Update deps, remove py37 and fix test warnings

tskit-dev · Oct 12, 2023 · 22d7199 · 22d7199
1 parent 113229b
commit 22d7199
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Showing 25 changed files with 53 additions and 89 deletions.
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -5,7 +5,7 @@ orbs:
 jobs:
   build:
     docker:
-      - image: cimg/python:3.7
+      - image: cimg/python:3.10
     working_directory: /home/circleci/msprime
     steps:
       - checkout

diff --git a/.github/workflows/docker/shared.env b/.github/workflows/docker/shared.env
@@ -1,7 +1,6 @@
 PYTHON_VERSIONS=(
     cp39-cp39
     cp38-cp38
-    cp37-cp37m
     cp310-cp310
     cp311-cp311
 )

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -26,7 +26,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python: [ 3.7, 3.11 ]
+        python: [ 3.8, 3.11 ]
         os:  [ macos-latest, ubuntu-latest, windows-latest ]
     defaults:
       run:
@@ -62,7 +62,6 @@ jobs:
           channels: conda-forge
           channel-priority: strict
           auto-update-conda: true
-          use-only-tar-bz2: true
 
       - name: Fix windows symlinks
         # This is horrible, but the "git config core.symlinks true" didn't work.

diff --git a/.github/workflows/wheels.yml b/.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
@@ -79,7 +79,7 @@ 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
@@ -105,7 +105,7 @@ 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]
     steps:
       - name: Download wheels
         uses: actions/download-artifact@v2

diff --git a/.mergify.yml b/.mergify.yml
@@ -4,11 +4,11 @@ queue_rules:
       - "#approved-reviews-by>=1"
       - status-success=Docs
       - status-success=Lint
-      - status-success=Python (3.7, macos-latest)
+      - status-success=Python (3.8, macos-latest)
       - status-success=Python (3.11, macos-latest)
-      - status-success=Python (3.7, ubuntu-latest)
+      - status-success=Python (3.8, ubuntu-latest)
       - status-success=Python (3.11, ubuntu-latest)
-      - status-success=Python (3.7, windows-latest)
+      - status-success=Python (3.8, windows-latest)
       - status-success=Python (3.11, windows-latest)
       - "status-success=ci/circleci: build"
 pull_request_rules:
@@ -20,11 +20,11 @@ pull_request_rules:
       - label=AUTOMERGE-REQUESTED
       - status-success=Docs
       - status-success=Lint
-      - status-success=Python (3.7, macos-latest)
+      - status-success=Python (3.8, macos-latest)
       - status-success=Python (3.11, macos-latest)
-      - status-success=Python (3.7, ubuntu-latest)
+      - status-success=Python (3.8, ubuntu-latest)
       - status-success=Python (3.11, ubuntu-latest)
-      - status-success=Python (3.7, windows-latest)
+      - status-success=Python (3.8, windows-latest)
       - status-success=Python (3.11, windows-latest)
       - "status-success=ci/circleci: build"
       #- status-success=codecov/patch

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -22,7 +22,7 @@ repos:
     rev: v3.2.2
     hooks:
       - id: pyupgrade
-        args: [--py37-plus]
+        args: [--py38-plus]
   - repo: https://github.com/psf/black
     rev: 22.10.0
     hooks:

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -22,8 +22,13 @@
   {user}`GertjanBisschop`)
 
 **Maintenance**:
+
 - Automatically flush edges whenever an edge with a different parent is added to the edge buffer. ({issue}`2182`, {pr}`2183`, {user}`GertjanBisschop`)
 
+**Breaking changes**:
+
+- msprime no longer supports Python 3.7
+
 ## [1.2.0] - 2022-05-18
 
 **New features**

diff --git a/benchmarks/benchmarks.py b/benchmarks/benchmarks.py
@@ -35,7 +35,6 @@
 
 
 class LargeSimulationBenchmark:
-
     # ASV is designed to accurately time functions that execute in a fraction
     # of a second. But, we're interested in profiling large simulations that
     # run in 10s of seconds (at least). We want to run the target function

diff --git a/msprime/ancestry.py b/msprime/ancestry.py
@@ -403,6 +403,8 @@ def _parse_random_seed(seed):
     """
     if seed is None:
         seed = core.get_random_seed()
+    if isinstance(seed, np.ndarray):
+        seed = seed[0]
     seed = int(seed)
     return seed
 

diff --git a/msprime/demography.py b/msprime/demography.py
@@ -2984,7 +2984,6 @@ class PopulationParametersChange(ParameterChangeEvent):
     _type_str: ClassVar[str] = "Population parameter change"
 
     def __post_init__(self):
-
         if self.population_id is not None and self.population is not None:
             raise ValueError(
                 "population_id and population are aliases; cannot supply both."

diff --git a/msprime/pedigrees.py b/msprime/pedigrees.py
@@ -215,7 +215,6 @@ def parse_pedigree(
 
 
 def write_pedigree(ts, out):
-
     print("# id\tparent0\tparent1\ttime\tis_sample\tpopulation", file=out)
     for ind in ts.individuals():
         if len(ind.nodes) != 2:

diff --git a/requirements/CI-complete/requirements.txt b/requirements/CI-complete/requirements.txt
@@ -1,17 +1,13 @@
 bintrees==2.2.0
-daiquiri==3.0.1
-demes==0.2.1
-mypy==0.910 
-newick==1.3.2
-numpy==1.21.6
-pytest==6.2.5
-pytest-cov==3.0.0
-pytest-xdist==2.5.0
-# https://github.com/tskit-dev/msprime/issues/1860
-# Required by python_jsonschema_objects
-jsonschema<4.0
-python_jsonschema_objects==0.4.1
-scipy==1.7.3
+daiquiri==3.2.1
+demes==0.2.3
+mypy==1.6.0 
+newick==1.9.0
+pytest==7.4.2
+pytest-cov==4.1.0
+pytest-xdist==3.3.1
+python_jsonschema_objects==0.5.0
+scipy==1.11.3
 stdpopsim==0.1.2
-tskit==0.5.3
+tskit==0.5.6
 kastore==0.3.2
diff --git a/requirements/CI-docs/requirements.txt b/requirements/CI-docs/requirements.txt
@@ -2,12 +2,12 @@ jupyter-book==0.15.1
 sphinx-issues==3.0.1
 sphinx-argparse==0.4.0
 sphinx-book-theme # not pinned to enable easy updates
-numpy==1.25.2
-tskit==0.5.5
+numpy==1.26.0
+tskit==0.5.6
 demes==0.2.3
-matplotlib==3.7.2
+matplotlib==3.8.0
 networkx==3.1
-scipy==1.11.1
+scipy==1.11.3
 daiquiri==3.2.1
 demesdraw==0.4.0
 newick==1.9.0
diff --git a/requirements/CI-tests-conda/requirements.txt b/requirements/CI-tests-conda/requirements.txt
@@ -1,8 +1,3 @@
-# https://github.com/tskit-dev/msprime/issues/1860
-# Version < 4 is required by python_jsonschema_objects,
-# but demes will pull in the latest so we pin here.
-jsonschema<4.0
 gsl
-tskit==0.5.3
 stdpopsim==0.1.2
-demes==0.2.1
+demes==0.2.3
diff --git a/requirements/CI-tests-pip/requirements.txt b/requirements/CI-tests-pip/requirements.txt
@@ -1,14 +1,9 @@
 bintrees==2.2.0
-daiquiri==3.0.1
-newick==1.3.1
-numpy==1.21.6; python_version < '3.11' # Held at 1.21.6 for Python 3.7 compatibility
-numpy==1.24.1; python_version > '3.10'
-pytest==6.2.5
-pytest-xdist==2.4.0
-# https://github.com/tskit-dev/msprime/issues/1860
-# Required by python_jsonschema_objects
-jsonschema<5.0
-python_jsonschema_objects==0.4.1
-scipy==1.7.3; python_version < '3.11'
-scipy==1.9.3; python_version > '3.10'
-tskit==0.5.3
+daiquiri==3.2.1
+newick==1.9.0
+pytest==7.4.2
+pytest-xdist==3.3.1
+python_jsonschema_objects==0.5.0
+scipy==1.11.3; python_version > '3.8'
+scipy==1.10.1; python_version <= '3.8'
+tskit==0.5.6
diff --git a/requirements/development.txt b/requirements/development.txt
@@ -26,10 +26,5 @@ sphinx-argparse
 sphinx-issues
 jupyter-book
 networkx
-
 newick>=1.3.0
-# https://github.com/tskit-dev/msprime/issues/1860
-# Required by python_jsonschema_objects
-jsonschema<4.0
-# We use JSON-schema to test out metadata handling.
 python_jsonschema_objects
diff --git a/setup.cfg b/setup.cfg
@@ -17,7 +17,6 @@ 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
@@ -45,7 +44,7 @@ platforms =
 
 [options]
 packages = msprime
-python_requires = >=3.7
+python_requires = >=3.8
 include_package_data = True
 install_requires =
     numpy

diff --git a/tests/test_ancestry.py b/tests/test_ancestry.py
@@ -1337,7 +1337,6 @@ def test_initial_state_errors(self):
             msprime.sim_ancestry(initial_state=ts1, random_seed=2)
 
     def test_initial_state(self):
-
         ts = msprime.sim_ancestry(10, end_time=0.01, random_seed=2)
         # Same if we use either the tables or tree sequence object.
         sim = ancestry._parse_sim_ancestry(initial_state=ts, population_size=1)

diff --git a/tests/test_cli.py b/tests/test_cli.py
@@ -1398,7 +1398,6 @@ def test_short_args(self, tmp_path):
         assert tree_sequence.get_num_mutations() == 0
 
     def test_run_yaml(self, tmp_path):
-
         yaml = """\
         time_units: generations
         demes:

diff --git a/tests/test_demography.py b/tests/test_demography.py
@@ -2597,7 +2597,6 @@ def test_full_arg_migration(self):
 
     def test_full_arg_migration_smc(self):
         for model in ["smc", "smc_prime"]:
-
             population_configurations = [
                 msprime.PopulationConfiguration(10),
                 msprime.PopulationConfiguration(10),
@@ -4262,7 +4261,6 @@ def test_debug(self):
         assert str(dbg1) == str(dbg2)
 
     def test_population_name(self):
-
         demography = msprime.Demography.isolated_model([1])
         assert demography.populations[0].name == "pop_0"
 

diff --git a/tests/test_lowlevel.py b/tests/test_lowlevel.py
@@ -1318,7 +1318,6 @@ def test_non_parametric_simulation_models(self):
             assert sim.model == model
 
     def test_dirac_simulation_model(self):
-
         for bad_type in [None, str, "sdf"]:
             model = get_simulation_model("dirac", psi=bad_type, c=1.0)
             with pytest.raises(TypeError):
@@ -2453,7 +2452,6 @@ def test_seed_bounds(self):
                 gen.seed = overflow
 
     def test_seed(self):
-
         for s in [1, 10, 2**32 - 1]:
             rng = _msprime.RandomGenerator()
             rng.seed = s

diff --git a/tests/test_mutations.py b/tests/test_mutations.py
@@ -202,8 +202,8 @@ def validate_state_independent(self, method, **kwargs):
 
     def verify_models_equivalent(self, model1, model2):
         assert len(model1.alleles) == len(model2.alleles)
-        assert np.alltrue(np.equal(model1.root_distribution, model2.root_distribution))
-        assert np.alltrue(np.equal(model1.transition_matrix, model2.transition_matrix))
+        assert np.all(np.equal(model1.root_distribution, model2.root_distribution))
+        assert np.all(np.equal(model1.transition_matrix, model2.transition_matrix))
 
     def test_bad_alleles(self):
         for alleles, err in [
@@ -1519,7 +1519,6 @@ def test_layer_mutation_models(self):
 
 
 class StatisticalTestMixin:
-
     p_threshold = 0.001
 
     def chisquare(self, observed, expected, p_th=p_threshold):
@@ -1604,7 +1603,6 @@ def run_mutate(
         mutation_id=0,
         slim_generation=1,
     ):
-
         model = msprime.SLiMMutationModel(
             type=mutation_type, next_id=mutation_id, slim_generation=slim_generation
         )
@@ -1719,7 +1717,6 @@ def validate_unique_alleles(self, ts):
             assert len(alleles) == len(set(alleles))
 
     def run_mutate(self, ts, rate=1, random_seed=42, start_allele=0):
-
         model = msprime.InfiniteAlleles(start_allele=start_allele)
         mts1 = msprime.sim_mutations(
             ts, rate=rate, random_seed=random_seed, model=model, discrete_genome=True
@@ -2132,7 +2129,10 @@ def populate_tables(self, tables):
                     mutation.derived_state,
                     parent=parent_id,
                     metadata=mutation.metadata,
-                    time=mutation.time,
+                    # Not sure why, but sometimes the time is a single-element array
+                    time=mutation.time[0]
+                    if isinstance(mutation.time, np.ndarray)
+                    else mutation.time,
                 )
                 assert mutation_id > parent_id
                 mutation.id = mutation_id

diff --git a/tests/test_pedigree.py b/tests/test_pedigree.py
@@ -414,7 +414,6 @@ def test_two_pedigrees(self):
         )
 
     def test_three_pedigrees(self):
-
         tables1 = simulate_pedigree(
             num_founders=2,
             num_generations=2,
@@ -778,7 +777,6 @@ class TestContinueSimulateThroughPedigree(TestSimulateThroughPedigree):
     """
 
     def verify(self, input_tables, recombination_rate=0):
-
         ts1 = msprime.sim_ancestry(
             model="fixed_pedigree",
             initial_state=input_tables,

diff --git a/tests/test_provenance.py b/tests/test_provenance.py
@@ -78,7 +78,10 @@ class TestBuildObjects:
     """
 
     def decode(self, prov):
-        builder = pjs.ObjectBuilder(tskit.provenance.get_schema())
+        # Supress warnings about schemas here - it's no big deal and
+        # not easy to fix
+        with pytest.warns(UserWarning):
+            builder = pjs.ObjectBuilder(tskit.provenance.get_schema())
         ns = builder.build_classes()
         return ns.TskitProvenance.from_json(prov)