WIP: Refresh Content

README.md

@@ -5,8 +5,17 @@ A lesson on creating and publishing packages in Python, implemented using the
 
 The website can be built locally using:
 
+Install R deps:
+```R
+> install.packages(c("sandpaper", "varnish", "pegboard"),
+  repos = c("https://carpentries.r-universe.dev/", getOption("repos")))
+```
+
+Build and serve website:
 ```bash
 $ Rscript build_script.R
 ```
 
 Please consult the Carpentries Workbench docs for info on setting up your R environment.
+
+For `vscode`, install the `R Extension for Visual Studio Code` plugin and install the `languageserver` to get syntax highlighting in R Markdown documents.

episodes/01-scripts-and-modules.Rmd

@@ -22,6 +22,8 @@ exercises: 2
 
 ## Python as a Scripting Language
 
+TODO: Cull text 
+
 Python is frequently used as a _scripting language_ by scientists and engineers due to
 its expressiveness, simplicity, and its rich ecosystem of third-party libraries. There
 isn't a hard line between a scripting language and a non-scripting language, but some
@@ -648,37 +650,9 @@ if __name__ == "__main__":
 ```
 An issue with our example is that it still requires the user to manually edit the file
 if they wish to change the input or outputs.  This problem can be solved by instead
-taking arguments from the command line. A simple interface can be created using
-`sys.argv`, which is a list of command line arguments in the form of strings:
-
-```python
-# file: SIR_model.py
-import sys
-
-def main():
-    # Note: sys.argv[0] is the name of our program!
-    pop_size = int(sys.argv[1])
-    beta = float(sys.argv[2])
-    gamma = float(sys.argv[3])
-    days = int(sys.argv[4])
-    I_0 = int(sys.argv[5])
-    output = sys.argv[6]
-
-    S, I, R = SIR_model(
-        pop_size=pop_size,
-        beta=beta,
-        gamma=gamma,
-        days=days,
-        I_0=I_0,
-    )
-    plot_SIR_model(S, I, R, save_to=output)
-
-if __name__ == "__main__":
-    main()
-```
+taking arguments from the command line.
 
-However, this requires the user to provide every argument in order, and doesn't allow
-default arguments. We can achieve a better interface using the built-in `argparse`
+We can achieve a better interface using the built-in `argparse`
 library. The comments in the code below explain how this works:
 
 ```python

episodes/03-building-and-installing.Rmd

@@ -575,7 +575,7 @@ This indicates that `pip` should install any version of `numpy` greater than 1.2
 that any version of `pyyaml` will do. If our installed `numpy` version is less than
 1.20, or if it isn't installed at all, `pip` will upgrade to the latest version that's
 compatible with the rest of our installed packages and our Python version. We'll cover
-software versioning in more detail in the [lesson on publishing](05-publishing.Rmd), but
+software versioning in more detail in the [lesson on publishing](04-publishing.Rmd), but
 now we'll simply cover some ways to specify which software versions we need:
 
 ```toml

episodes/04-publishing.Rmd

@@ -747,7 +747,7 @@ We can test the distribution of our package by uploading to TestPyPI.
 First we will need to create a "token" on test-pypi to use as a temporary password.
 
 ```bash
-$ hatch publish --repo testpypi --user __token__ --auth <your_token_here>
+$ hatch publish --repo https://test.pypi.org/legacy/ --user __token__ --auth pypi-token-here
 ```
 
 To avoid entering you token on the cmd line you can provide details as env variables

learners/setup.md

@@ -117,6 +117,15 @@ Setup your test-pypi account:
 
 ## Create project repo
 
+TODO: Create github template with init script + license + .gitignore
+
 Create a new repo in your github account called `learn-hatch` and clone it to your local machine.
 
-Tutor to discuss `.gitignore` and licences.
+Tutor to discuss `.gitignore` and licences.
+
+
+## Create Conda env
+
+TODO: create new conda env.yml to include in template repo
+
+- inc biopython, seaborn