Fix osx tests

.github/workflows/tests.yml

@@ -74,27 +74,27 @@ jobs:
       - name: Checkout
         uses: actions/checkout@v3
 
+      - name: Install OSX libs
+        if: matrix.os == 'macos-latest'
+        run: |
+          brew install libxml2 libxslt
+
       - name: Cache conda and dependencies
         id: cache
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         with:
-          path: |
-            c:\Miniconda\envs\anaconda-client-env
-            /usr/share/miniconda/envs/anaconda-client-env
-            ~/osx-conda
-            ~/.profile
-          key: ${{ runner.os }}-${{ matrix.python}}-conda-v12-${{ hashFiles('python/requirements/CI-tests-conda/requirements.txt') }}-${{ hashFiles('python/requirements/CI-tests-pip/requirements.txt') }}
+          path: ${{ env.CONDA }}/envs
+          key: ${{ runner.os }}-${{ runner.arch }}-${{ matrix.python}}-conda-v1-${{ hashFiles('python/requirements/CI-tests-conda/requirements.txt') }}-${{ hashFiles('python/requirements/CI-tests-pip/requirements.txt') }}
 
       - name: Install Conda
-        uses: conda-incubator/setup-miniconda@v2
+        uses: conda-incubator/setup-miniconda@v3
         if: steps.cache.outputs.cache-hit != 'true'
         with:
           activate-environment: anaconda-client-env
           python-version: ${{ matrix.python }}
           channels: conda-forge
           channel-priority: strict
           auto-update-conda: true
-          use-only-tar-bz2: true
 
       - name: Fix windows symlinks
         working-directory: python
@@ -123,17 +123,8 @@ jobs:
         run: |
           pip install setuptools==57.5.0 #v58 broke some deps https://setuptools.pypa.io/en/latest/history.html#v58-0-0
           pip install -r python/requirements/CI-tests-pip/requirements.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
-
-      - name: Fix OSX Cache Restore
-        if: steps.cache.outputs.cache-hit == 'true' && matrix.os == 'macos-latest'
-        run: |
-          mkdir -p /usr/local/miniconda/envs
-          sudo cp -r ~/osx-conda /usr/local/miniconda/envs/anaconda-client-env
+          # Remove tskit installed by conda
+          pip uninstall -y tskit
 
       - name: Build module
         working-directory: python

python/requirements/CI-tests-conda/requirements.txt

@@ -1,4 +1,2 @@
 msprime==1.2.0
-kastore==0.3.2
-jsonschema==4.16.0
 h5py==3.7.0

python/requirements/CI-tests-pip/requirements.txt

@@ -12,3 +12,5 @@ networkx==3.1
 msgpack==1.0.4
 newick==1.3.2
 tszip==0.2.2
+kastore==0.3.2
+lxml==4.9.2

python/tests/test_balance_metrics.py

@@ -1,6 +1,6 @@
 # MIT License
 #
-# Copyright (c) 2022 Tskit Developers
+# Copyright (c) 2024 Tskit Developers
 #
 # Permission is hereby granted, free of charge, to any person obtaining a copy
 # of this software and associated documentation files (the "Software"), to deal
@@ -119,7 +119,7 @@ def test_b2(self, ts):
                 with pytest.raises(ValueError):
                     b2_index_definition(tree)
             else:
-                assert tree.b2_index() == b2_index_definition(tree)
+                assert tree.b2_index() == pytest.approx(b2_index_definition(tree))
 
     @pytest.mark.parametrize("ts", get_example_tree_sequences())
     @pytest.mark.parametrize("base", [0.1, 1.1, 2, 10, math.e, np.array([3])[0]])
@@ -131,7 +131,9 @@ def test_b2_base(self, ts, base):
                 with pytest.raises(ValueError):
                     b2_index_definition(tree, base)
             else:
-                assert tree.b2_index(base) == b2_index_definition(tree, base)
+                assert tree.b2_index(base) == pytest.approx(
+                    b2_index_definition(tree, base)
+                )
 
 
 class TestBalancedBinaryOdd:

python/tests/test_ld_matrix.py

@@ -1035,7 +1035,7 @@ def test_sample_sets(partition):
     :param partition: length 2 list of [ss_1, ss_2].
     """
     ts = get_paper_ex_ts()
-    np.testing.assert_equal(
+    np.testing.assert_array_almost_equal(
         ld_matrix(ts, sample_sets=partition), ts.ld_matrix(sample_sets=partition)
     )
 
@@ -1055,7 +1055,9 @@ def test_multiallelic_with_back_mutation(stat):
         samples=4, recombination_rate=0.2, sequence_length=10, random_seed=1
     )
     ts = msprime.sim_mutations(ts, rate=0.5, random_seed=1)
-    np.testing.assert_array_equal(ld_matrix(ts, stat=stat), ts.ld_matrix(stat=stat))
+    np.testing.assert_array_almost_equal(
+        ld_matrix(ts, stat=stat), ts.ld_matrix(stat=stat)
+    )
 
 
 @pytest.mark.parametrize(
@@ -1068,7 +1070,9 @@ def test_multiallelic_with_back_mutation(stat):
 )
 @pytest.mark.parametrize("stat", SUMMARY_FUNCS.keys())
 def test_ld_matrix(ts, stat):
-    np.testing.assert_array_equal(ld_matrix(ts, stat=stat), ts.ld_matrix(stat=stat))
+    np.testing.assert_array_almost_equal(
+        ld_matrix(ts, stat=stat), ts.ld_matrix(stat=stat)
+    )
 
 
 @pytest.mark.parametrize(