diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index b61ba4104..752167406 100644 --- a/.github/workflows/tests.yml +++ b/.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 diff --git a/requirements/CI/requirements.txt b/requirements/CI/requirements.txt index a2a805a09..e03d2ffa8 100644 --- a/requirements/CI/requirements.txt +++ b/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 diff --git a/requirements/development.txt b/requirements/development.txt index e1d09d9da..061f2e2db 100644 --- a/requirements/development.txt +++ b/requirements/development.txt @@ -17,7 +17,7 @@ attrs appdirs humanize pre-commit -pyslim>=1.0.1 +pyslim>=1.0.4 numpy scikit-allel biopython diff --git a/setup.cfg b/setup.cfg index d581ae3bc..9177c1ea8 100644 --- a/setup.cfg +++ b/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 diff --git a/stdpopsim/slim_engine.py b/stdpopsim/slim_engine.py index f5d163601..b819e12b1 100644 --- a/stdpopsim/slim_engine.py +++ b/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: