Fixup CI

.flake8

@@ -0,0 +1,6 @@
+[flake8]
+# Based directly on Black's recommendations:
+# https://black.readthedocs.io/en/stable/the_black_code_style.html#line-length
+max-line-length = 81
+select = A,C,E,F,W,B,B950
+ignore = E203, E501, W503

.github/workflows/docs.yml

@@ -7,13 +7,6 @@ on:
     tags:
       - '*'
 
-env:
-  COMMIT_EMAIL: [email protected]
-  MAKE_TARGET: -C python
-  OWNER: tskit-dev
-  REPO: tskit
-  REQUIREMENTS: python/requirements/CI-docs/requirements.txt
-
 jobs:
   build-deploy-docs:
     name: Docs
@@ -29,26 +22,25 @@ jobs:
 
       - uses: actions/checkout@v4
 
-      - name: Setup Conda
-        uses: conda-incubator/setup-miniconda@v3
-        with:
-          miniforge-version: latest
-          activate-environment: tskit-docs-env
-
-      - name: Cache Conda env
-        uses: actions/cache@v4
+      - uses: actions/[email protected]
         with:
-          path: ${{ env.CONDA }}/envs
-          key: conda-${{ runner.os }}--${{ runner.arch }}--${{ hashFiles(env.REQUIREMENTS) }}-${{ env.CACHE_NUMBER }}
-        env:
-          CACHE_NUMBER: 0
-        id: cache
+          python-version: "3.11"
+          cache: "pip"
 
-      - name: Update environment
+      - name: Create venv and install deps (one by one to avoid conflict errors)
         run: |
-          mamba install -y python=3.12 doxygen pip
-          pip install -r ${{ env.REQUIREMENTS }}
-        if: steps.cache.outputs.cache-hit != 'true'
+          pip install --upgrade pip wheel
+          pip install -r requirements/CI-docs-pip/requirements.txt
 
       - name: Build Docs
-        run: make -C docs
+        run: |
+          cd docs
+          make
+
+      - name: Trigger docs site rebuild
+        if: github.ref == 'refs/heads/main'
+        run: |
+          curl -X POST https://api.github.com/repos/tskit-dev/tskit-site/dispatches \
+                    -H 'Accept: application/vnd.github.everest-preview+json' \
+                    -u AdminBot-tskit:${{ secrets.ADMINBOT_TOKEN }} \
+                    --data '{"event_type":"build-docs"}'

.github/workflows/tests.yml

@@ -26,7 +26,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python: [ 3.9, 3.12 ]
+        python: [ "3.10", 3.12 ]
         os:  [ macos-latest, ubuntu-24.04, windows-latest ]
     defaults:
       run:

.pre-commit-config.yaml

@@ -0,0 +1,29 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: check-merge-conflict
+      - id: debug-statements
+      - id: mixed-line-ending
+      - id: check-case-conflict
+      - id: check-yaml
+  - repo: https://github.com/asottile/reorder_python_imports
+    rev: v3.14.0
+    hooks:
+      - id: reorder-python-imports
+  - repo: https://github.com/asottile/pyupgrade
+    rev: v3.19.0
+    hooks:
+      - id: pyupgrade
+        args: [--py39-plus]
+  - repo: https://github.com/psf/black
+    rev: 24.10.0
+    hooks:
+      - id: black
+        language_version: python3
+  - repo: https://github.com/pycqa/flake8
+    rev: 7.1.1
+    hooks:
+      - id: flake8
+        args: [--config=.flake8]
+        additional_dependencies: ["flake8-bugbear==24.12.12", "flake8-builtins==2.5.0"]

requirements/CI-docs-pip/requirements.txt

@@ -5,6 +5,7 @@ sphinx-issues==4.1.0
 sphinx-argparse==0.4.0
 svgwrite==1.4.3
 tskit==0.6.0
+tsinfer==0.3.3
 scipy==1.14.1
 msprime==1.3.2
 sphinx-book-theme

tests/test_methods.py

@@ -23,7 +23,6 @@
 """
 Test tools for mapping between node sets of different tree sequences
 """
-
 from collections import defaultdict
 from itertools import combinations
 
@@ -99,10 +98,13 @@ def naive_compare(ts, other, transform=None):
     Ineffiecient but transparent function to compute dissimilarity
     and root-mean-square-error between two tree sequences.
     """
+
     def f(t):
         return np.log(1 + t)
-    if transform is not None:
-        f = transform
+
+    if transform is None:
+        transform = f
+
     shared_spans = naive_shared_node_spans(ts, other).toarray()
     max_span = np.max(shared_spans, axis=1)
     assert len(max_span) == ts.num_nodes
@@ -115,7 +117,9 @@ def f(t):
         else:
             for j in range(other.num_nodes):
                 if shared_spans[i, j] == max_span[i]:
-                    time_array[i, j] = np.abs(f(ts.nodes_time[i]) - f(other.nodes_time[j]))
+                    time_array[i, j] = np.abs(
+                        transform(ts.nodes_time[i]) - transform(other.nodes_time[j])
+                    )
                     dissimilarity_matrix[i, j] = 1 / (1 + time_array[i, j])
     best_match = np.argmax(dissimilarity_matrix, axis=1)
     best_match_spans = np.zeros((ts.num_nodes,))
@@ -180,9 +184,7 @@ def test_node_spans(self, ts):
         naive_ns = naive_node_span(ts)
         assert np.allclose(eval_ns, naive_ns)
 
-    @pytest.mark.parametrize(
-        "pair", combinations([true_simpl, true_unary], 2)
-    )
+    @pytest.mark.parametrize("pair", combinations([true_simpl, true_unary], 2))
     def test_shared_spans(self, pair):
         """
         Check that efficient implementation returns same answer as naive
@@ -205,13 +207,16 @@ def test_match_self(self, ts):
         assert np.allclose(time, ts.nodes_time)
         assert np.array_equal(hit, np.arange(ts.num_nodes))
 
+
 class TestDissimilarity:
 
     def verify_compare(self, ts, other, transform=None):
-        match_span, ts_span, other_span, rmse = naive_compare(ts, other, transform=transform)
+        match_span, ts_span, other_span, rmse = naive_compare(
+            ts, other, transform=transform
+        )
         dis = tscompare.compare(ts, other, transform=transform)
-        assert np.isclose(1.0 - match_span/ts_span, dis.arf)
-        assert np.isclose(match_span/other_span, dis.tpr)
+        assert np.isclose(1.0 - match_span / ts_span, dis.arf)
+        assert np.isclose(match_span / other_span, dis.tpr)
         assert np.isclose(ts_span - match_span, dis.dissimilarity)
         assert np.isclose(ts_span, dis.total_span[0])
         assert np.isclose(other_span, dis.total_span[1])
@@ -235,15 +240,15 @@ def test_basic_comparison(self, pair):
     def test_zero_dissimilarity(self, pair):
         dis = tscompare.compare(pair[0], pair[1])
         assert np.isclose(dis.dissimilarity, 0)
-        assert np.isclose(dis.arf,  0)
+        assert np.isclose(dis.arf, 0)
         assert np.isclose(dis.rmse, 0)
 
     def test_transform(self):
         dis1 = tscompare.compare(true_simpl, true_simpl, transform=lambda t: t)
         dis2 = tscompare.compare(true_simpl, true_simpl, transform=None)
         assert dis1.dissimilarity == dis2.dissimilarity
         assert dis1.rmse == dis2.rmse
-        self.verify_compare(true_simpl, true_ext, transform=lambda t: 1/(1 + t))
+        self.verify_compare(true_simpl, true_ext, transform=lambda t: 1 / (1 + t))
 
     def get_simple_ts(self, samples=None, time=False, span=False, no_match=False):
         # A simple tree sequence we can use to properly test various
@@ -397,12 +402,17 @@ def test_rmse(self):
         true_total_span = 46
         assert dis.total_span[0] == true_total_span
         assert dis.total_span[1] == true_total_span
+
         def f(t):
             return np.log(1 + t)
-        true_rmse = np.sqrt((
-            2 * 6 * (f(500) - f(200))**2 # nodes 4, 5
-            + 2 * 2 * (f(750) - f(600))**2 # nodes, 7, 8
-        ) / true_total_span)
+
+        true_rmse = np.sqrt(
+            (
+                2 * 6 * (f(500) - f(200)) ** 2  # nodes 4, 5
+                + 2 * 2 * (f(750) - f(600)) ** 2  # nodes, 7, 8
+            )
+            / true_total_span
+        )
         assert np.isclose(dis.arf, 0.0)
         assert np.isclose(dis.tpr, 1.0)
         assert np.isclose(dis.dissimilarity, 0.0)
@@ -414,12 +424,17 @@ def test_value_and_error(self):
         dis = tscompare.compare(ts, other)
         true_total_spans = (46, 47)
         assert dis.total_span == true_total_spans
+
         def f(t):
             return np.log(1 + t)
-        true_rmse = np.sqrt((
-            2 * 6 * (f(500) - f(200))**2 # nodes 4, 5
-            + 2 * 2 * (f(750) - f(600))**2 # nodes, 7, 8
-        ) / true_total_spans[0])
+
+        true_rmse = np.sqrt(
+            (
+                2 * 6 * (f(500) - f(200)) ** 2  # nodes 4, 5
+                + 2 * 2 * (f(750) - f(600)) ** 2  # nodes, 7, 8
+            )
+            / true_total_spans[0]
+        )
         assert np.isclose(dis.arf, 4 / true_total_spans[0])
         assert np.isclose(dis.tpr, (true_total_spans[0] - 4) / true_total_spans[1])
         assert np.isclose(dis.dissimilarity, 4)

tscompare/__init__.py

@@ -22,5 +22,10 @@
 """
 Tools for comparing tree sequences
 """
-from .methods import compare, node_spans, CladeMap, shared_node_spans, match_node_ages, ARFResult
-from .provenance import __version__
+from .methods import ARFResult  # noqa F401
+from .methods import CladeMap  # noqa F401
+from .methods import compare  # noqa F401
+from .methods import match_node_ages  # noqa F401
+from .methods import node_spans  # noqa F401
+from .methods import shared_node_spans  # noqa F401
+from .provenance import __version__  # noqa F401