Merge pull request #59 from benjeffery/ci

Add tests and lint to CI

Author: jeromekelleher

.flake8

@@ -0,0 +1,7 @@
+[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
+#B305 doesn't like `.next()` that is a key Tree method.
+ignore = E203, E501, W503, B305

.github/workflows/tests.yml

@@ -0,0 +1,48 @@
+name: Tests
+
+on:
+  pull_request:
+  push:
+    branches: [main, test]
+
+jobs:
+  pre-commit:
+    name: Lint
+    runs-on: ubuntu-latest
+    steps:
+      - name: Cancel Previous Runs
+        uses: styfle/[email protected]
+        with:
+          access_token: ${{ github.token }}
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+          python-version: '3.11'
+      - uses: pre-commit/[email protected]
+
+  test:
+    name: Python
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        python: [ "3.11" ]
+        os:  [ ubuntu-latest, ]
+    defaults:
+      run:
+        shell: bash
+    steps:
+      - name: Cancel Previous Runs
+        uses: styfle/[email protected]
+        with:
+          access_token: ${{ github.token }}
+
+      - name: Checkout
+        uses: actions/checkout@v3
+
+      - uses: actions/setup-python@v4
+        with:
+          python-version: '3.11'
+          cache: 'pip'
+      - run: pip install -r requirements.txt
+      - run: python -m pytest tests

.pre-commit-config.yaml

@@ -0,0 +1,37 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    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: v3.10.0
+    hooks:
+      - id: reorder-python-imports
+        args: [ --unclassifiable-application-module=_tsinfer ]
+  - repo: https://github.com/asottile/pyupgrade
+    rev: v3.10.1
+    hooks:
+      - id: pyupgrade
+        args: [ --py3-plus, --py310-plus ]
+  - repo: https://github.com/psf/black
+    rev: 23.7.0
+    hooks:
+      - id: black
+        language_version: python3
+  - repo: https://github.com/asottile/blacken-docs
+    rev: 1.16.0
+    hooks:
+      - id: blacken-docs
+        args: [--skip-errors]
+        additional_dependencies: [black==22.3.0]
+        language_version: python3
+  - repo: https://github.com/pycqa/flake8
+    rev: 6.1.0
+    hooks:
+      - id: flake8
+        args: [--config=.flake8]
+        additional_dependencies: ["flake8-bugbear==23.7.10", "flake8-builtins==2.1.0"]

model.py

@@ -2,7 +2,6 @@
 
 import tskit
 import numpy as np
-import utils
 import numba
 import pandas as pd
 import numba
@@ -156,11 +155,13 @@ def compute_per_tree_stats(ts):
         ts.edges_child,
     )
 
+
 class TSModel:
     """
     A wrapper around a tskit.TreeSequence object that provides some
     convenience methods for analysing the tree sequence.
     """
+
     def __init__(self, ts, name=None):
         self.ts = ts
         self.name = name

requirements.txt

@@ -3,4 +3,6 @@ hvplot
 xarray
 datashader
 tskit
-seaborn
+seaborn
+pre-commit
+pytest

tests/test_data_model.py

@@ -1,10 +1,8 @@
-import pytest
-import tskit
-import numpy.testing as nt
 import numpy as np
-
 import model
-import utils
+import numpy.testing as nt
+import tskit
+
 
 
 def single_tree_example_ts():
@@ -42,6 +40,7 @@ def single_tree_recurrent_mutation_example_ts():
     ts = tables.tree_sequence()
     return tables.tree_sequence()
 
+
 def multiple_trees_example_ts():
     # 2.00┊   4   ┊   4   ┊
     #     ┊ ┏━┻┓  ┊  ┏┻━┓ ┊
@@ -162,8 +161,7 @@ def test_single_tree_example(self):
         assert len(df) == 7
         nt.assert_array_equal(df.time, [0.0, 0.0, 0.0, 0.0, 1.0, 1.0, 2.0])
         nt.assert_array_equal(df.num_mutations, [1, 1, 1, 1, 1, 1, 0])
-        nt.assert_array_equal(df.ancestors_span, [
-                              10, 10, 10, 10, 10, 10, -np.inf])
+        nt.assert_array_equal(df.ancestors_span, [10, 10, 10, 10, 10, 10, -np.inf])
 
     def test_multiple_tree_example(self):
         ts = multiple_trees_example_ts()