From 556b1112abcd02d6c37d0cb5ae78281ae3f770fd Mon Sep 17 00:00:00 2001 From: Jover Lee Date: Fri, 24 Jul 2026 14:08:21 -0700 Subject: [PATCH] Isolate fauna in Python venv Fauna is the only blocker on pandas v2 and we don't want to spend the time to upgrading fauna to work with pandas v2, so just isolate it in its own Python venv. This does require downstream workflows to activate the venv before running any fauna scripts. The only workflow actively using fauna is the seasonal-flu/upload workflow, so this should have minimal impact. Part of https://github.com/nextstrain/public/issues/12 --- Dockerfile | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index ab8e5ea..9662f4b 100644 --- a/Dockerfile +++ b/Dockerfile @@ -301,7 +301,8 @@ COPY builder-scripts/ /builder-scripts/ # Fauna WORKDIR /nextstrain/fauna RUN /builder-scripts/download-repo https://github.com/nextstrain/fauna master . \ - && pip3 install --requirement=requirements.txt + && python3 -m venv .venv \ + && .venv/bin/pip3 install --requirement=requirements.txt # Add Treetime RUN pip3 install phylo-treetime