From 8c1b8a6796df0aac175d97e7cf50b60cfdda01d2 Mon Sep 17 00:00:00 2001
From: Ben Jeffery <ben.jeffery@bdi.ox.ac.uk>
Date: Thu, 19 May 2022 00:56:02 +0100
Subject: [PATCH] Fix linux wheel building and testing

---
 .github/workflows/docker/buildwheel.sh | 6 ++++--
 .github/workflows/docker/shared.env    | 2 +-
 .github/workflows/wheels.yml           | 8 ++++++--
 3 files changed, 11 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/docker/buildwheel.sh b/.github/workflows/docker/buildwheel.sh
index 0054f3067..0d1d9f392 100644
--- a/.github/workflows/docker/buildwheel.sh
+++ b/.github/workflows/docker/buildwheel.sh
@@ -21,12 +21,14 @@ git config --global --add safe.directory /project
 # Fetch the full history as we'll be missing tags otherwise.
 git fetch --unshallow
 for V in "${PYTHON_VERSIONS[@]}"; do
+    git reset --hard
+    git clean -fd
     PYBIN=/opt/python/$V/bin
     rm -rf build/       # Avoid lib build by one Python is used by another
     $PYBIN/python -m venv env
     source env/bin/activate
-    python -m pip install --upgrade build
-    SETUPTOOLS_SCM_DEBUG=1 python -m build
+    $PYBIN/python -m pip install --upgrade build
+    SETUPTOOLS_SCM_DEBUG=1 $PYBIN/python -m build
 done
 
 cd dist
diff --git a/.github/workflows/docker/shared.env b/.github/workflows/docker/shared.env
index 9f0c3fa06..8e088f14d 100644
--- a/.github/workflows/docker/shared.env
+++ b/.github/workflows/docker/shared.env
@@ -1,7 +1,7 @@
 PYTHON_VERSIONS=(
-    cp310-cp310
     cp39-cp39
     cp38-cp38
     cp37-cp37m
+    cp310-cp310
 )
 GSL_VERSION=2.6
diff --git a/.github/workflows/wheels.yml b/.github/workflows/wheels.yml
index 583182307..d46883876 100644
--- a/.github/workflows/wheels.yml
+++ b/.github/workflows/wheels.yml
@@ -93,7 +93,9 @@ jobs:
         run: |
           python -VV
           # Install the local wheel
-          pip install msprime --only-binary msprime -f .
+          pip install msprime
+          pip uninstall --yes msprime
+          pip install msprime --no-index --only-binary msprime -f .
           python -c "import msprime"
           msp simulate 10 tmp.trees
           tskit info tmp.trees
@@ -118,7 +120,9 @@ jobs:
         run: |
           python -VV
           # Install the local wheel
-          pip install msprime --only-binary msprime -f .
+          pip install msprime
+          pip uninstall --yes msprime
+          pip install msprime --no-index --only-binary msprime -f .
           python -c "import msprime"
           msp simulate 10 tmp.trees
           tskit info tmp.trees