Remove 3.7 and update pre-commit to 3.8

.github/workflows/docker/shared.env

@@ -3,5 +3,4 @@ PYTHON_VERSIONS=(
     cp310-cp310
     cp39-cp39
     cp38-cp38
-    cp37-cp37m
 )

.github/workflows/wheels.yml

@@ -15,7 +15,7 @@ jobs:
     runs-on: macos-latest
     strategy:
       matrix:
-        python: [3.7, 3.8, 3.9, "3.10", 3.11]
+        python: [3.8, 3.9, "3.10", 3.11]
     steps:
       - name: Checkout
         uses: actions/checkout@v2
@@ -55,7 +55,7 @@ jobs:
     runs-on: windows-latest
     strategy:
       matrix:
-        python: [3.7, 3.8, 3.9, "3.10", 3.11]
+        python: [3.8, 3.9, "3.10", 3.11]
         wordsize: [64]
     steps:
       - name: Checkout
@@ -140,7 +140,7 @@ jobs:
     runs-on: macos-latest
     strategy:
       matrix:
-        python: [3.7, 3.8, 3.9, "3.10", 3.11]
+        python: [3.8, 3.9, "3.10", 3.11]
     steps:
       - name: Download wheels
         uses: actions/download-artifact@v2
@@ -162,7 +162,7 @@ jobs:
     runs-on: windows-latest
     strategy:
       matrix:
-        python: [3.7, 3.8, 3.9, "3.10", 3.11]
+        python: [3.8, 3.9, "3.10", 3.11]
         wordsize: [64]
     steps:
       - name: Download wheels
@@ -186,10 +186,9 @@ jobs:
     needs: ['manylinux']
     strategy:
       matrix:
-        python: [3.7, 3.8, 3.9, "3.10", 3.11]
+        python: [3.8, 3.9, "3.10", 3.11]
         include:
-          - python: 3.7
-            wheel: cp37
+
           - python: 3.8
             wheel: cp38
           - python: 3.9

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.3.0
+    rev: v4.5.0
     hooks:
       - id: check-merge-conflict
       - id: debug-statements
@@ -18,29 +18,29 @@ repos:
       exclude: dev-tools|examples
       verbose: true
   - repo: https://github.com/asottile/reorder_python_imports
-    rev: v3.9.0
+    rev: v3.12.0
     hooks:
       - id: reorder-python-imports
         args: [--application-directories=python,
                --unclassifiable-application-module=_tskit]
   - repo: https://github.com/asottile/pyupgrade
-    rev: v3.2.2
+    rev: v3.15.0
     hooks:
       - id: pyupgrade
-        args: [--py3-plus, --py37-plus]
+        args: [--py3-plus, --py38-plus]
   - repo: https://github.com/psf/black
-    rev: 22.10.0
+    rev: 23.9.1
     hooks:
       - id: black
         language_version: python3
   - repo: https://github.com/pycqa/flake8
-    rev: 5.0.4
+    rev: 6.1.0
     hooks:
       - id: flake8
         args: [--config=python/.flake8]
-        additional_dependencies: ["flake8-bugbear==22.10.27", "flake8-builtins==2.0.1"]
+        additional_dependencies: ["flake8-bugbear==23.9.16", "flake8-builtins==2.1.0"]
   - repo: https://github.com/asottile/blacken-docs
-    rev: v1.12.1
+    rev: 1.16.0
     hooks:
       - id: blacken-docs
         args: [--skip-errors]

docs/development.md

@@ -71,7 +71,7 @@ an overview of how to contribute a new feature to `tskit`.
 ### Requirements
 
 To develop the Python code you will need a working C compiler and a
-development installation of Python (>= 3.7). On Debian/Ubuntu we can install these
+development installation of Python (>= 3.8). On Debian/Ubuntu we can install these
 with:
 
 ```bash
@@ -429,7 +429,7 @@ $ make
 
 If this has completed successfully you should see a file `_tskit.cpython-XXXXXX.so`
 in the current directory (the suffix depends on your platform and Python version;
-with Python 3.7 on Linux it's `_tskit.cpython-37m-x86_64-linux-gnu.so`).
+with Python 3.11 on Linux it's `_tskit.cpython-311-x86_64-linux-gnu.so`).
 
 To make sure that your development environment is working, run some
 {ref}`tests <sec_development_python_tests>`.
@@ -1050,10 +1050,10 @@ For instance:
 
 ```bash
 > git commit -a -m 'fixed all the things'
-/usr/bin/env: ‘python3.7’: No such file or directory
+/usr/bin/env: ‘python3.8’: No such file or directory
 ```
 
-What the heck? Why is this even looking for python3.7?
+What the heck? Why is this even looking for python3.8?
 This is because of the "pre-commit hook", mentioned above.
 As above, you can proceed by just appending `--no-verify`:
 

docs/installation.md

@@ -32,7 +32,7 @@ so it may already be installed if you use such software.
 
 ## Requirements
 
-Tskit requires Python 3.7+. There are no external C library dependencies. Python
+Tskit requires Python 3.8+. There are no external C library dependencies. Python
 dependencies are installed automatically by `pip` or `conda`.
 
 (sec_installation_conda)=

python/CHANGELOG.rst

@@ -2,6 +2,10 @@
 [0.5.6] - 2023-XX-XX
 --------------------
 
+**Breaking Changes**
+
+- tskit now requires Python 3.8, as Python 3.7 became end-of-life on 2023-06-27
+
 **Features**
 
 - Tree.trmca now accepts >2 nodes and returns nicer errors

python/setup.cfg

@@ -16,7 +16,6 @@ classifiers =
     Programming Language :: C
     Programming Language :: Python
     Programming Language :: Python :: 3
-    Programming Language :: Python :: 3.7
     Programming Language :: Python :: 3.8
     Programming Language :: Python :: 3.9
     Programming Language :: Python :: 3.10
@@ -46,7 +45,7 @@ platforms =
 
 [options]
 packages = tskit
-python_requires = >=3.7
+python_requires = >=3.8
 include_package_data = True
 install_requires =
     jsonschema>=3.0.0

python/tests/simplify.py

@@ -725,7 +725,6 @@ def flush_edges(self):
         return num_edges
 
     def check_state(self):
-
         num_nodes = len(self.A_head)
         for j in range(num_nodes):
             head = self.A_head[j]
@@ -771,7 +770,6 @@ def print_state(self):
     ts = tskit.load(sys.argv[2])
 
     if class_to_implement == "Simplifier":
-
         samples = list(map(int, sys.argv[3:]))
 
         print("When keep_unary = True:")
@@ -805,7 +803,6 @@ def print_state(self):
         print(tables.mutations)
 
     elif class_to_implement == "AncestorMap":
-
         samples = sys.argv[3]
         samples = samples.split(",")
         samples = list(map(int, samples))

python/tests/test_file_format.py

@@ -487,7 +487,7 @@ def test_unsupported_version(self):
         # Cannot read current files.
         ts.dump(self.temp_file)
         # Catch Exception here because h5py throws different exceptions on py2 and py3
-        with pytest.raises(Exception):
+        with pytest.raises(Exception):  # noqa B017
             tskit.load_legacy(self.temp_file)
 
     def test_no_version_number(self):

python/tests/test_highlevel.py

@@ -207,7 +207,7 @@ def insert_gap(ts, position, length):
     return tables.tree_sequence()
 
 
-@functools.lru_cache()
+@functools.lru_cache
 def get_gap_examples():
     """
     Returns example tree sequences that contain gaps within the list of
@@ -239,7 +239,7 @@ def get_gap_examples():
     return ret
 
 
-@functools.lru_cache()
+@functools.lru_cache
 def get_internal_samples_examples():
     """
     Returns example tree sequences with internal samples.
@@ -270,7 +270,7 @@ def get_internal_samples_examples():
     return ret
 
 
-@functools.lru_cache()
+@functools.lru_cache
 def get_decapitated_examples():
     """
     Returns example tree sequences in which the oldest edges have been removed.

python/tests/test_ibd.py

@@ -285,7 +285,6 @@ def test_empty_in_between(self, ts):
 
 
 class TestIbdTwoSamplesTwoTrees:
-
     # 2
     #             |     3
     # 1      2    |    / \
@@ -339,15 +338,13 @@ def test_length(self):
 
 
 class TestIbdUnrelatedSamples:
-
     #
     #    2   3
     #    |   |
     #    0   1
 
     @tests.cached_example
     def ts(self):
-
         nodes = io.StringIO(
             """\
         id      is_sample   time

python/tests/test_lowlevel.py

@@ -4044,7 +4044,7 @@ def test_uninitialised():
     ]
     for cls_name, cls in inspect.getmembers(_tskit):
         if (
-            type(cls) == type
+            isinstance(cls, type)
             and not issubclass(cls, Exception)
             and not issubclass(cls, tuple)
         ):

python/tests/test_table_transforms.py

@@ -96,7 +96,6 @@ def test_mutation_parents(self, ts):
 
 
 class TestDeleteOlderSimpleTree:
-
     # 2.00┊   4   ┊
     #     ┊ ┏━┻┓  ┊
     # 1.00┊ ┃  3  ┊
@@ -357,7 +356,6 @@ def split_edges_definition(ts, time, *, flags=0, population=None, metadata=None)
 
 
 class TestSplitEdgesSimpleTree:
-
     # 2.00┊   4   ┊
     #     ┊ ┏━┻┓  ┊
     # 1.00┊ ┃  3  ┊
@@ -757,7 +755,6 @@ def test_no_population(self, ts):
 
 
 class TestDecapitateSimpleTree:
-
     # 2.00┊   4   ┊
     #     ┊ ┏━┻┓  ┊
     # 1.00┊ ┃  3  ┊

python/tests/test_tables.py

@@ -1772,7 +1772,6 @@ def test_keep_rows_data(self):
 
 
 class TestNodeTable(*common_tests):
-
     columns = [
         UInt32Column("flags"),
         DoubleColumn("time"),
@@ -1853,7 +1852,6 @@ def test_add_row_bad_data(self):
 
 
 class TestEdgeTable(*common_tests):
-
     columns = [
         DoubleColumn("left"),
         DoubleColumn("right"),
@@ -3856,13 +3854,13 @@ def check_concordance(d1, d2):
             assert set(d1.keys()) == set(d2.keys())
             for k1, v1 in d1.items():
                 v2 = d2[k1]
-                assert type(v1) == type(v2)
-                if type(v1) == dict:
+                assert type(v1) is type(v2)
+                if type(v1) is dict:
                     assert set(v1.keys()) == set(v2.keys())
                     for sk1, sv1 in v1.items():
                         sv2 = v2[sk1]
-                        assert type(sv1) == type(sv2)
-                        if type(sv1) == np.ndarray:
+                        assert type(sv1) is type(sv2)
+                        if isinstance(sv1, np.ndarray):
                             assert np.array_equal(sv1, sv2) or (
                                 np.all(tskit.is_unknown_time(sv1))
                                 and np.all(tskit.is_unknown_time(sv2))
@@ -4172,7 +4170,6 @@ def test_kwargs_only(self):
 
 
 class TestTableCollectionMetadata:
-
     metadata_schema = metadata.MetadataSchema(
         {
             "codec": "json",

python/tests/test_text_formats.py

@@ -92,7 +92,7 @@ def test_insufficient_cols(self, n_cols):
         entry = FamEntry(iid="1")
         for field in fields[n_cols:]:
             entry.__setattr__(field, None)
-        with pytest.raises(
+        with pytest.raises(  # noqa B017
             Exception
         ):  # Have to be non-specific here as numpy 1.23 changed the exception type
             self.get_parsed_fam(entries=[entry])
@@ -137,7 +137,7 @@ def test_bad_sex_value(self, sex):
 
     def test_empty_sex_value(self):
         entries = [FamEntry(iid="1", sex="")]
-        with pytest.raises(
+        with pytest.raises(  # noqa B017
             Exception
         ):  # Have to be non-specific here as numpy 1.23 changed the exception type
             self.get_parsed_fam(entries=entries)

python/tskit/combinatorics.py

@@ -1126,7 +1126,7 @@ def is_symmetrical(self):
 # so we should compute a vector of those results up front instead of using
 # repeated calls to this function.
 # Put an lru_cache on for now as a quick replacement (cuts test time down by 80%)
-@functools.lru_cache()
+@functools.lru_cache
 def num_shapes(n):
     """
     The cardinality of the set of unlabelled trees with n leaves,