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behinger (s-ccs 001) 2023-09-28 14:09:08 +00:00
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125
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
```
:::

8
material/1_mon/envs/tasks.qmd Normal file
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@ -0,0 +1,8 @@
# Task
1. Create a new package `MyStatsPackage` using `generate`
2. Add your `statistic.jl` & "include" it.
3. Export all functions
4. Create a new environment in a separate folder and add the package.
5. Does `using MyStatsPackage` work now? :tada: congratulations!
6. Go back to your package environment. Now add a dependency (e.g. ProgressMeter) and a `compat`-entry
7. Go back to your project environment, has the dependency been updated? Think: should you use `resolve` or `instantiate`?

3
material/1_mon/firststeps/statistic_functions.jl
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@ -1,8 +1,9 @@
#---
using ProgressMeter
function rse_sum(x)
s = 0
for k = eachindex(x)
@showprogress for k = eachindex(x)
s = s+x[k]
end
return s

11
material/1_mon/firststeps/tasks.qmd
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@ -19,7 +19,18 @@ You can mark some code and execute it using `ctrl` + `enter` - you can also gene
Well done! You now have all functions defined with which we will continue our journey.
::: callout
## Bonus Task ProgressMeter
for very large sums we might want to add a progressmeter. To do so:
```julia
]add ProgressMeter
using ProgressMeter
...
@showprogress for ...
```
And that's it! You should have a nice progress bar now
# Task 2 {#2}
1. Implement a type `StatResult` with fields for `x`, `n`, `std` and `tvalue`

2
material/3_wed/vis/Manifest.toml
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@ -2,7 +2,7 @@
julia_version = "1.9.2"
manifest_format = "2.0"
project_hash = "72e4df15571f2f16bde88622e0b2d85533f8eea7"
project_hash = "6b7e018e1e42b9e8dc72df15bdc780c4b72357b0"
[[deps.AbstractFFTs]]
deps = ["LinearAlgebra"]

1
material/3_wed/vis/Project.toml
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@ -3,3 +3,4 @@ AlgebraOfGraphics = "cbdf2221-f076-402e-a563-3d30da359d67"
DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
GLMakie = "e9467ef8-e4e7-5192-8a1a-b1aee30e663a"
PalmerPenguins = "8b842266-38fa-440a-9b57-31493939ab85"
ProgressMeter = "92933f4c-e287-5a05-a399-4b506db050ca"