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docs/Software/Reproducible_Software.md

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+---
+tags:
+    - software
+    - reproducible
+    - reproducibility
+    - environments
+    - containers
+---
+
+## Research Software
+
+According to [this article in Nature](https://www.nature.com/articles/s41597-022-01710-x):
+
+> Research software is a fundamental and vital part of research, yet significant challenges 
+> to discoverability, productivity, quality, reproducibility, and sustainability exist.
+
+So what can we as researchers and technologists do to make our software easier to reproduce and use?
+Below are some tips, tricks and best practice to help get you started.
+
+```mermaid
+flowchart TD
+        A{"Do you require a specific operating system?"}
+        A -- "Yes" ---> CON
+        A -- "No" ---> B
+
+        B{"What software are you using?"}
+        B -- "Python" ---> D
+        B -- "Other" ---> C
+
+        C{"Do you need to match environments with another computer?"}
+        C -- "Yes" ---> E
+        C -- "No" ---> ENVM
+
+        D{"How many packages are you using?"}
+        D -- "Few" ---> ENVM
+        D -- "Dozens" ---> VENV
+        D -- "Hundreds" ---> CONDA
+
+        E{"Can you build it yourself?"}
+        E -- "Yes" ---> BLD
+        E -- "No" --->  CON
+
+        BLD["Build the software from source"]
+        ENVM["Use the Environment Module"]
+        CON["Use a Apptainer container"]
+        CONDA["Use Conda / Mamba"]
+        VENV["Use Python Virtual Environment"]
+```
+
+
+## Established Software Environment Tools
+
+### Environment Modules
+
+The most simple way to access software on the cluster is using [Environment Modules]().
+
+This will get you access to a specific version of your software, built for the clusters hardware.
+
+If you want to exactly replicate your local environment this may not be suitable.
+
+### Conda/Mamba Environments
+
+Conda environments are supported via the [Miniforge3](../Software/Available_Applications/Miniforge3.md) module.
+
+### Python Virtual Environments
+
+TODO: find and point to venv
+
+## New Tools for Reproducible Environments
+
+### uv
+
+The [uv](../Software/Available_Applications/uv.md) package manager is available as module.
+
+### pixi
+
+TODO: new page
+
+### anything else work mentioning?
+
+
+## Containerisation
+
+Containers are supported on Mahuika via [Apptainer](Available_Applications/Apptainer.md).
+
+## Compiled Software
+
+In addition to the ability to search available modules using `module spider <search-term>`, all installed modules and available versions can be found in [this table](Available_Applications/index.md).