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improved materials

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behinger (s-ccs 001)
2023-09-28 14:09:08 +00:00
parent a14fbfbf67
commit 22258b264c
6 changed files with 97 additions and 53 deletions
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material/1_mon/envs/envs_handout.qmd
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@@ -139,6 +139,64 @@ version = "0.3.4"
[...]
```
## Projects in Julia
Formally, projects don't have specific requirements. You should activate an environment (`Project.toml`+`Manifest.toml`) in the main folder though. I recommend the following minimal structure:
- `./src/` - all functions should go there
- `./scripts/` - all actual scripts should go here,
- `./README.md` - Write what this is about, who you are etc.
- `./Project.toml` - Your explicit dependencies
- `./Manifest.toml` - Your implicit dependencies + versions <-- this makes it reproducible!
::: callout-tip
One recommendation is to use `DrWatson.initialize_project([path])` to start a new project - it will generate a nice folder structure + provide some other helpful `DrWatson.jl` features.
:::
:::{.callout-tip collapse="true"}
## Click to expand the full datastructure
```
│projectdir <- Project's main folder. It is initialized as a Git
│ repository with a reasonable .gitignore file.
│
├── _research <- WIP scripts, code, notes, comments,
│ | to-dos and anything in an alpha state.
│ └── tmp <- Temporary data folder.
│
├── data <- **Immutable and add-only!**
│ ├── sims <- Data resulting directly from simulations.
│ ├── exp_pro <- Data from processing experiments.
│ └── exp_raw <- Raw experimental data.
│
├── plots <- Self-explanatory.
├── notebooks <- Jupyter, Weave or any other mixed media notebooks.
│
├── papers <- Scientific papers resulting from the project.
│
├── scripts <- Various scripts, e.g. simulations, plotting, analysis,
│ │ The scripts use the `src` folder for their base code.
│ └── intro.jl <- Simple file that uses DrWatson and uses its greeting.
│
├── src <- Source code for use in this project. Contains functions,
│ structures and modules that are used throughout
│ the project and in multiple scripts.
│
├── README.md <- Optional top-level README for anyone using this project.
├── .gitignore <- by default ignores _research, data, plots, videos,
│ notebooks and latex-compilation related files.
│
├── Manifest.toml <- Contains full list of exact package versions used currently.
└── Project.toml <- Main project file, allows activation and installation.
Includes DrWatson by default.
```
:::
## Packages in Julia
Several thousand packages exist in Julia already. Take a thorough look before starting something new!
@@ -181,10 +239,10 @@ The default registry is [JuliaRegistries/General](https://github.com/JuliaRegist
### Adding dependencies
```julia
]activate ./path/to/MyStatsPackage
]add UnicodePlots
]add ProgressMeter
]compat # <1>
```
1. let's directly add a compat entry for UnicodePlots
1. let's directly add a compat entry for ProgressMeter
### Semantic Versioning
Following `semver` - three parts:
@@ -234,57 +292,22 @@ As you can see, develop version (`version < 1`) are treated a bit special in Jul
keep the compat list in alphabetical order - github-actions might behave very strange else.
:::
## Projects in Julia
### Internals of a package
Formally, projects don't have specific requirements. You should activate an environment (`Project.toml`+`Manifest.toml`) in the main folder though. I recommend the following minimal structure:
The file `./src/MyStatsPackage.jl` should contain:
```julia
module MyStatsPackage
using ProgressMeter # <1>
include("src/stats_functions.jl")
- `./src/` - all functions should go there
- `./scripts/` - all actual scripts should go here,
- `./README.md` - Write what this is about, who you are etc.
- `./Project.toml` - Your explicit dependencies
- `./Manifest.toml` - Your implicit dependencies + versions <-- this makes it reproducible!
export sum
export mean, tstat
::: callout-tip
One recommendation is to use `DrWatson.initialize_project([path])` to start a new project - it will generate a nice folder structure + provide some other helpful `DrWatson.jl` features.
(click the following tipp to expand the full datastructure)
:::
:::{.callout-tip collapse="true"}
end
```
│projectdir <- Project's main folder. It is initialized as a Git
│ repository with a reasonable .gitignore file.
│
├── _research <- WIP scripts, code, notes, comments,
│ | to-dos and anything in an alpha state.
│ └── tmp <- Temporary data folder.
│
├── data <- **Immutable and add-only!**
│ ├── sims <- Data resulting directly from simulations.
│ ├── exp_pro <- Data from processing experiments.
│ └── exp_raw <- Raw experimental data.
│
├── plots <- Self-explanatory.
├── notebooks <- Jupyter, Weave or any other mixed media notebooks.
│
├── papers <- Scientific papers resulting from the project.
│
├── scripts <- Various scripts, e.g. simulations, plotting, analysis,
│ │ The scripts use the `src` folder for their base code.
│ └── intro.jl <- Simple file that uses DrWatson and uses its greeting.
│
├── src <- Source code for use in this project. Contains functions,
│ structures and modules that are used throughout
│ the project and in multiple scripts.
│
├── README.md <- Optional top-level README for anyone using this project.
├── .gitignore <- by default ignores _research, data, plots, videos,
│ notebooks and latex-compilation related files.
│
├── Manifest.toml <- Contains full list of exact package versions used currently.
└── Project.toml <- Main project file, allows activation and installation.
Includes DrWatson by default.
1. We use GLMakie as a simple example as you need it on Wednesday again anyway - it does take a while to install though!
Now we are ready to use the package from a different environment
```julia
]dev ./path/to/MyStatsPackage
```
:::