From f41827650b3cf60a7df2a6505c59fdaf6966283f Mon Sep 17 00:00:00 2001
From: Daniel Weindl <daniel.weindl@helmholtz-munich.de>
Date: Wed, 29 Nov 2023 12:38:05 +0100
Subject: [PATCH] update docs / workflow

---
 .github/workflows/test_doc.yml |  4 ++--
 documentation/README.md        |  8 +-------
 scripts/run-sphinx-hasenv.sh   | 17 -----------------
 scripts/run-sphinx.sh          | 16 ----------------
 4 files changed, 3 insertions(+), 42 deletions(-)
 delete mode 100755 scripts/run-sphinx-hasenv.sh
 delete mode 100755 scripts/run-sphinx.sh

diff --git a/.github/workflows/test_doc.yml b/.github/workflows/test_doc.yml
index 07e0afdcc8..ca4766c5eb 100644
--- a/.github/workflows/test_doc.yml
+++ b/.github/workflows/test_doc.yml
@@ -67,10 +67,10 @@ jobs:
           sudo apt-get update \
             && sudo apt-get install -y \
               pandoc \
-              python3-venv
+            && pip install tox
 
       - name: Set up SWIG
         uses: ./.github/actions/setup-swig
 
       - name: Run sphinx
-        run: scripts/run-sphinx.sh
+        run: tox -e doc
diff --git a/documentation/README.md b/documentation/README.md
index af9f33320e..eece1de90e 100644
--- a/documentation/README.md
+++ b/documentation/README.md
@@ -12,7 +12,7 @@ The legacy GitHub Pages URL https://amici-dev.github.io/AMICI/ is set up as a
 redirect to RTD.
 
 The main configuration file is `documentation/conf.py` and the documentation
-is generated using `scripts/run-sphinx.sh`. The documentation is written to
+is generated using `tox -e doc`. The documentation is written to
 `documentation/_build/`.
 
 The documentation comprises:
@@ -50,12 +50,6 @@ Matlab documentation is processed by
 [mtoc++](https://www.morepas.org/software/mtocpp/docs/tools.html).
 This is configured in `matlab/mtoc/config`.
 
-#### Python documentation
-
-Python documentation is processed by doxygen and doxypypy using the script and
-filters in `scripts/`.
-
-
 ## Writing documentation
 
 ### Out-of-source documentation
diff --git a/scripts/run-sphinx-hasenv.sh b/scripts/run-sphinx-hasenv.sh
deleted file mode 100755
index e401737022..0000000000
--- a/scripts/run-sphinx-hasenv.sh
+++ /dev/null
@@ -1,17 +0,0 @@
-#!/bin/bash
-# Build the sphinx documentation in an environment prepared
-# as in run-sphinx.sh already
-
-SCRIPT_PATH=$(dirname $BASH_SOURCE)
-AMICI_PATH=$(cd $SCRIPT_PATH/.. && pwd)
-
-source ${AMICI_PATH}/doc-venv/bin/activate
-
-cd ${AMICI_PATH}/documentation
-
-rm -rf ${AMICI_PATH}/documentation/generated
-
-sphinx-build -T -E -W --keep-going -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html
-
-ret=$?
-if [[ $ret != 0 ]]; then exit $ret; fi
diff --git a/scripts/run-sphinx.sh b/scripts/run-sphinx.sh
deleted file mode 100755
index e7b1ce0861..0000000000
--- a/scripts/run-sphinx.sh
+++ /dev/null
@@ -1,16 +0,0 @@
-#!/bin/bash
-# generate code documentation via sphinx for upload to rtd
-
-SCRIPT_PATH=$(dirname $BASH_SOURCE)
-AMICI_PATH=$(cd $SCRIPT_PATH/.. && pwd)
-
-python3 -m venv ${AMICI_PATH}/doc-venv --clear
-source ${AMICI_PATH}/doc-venv/bin/activate
-python -m pip install --upgrade --no-cache-dir pip setuptools wheel
-(cd ${AMICI_PATH}/ && python -m pip install --exists-action=w --no-cache-dir -r documentation/rtd_requirements.txt)
-(cd ${AMICI_PATH}/ && python -m pip install --exists-action=w --no-cache-dir -r documentation/rtd_requirements2.txt)
-
-${AMICI_PATH}/scripts/run-sphinx-hasenv.sh
-
-ret=$?
-if [[ $ret != 0 ]]; then exit $ret; fi