From 7f63d32ede3be6ba5f3c298508db8987fc79a013 Mon Sep 17 00:00:00 2001
From: Ekaterina Noskova <ekaterina.e.noskova@gmail.com>
Date: Mon, 4 Nov 2024 20:45:59 +0100
Subject: [PATCH] Change tests

---
 .github/workflows/tests.yml | 49 +++++++++++++++++++++++++++++++------
 1 file changed, 42 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index f7b7538..31cdc85 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -31,15 +31,50 @@ jobs:
       - name: Checkout.
         uses: actions/checkout@v2
 
-      - name: Set up Conda environment.
-        uses: conda-incubator/setup-miniconda@v3
+      - name: find conda
+        id: find-conda
+        run: |
+          echo "CONDA=$CONDA" >> $GITHUB_OUTPUT
+
+      - name: fix conda permissions
+        if: runner.os == 'macOS'
+        run: |
+          # Fix incorrect conda permissions on mac that prevent cache restore.
+          sudo chown -R $USER:staff ${{ steps.find-conda.outputs.CONDA }}
+
+      - name: cache conda
+        id: cache
+        uses: actions/cache@v3
+        env:
+          # Increase this to reset the cache if the key hasn't changed.
+          CACHE_NUM: 9
+        with:
+          path: |
+            ${{ steps.find-conda.outputs.CONDA }}/envs/${{ env.CONDA_ENV_NAME }}
+            ~/.bash_profile
+          key: ${{ runner.os }}-${{ matrix.python }}-conda-${{ hashFiles('requirements/CI/*') }}-${{ env.CACHE_NUM }}
+
+      - name: install conda
+        uses: conda-incubator/setup-miniconda@v2
+        if: steps.cache.outputs.cache-hit != 'true'
         with:
-          auto-update-conda: true
-          python-version: ${{ matrix.python-version }}
-          channels: conda-forge,bioconda
           activate-environment: ${{ env.CONDA_ENV_NAME }}
-          
-      - name: Install dadi and scikit-allel using conda.
+          python-version: ${{ matrix.python }}
+          channels: conda-forge, bioconda
+          channel-priority: strict
+          auto-update-conda: true
+          use-only-tar-bz2: true
+
+      - name: move profile
+        if: steps.cache.outputs.cache-hit != 'true' && runner.os != 'Windows'
+        run: |
+          # The setup-miniconda action leaves different shell init files for
+          # different OSes. Bash gives priority to ~/.bash_profile, so here we
+          # ensure that's used for all platforms.
+          mv ~/.profile ~/.bash_profile
+
+      - name: install dadi and scikit-allel using conda.
+        if: steps.cache.outputs.cache-hit != 'true'
         run: |
           conda install dadi
           conda install scikit-allel