enable tests (this will not work)

use tempdir, closes #427 . temp file names better context handling extra level of escaping in eidos escape logfile cache bump .
popsim-consortium · Mar 21, 2023 · 5dc0c4f · 5dc0c4f
1 parent 5bb5b71
commit 5dc0c4f
Show file tree

Hide file tree

Showing 6 changed files with 64 additions and 103 deletions.
diff --git a/stdpopsim/cli.py b/stdpopsim/cli.py
@@ -35,8 +35,6 @@
     pass
 
 
-IS_WINDOWS = sys.platform.startswith("win")
-
 logger = logging.getLogger(__name__)
 
 
@@ -1040,47 +1038,44 @@ 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

diff --git a/stdpopsim/slim_engine.py b/stdpopsim/slim_engine.py
@@ -40,13 +40,13 @@
 
 import os
 import sys
+import contextlib
 import copy
 import string
 import tempfile
 import subprocess
 import functools
 import itertools
-import contextlib
 import random
 import textwrap
 import logging
@@ -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"))
@@ -1135,7 +1141,7 @@ 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})",
         )
     )
@@ -1410,7 +1416,7 @@ def matrix2str(
     if logfile is not None:
         printsc(
             string.Template(_slim_logfile).substitute(
-                logfile=logfile,
+                logfile=_escape_eidos(str(logfile)),
                 loginterval=logfile_interval,
             )
         )
@@ -1552,21 +1558,27 @@ 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,
@@ -1584,7 +1596,7 @@ def script_file_f():
                 return None
 
             self._run_slim(
-                script_file.name,
+                script_filename,
                 slim_path=slim_path,
                 seed=seed,
                 dry_run=dry_run,
@@ -1594,7 +1606,7 @@ 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:
@@ -1634,8 +1646,7 @@ 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("3.6", slim_path)
+        self._assert_min_version("4.0", slim_path)
 
         slim_cmd = [slim_path]
         if seed is not None:
@@ -1921,6 +1932,4 @@ 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())
diff --git a/tests/test_cli.py b/tests/test_cli.py
@@ -543,9 +543,6 @@ def test_gutenkunst_three_pop_ooa(self):
     def test_browning_america(self):
         self.verify_bad_samples("HomSap -d AmericanAdmixture_4B11 2 3 4 5 6")
 
-    IS_WINDOWS = sys.platform.startswith("win")
-
-    @pytest.mark.skipif(IS_WINDOWS, reason="SLiM not available on windows")
     def test_browning_america_dfe(self):
         self.verify_bad_samples(
             "HomSap -d AmericanAdmixture_4B11 --dfe Gamma_K17 2 3 4 5 6"

diff --git a/tests/test_dfes.py b/tests/test_dfes.py
@@ -9,8 +9,6 @@
 from stdpopsim import dfe
 from stdpopsim import utils
 
-IS_WINDOWS = sys.platform.startswith("win")
-
 
 class TestCreateMutationType:
     """
@@ -554,7 +552,6 @@ def test_dfe_is_neutral(self):
                 )
                 assert d.is_neutral is (neutral and dist == "f")
 
-    @pytest.mark.skipif(IS_WINDOWS, reason="SLiM not available on windows")
     def test_no_msprime_dfe(self):
         # test we cannot simulate a non-neutral DFE with msprime
         m1 = dfe.MutationType(
@@ -644,7 +641,6 @@ def test_bad_qc_dfe(self):
             )
 
 
-@pytest.mark.skipif(IS_WINDOWS, reason="SLiM not available on windows")
 class DFETestMixin:
     """
     Mixin for testing specific DFEs. Subclass should extend
@@ -694,7 +690,6 @@ def test_simulation_runs(self):
         assert num_nonneutral > 0  # nonneutral mutations
 
 
-@pytest.mark.skipif(IS_WINDOWS, reason="SLiM not available on windows")
 class CatalogDFETestMixin(DFETestMixin):
     """
     Mixin for DFEs in the catalog.
@@ -704,7 +699,6 @@ def test_id_valid(self):
         assert utils.is_valid_dfe_id(self.dfe.id)
 
 
-@pytest.mark.skipif(IS_WINDOWS, reason="SLiM not available on windows")
 class QcdCatalogDFETestMixin(CatalogDFETestMixin):
     """
     Extends the tests to also check that the qc DFE is equal to

diff --git a/tests/test_masking.py b/tests/test_masking.py
@@ -1,16 +1,13 @@
 """
 Tests for the genetic maps management.
 """
-import sys
 
 import numpy as np
 import msprime
 import pytest
 
 import stdpopsim.utils
 
-IS_WINDOWS = sys.platform.startswith("win")
-
 
 class TestMasking:
     @pytest.mark.usefixtures("tmp_path")
@@ -119,7 +116,6 @@ def test_mask_tree_sequence(self):
         assert np.all(np.logical_and(100 <= positions, positions < 200))
 
 
-@pytest.mark.skipif(IS_WINDOWS, reason="SLiM not available on windows")
 class TestSimulate:
     @pytest.mark.filterwarnings("ignore::msprime.IncompletePopulationMetadataWarning")
     def test_simulate_with_mask(self):