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Migrate from conda/micromamba to pixi for environment management
Replace conda environment.yml files and micromamba-based CI with pixi configuration embedded in pyproject.toml. This simplifies environment management by using a single source of truth for all dependencies. - Add [tool.pixi.*] sections to pyproject.toml with all environments - Rewrite CI workflow to use prefix-dev/setup-pixi - Update .readthedocs.yml to use pixi via asdf - Remove old conda files (environment.yml, testenv-*.yml, update_envs.py) - Update check_mypy_versions.py to read from pyproject.toml - Update developer docs to reference pixi commands - Bump check-added-large-files maxkb to accommodate pixi.lock Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
1 parent 9a4c2d3 commit 4e5d0ab

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‎.github/workflows/main.yml‎

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---
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name: main
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# Automatically cancel a previous run.
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concurrency:
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group: ${{ github.head_ref || github.run_id }}
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cancel-in-progress: true
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- '*'
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jobs:
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run-tests-linux:
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name: Run tests for ${{ matrix.os }} on ${{ matrix.python-version }}
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runs-on: ${{ matrix.os }}
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name: Run tests on ubuntu-latest py${{ matrix.python-version }}
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runs-on: ubuntu-latest
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strategy:
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fail-fast: false
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matrix:
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os:
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- ubuntu-latest
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python-version:
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- '3.10'
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- '3.11'
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- '3.12'
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- '3.13'
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- '310'
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- '311'
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- '312'
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- '313'
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steps:
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- uses: actions/checkout@v4
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- name: create build environment
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uses: mamba-org/setup-micromamba@v1
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- uses: prefix-dev/setup-pixi@v0.9.4
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with:
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environment-file: ./.tools/envs/testenv-linux.yml
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cache-environment: true
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create-args: |
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python=${{ matrix.python-version }}
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- name: run pytest
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shell: bash -l {0}
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run: |
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micromamba activate optimagic
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pytest --cov-report=xml --cov=./
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pixi-version: v0.65.0
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cache: true
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cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }}
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frozen: true
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environments: test-linux-py${{ matrix.python-version }}
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- name: Run pytest
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shell: bash -el {0}
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run: pixi run -e test-linux-py${{ matrix.python-version }} tests-with-cov
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- name: Upload coverage report.
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if: runner.os == 'Linux' && matrix.python-version == '3.10'
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if: matrix.python-version == '310'
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uses: codecov/codecov-action@v4
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with:
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token: ${{ secrets.CODECOV_TOKEN }}
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run-tests-win-and-mac:
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name: Run tests for ${{ matrix.os }} on ${{ matrix.python-version }}
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name: Run tests on ${{ matrix.os }} py${{ matrix.python-version }}
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runs-on: ${{ matrix.os }}
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strategy:
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fail-fast: false
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- macos-latest
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- windows-latest
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python-version:
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- '3.10'
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- '3.11'
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- '3.12'
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- '3.13'
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- '310'
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- '311'
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- '312'
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- '313'
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steps:
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- uses: actions/checkout@v4
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- name: create build environment
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uses: mamba-org/setup-micromamba@v1
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- uses: prefix-dev/setup-pixi@v0.9.4
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with:
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micromamba-version: 1.5.6-0
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environment-file: ./.tools/envs/testenv-others.yml
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cache-environment: true
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create-args: |
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python=${{ matrix.python-version }}
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- name: run pytest
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shell: bash -l {0}
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run: |
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micromamba activate optimagic
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pytest -m "not slow and not jax"
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pixi-version: v0.65.0
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cache: true
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cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }}
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frozen: true
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environments: test-py${{ matrix.python-version }}
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- name: Run pytest
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shell: bash -el {0}
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run: pixi run -e test-py${{ matrix.python-version }} tests-fast
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run-tests-with-old-pandas:
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# This job is only for testing if optimagic works with pandas<2, as many pandas
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# functions we use will be deprecated in pandas 3. optimagic's behavior for older
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# verions is handled in src/optimagic/compat.py. For compatibility with we have to
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# restrict numpy<2.
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name: Run tests for ${{ matrix.os}} on ${{ matrix.python-version }} with pandas 1
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runs-on: ${{ matrix.os }}
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strategy:
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fail-fast: false
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matrix:
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os:
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- ubuntu-latest
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python-version:
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- '3.10'
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name: Run tests on ubuntu-latest with pandas < 2
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- name: create build environment
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uses: mamba-org/setup-micromamba@v1
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- uses: prefix-dev/setup-pixi@v0.9.4
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with:
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environment-file: ./.tools/envs/testenv-pandas.yml
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cache-environment: true
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create-args: |
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python=${{ matrix.python-version }}
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- name: run pytest
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shell: bash -l {0}
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run: |
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micromamba activate optimagic
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pytest -m "not slow and not jax"
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pixi-version: v0.65.0
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cache: true
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cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }}
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frozen: true
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environments: test-old-pandas
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- name: Run pytest
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shell: bash -el {0}
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run: pixi run -e test-old-pandas tests-fast
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run-tests-with-old-numpy:
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# This job is only for testing if optimagic works with numpy<2. Because we already
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# test pandas<2 with numpy<2, in this environment we restrict pandas>=2.
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name: Run tests for ${{ matrix.os}} on ${{ matrix.python-version }} with numpy 1
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runs-on: ${{ matrix.os }}
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strategy:
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fail-fast: false
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matrix:
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os:
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- ubuntu-latest
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python-version:
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- '3.10'
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name: Run tests on ubuntu-latest with numpy < 2
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- name: create build environment
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uses: mamba-org/setup-micromamba@v1
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- uses: prefix-dev/setup-pixi@v0.9.4
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with:
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environment-file: ./.tools/envs/testenv-numpy.yml
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cache-environment: true
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create-args: |
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python=${{ matrix.python-version }}
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- name: run pytest
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shell: bash -l {0}
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run: |
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micromamba activate optimagic
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pytest -m "not slow and not jax"
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pixi-version: v0.65.0
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cache: true
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cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }}
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frozen: true
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environments: test-old-numpy
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- name: Run pytest
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shell: bash -el {0}
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run: pixi run -e test-old-numpy tests-fast
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run-tests-with-old-plotly:
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name: Run tests for ubuntu-latest on 3.10 with plotly < 6 and kaleido < 0.3
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name: Run tests on ubuntu-latest with plotly < 6
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runs-on: ubuntu-latest
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strategy:
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fail-fast: false
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steps:
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- uses: actions/checkout@v4
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- name: create build environment
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uses: mamba-org/setup-micromamba@v1
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- uses: prefix-dev/setup-pixi@v0.9.4
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with:
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environment-file: ./.tools/envs/testenv-plotly.yml
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cache-environment: true
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create-args: |
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python=3.10
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- name: run pytest
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shell: bash -l {0}
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run: |
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micromamba activate optimagic
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pytest -m "not slow and not jax"
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pixi-version: v0.65.0
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cache: true
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cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }}
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frozen: true
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environments: test-old-plotly
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- name: Run pytest
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shell: bash -el {0}
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run: pixi run -e test-old-plotly tests-fast
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run-tests-nevergrad:
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# This job is for running test related to nevergrad with pinned version of
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# bayesian_optimization == 1.4.0
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name: Run tests for ubuntu-latest on ${{ matrix.python-version }} bayes_opt==1.4.0
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runs-on: ${{ matrix.os }}
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name: Run nevergrad tests py${{ matrix.python-version }}
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runs-on: ubuntu-latest
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strategy:
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fail-fast: false
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matrix:
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os:
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- ubuntu-latest
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python-version:
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- '3.10'
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- '3.11'
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- '3.12'
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- '3.13'
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- '310'
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- '311'
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- '312'
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- '313'
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steps:
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- uses: actions/checkout@v4
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- name: create build environment
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uses: mamba-org/setup-micromamba@v1
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- uses: prefix-dev/setup-pixi@v0.9.4
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with:
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environment-file: ./.tools/envs/testenv-nevergrad.yml
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cache-environment: true
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create-args: |
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python=${{ matrix.python-version }}
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- name: run pytest
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shell: bash -l {0}
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run: |
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micromamba activate optimagic
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pixi-version: v0.65.0
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cache: true
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cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }}
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frozen: true
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environments: test-nevergrad-py${{ matrix.python-version }}
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- name: Run pytest
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shell: bash -el {0}
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run: >-
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pixi run -e test-nevergrad-py${{ matrix.python-version }}
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pytest tests/optimagic/optimizers/test_nevergrad.py
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code-in-docs:
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name: Run code snippets in documentation
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- name: create build environment
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uses: mamba-org/setup-micromamba@v1
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- uses: prefix-dev/setup-pixi@v0.9.4
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with:
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environment-file: ./.tools/envs/testenv-linux.yml
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environment-name: optimagic
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cache-environment: true
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create-args: |
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python=3.12
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- name: run sphinx
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shell: bash -l {0}
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run: |-
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micromamba activate optimagic
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cd docs/source
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python -m doctest -v how_to/how_to_constraints.md
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pixi-version: v0.65.0
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cache: true
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cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }}
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frozen: true
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environments: test-linux-py312
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- name: Run doctest
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shell: bash -el {0}
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run: >-
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pixi run -e test-linux-py312
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python -m doctest -v docs/source/how_to/how_to_constraints.md
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run-mypy:
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name: Run mypy
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runs-on: ubuntu-latest
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strategy:
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fail-fast: false
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steps:
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- uses: actions/checkout@v4
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- name: create build environment
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uses: mamba-org/setup-micromamba@v1
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- uses: prefix-dev/setup-pixi@v0.9.4
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with:
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environment-file: ./.tools/envs/testenv-linux.yml
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environment-name: optimagic
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cache-environment: true
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create-args: |
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python=3.10
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pixi-version: v0.65.0
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cache: true
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cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }}
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frozen: true
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environments: test-linux-py310
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- name: Run mypy
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shell: bash -l {0}
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run: |-
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micromamba activate optimagic
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mypy
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shell: bash -el {0}
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run: pixi run -e test-linux-py310 mypy

‎.gitignore‎

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ENV/
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env.bak/
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venv.bak/
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.pixi/
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# Spyder project settings
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.spyderproject

‎.pre-commit-config.yaml‎

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hooks:
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- id: yamlfix
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exclude: tests/optimagic/optimizers/_pounders/fixtures
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- repo: local
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hooks:
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- id: update-environment-files
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name: check environment file updates
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entry: python .tools/update_envs.py
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language: python
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always_run: true
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require_serial: true
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- repo: local
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hooks:
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- id: check-mypy-versions
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name: verify that pre-commits and dev env use the same mypy version
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name: verify that pre-commits and pixi use the same mypy version
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entry: python .tools/check_mypy_versions.py
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language: python
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always_run: true
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hooks:
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- id: check-added-large-files
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args:
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- --maxkb=1300
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- --maxkb=2500
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exclude: tests/optimagic/optimizers/_pounders/fixtures/
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- id: check-case-conflict
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- id: check-merge-conflict

‎.readthedocs.yml‎

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---
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version: 2
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build:
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os: ubuntu-22.04
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os: ubuntu-24.04
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tools:
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python: mambaforge-4.10
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conda:
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environment: docs/rtd_environment.yml
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python: '3.12'
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jobs:
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create_environment:
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- asdf plugin add pixi
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- asdf install pixi latest
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- asdf global pixi latest
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install:
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- pixi install -e docs
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build:
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- pixi run -e docs docs
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post_build:
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- mkdir --parents $READTHEDOCS_OUTPUT/html/
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- cp -a docs/build/html/. "$READTHEDOCS_OUTPUT/html" && rm -r docs/build
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sphinx:
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builder: html
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configuration: docs/source/conf.py
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fail_on_warning: false

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