From abb5726a583c0ac3ae1b0f936d43cb9fb1a009fc Mon Sep 17 00:00:00 2001
From: Liam Keegan <liam@keegan.ch>
Date: Tue, 17 Dec 2024 15:12:35 +0100
Subject: [PATCH] update model python lib install instructions, add
 requriements/env files to web page for download

---
 .github/workflows/docs.yml |  1 +
 docs/models.md             | 28 +++++++++++++++++++++++++---
 2 files changed, 26 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
index 1c377f9..78bf197 100644
--- a/.github/workflows/docs.yml
+++ b/.github/workflows/docs.yml
@@ -25,4 +25,5 @@ jobs:
           restore-keys: |
             mkdocs-material-
       - run: pip install mkdocs-material
+      - run: cp requirements.txt environment.yml docs/.
       - run: mkdocs gh-deploy --force
diff --git a/docs/models.md b/docs/models.md
index 045f135..64bc5ef 100644
--- a/docs/models.md
+++ b/docs/models.md
@@ -2,7 +2,29 @@
 
 Example models and data are provided at [github.com/ZhaoWenzhao/QHCC](https://github.com/ZhaoWenzhao/QHCC).
 
-In order to run the provided example scripts, you will need to use Python 3.8 or 3.9, and install the required Python libraries:
+In order to run the provided example scripts, you will need to use Python 3.8 or 3.9, and install the required Python libraries.
+You can do this with pip, by first [downloading requirements.txt](requirements.txt) and then running:
+
+=== "pip"
+    ```bash
+    pip install -r requirements.txt
+    ```
+
+Or with conda or micromamba, by first [downloading environment.yml](environment.yml) and then running:
+
+=== "conda"
+    ```bash
+    conda env create -f environment.yml
+    conda activate QHCC
+    ```
+
+=== "micromamba"
+    ```bash
+    micromamba env create -f environment.yml
+    micromamba activate QHCC
+    ```
+
+Alternatively you can install the required Python libraries directly:
 
 === "pip"
     ```bash
@@ -11,12 +33,12 @@ In order to run the provided example scripts, you will need to use Python 3.8 or
 
 === "conda"
     ```bash
-    conda env create -n QHCC2 jupyter numpy pandas pooch python radiomics::pyradiomics simpleitk scikit-learn xgboost -c conda-forge -c radiomics
+    conda env create -n QHCC jupyter numpy pandas pooch python radiomics::pyradiomics simpleitk scikit-learn xgboost -c conda-forge -c radiomics
     conda activate QHCC
     ```
 
 === "micromamba"
     ```bash
-    micromamba env create -n QHCC2 jupyter numpy pandas pooch python radiomics::pyradiomics simpleitk scikit-learn xgboost -c conda-forge -c radiomics
+    micromamba env create -n QHCC jupyter numpy pandas pooch python radiomics::pyradiomics simpleitk scikit-learn xgboost -c conda-forge -c radiomics
     micromamba activate QHCC
     ```