From a1dc9456368fa21ba2782c34118adcb7b2f379a6 Mon Sep 17 00:00:00 2001
From: Ben Jeffery <ben.jeffery@bdi.ox.ac.uk>
Date: Tue, 17 Oct 2023 16:48:29 +0100
Subject: [PATCH] Simplify testing

---
 .github/workflows/tests.yml                 | 58 +++++----------------
 .mergify.yml                                | 24 ++++-----
 requirements/{CI-tests-conda.txt => ci.txt} |  0
 3 files changed, 24 insertions(+), 58 deletions(-)
 rename requirements/{CI-tests-conda.txt => ci.txt} (100%)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 948a630..e192f07 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -23,66 +23,32 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python: [ 3.7, 3.9 ]
-        os:  [ macos-latest, ubuntu-latest, windows-latest ]
-    defaults:
-      run:
-        shell: bash
+        python: [ 3.8, 3.11 ]
+        # Reinstate windows-latest when msprime has wheels
+        os:  [ macos-latest, ubuntu-latest] #, windows-latest ]
     steps:
       - name: Cancel Previous Runs
-        uses: styfle/cancel-workflow-action@0.6.0
+        uses: styfle/cancel-workflow-action@0.12.0
         with:
           access_token: ${{ github.token }}
 
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
         with:
           submodules: true
 
-      - name: Cache conda and dependancies
-        id: cache
-        uses: actions/cache@v2
-        with:
-          path: |
-            c:\Miniconda\envs\anaconda-client-env
-            /usr/share/miniconda/envs/anaconda-client-env
-            ~/osx-conda
-            ~/.profile
-          key: ${{ runner.os }}-${{ matrix.python}}-conda-v10-${{ hashFiles('requirements/CI-tests-conda.txt') }}
-
-      - name: Install Conda
-        uses: conda-incubator/setup-miniconda@v2
-        if: steps.cache.outputs.cache-hit != 'true'
+      - name: Set up Python ${{ matrix.python }}
+        uses: actions/setup-python@v4
         with:
-          activate-environment: anaconda-client-env
           python-version: ${{ matrix.python }}
-          channels: conda-forge
-          channel-priority: strict
-          auto-update-conda: true
-
-      - name: Fix windows .profile
-        if: steps.cache.outputs.cache-hit != 'true' && matrix.os == 'windows-latest'
-        run: |
-          cp ~/.bash_profile ~/.profile
-
-      - name: Install conda deps
-        if: steps.cache.outputs.cache-hit != 'true'
-        shell: bash -l {0} #We need a login shell to get conda
-        run: conda install --yes --file=requirements/CI-tests-conda.txt
-
-      - name: Fix OSX Cache Write #OSX Won't let the cache restore due to file perms
-        if: steps.cache.outputs.cache-hit != 'true' && matrix.os == 'macos-latest'
-        run: |
-          cp -r /usr/local/miniconda/envs/anaconda-client-env ~/osx-conda
+          cache: 'pip'
 
-      - name: Fix OSX Cache Restore
-        if: steps.cache.outputs.cache-hit == 'true' && matrix.os == 'macos-latest'
+      - name: Install dependencies
         run: |
-          mkdir -p /usr/local/miniconda/envs
-          sudo cp -r ~/osx-conda /usr/local/miniconda/envs/anaconda-client-env
+          which python
+          which python3
+          python -m pip install -r requirements/ci.txt
 
       - name: Run tests
         run: |
-          source ~/.profile
-          conda activate anaconda-client-env
           python -m pytest -xv -n2
diff --git a/.mergify.yml b/.mergify.yml
index 018c8fa..d02c7a8 100644
--- a/.mergify.yml
+++ b/.mergify.yml
@@ -4,12 +4,12 @@ queue_rules:
       - "#approved-reviews-by>=1"
       - "#changes-requested-reviews-by=0"
       - status-success=Lint
-      - status-success=Python (3.7, macos-latest)
-      - status-success=Python (3.9, macos-latest)
-      - status-success=Python (3.7, ubuntu-latest)
-      - status-success=Python (3.9, ubuntu-latest)
-      - status-success=Python (3.7, windows-latest)
-      - status-success=Python (3.9, windows-latest)
+      - status-success=Python (3.8, macos-latest)
+      - status-success=Python (3.11, macos-latest)
+      - status-success=Python (3.8, ubuntu-latest)
+      - status-success=Python (3.11, ubuntu-latest)
+      - status-success=Python (3.8, windows-latest)
+      - status-success=Python (3.11, windows-latest)
       - "status-success=ci/circleci: build"
 pull_request_rules:
   - name: Automatic rebase, CI and merge
@@ -20,12 +20,12 @@ pull_request_rules:
       - base=main
       - label=AUTOMERGE-REQUESTED
       - status-success=Lint
-      - status-success=Python (3.7, macos-latest)
-      - status-success=Python (3.9, macos-latest)
-      - status-success=Python (3.7, ubuntu-latest)
-      - status-success=Python (3.9, ubuntu-latest)
-      - status-success=Python (3.7, windows-latest)
-      - status-success=Python (3.9, windows-latest)
+      - status-success=Python (3.8, macos-latest)
+      - status-success=Python (3.11, macos-latest)
+      - status-success=Python (3.8, ubuntu-latest)
+      - status-success=Python (3.11, ubuntu-latest)
+      - status-success=Python (3.8, windows-latest)
+      - status-success=Python (3.11, windows-latest)
       - "status-success=ci/circleci: build"
     actions:
       queue:
diff --git a/requirements/CI-tests-conda.txt b/requirements/ci.txt
similarity index 100%
rename from requirements/CI-tests-conda.txt
rename to requirements/ci.txt