Fix SLiM time units warning, bump minimum version to 4.0 (popsim-cons…

…ortium#1567)

* Fix TimeUnitsMismatchWarning

* Bump slim version assert to 4.0

* Bump pyslim version to 1.0.4

* Bump numpy version in CI

* Bump macos runner version to 13

* Debugging CI

* Debugging CI

* Debugging CI

* Downgrade to macos-12 as later versions drop miniconda

.github/workflows/tests.yml

@@ -17,7 +17,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-20.04, macos-11, windows-latest]
+        os: [ubuntu-20.04, macos-12, windows-latest]
         python: ["3.8", "3.10"]
     env:
       CONDA_ENV_NAME: stdpopsim
@@ -41,7 +41,8 @@ jobs:
         if: runner.os == 'macOS'
         run: |
           # Fix incorrect conda permissions on mac that prevent cache restore.
-          sudo chown -R $USER:staff $CONDA
+          echo "$USER:staff ${{ steps.find-conda.outputs.CONDA }}"
+          sudo chown -R $USER:staff ${{ steps.find-conda.outputs.CONDA }}
 
       - name: cache conda
         id: cache

requirements/CI/requirements.txt

@@ -13,8 +13,8 @@ msprime==1.2.0
 attrs==21.4.0
 appdirs==1.4.4
 humanize==4.6.0
-pyslim==1.0.1
-numpy==1.22.3
+pyslim==1.0.4
+numpy==1.23.5
 scipy==1.10.1
 scikit-allel==1.3.6
 biopython==1.80

requirements/development.txt

@@ -17,7 +17,7 @@ attrs
 appdirs
 humanize
 pre-commit
-pyslim>=1.0.1
+pyslim>=1.0.4
 numpy
 scikit-allel
 biopython

setup.cfg

@@ -37,7 +37,7 @@ install_requires =
     attrs >= 19.1.0
     appdirs
     humanize
-    pyslim >= 1.0.1
+    pyslim >= 1.0.4
     numpy
 setup_requires =
     setuptools

stdpopsim/slim_engine.py

@@ -94,7 +94,7 @@
 _slim_lower = """
     defineConstant("N", asInteger(_N/Q));
 
-    initializeTreeSeq();
+    initializeTreeSeq(timeUnit="generations");
     initializeRecombinationRate(recombination_rates, recombination_ends);
 }
 
@@ -1714,7 +1714,7 @@ def _run_slim(
             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: