Merge pull request #669 from petrelharp/fix_666

error in schema and test machinery

Author: bhaller

core/slim_globals.cpp

@@ -2355,7 +2355,7 @@ const std::string gSLiM_tsk_individual_metadata_schema_FORMAT_SOURCE = R"V0G0N({
         "sex": {
             "index": 8,
             "type": "integer",
-            "binaryFormat": "i",
+            "binaryFormat": "h",
             "description": "The sex of the individual (0 for female, 1 for male, -1 for hermaphrodite)."
         },
         "tagL0_set": {

treerec/tests/.python-version

@@ -0,0 +1 @@
+3.13

treerec/tests/README.md

@@ -1,8 +1,8 @@
 # Test suite for tree sequence output from SLiM
 
 ## Running the tests
-Just do `python3 -m pytest` from within this directory to run the tests on the results of SLiM scripts listed in the `testRecipes/` directory. Alternatively, to run just one of the recipes do e.g.
-`python3 -m pytest -k test_000_sexual_nonwf`
+Just do `uv run pytest` from within this directory to run the tests on the results of SLiM scripts listed in the `testRecipes/` directory. Alternatively, to run just one of the recipes do e.g.
+`uv run pytest -k test_000_sexual_nonwf`
 
 ## Recaching in GitHub Actions to get a new tskit/msprime version
 GitHub Actions caches its install of `tskit`, `msprime`, and other software.  When a new version of such software is released, a recache needs to be forced or these tests will likely fail in CI.  This cannot presently be gone in GitHub's UI; see [this GitHub issue](https://github.com/actions/cache/issues/2).  So to trigger a recache, you need to increment the cache version number.  It is found in `.github/workflows/tests.yml` in the line:

treerec/tests/pip-requirements.txt

@@ -3,3 +3,6 @@ filelock
 numpy
 pytest
 pytest-xdist
+tskit>=0.4.1
+msprime>=1.2.0
+pyslim>=1.0.4

treerec/tests/pyproject.toml

@@ -0,0 +1,14 @@
+[project]
+name = "SLiM_python_tests"
+version = "0.1.0"
+requires-python = ">=3.13"
+dependencies = [
+    "filelock>=3.32.4",
+    "msprime>=1.2.0",
+    "numpy>=2.5.2",
+    "pyslim>=1.0.4",
+    "pytest>=9.1.1",
+    "pytest-xdist>=3.8.0",
+    "setuptools>=84.0.0",
+    "tskit>=0.4.1",
+]

treerec/tests/test_consistency.py

@@ -290,11 +290,12 @@ def test_chromosome_consistency(self, recipe):
             for tsl in result.get_ts():
                 for chrom_id in tsl:
                     ts = tsl[chrom_id]
-                    chrom_type = ts.metadata['SLiM']['this_chromosome']['type']
-                    chrom_index = ts.metadata['SLiM']['this_chromosome']['index']
+                    ts_metadata = ts.metadata
+                    chrom_type = ts_metadata['SLiM']['this_chromosome']['type']
+                    chrom_index = ts_metadata['SLiM']['this_chromosome']['index']
                     details = self.chrom_details(chrom_type)
                     if chrom_type in ['X', 'Y', 'Z', 'W', 'HF', 'FL', 'HM', 'ML']:
-                        assert ts.metadata['SLiM']['separate_sexes']
+                        assert ts_metadata['SLiM']['separate_sexes']
                     for ind in ts.individuals():
                         if ind.flags & (pyslim.INDIVIDUAL_ALIVE | pyslim.INDIVIDUAL_REMEMBERED) > 0:
                             sex = {0 : "F", 1 : "M", -1 : "H"}[ind.metadata['sex']]
@@ -322,10 +323,11 @@ def test_chromosome_inheritance(self, recipe):
             for tsl in result.get_ts():
                 for chrom_id in tsl:
                     ts = tsl[chrom_id]
-                    chrom_type = ts.metadata['SLiM']['this_chromosome']['type']
+                    ts_metadata = ts.metadata
+                    chrom_type = ts_metadata['SLiM']['this_chromosome']['type']
                     if chrom_type == "H":
                         continue
-                    chrom_index = ts.metadata['SLiM']['this_chromosome']['index']
+                    chrom_index = ts_metadata['SLiM']['this_chromosome']['index']
                     inheritance = self.chrom_inheritance(chrom_type)
                     for ind in ts.individuals():
                         if len(ind.parents) > 0: