From b647f53655c8bc48abc25453f96980c1eaca416b Mon Sep 17 00:00:00 2001
From: Daniel Weindl <daniel.weindl@uni-bonn.de>
Date: Wed, 27 Nov 2024 09:07:35 +0100
Subject: [PATCH] CI: don't cache amici; pytest ignore amici_models; passenv
 BNGPATH

* Don't cache the amici installation.
  We are using amici/develop on purpose to detect problems early on. E.g., #1520 should have been detected much earlier.
* Ignore `amici_models` when collecting tests
* Use external BNGPATH if set
---
 .github/workflows/ci.yml |  2 +-
 pytest.ini               |  1 +
 tox.ini                  | 10 +++++++---
 3 files changed, 9 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 4db56ab55..f55f8f6b5 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -157,7 +157,7 @@ jobs:
 
     - name: Run tests
       timeout-minutes: 35
-      run: tox -e petab
+      run: tox -e petab && tox e -e petab -- pip uninstall -y amici
       env:
         CC: clang
         CXX: clang++
diff --git a/pytest.ini b/pytest.ini
index c852c729e..82ae58578 100644
--- a/pytest.ini
+++ b/pytest.ini
@@ -2,3 +2,4 @@
 addopts = "--doctest-modules"
 filterwarnings =
     ignore:.*inspect.getargspec\(\) is deprecated.*:DeprecationWarning
+norecursedirs = amici_models
diff --git a/tox.ini b/tox.ini
index e9193e0ad..d1937e4ee 100644
--- a/tox.ini
+++ b/tox.ini
@@ -29,7 +29,7 @@ envlist =
 # Base-environment
 
 [testenv]
-passenv = AMICI_PARALLEL_COMPILE,CC,CXX,MPLBACKEND
+passenv = AMICI_PARALLEL_COMPILE,CC,CXX,MPLBACKEND,BNGPATH
 
 # Sub-environments
 #  inherit settings defined in the base
@@ -75,10 +75,14 @@ description =
     Test basic functionality on Windows
 
 [testenv:petab]
-extras = test,amici,petab,pyswarm,roadrunner
+extras = test,petab,pyswarm,roadrunner
 deps =
     git+https://github.com/Benchmarking-Initiative/Benchmark-Models-PEtab.git@master\#subdirectory=src/python
-    git+https://github.com/AMICI-dev/amici.git@develop\#egg=amici&subdirectory=python/sdist
+# always install amici from develop branch, avoid caching
+#  to skip re-installation, run `tox -e petab --override testenv:petab.commands_pre=`
+commands_pre =
+    python3 -m pip uninstall -y amici
+    python3 -m pip install git+https://github.com/AMICI-dev/amici.git@develop\#egg=amici&subdirectory=python/sdist
 commands =
     python3 -m pip install git+https://github.com/PEtab-dev/petab_test_suite@main
     python3 -m pip install git+https://github.com/pysb/pysb@master