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GHA: Test macos-14 #1387

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May 5, 2024
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GHA: Test macos-14 #1387

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3ab9783
GHA: Test macos-latest
dweindl May 3, 2024
bad42df
imports
dweindl May 3, 2024
c08871c
py312
dweindl May 4, 2024
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28 changes: 14 additions & 14 deletions .github/workflows/ci.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -41,7 +41,7 @@ jobs:
path: |
~/.cache/pip
.tox/
key: ${{ runner.os }}-${{ matrix.python-version }}-ci-${{ github.job }}
key: "${{ runner.os }}-${{ runner.arch }}-py${{ matrix.python-version }}-ci-${{ github.job }}"

- name: Install dependencies
run: .github/workflows/install_deps.sh amici
Expand All @@ -60,7 +60,7 @@ jobs:
file: ./coverage.xml

mac:
runs-on: macos-12
runs-on: macos-latest
strategy:
matrix:
python-version: ['3.12']
Expand All @@ -80,14 +80,14 @@ jobs:
path: |
~/.cache/pip
.tox/
key: ${{ runner.os }}-${{ matrix.python-version }}-ci
key: "${{ runner.os }}-${{ runner.arch }}-py${{ matrix.python-version }}-ci-${{ github.job }}"

- name: Install dependencies
run: .github/workflows/install_deps.sh amici

- name: Run tests
timeout-minutes: 30
run: tox -e base
run: ulimit -n 65536 65536 && tox -e base

- name: Coverage
uses: codecov/codecov-action@v3
Expand Down Expand Up @@ -116,7 +116,7 @@ jobs:
path: |
~\AppData\Local\pip\Cache
.tox
key: ${{ runner.os }}-${{ matrix.python-version }}-ci
key: "${{ runner.os }}-${{ runner.arch }}-py${{ matrix.python-version }}-ci-${{ github.job }}"

- name: Install dependencies
run: |
Expand Down Expand Up @@ -149,7 +149,7 @@ jobs:
path: |
~/.cache/pip
.tox/
key: ${{ runner.os }}-${{ matrix.python-version }}-ci-${{ github.job }}
key: "${{ runner.os }}-${{ runner.arch }}-py${{ matrix.python-version }}-ci-${{ github.job }}"

- name: Install dependencies
run: .github/workflows/install_deps.sh amici pysb
Expand Down Expand Up @@ -193,7 +193,7 @@ jobs:
path: |
~/.cache/pip
.tox/
key: ${{ runner.os }}-${{ matrix.python-version }}-ci-${{ github.job }}
key: "${{ runner.os }}-${{ runner.arch }}-py${{ matrix.python-version }}-ci-${{ github.job }}"

- name: Install julia
uses: julia-actions/setup-julia@v1
Expand Down Expand Up @@ -242,7 +242,7 @@ jobs:
path: |
~/.cache/pip
.tox/
key: ${{ runner.os }}-${{ matrix.python-version }}-ci-${{ github.job }}
key: "${{ runner.os }}-${{ runner.arch }}-py${{ matrix.python-version }}-ci-${{ github.job }}"

- name: Install dependencies
run: .github/workflows/install_deps.sh ipopt
Expand Down Expand Up @@ -278,7 +278,7 @@ jobs:
path: |
~/.cache/pip
.tox/
key: ${{ runner.os }}-${{ matrix.python-version }}-ci-${{ github.job }}
key: "${{ runner.os }}-${{ runner.arch }}-py${{ matrix.python-version }}-ci-${{ github.job }}"

- name: Install dependencies
run: .github/workflows/install_deps.sh amici
Expand Down Expand Up @@ -314,7 +314,7 @@ jobs:
path: |
~/.cache/pip
.tox/
key: ${{ runner.os }}-${{ matrix.python-version }}-ci-${{ github.job }}
key: "${{ runner.os }}-${{ runner.arch }}-py${{ matrix.python-version }}-ci-${{ github.job }}"

- name: Install dependencies
run: .github/workflows/install_deps.sh amici
Expand Down Expand Up @@ -350,7 +350,7 @@ jobs:
path: |
~/.cache/pip
.tox/
key: ${{ runner.os }}-${{ matrix.python-version }}-ci-${{ github.job }}
key: "${{ runner.os }}-${{ runner.arch }}-py${{ matrix.python-version }}-ci-${{ github.job }}"

- name: Install dependencies
run: pip install tox pre-commit
Expand Down Expand Up @@ -382,7 +382,7 @@ jobs:
path: |
~/.cache/pip
.tox/
key: ${{ runner.os }}-${{ matrix.python-version }}-ci-${{ github.job }}
key: "${{ runner.os }}-${{ runner.arch }}-py${{ matrix.python-version }}-ci-${{ github.job }}"

- name: Install dependencies
run: .github/workflows/install_deps.sh doc amici
Expand Down Expand Up @@ -415,7 +415,7 @@ jobs:
path: |
~/.cache/pip
.tox/
key: ${{ runner.os }}-${{ matrix.python-version }}-ci-${{ github.job }}
key: "${{ runner.os }}-${{ runner.arch }}-py${{ matrix.python-version }}-ci-${{ github.job }}"

- name: Install dependencies
run: .github/workflows/install_deps.sh amici ipopt
Expand Down Expand Up @@ -445,7 +445,7 @@ jobs:
path: |
~/.cache/pip
.tox/
key: ${{ runner.os }}-${{ matrix.python-version }}-ci-${{ github.job }}
key: "${{ runner.os }}-${{ runner.arch }}-py${{ matrix.python-version }}-ci-${{ github.job }}"

- name: Install dependencies
run: .github/workflows/install_deps.sh amici
Expand Down
9 changes: 6 additions & 3 deletions test/sample/test_sample.py
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -3,18 +3,15 @@
import os

import numpy as np
import petab
import pytest
import scipy.optimize as so
from scipy.integrate import quad
from scipy.stats import ks_2samp, kstest, multivariate_normal, norm, uniform

import pypesto
import pypesto.optimize as optimize
import pypesto.petab
import pypesto.sample as sample
from pypesto.C import OBJECTIVE_NEGLOGLIKE, OBJECTIVE_NEGLOGPOST
from pypesto.sample.pymc import PymcSampler


def gaussian_llh(x):
Expand Down Expand Up @@ -96,6 +93,10 @@ def rosenbrock_problem():


def create_petab_problem():
import petab

import pypesto.petab

current_path = os.path.dirname(os.path.realpath(__file__))
dir_path = os.path.abspath(
os.path.join(current_path, "..", "..", "doc", "example")
Expand Down Expand Up @@ -187,6 +188,8 @@ def sampler(request):
n_chains=5,
)
elif request.param == "Pymc":
from pypesto.sample.pymc import PymcSampler

return PymcSampler(tune=5, progressbar=False)
elif request.param == "Emcee":
return sample.EmceeSampler(nwalkers=10)
Expand Down
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