.

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

@@ -62,6 +62,12 @@
 
 logger = logging.getLogger(__name__)
 
+
+def _escape_eidos(s):
+    # this is for Windows paths passed as strings in Eidos
+    return "\\\\".join(s.split("\\"))
+
+
 _slim_upper = """
 initialize() {
     if (!exists("dry_run"))
@@ -1171,7 +1177,7 @@ def fix_time(event):
             recombination_rates=recomb_rates_str,
             recombination_ends=recomb_ends_str,
             generation_time=demographic_model.generation_time,
-            trees_file=trees_file,
+            trees_file=_escape_eidos(trees_file),
             pop_names=f"c({pop_names_str})",
         )
     )
@@ -1489,7 +1495,7 @@ def matrix2str(
     if logfile is not None:
         printsc(
             string.Template(_slim_logfile).substitute(
-                logfile=logfile,
+                logfile=_escape_eidos(str(logfile)),
                 loginterval=logfile_interval,
             )
         )
@@ -1631,21 +1637,27 @@ 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 +1675,7 @@ 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 +1685,7 @@ 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 +1725,6 @@ 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 +2013,4 @@ 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

@@ -56,41 +56,6 @@ def test_bad_params(self):
                     dry_run=True,
                 )
 
-    def test_bad_samples(self):
-        engine = stdpopsim.get_engine("slim")
-        species = stdpopsim.get_species("HomSap")
-        contig = species.get_contig("chr1")
-        model = stdpopsim.PiecewiseConstantSize(species.population_size)
-        samples = [1, 2, ["foo"]]
-        with pytest.raises(ValueError, match="Samples must be a dict"):
-            engine.simulate(
-                demographic_model=model,
-                contig=contig,
-                samples=samples,
-                dry_run=True,
-            )
-        with pytest.raises(ValueError, match="Samples must be a dict"):
-            engine.recap_and_rescale(
-                ts=None,
-                demographic_model=model,
-                contig=contig,
-                samples=samples,
-            )
-        samples = [
-            msprime.SampleSet(
-                num_samples=2,
-                population=0,
-                ploidy=3,
-            )
-        ]
-        with pytest.raises(ValueError, match="Sample ploidy other than 1 or 2"):
-            engine.simulate(
-                demographic_model=model,
-                contig=contig,
-                samples=samples,
-                dry_run=True,
-            )
-
     @pytest.mark.filterwarnings("ignore::stdpopsim.SLiMScalingFactorWarning")
     @pytest.mark.filterwarnings(
         "ignore:.*model has mutation rate.*but this simulation used.*"