpha`)
-   - the human language the lesson is written in (e.g. `deutsch`)
-1. **Adjust the 
-   `CODE_OF_CONDUCT.md`, `CONTRIBUTING.md`, and `LICENSE.md` files**
-   as appropriate for your project.
-   -  `CODE_OF_CONDUCT.md`: 
-      if you are using this template for a project outside The Carpentries,
-      you should adjust this file to describe 
-      who should be contacted with Code of Conduct reports,
-      and how those reports will be handled.
-   -  `CONTRIBUTING.md`:
-      depending on the current state and maturity of your project,
-      the contents of the template Contributing Guide may not be appropriate.
-      You should adjust the file to help guide contributors on how best
-      to get involved and make an impact on your lesson.
-   -  `LICENSE.md`:
-      in line with the terms of the CC-BY license,
-      you should ensure that the copyright information 
-      provided in the license file is accurate for your project.
-1. **Update this README with 
-   [relevant information about your lesson](https://carpentries.github.io/lesson-development-training/collaborating-newcomers.html#readme)**
-   and delete this section.
+To render these pages locally you need to have [R][r] installed. Instructions are
+[available](https://carpentries.github.io/workbench/#installation) but some additional steps have been taken to make
+sure the environment is reproducible.
 
+Once you have installed the dependencies you can render the pages locally by starting R in the project root and
+running...
+
+``` r
+sandpaper::serve()
+```
+
+This will build the pages and start a local web-server in R and open it in your default browser. These pages are "live"
+and as you edit and save them the web-site will be rebuilt and the pages updated.
+
+## Licensing
+
+Please refer to the `LICENSING.md` at the top level of this repository.
+
+[r]: https://www.r-project.org/
+[topostats]: https://afm-spm.github.io/topostats
+[topostats-training]: https://afm-spm.github.io/topostats-training
 [workbench]: https://carpentries.github.io/sandpaper-docs/

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
-

instructors/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.

learners/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