enable slim on windows

stdpopsim/cli.py

@@ -35,8 +35,6 @@
     pass
 
 
-IS_WINDOWS = sys.platform.startswith("win")
-
 logger = logging.getLogger(__name__)
 
 
@@ -1041,47 +1039,44 @@ def time_or_model(
         "This option may provided multiple times.",
     )
 
-    # SLiM is not available for windows.
-    if not IS_WINDOWS:
-
-        def slim_exec(path):
-            # Hack to set the SLIM environment variable at parse time,
-            # before get_version() can be called.
-            os.environ["SLIM"] = path
-            return path
-
-        slim_parser = top_parser.add_argument_group("SLiM specific parameters")
-        slim_parser.add_argument(
-            "--slim-path",
-            metavar="PATH",
-            type=slim_exec,
-            default=None,
-            help="Full path to `slim' executable.",
-        )
-        slim_parser.add_argument(
-            "--slim-script",
-            action="store_true",
-            default=False,
-            help="Write script to stdout and exit without running SLiM.",
-        )
-        slim_parser.add_argument(
-            "--slim-scaling-factor",
-            metavar="Q",
-            default=1,
-            type=float,
-            help="Rescale model parameters by Q to speed up simulation. "
-            "See SLiM manual: `5.5 Rescaling population sizes to "
-            "improve simulation performance`. "
-            "[default=%(default)s].",
-        )
-        slim_parser.add_argument(
-            "--slim-burn-in",
-            metavar="X",
-            default=10,
-            type=float,
-            help="Length of the burn-in phase, in units of N generations "
-            "[default=%(default)s].",
-        )
+    def slim_exec(path):
+        # Hack to set the SLIM environment variable at parse time,
+        # before get_version() can be called.
+        os.environ["SLIM"] = path
+        return path
+
+    slim_parser = top_parser.add_argument_group("SLiM specific parameters")
+    slim_parser.add_argument(
+        "--slim-path",
+        metavar="PATH",
+        type=slim_exec,
+        default=None,
+        help="Full path to `slim' executable.",
+    )
+    slim_parser.add_argument(
+        "--slim-script",
+        action="store_true",
+        default=False,
+        help="Write script to stdout and exit without running SLiM.",
+    )
+    slim_parser.add_argument(
+        "--slim-scaling-factor",
+        metavar="Q",
+        default=1,
+        type=float,
+        help="Rescale model parameters by Q to speed up simulation. "
+        "See SLiM manual: `5.5 Rescaling population sizes to "
+        "improve simulation performance`. "
+        "[default=%(default)s].",
+    )
+    slim_parser.add_argument(
+        "--slim-burn-in",
+        metavar="X",
+        default=10,
+        type=float,
+        help="Length of the burn-in phase, in units of N generations "
+        "[default=%(default)s].",
+    )
 
     subparsers = top_parser.add_subparsers(dest="subcommand")
     subparsers.required = True

stdpopsim/slim_engine.py

@@ -1631,21 +1631,27 @@ def simulate(
 
         run_slim = not slim_script
 
-        mktemp = functools.partial(tempfile.NamedTemporaryFile, mode="w")
+        tempdir = tempfile.TemporaryDirectory(prefix="stdpopsim_")
+        ts_filename = os.path.join(tempdir.name, f"{os.urandom(3).hex()}.trees")
 
         @contextlib.contextmanager
         def script_file_f():
-            f = mktemp(suffix=".slim") if not slim_script else sys.stdout
-            yield f
+            if run_slim:
+                fname = os.path.join(tempdir.name, f"{os.urandom(3).hex()}.slim")
+                f = open(fname, "w")
+            else:
+                fname = "stdout"
+                f = sys.stdout
+            yield f, fname
             # Don't close sys.stdout.
-            if not slim_script:
+            if run_slim:
                 f.close()
 
-        with script_file_f() as script_file, mktemp(suffix=".ts") as ts_file:
-
+        with script_file_f() as sf:
+            script_file, script_filename = sf
             recap_epoch = slim_makescript(
                 script_file,
-                ts_file.name,
+                ts_filename,
                 demographic_model,
                 contig,
                 sample_sets,
@@ -1663,7 +1669,7 @@ def script_file_f():
                 return None
 
             self._run_slim(
-                script_file.name,
+                script_filename,
                 slim_path=slim_path,
                 seed=seed,
                 dry_run=dry_run,
@@ -1673,7 +1679,7 @@ def script_file_f():
             if dry_run:
                 return None
 
-            ts = tskit.load(ts_file.name)
+            ts = tskit.load(ts_filename)
 
         ts = _add_dfes_to_metadata(ts, contig)
         if _recap_and_rescale:
@@ -1713,7 +1719,6 @@ def _run_slim(
         if slim_path is None:
             slim_path = self.slim_path()
 
-        # SLiM v3.6 sends `stop()` output to stderr, which we rely upon.
         self._assert_min_version("4.0", slim_path)
 
         slim_cmd = [slim_path]
@@ -2002,6 +2007,4 @@ def recap_and_rescale(
         return ts
 
 
-# SLiM does not currently work on Windows.
-if sys.platform != "win32":
-    stdpopsim.register_engine(_SLiMEngine())
+stdpopsim.register_engine(_SLiMEngine())

tests/test_slim_engine.py

@@ -3,7 +3,6 @@
 """
 import os
 import io
-import sys
 import tempfile
 import math
 from unittest import mock
@@ -21,7 +20,6 @@
 import stdpopsim.cli
 from .test_cli import capture_output
 
-IS_WINDOWS = sys.platform.startswith("win")
 slim_path = os.environ.get("SLIM", "slim")
 
 
@@ -33,7 +31,6 @@ def count_mut_types(ts):
     return [num_neutral, abs(len(selection_coeffs) - num_neutral)]
 
 
-@pytest.mark.skipif(IS_WINDOWS, reason="SLiM not available on windows")
 class TestAPI:
     def test_bad_params(self):
         engine = stdpopsim.get_engine("slim")
@@ -151,7 +148,7 @@ def test_script_generation(self):
     def test_recombination_map(self):
         engine = stdpopsim.get_engine("slim")
         species = stdpopsim.get_species("HomSap")
-        contig = species.get_contig("chr1", genetic_map="HapMapII_GRCh37")
+        contig = species.get_contig("chr21", genetic_map="HapMapII_GRCh37")
         model = stdpopsim.PiecewiseConstantSize(100)
         samples = {"pop_0": 5}
         engine.simulate(
@@ -277,8 +274,8 @@ def test_recap_and_rescale_on_external_slim_run(self, tmp_path):
         scriptfile = tmp_path / "slim.script"
         engine = stdpopsim.get_engine("slim")
         species = stdpopsim.get_species("HomSap")
-        contig = species.get_contig("chr1", length_multiplier=0.01)
-        model = stdpopsim.PiecewiseConstantSize(species.population_size)
+        contig = species.get_contig("chr19", length_multiplier=0.01)
+        model = stdpopsim.PiecewiseConstantSize(species.population_size / 10)
         samples = {"pop_0": 5}
         seed = 1024
         out, _ = capture_output(
@@ -291,8 +288,8 @@ def test_recap_and_rescale_on_external_slim_run(self, tmp_path):
             seed=seed,
         )
         out = re.sub(
-            'defineConstant\\("trees_file.+;',
-            f'defineConstant("trees_file", "{treefile}");',
+            r'defineConstant\("trees_file.+;',
+            rf'defineConstant("trees_file", "{treefile}");',
             out,
         )
         with open(scriptfile, "w") as f:
@@ -404,7 +401,6 @@ def test_allele_codes(self):
             assert all([x.isnumeric() for x in alleles])
 
 
-@pytest.mark.skipif(IS_WINDOWS, reason="SLiM not available on windows")
 class TestCLI:
     def docmd(self, _cmd):
         cmd = (f"-q -e slim --slim-burn-in 0 {_cmd} -l 0.001 -c chr1 -s 1234").split()
@@ -642,8 +638,8 @@ def test_chromosomal_segment_with_dfe_annotation(self):
         assert ts.sequence_length == contig.length
         self.verify_slim_sim(ts, num_samples=10)
 
-    # tmp_path is a pytest fixture
     @pytest.mark.filterwarnings("ignore::stdpopsim.SLiMScalingFactorWarning")
+    @pytest.mark.usefixtures("tmp_path")
     def test_errors(self, tmp_path):
         lines = [
             "\t".join(["chr22", "100000", "145000"]),
@@ -763,7 +759,6 @@ def test_bad_slim_path(self):
             os.environ["SLIM"] = saved_slim_env
 
 
-@pytest.mark.skipif(IS_WINDOWS, reason="SLiM not available on windows")
 class TestWarningsAndErrors:
     """
     Checks that warning messages are printed when appropriate.
@@ -1050,19 +1045,15 @@ def test_warning_when_scaling(self, scaling_factor):
 
 class TestSlimAvailable:
     """
-    Checks whether SLiM is available or not on platforms that support it.
+    Checks whether SLiM is available or not.
     """
 
     def test_parser_has_options(self):
         parser = stdpopsim.cli.stdpopsim_cli_parser()
         with mock.patch("sys.exit", autospec=True):
             _, stderr = capture_output(parser.parse_args, ["--help"])
             # On windows we should have no "slim" options
-            assert IS_WINDOWS == ("slim" not in stderr)
-
-    def test_engine_available(self):
-        all_engines = [engine.id for engine in stdpopsim.all_engines()]
-        assert IS_WINDOWS == ("slim" not in all_engines)
+            assert "slim" in stderr
 
 
 def get_test_contig(
@@ -1110,7 +1101,6 @@ def allele_frequency(self, ts):
         return af
 
 
-@pytest.mark.skipif(IS_WINDOWS, reason="SLiM not available on windows")
 class TestRecombinationMap(PiecewiseConstantSizeMixin):
     def verify_recombination_map(self, contig, ts):
         Q = ts.metadata["SLiM"]["user_metadata"]["Q"]
@@ -1176,7 +1166,6 @@ def test_off_by_one(self):
         assert list(ts.breakpoints()) == [0.0, midpoint, contig.length]
 
 
-@pytest.mark.skipif(IS_WINDOWS, reason="SLiM not available on windows")
 class TestGenomicElementTypes(PiecewiseConstantSizeMixin):
 
     mut_params = {
@@ -1786,7 +1775,6 @@ def test_dominance_coeff_list(self):
         self.verify_mutation_rates(contig, ts)
 
 
-@pytest.mark.skipif(IS_WINDOWS, reason="SLiM not available on windows")
 class TestLogfile(PiecewiseConstantSizeMixin):
     # tmp_path is a pytest fixture
     def test_logfile(self, tmp_path):
@@ -1810,7 +1798,6 @@ def test_logfile(self, tmp_path):
         assert np.all(data[:, 2] == 0.0)
 
 
-@pytest.mark.skipif(IS_WINDOWS, reason="SLiM not available on windows")
 class TestDrawMutation(PiecewiseConstantSizeMixin):
     def test_draw_mutation(self):
         contig = get_test_contig()
@@ -2115,7 +2102,6 @@ def test_bad_time(self):
                 )
 
 
-@pytest.mark.skipif(IS_WINDOWS, reason="SLiM not available on windows")
 class TestAlleleFrequencyConditioning(PiecewiseConstantSizeMixin):
     @pytest.mark.filterwarnings("ignore::stdpopsim.SLiMScalingFactorWarning")
     def test_drawn_mutation_not_lost(self):
@@ -2325,7 +2311,6 @@ def test_no_drawn_mutation(self):
             )
 
 
-@pytest.mark.skipif(IS_WINDOWS, reason="SLiM not available on windows")
 class TestChangeMutationFitness(PiecewiseConstantSizeMixin):
     # Testing stdpopsim.ChangeMutationFitness is challenging, because
     # the side-effects are not deterministic. But if we condition on fixation
@@ -2503,7 +2488,6 @@ def test_bad_GenerationAfter_times(self):
                 )
 
 
-@pytest.mark.skipif(IS_WINDOWS, reason="SLiM not available on windows")
 class TestExtendedEvents(PiecewiseConstantSizeMixin):
     def test_bad_extended_events(self):
         engine = stdpopsim.get_engine("slim")
@@ -2523,7 +2507,6 @@ def test_bad_extended_events(self):
                 )
 
 
-@pytest.mark.skipif(IS_WINDOWS, reason="SLiM not available on windows")
 class TestSelectiveSweep(PiecewiseConstantSizeMixin):
     @staticmethod
     def _get_island_model(Ne=1000, migration_rate=0.01):
@@ -2969,7 +2952,6 @@ def test_sweep_with_background_selection(self, tmp_path):
         assert np.all(p1_outside_sweep <= 1)
 
 
-@pytest.mark.skipif(IS_WINDOWS, reason="SLiM not available on windows")
 class TestSelectionCoeffFromMutation:
 
     species = stdpopsim.get_species("HomSap")
@@ -3043,7 +3025,6 @@ def test_errors(self):
             stdpopsim.selection_coeff_from_mutation(ts, "bar")
 
 
-@pytest.mark.skipif(IS_WINDOWS, reason="SLiM not available on windows")
 class TestPloidy:
     """
     Test that population sizes used in SLiM engine are scaled correctly