slides and tweak container config

.devcontainer/Dockerfile

@@ -1,17 +1,9 @@
 FROM mcr.microsoft.com/devcontainers/base:jammy
-
 ARG PIXI_VERSION=v0.33.0
-
 RUN curl -L -o /usr/local/bin/pixi -fsSL --compressed "https://github.com/prefix-dev/pixi/releases/download/${PIXI_VERSION}/pixi-$(uname -m)-unknown-linux-musl" \
-
     && chmod +x /usr/local/bin/pixi \
-
     && pixi info
-
 # set some user and workdir settings to work nicely with vscode
-
 USER vscode
-
 WORKDIR /home/vscode
-
 RUN echo 'eval "$(pixi completion -s bash)"' >> /home/vscode/.bashrc

.devcontainer/devcontainer.json

@@ -1,16 +1,12 @@
 {
-  "name": "rypyr",
-
+  "name": "rypyrx",
   "build": {
     "dockerfile": "Dockerfile",
-
     "context": ".."
   },
-
   "customizations": {
     "vscode": {
       "settings": {},
-
       "extensions": [
         "ms-python.python",
         "ms-python.vscode-pylance",
@@ -28,18 +24,17 @@
         "quarto.quarto",
         "shd101wyy.markdown-preview-enhanced",
         "notzaki.pandocciter"
-
       ]
     }
   },
-
+  "hostRequirements": {
+    "memory": "4gb"
+  },
   "features": {
     "ghcr.io/devcontainers/features/docker-in-docker:2": {}
   },
-
   "mounts": [
     "source=${localWorkspaceFolderBasename}-pixi,target=${containerWorkspaceFolder}/.pixi,type=volume"
   ],
-
   "postCreateCommand": "sudo chown vscode .pixi && pixi install"
-}
+}

README.md

@@ -1,10 +1,19 @@
-# `rypyr`
+# `rypyrx`
 
-[![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://codespaces.new/knaaptime/rypyr)
+reproducible research environments, cross language/cross-platform
 
-pronounced 'ripper', like [repr](), but so that R people can grok reproducible Python environments
+[![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://codespaces.new/knaaptime/rypyrx)
 
-tl;dr: I write in quarto and do my work in both python and R. But lots of people still hate Python environments. I swear they are straightforward for this task now!
+pronounced 'rip-rex', like [reprex](https://reprex.tidyverse.org/), but so that R people can grok reproducible Python environments for papers et al
+
+tl;dr: I write in quarto and do my work in both Python and R. I work with lots of people who are new to Python environments, or hate them altogether. I swear they are straightforward for this task now!
+
+the important pieces are:
+
+- the `pixi.toml` file defines the dependencies and when installed pixi creates a lockfile to make sure you can re-create that *exact* environment anywhere
+- the files in `.devcontainer` setup codespaces to install the project dependencies and some useful vscode extensions (so you can run whatever notebooks you create in the cloud)
+- the files in `.github/workflows` setup the repo to serve a static website from the `slides` directory, so when you use quarto to generate slides in that directory, they're available immediately at `<{your-github}.github.io/{project_name}>` 
+  - the slides and paper are separate quarto projects which allows you to keep the repo private while you work on code and paper, but publish the slides (using the same materials) for giving conference talks etc while the paper is in draft.
 
 ## Goals
 
@@ -42,10 +51,14 @@ edit the notebooks as you like
 
 ## Execute and Build
 
-`cd paper`
+`cd paper`  
 `pixi run quarto render`
 
 will run the python and r noteooks and generate the html and pdf in `paper/_manuscript`
 
+**note** this workflow works perfectly when run locally (on my mac). Currently, quarto's default latex engine (tinytex) has a `PATH` issue when running through pixi in codespaces (which, given pixi's hyper-sandboxing, is not terribly surprising). You can get around that at the moment by using the tectonic engine for the pdf, like:
+
+`pixi run quarto render --pdf-engine tectonic`
+
 you can use `pixi run quarto preview` to preview while you work
 

pixi.toml

@@ -2,7 +2,7 @@
 channels = ["conda-forge", "r", "main"]
 description = "A demo project using quarto and pixi for full-stack reproducibility"
 name = "rypyr"
-platforms = ["linux-64", "win-64", "osx-64"] # I left osx-arm because theres no r-satellite <https://pixi.sh/v0.27.1/reference/project_configuration/#the-project-table>
+platforms = ["linux-64", "win-64", "osx-64", "linux-aarch64"] # I left out osx-arm because theres no r-satellite build <https://pixi.sh/v0.27.1/reference/project_configuration/#the-project-table>
 version = "0.1.0"
 
 [tasks]
@@ -34,7 +34,7 @@ rpy2 = "*"
 # R deps
 r-irkernel = "*"
 r-tidymodels = "*"
-#r-spdep = "*" # sfdep hasn't made it onto conda-forge yet
+#r-spdep = "*"  # sfdep hasn't made it onto conda-forge yet
 r-nlme = "*"
 r-lme4 = "*"
 r-tidycensus = "*"
@@ -43,3 +43,4 @@ r-reticulate = "*"
 r-mapview = "*" 
 r-languageserver = "*"
 r-tinytex = "*"
+r-devtools = "*"  # use install.packages() to get whatever, but you wont have a lockfile for those

slides/.gitignore

@@ -0,0 +1 @@
+/.quarto/

slides/_quarto.yml

@@ -0,0 +1,11 @@
+project:
+  type: website
+  output-dir: "." # publish from root of this dir
+format:
+  html:
+    embed-resources: true
+    theme: 
+      light: 
+        - flatly
+      dark: 
+        - cyborg