enable slim on windows

CHANGELOG.rst

@@ -1,3 +1,7 @@
+**New features**:
+
+- Added support for the SLiM engine on Windows. (:user:`petrelharp`, :pr:`1571`)
+
 ---------------------
 [0.2.1a] - 2024-07-06
 ---------------------

stdpopsim/cli.py

@@ -36,8 +36,6 @@
     pass
 
 
-IS_WINDOWS = sys.platform.startswith("win")
-
 logger = logging.getLogger(__name__)
 
 
@@ -1066,47 +1064,44 @@ 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"))
@@ -1198,7 +1204,7 @@ 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})",
         )
     )
@@ -1517,7 +1523,7 @@ def matrix2str(
     if logfile is not None:
         printsc(
             string.Template(_slim_logfile).substitute(
-                logfile=logfile,
+                logfile=_escape_eidos(str(logfile)),
                 loginterval=logfile_interval,
             )
         )
@@ -1658,21 +1664,32 @@ def simulate(
 
         run_slim = not slim_script
 
-        mktemp = functools.partial(tempfile.NamedTemporaryFile, mode="w")
-
         @contextlib.contextmanager
-        def script_file_f():
-            f = mktemp(suffix=".slim") if not slim_script else sys.stdout
-            yield f
-            # Don't close sys.stdout.
-            if not slim_script:
-                f.close()
+        def _slim_tempdir():
+            tempdir = tempfile.TemporaryDirectory(
+                prefix="stdpopsim_", ignore_cleanup_errors=True
+            )
+            ts_filename = os.path.join(tempdir.name, f"{os.urandom(3).hex()}.trees")
 
-        with script_file_f() as script_file, mktemp(suffix=".ts") as ts_file:
+            if run_slim:
+                script_filename = os.path.join(
+                    tempdir.name, f"{os.urandom(3).hex()}.slim"
+                )
+                script_file = open(script_filename, "w", encoding="utf-8")
+            else:
+                script_filename = "stdout"
+                script_file = sys.stdout
+            yield script_file, script_filename, ts_filename
+            if run_slim:
+                script_file.close()
+            tempdir.cleanup()
+
+        with _slim_tempdir() as st:
+            script_file, script_filename, ts_filename = st
 
             recap_epoch = slim_makescript(
                 script_file,
-                ts_file.name,
+                ts_filename,
                 demographic_model,
                 contig,
                 sample_sets,
@@ -1690,7 +1707,7 @@ def script_file_f():
                 return None
 
             self._run_slim(
-                script_file.name,
+                script_filename,
                 slim_path=slim_path,
                 seed=seed,
                 dry_run=dry_run,
@@ -1700,24 +1717,26 @@ 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:
-            ts = self._recap_and_rescale(
-                ts,
-                seed,
-                recap_epoch,
-                contig,
-                slim_scaling_factor,
-                keep_mutation_ids_as_alleles,
-                extended_events,
-            )
+            ts = _add_dfes_to_metadata(ts, contig)
+            if _recap_and_rescale:
+                ts = self._recap_and_rescale(
+                    ts,
+                    seed,
+                    recap_epoch,
+                    contig,
+                    slim_scaling_factor,
+                    keep_mutation_ids_as_alleles,
+                    extended_events,
+                )
 
-        if contig.inclusion_mask is not None:
-            ts = stdpopsim.utils.mask_tree_sequence(ts, contig.inclusion_mask, False)
-        if contig.exclusion_mask is not None:
-            ts = stdpopsim.utils.mask_tree_sequence(ts, contig.exclusion_mask, True)
+            if contig.inclusion_mask is not None:
+                ts = stdpopsim.utils.mask_tree_sequence(
+                    ts, contig.inclusion_mask, False
+                )
+            if contig.exclusion_mask is not None:
+                ts = stdpopsim.utils.mask_tree_sequence(ts, contig.exclusion_mask, True)
 
         return ts
 
@@ -1740,7 +1759,6 @@ 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]
@@ -1759,7 +1777,19 @@ def _run_slim(
             stdout=subprocess.PIPE,
             stderr=subprocess.PIPE,
         ) as proc:
-            for line in proc.stdout:
+            procout = proc.communicate()
+            try:
+                # we get procout == None with the patching of suprocess.Popen
+                # that we do in test_slim_engine.py::TestCLI::test_dry_run
+                outs, errs = procout
+            except ValueError:
+                warnings.warn(
+                    stdpopsim.UnspecifiedSLiMWarning(
+                        "Cannot get output from SLiM " "for unknown reasons."
+                    )
+                )
+                outs, errs = "", ""
+            for line in outs.splitlines():
                 line = line.rstrip()
                 if line.startswith("WARNING: "):
                     warnings.warn(
@@ -1770,14 +1800,13 @@ def _run_slim(
                     line = line.replace("dbg(self.source); ", "")
                     logger.debug(line)
 
-            stderr = proc.stderr.read()
-            for line in stderr.splitlines():
+            for line in errs.splitlines():
                 if line.startswith("ERROR: "):
                     logger.error(line[len("ERROR: ") :])
 
         if proc.returncode != 0:
             raise SLiMException(
-                f"{slim_path} exited with code {proc.returncode}.\n{stderr}"
+                f"{slim_path} exited with code {proc.returncode}.\n{errs}"
             )
 
     def _simplify_remembered(self, ts):
@@ -2029,6 +2058,4 @@ 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())