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Fix SLiM time units warning, bump minimum version to 4.0 #1567

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merged 9 commits into from
Jul 5, 2024
Merged

Fix SLiM time units warning, bump minimum version to 4.0 #1567

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84a25a2
Fix TimeUnitsMismatchWarning
nspope Jul 5, 2024
2043688
Bump slim version assert to 4.0
nspope Jul 5, 2024
eedacb7
Bump pyslim version to 1.0.4
nspope Jul 5, 2024
d1f1f8e
Bump numpy version in CI
nspope Jul 5, 2024
28d5924
Bump macos runner version to 13
nspope Jul 5, 2024
d6aa379
Debugging CI
nspope Jul 5, 2024
adfb484
Debugging CI
nspope Jul 5, 2024
6221125
Debugging CI
nspope Jul 5, 2024
b9db1db
Downgrade to macos-12 as later versions drop miniconda
nspope Jul 5, 2024
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5 changes: 3 additions & 2 deletions .github/workflows/tests.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand All @@ -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
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4 changes: 2 additions & 2 deletions requirements/CI/requirements.txt
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion requirements/development.txt
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Expand Up @@ -17,7 +17,7 @@ attrs
appdirs
humanize
pre-commit
pyslim>=1.0.1
pyslim>=1.0.4
numpy
scikit-allel
biopython
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2 changes: 1 addition & 1 deletion setup.cfg
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Expand Up @@ -37,7 +37,7 @@ install_requires =
attrs >= 19.1.0
appdirs
humanize
pyslim >= 1.0.1
pyslim >= 1.0.4
numpy
setup_requires =
setuptools
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4 changes: 2 additions & 2 deletions stdpopsim/slim_engine.py
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Expand Up @@ -94,7 +94,7 @@
_slim_lower = """
defineConstant("N", asInteger(_N/Q));

initializeTreeSeq();
initializeTreeSeq(timeUnit="generations");
initializeRecombinationRate(recombination_rates, recombination_ends);
}

Expand Down Expand Up @@ -1714,7 +1714,7 @@
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)

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slim_cmd = [slim_path]
if seed is not None:
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