From 4e5d0abaf8655e6a7722ab3897480af9b50ad4b5 Mon Sep 17 00:00:00 2001 From: timmens Date: Tue, 10 Mar 2026 11:48:58 +0100 Subject: [PATCH 01/18] 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 --- .github/workflows/main.yml | 241 +- .gitignore | 1 + .pre-commit-config.yaml | 12 +- .readthedocs.yml | 19 +- .tools/check_mypy_versions.py | 17 +- .tools/envs/testenv-linux.yml | 52 - .tools/envs/testenv-nevergrad.yml | 51 - .tools/envs/testenv-numpy.yml | 49 - .tools/envs/testenv-others.yml | 50 - .tools/envs/testenv-pandas.yml | 49 - .tools/envs/testenv-plotly.yml | 50 - .tools/update_envs.py | 91 - docs/rtd_environment.yml | 49 - docs/source/development/how_to_contribute.md | 14 +- .../source/how_to/how_to_add_optimizers.ipynb | 28 +- environment.yml | 66 - pixi.lock | 33712 ++++++++++++++++ pyproject.toml | 165 + src/optimagic/algorithms.py | 64 +- 19 files changed, 34035 insertions(+), 745 deletions(-) delete mode 100644 .tools/envs/testenv-linux.yml delete mode 100644 .tools/envs/testenv-nevergrad.yml delete mode 100644 .tools/envs/testenv-numpy.yml delete mode 100644 .tools/envs/testenv-others.yml delete mode 100644 .tools/envs/testenv-pandas.yml delete mode 100644 .tools/envs/testenv-plotly.yml delete mode 100644 .tools/update_envs.py delete mode 100644 docs/rtd_environment.yml delete mode 100644 environment.yml create mode 100644 pixi.lock diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 631cb3985..28a9added 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -1,6 +1,5 @@ --- name: main -# Automatically cancel a previous run. concurrency: group: ${{ github.head_ref || github.run_id }} cancel-in-progress: true @@ -13,39 +12,35 @@ on: - '*' jobs: run-tests-linux: - name: Run tests for ${{ matrix.os }} on ${{ matrix.python-version }} - runs-on: ${{ matrix.os }} + name: Run tests on ubuntu-latest py${{ matrix.python-version }} + runs-on: ubuntu-latest strategy: fail-fast: false matrix: - os: - - ubuntu-latest python-version: - - '3.10' - - '3.11' - - '3.12' - - '3.13' + - '310' + - '311' + - '312' + - '313' steps: - uses: actions/checkout@v4 - - name: create build environment - uses: mamba-org/setup-micromamba@v1 + - uses: prefix-dev/setup-pixi@v0.9.4 with: - environment-file: ./.tools/envs/testenv-linux.yml - cache-environment: true - create-args: | - python=${{ matrix.python-version }} - - name: run pytest - shell: bash -l {0} - run: | - micromamba activate optimagic - pytest --cov-report=xml --cov=./ + pixi-version: v0.65.0 + cache: true + cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }} + frozen: true + environments: test-linux-py${{ matrix.python-version }} + - name: Run pytest + shell: bash -el {0} + run: pixi run -e test-linux-py${{ matrix.python-version }} tests-with-cov - name: Upload coverage report. - if: runner.os == 'Linux' && matrix.python-version == '3.10' + if: matrix.python-version == '310' uses: codecov/codecov-action@v4 with: token: ${{ secrets.CODECOV_TOKEN }} run-tests-win-and-mac: - name: Run tests for ${{ matrix.os }} on ${{ matrix.python-version }} + name: Run tests on ${{ matrix.os }} py${{ matrix.python-version }} runs-on: ${{ matrix.os }} strategy: fail-fast: false @@ -54,163 +49,121 @@ jobs: - macos-latest - windows-latest python-version: - - '3.10' - - '3.11' - - '3.12' - - '3.13' + - '310' + - '311' + - '312' + - '313' steps: - uses: actions/checkout@v4 - - name: create build environment - uses: mamba-org/setup-micromamba@v1 + - uses: prefix-dev/setup-pixi@v0.9.4 with: - micromamba-version: 1.5.6-0 - environment-file: ./.tools/envs/testenv-others.yml - cache-environment: true - create-args: | - python=${{ matrix.python-version }} - - name: run pytest - shell: bash -l {0} - run: | - micromamba activate optimagic - pytest -m "not slow and not jax" + pixi-version: v0.65.0 + cache: true + cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }} + frozen: true + environments: test-py${{ matrix.python-version }} + - name: Run pytest + shell: bash -el {0} + run: pixi run -e test-py${{ matrix.python-version }} tests-fast run-tests-with-old-pandas: - # This job is only for testing if optimagic works with pandas<2, as many pandas - # functions we use will be deprecated in pandas 3. optimagic's behavior for older - # verions is handled in src/optimagic/compat.py. For compatibility with we have to - # restrict numpy<2. - name: Run tests for ${{ matrix.os}} on ${{ matrix.python-version }} with pandas 1 - runs-on: ${{ matrix.os }} - strategy: - fail-fast: false - matrix: - os: - - ubuntu-latest - python-version: - - '3.10' + name: Run tests on ubuntu-latest with pandas < 2 + runs-on: ubuntu-latest steps: - uses: actions/checkout@v4 - - name: create build environment - uses: mamba-org/setup-micromamba@v1 + - uses: prefix-dev/setup-pixi@v0.9.4 with: - environment-file: ./.tools/envs/testenv-pandas.yml - cache-environment: true - create-args: | - python=${{ matrix.python-version }} - - name: run pytest - shell: bash -l {0} - run: | - micromamba activate optimagic - pytest -m "not slow and not jax" + pixi-version: v0.65.0 + cache: true + cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }} + frozen: true + environments: test-old-pandas + - name: Run pytest + shell: bash -el {0} + run: pixi run -e test-old-pandas tests-fast run-tests-with-old-numpy: - # This job is only for testing if optimagic works with numpy<2. Because we already - # test pandas<2 with numpy<2, in this environment we restrict pandas>=2. - name: Run tests for ${{ matrix.os}} on ${{ matrix.python-version }} with numpy 1 - runs-on: ${{ matrix.os }} - strategy: - fail-fast: false - matrix: - os: - - ubuntu-latest - python-version: - - '3.10' + name: Run tests on ubuntu-latest with numpy < 2 + runs-on: ubuntu-latest steps: - uses: actions/checkout@v4 - - name: create build environment - uses: mamba-org/setup-micromamba@v1 + - uses: prefix-dev/setup-pixi@v0.9.4 with: - environment-file: ./.tools/envs/testenv-numpy.yml - cache-environment: true - create-args: | - python=${{ matrix.python-version }} - - name: run pytest - shell: bash -l {0} - run: | - micromamba activate optimagic - pytest -m "not slow and not jax" + pixi-version: v0.65.0 + cache: true + cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }} + frozen: true + environments: test-old-numpy + - name: Run pytest + shell: bash -el {0} + run: pixi run -e test-old-numpy tests-fast run-tests-with-old-plotly: - name: Run tests for ubuntu-latest on 3.10 with plotly < 6 and kaleido < 0.3 + name: Run tests on ubuntu-latest with plotly < 6 runs-on: ubuntu-latest - strategy: - fail-fast: false steps: - uses: actions/checkout@v4 - - name: create build environment - uses: mamba-org/setup-micromamba@v1 + - uses: prefix-dev/setup-pixi@v0.9.4 with: - environment-file: ./.tools/envs/testenv-plotly.yml - cache-environment: true - create-args: | - python=3.10 - - name: run pytest - shell: bash -l {0} - run: | - micromamba activate optimagic - pytest -m "not slow and not jax" + pixi-version: v0.65.0 + cache: true + cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }} + frozen: true + environments: test-old-plotly + - name: Run pytest + shell: bash -el {0} + run: pixi run -e test-old-plotly tests-fast run-tests-nevergrad: - # This job is for running test related to nevergrad with pinned version of - # bayesian_optimization == 1.4.0 - name: Run tests for ubuntu-latest on ${{ matrix.python-version }} bayes_opt==1.4.0 - runs-on: ${{ matrix.os }} + name: Run nevergrad tests py${{ matrix.python-version }} + runs-on: ubuntu-latest strategy: fail-fast: false matrix: - os: - - ubuntu-latest python-version: - - '3.10' - - '3.11' - - '3.12' - - '3.13' + - '310' + - '311' + - '312' + - '313' steps: - uses: actions/checkout@v4 - - name: create build environment - uses: mamba-org/setup-micromamba@v1 + - uses: prefix-dev/setup-pixi@v0.9.4 with: - environment-file: ./.tools/envs/testenv-nevergrad.yml - cache-environment: true - create-args: | - python=${{ matrix.python-version }} - - name: run pytest - shell: bash -l {0} - run: | - micromamba activate optimagic + pixi-version: v0.65.0 + cache: true + cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }} + frozen: true + environments: test-nevergrad-py${{ matrix.python-version }} + - name: Run pytest + shell: bash -el {0} + run: >- + pixi run -e test-nevergrad-py${{ matrix.python-version }} pytest tests/optimagic/optimizers/test_nevergrad.py code-in-docs: name: Run code snippets in documentation runs-on: ubuntu-latest steps: - uses: actions/checkout@v4 - - name: create build environment - uses: mamba-org/setup-micromamba@v1 + - uses: prefix-dev/setup-pixi@v0.9.4 with: - environment-file: ./.tools/envs/testenv-linux.yml - environment-name: optimagic - cache-environment: true - create-args: | - python=3.12 - - name: run sphinx - shell: bash -l {0} - run: |- - micromamba activate optimagic - cd docs/source - python -m doctest -v how_to/how_to_constraints.md + pixi-version: v0.65.0 + cache: true + cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }} + frozen: true + environments: test-linux-py312 + - name: Run doctest + shell: bash -el {0} + run: >- + pixi run -e test-linux-py312 + python -m doctest -v docs/source/how_to/how_to_constraints.md run-mypy: name: Run mypy runs-on: ubuntu-latest - strategy: - fail-fast: false steps: - uses: actions/checkout@v4 - - name: create build environment - uses: mamba-org/setup-micromamba@v1 + - uses: prefix-dev/setup-pixi@v0.9.4 with: - environment-file: ./.tools/envs/testenv-linux.yml - environment-name: optimagic - cache-environment: true - create-args: | - python=3.10 + pixi-version: v0.65.0 + cache: true + cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }} + frozen: true + environments: test-linux-py310 - name: Run mypy - shell: bash -l {0} - run: |- - micromamba activate optimagic - mypy + shell: bash -el {0} + run: pixi run -e test-linux-py310 mypy diff --git a/.gitignore b/.gitignore index 5c92ba19e..5a6169c6e 100644 --- a/.gitignore +++ b/.gitignore @@ -104,6 +104,7 @@ venv/ ENV/ env.bak/ venv.bak/ +.pixi/ # Spyder project settings .spyderproject diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 68f8ec826..ea6cc9885 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -10,18 +10,10 @@ repos: hooks: - id: yamlfix exclude: tests/optimagic/optimizers/_pounders/fixtures - - repo: local - hooks: - - id: update-environment-files - name: check environment file updates - entry: python .tools/update_envs.py - language: python - always_run: true - require_serial: true - repo: local hooks: - id: check-mypy-versions - name: verify that pre-commits and dev env use the same mypy version + name: verify that pre-commits and pixi use the same mypy version entry: python .tools/check_mypy_versions.py language: python always_run: true @@ -44,7 +36,7 @@ repos: hooks: - id: check-added-large-files args: - - --maxkb=1300 + - --maxkb=2500 exclude: tests/optimagic/optimizers/_pounders/fixtures/ - id: check-case-conflict - id: check-merge-conflict diff --git a/.readthedocs.yml b/.readthedocs.yml index e35e92185..ff31076ee 100644 --- a/.readthedocs.yml +++ b/.readthedocs.yml @@ -1,12 +1,21 @@ --- version: 2 build: - os: ubuntu-22.04 + os: ubuntu-24.04 tools: - python: mambaforge-4.10 -conda: - environment: docs/rtd_environment.yml + python: '3.12' + jobs: + create_environment: + - asdf plugin add pixi + - asdf install pixi latest + - asdf global pixi latest + install: + - pixi install -e docs + build: + - pixi run -e docs docs + post_build: + - mkdir --parents $READTHEDOCS_OUTPUT/html/ + - cp -a docs/build/html/. "$READTHEDOCS_OUTPUT/html" && rm -r docs/build sphinx: - builder: html configuration: docs/source/conf.py fail_on_warning: false diff --git a/.tools/check_mypy_versions.py b/.tools/check_mypy_versions.py index d85b0b02c..51f1b6993 100644 --- a/.tools/check_mypy_versions.py +++ b/.tools/check_mypy_versions.py @@ -12,29 +12,28 @@ def _get_mypy_version_from_precommit_config() -> str: for hook in config["repos"] if hook["repo"] == "https://github.com/pre-commit/mirrors-mypy" ][0] - match = re.search(r"v([\d.]+)", mypy_config["rev"]) # Remove "v" prefix + match = re.search(r"v([\d.]+)", mypy_config["rev"]) if match: return match.group(1) raise ValueError("Mypy version not found in pre-commit config.") -def _get_mypy_version_from_conda_environment() -> str: - config = yaml.safe_load(Path("environment.yml").read_text()) - mypy_line = [dep for dep in config["dependencies"] if "mypy" in dep][0] - match = re.search(r"mypy=([\d.]+)", mypy_line) +def _get_mypy_version_from_pixi() -> str: + text = Path("pyproject.toml").read_text() + match = re.search(r'mypy\s*=\s*"==([\d.]+)"', text) if match: return match.group(1) - raise ValueError("Mypy version not found in conda environment.") + raise ValueError("Mypy version not found in pyproject.toml pixi config.") def main() -> None: v_precommit = _get_mypy_version_from_precommit_config() - v_conda = _get_mypy_version_from_conda_environment() - if v_precommit != v_conda: + v_pixi = _get_mypy_version_from_pixi() + if v_precommit != v_pixi: print( f"Error: Mypy versions do not match:\n" f" Pre-commit config: {v_precommit}\n" - f" Conda environment: {v_conda}\n" + f" Pixi config: {v_pixi}\n" ) sys.exit(1) sys.exit(0) diff --git a/.tools/envs/testenv-linux.yml b/.tools/envs/testenv-linux.yml deleted file mode 100644 index fcdbb44b5..000000000 --- a/.tools/envs/testenv-linux.yml +++ /dev/null @@ -1,52 +0,0 @@ ---- -name: optimagic -channels: - - conda-forge - - nodefaults -dependencies: - - petsc4py<=3.23.4 - - jax - - cyipopt>=1.4.0 # dev, tests - - pygmo>=2.19.0 # dev, tests, docs - - nlopt # dev, tests, docs - - pip # dev, tests, docs - - pytest # dev, tests - - pytest-cov # tests - - pytest-xdist # dev, tests - - statsmodels # dev, tests - - cloudpickle # run, tests - - joblib # run, tests - - numpy >= 2 # run, tests - - pandas # run, tests - - plotly>=6.2 # run, tests - - matplotlib # tests - - bokeh # tests - - altair # tests - - pybaum>=0.1.2 # run, tests - - scipy>=1.2.1 # run, tests - - sqlalchemy # run, tests - - seaborn # dev, tests - - mypy=1.19.1 # dev, tests - - pyyaml # dev, tests - - jinja2 # dev, tests - - annotated-types # dev, tests - - tranquilo>=0.1.1 # tests - - iminuit # dev, tests - - cma # dev, tests - - pygad # dev, tests - - pytorch-cpu # dev, tests - - pip: # dev, tests, docs - - bayesian-optimization>=2.0.4 # dev, tests - - DFO-LS>=1.5.3 # dev, tests - - Py-BOBYQA # dev, tests - - fides==0.7.4 # dev, tests - - kaleido>=1.0 # dev, tests - - gradient_free_optimizers # dev, tests - - pyswarms # dev, tests - - pandas-stubs # dev, tests - - types-cffi # dev, tests - - types-openpyxl # dev, tests - - types-jinja2 # dev, tests - - sqlalchemy-stubs # dev, tests - - sphinxcontrib-mermaid # dev, tests, docs - - -e ../../ diff --git a/.tools/envs/testenv-nevergrad.yml b/.tools/envs/testenv-nevergrad.yml deleted file mode 100644 index fb26f7861..000000000 --- a/.tools/envs/testenv-nevergrad.yml +++ /dev/null @@ -1,51 +0,0 @@ ---- -name: optimagic -channels: - - conda-forge - - nodefaults -dependencies: - - cyipopt>=1.4.0 # dev, tests - - pygmo>=2.19.0 # dev, tests, docs - - nlopt # dev, tests, docs - - pip # dev, tests, docs - - pytest # dev, tests - - pytest-cov # tests - - pytest-xdist # dev, tests - - statsmodels # dev, tests - - cloudpickle # run, tests - - joblib # run, tests - - numpy >= 2 # run, tests - - pandas # run, tests - - plotly>=6.2 # run, tests - - matplotlib # tests - - bokeh # tests - - altair # tests - - pybaum>=0.1.2 # run, tests - - scipy>=1.2.1 # run, tests - - sqlalchemy # run, tests - - seaborn # dev, tests - - mypy=1.19.1 # dev, tests - - pyyaml # dev, tests - - jinja2 # dev, tests - - annotated-types # dev, tests - - tranquilo>=0.1.1 # tests - - iminuit # dev, tests - - cma # dev, tests - - pygad # dev, tests - - pytorch-cpu # dev, tests - - pip: # dev, tests, docs - - DFO-LS>=1.5.3 # dev, tests - - Py-BOBYQA # dev, tests - - fides==0.7.4 # dev, tests - - kaleido>=1.0 # dev, tests - - gradient_free_optimizers # dev, tests - - pyswarms # dev, tests - - pandas-stubs # dev, tests - - types-cffi # dev, tests - - types-openpyxl # dev, tests - - types-jinja2 # dev, tests - - sqlalchemy-stubs # dev, tests - - sphinxcontrib-mermaid # dev, tests, docs - - bayesian_optimization==1.4.0 - - nevergrad - - -e ../../ diff --git a/.tools/envs/testenv-numpy.yml b/.tools/envs/testenv-numpy.yml deleted file mode 100644 index 516a333c2..000000000 --- a/.tools/envs/testenv-numpy.yml +++ /dev/null @@ -1,49 +0,0 @@ ---- -name: optimagic -channels: - - conda-forge - - nodefaults -dependencies: - - pandas>=2 - - numpy<2 - - cyipopt>=1.4.0 # dev, tests - - pygmo>=2.19.0 # dev, tests, docs - - nlopt # dev, tests, docs - - pip # dev, tests, docs - - pytest # dev, tests - - pytest-cov # tests - - pytest-xdist # dev, tests - - statsmodels # dev, tests - - cloudpickle # run, tests - - joblib # run, tests - - plotly>=6.2 # run, tests - - matplotlib # tests - - bokeh # tests - - altair # tests - - pybaum>=0.1.2 # run, tests - - scipy>=1.2.1 # run, tests - - sqlalchemy # run, tests - - seaborn # dev, tests - - mypy=1.19.1 # dev, tests - - pyyaml # dev, tests - - jinja2 # dev, tests - - annotated-types # dev, tests - - tranquilo>=0.1.1 # tests - - iminuit # dev, tests - - cma # dev, tests - - pygad # dev, tests - - pytorch-cpu # dev, tests - - pip: # dev, tests, docs - - bayesian-optimization>=2.0.4 # dev, tests - - DFO-LS>=1.5.3 # dev, tests - - Py-BOBYQA # dev, tests - - fides==0.7.4 # dev, tests - - kaleido>=1.0 # dev, tests - - gradient_free_optimizers # dev, tests - - pyswarms # dev, tests - - types-cffi # dev, tests - - types-openpyxl # dev, tests - - types-jinja2 # dev, tests - - sqlalchemy-stubs # dev, tests - - sphinxcontrib-mermaid # dev, tests, docs - - -e ../../ diff --git a/.tools/envs/testenv-others.yml b/.tools/envs/testenv-others.yml deleted file mode 100644 index 6786f831d..000000000 --- a/.tools/envs/testenv-others.yml +++ /dev/null @@ -1,50 +0,0 @@ ---- -name: optimagic -channels: - - conda-forge - - nodefaults -dependencies: - - cyipopt>=1.4.0 # dev, tests - - pygmo>=2.19.0 # dev, tests, docs - - nlopt # dev, tests, docs - - pip # dev, tests, docs - - pytest # dev, tests - - pytest-cov # tests - - pytest-xdist # dev, tests - - statsmodels # dev, tests - - cloudpickle # run, tests - - joblib # run, tests - - numpy >= 2 # run, tests - - pandas # run, tests - - plotly>=6.2 # run, tests - - matplotlib # tests - - bokeh # tests - - altair # tests - - pybaum>=0.1.2 # run, tests - - scipy>=1.2.1 # run, tests - - sqlalchemy # run, tests - - seaborn # dev, tests - - mypy=1.19.1 # dev, tests - - pyyaml # dev, tests - - jinja2 # dev, tests - - annotated-types # dev, tests - - tranquilo>=0.1.1 # tests - - iminuit # dev, tests - - cma # dev, tests - - pygad # dev, tests - - pytorch-cpu # dev, tests - - pip: # dev, tests, docs - - bayesian-optimization>=2.0.4 # dev, tests - - DFO-LS>=1.5.3 # dev, tests - - Py-BOBYQA # dev, tests - - fides==0.7.4 # dev, tests - - kaleido>=1.0 # dev, tests - - gradient_free_optimizers # dev, tests - - pyswarms # dev, tests - - pandas-stubs # dev, tests - - types-cffi # dev, tests - - types-openpyxl # dev, tests - - types-jinja2 # dev, tests - - sqlalchemy-stubs # dev, tests - - sphinxcontrib-mermaid # dev, tests, docs - - -e ../../ diff --git a/.tools/envs/testenv-pandas.yml b/.tools/envs/testenv-pandas.yml deleted file mode 100644 index ead41b5eb..000000000 --- a/.tools/envs/testenv-pandas.yml +++ /dev/null @@ -1,49 +0,0 @@ ---- -name: optimagic -channels: - - conda-forge - - nodefaults -dependencies: - - pandas<2 - - numpy<2 - - cyipopt>=1.4.0 # dev, tests - - pygmo>=2.19.0 # dev, tests, docs - - nlopt # dev, tests, docs - - pip # dev, tests, docs - - pytest # dev, tests - - pytest-cov # tests - - pytest-xdist # dev, tests - - statsmodels # dev, tests - - cloudpickle # run, tests - - joblib # run, tests - - plotly>=6.2 # run, tests - - matplotlib # tests - - bokeh # tests - - altair # tests - - pybaum>=0.1.2 # run, tests - - scipy>=1.2.1 # run, tests - - sqlalchemy # run, tests - - seaborn # dev, tests - - mypy=1.19.1 # dev, tests - - pyyaml # dev, tests - - jinja2 # dev, tests - - annotated-types # dev, tests - - tranquilo>=0.1.1 # tests - - iminuit # dev, tests - - cma # dev, tests - - pygad # dev, tests - - pytorch-cpu # dev, tests - - pip: # dev, tests, docs - - bayesian-optimization>=2.0.4 # dev, tests - - DFO-LS>=1.5.3 # dev, tests - - Py-BOBYQA # dev, tests - - fides==0.7.4 # dev, tests - - kaleido>=1.0 # dev, tests - - gradient_free_optimizers # dev, tests - - pyswarms # dev, tests - - types-cffi # dev, tests - - types-openpyxl # dev, tests - - types-jinja2 # dev, tests - - sqlalchemy-stubs # dev, tests - - sphinxcontrib-mermaid # dev, tests, docs - - -e ../../ diff --git a/.tools/envs/testenv-plotly.yml b/.tools/envs/testenv-plotly.yml deleted file mode 100644 index b25f14475..000000000 --- a/.tools/envs/testenv-plotly.yml +++ /dev/null @@ -1,50 +0,0 @@ ---- -name: optimagic -channels: - - conda-forge - - nodefaults -dependencies: - - plotly<6 - - cyipopt>=1.4.0 # dev, tests - - pygmo>=2.19.0 # dev, tests, docs - - nlopt # dev, tests, docs - - pip # dev, tests, docs - - pytest # dev, tests - - pytest-cov # tests - - pytest-xdist # dev, tests - - statsmodels # dev, tests - - cloudpickle # run, tests - - joblib # run, tests - - numpy >= 2 # run, tests - - pandas # run, tests - - matplotlib # tests - - bokeh # tests - - altair # tests - - pybaum>=0.1.2 # run, tests - - scipy>=1.2.1 # run, tests - - sqlalchemy # run, tests - - seaborn # dev, tests - - mypy=1.19.1 # dev, tests - - pyyaml # dev, tests - - jinja2 # dev, tests - - annotated-types # dev, tests - - tranquilo>=0.1.1 # tests - - iminuit # dev, tests - - cma # dev, tests - - pygad # dev, tests - - pytorch-cpu # dev, tests - - pip: # dev, tests, docs - - bayesian-optimization>=2.0.4 # dev, tests - - DFO-LS>=1.5.3 # dev, tests - - Py-BOBYQA # dev, tests - - fides==0.7.4 # dev, tests - - gradient_free_optimizers # dev, tests - - pyswarms # dev, tests - - pandas-stubs # dev, tests - - types-cffi # dev, tests - - types-openpyxl # dev, tests - - types-jinja2 # dev, tests - - sqlalchemy-stubs # dev, tests - - sphinxcontrib-mermaid # dev, tests, docs - - kaleido<0.3 - - -e ../../ diff --git a/.tools/update_envs.py b/.tools/update_envs.py deleted file mode 100644 index d2cb813fe..000000000 --- a/.tools/update_envs.py +++ /dev/null @@ -1,91 +0,0 @@ -from copy import deepcopy -from pathlib import Path - - -def _keep_line(line: str, flag: str) -> bool: - """Return True if line contains flag and does not include a comment. - - Examples: - >>> assert _keep_line(" - jax # tests", "tests") is True - >>> assert _keep_line("name: env", "tests") is True - >>> assert _keep_line(" - jax # run", "tests") is False - - """ - return flag in line or "#" not in line - - -def main() -> None: - lines = Path("environment.yml").read_text().splitlines() - - # create standard testing environments - - test_env = [line for line in lines if _keep_line(line, "tests")] - test_env.append(" - -e ../../") # add local installation - - # find index to insert additional dependencies - _insert_idx = [i for i, line in enumerate(lines) if "dependencies:" in line][0] + 1 - _insert_idx_pip = [i for i, line in enumerate(lines) if " - pip:" in line][0] + 1 - - ## linux - test_env_linux = deepcopy(test_env) - test_env_linux.insert(_insert_idx, " - jax") - # pinned petsc4py due to failing test on python 3.11 , revert later - test_env_linux.insert(_insert_idx, " - petsc4py<=3.23.4") - - ## test environment others - test_env_others = deepcopy(test_env) - - ## test environment for pandas version < 2 (requires numpy < 2) - test_env_pandas = deepcopy(test_env) - for pkg in ["numpy", "pandas"]: - test_env_pandas = [line for line in test_env_pandas if pkg not in line] - test_env_pandas.insert(_insert_idx, f" - {pkg}<2") - - ## test environment for numpy version < 2 (with pandas >= 2) - test_env_numpy = deepcopy(test_env) - for pkg in ["numpy", "pandas"]: - test_env_numpy = [line for line in test_env_numpy if pkg not in line] - test_env_numpy.insert(_insert_idx, " - numpy<2") - test_env_numpy.insert(_insert_idx, " - pandas>=2") - - ## test environment for plotly < 6, kaleido < 1.0 - test_env_plotly = deepcopy(test_env) - for pkg in ["plotly", "kaleido"]: - test_env_plotly = [line for line in test_env_plotly if pkg not in line] - test_env_plotly.insert(_insert_idx, " - plotly<6") - test_env_plotly.insert(_insert_idx_pip, " - kaleido<0.3") - - test_env_nevergrad = deepcopy(test_env) - for pkg in ["bayesian-optimization"]: - test_env_nevergrad = [line for line in test_env_nevergrad if pkg not in line] - test_env_nevergrad.insert(_insert_idx_pip, " - nevergrad") - test_env_nevergrad.insert( - _insert_idx_pip, " - bayesian_optimization==1.4.0" - ) - - # test environment for documentation - docs_env = [line for line in lines if _keep_line(line, "docs")] - docs_env.append(" - -e ../../") # add local installation - - # write environments - for name, env in zip( - ["linux", "others", "pandas", "numpy", "plotly", "nevergrad"], - [ - test_env_linux, - test_env_others, - test_env_pandas, - test_env_numpy, - test_env_plotly, - test_env_nevergrad, - ], - strict=False, - ): - # Specify newline to avoid wrong line endings on Windows. - # See: https://stackoverflow.com/a/69869641 - Path(f".tools/envs/testenv-{name}.yml").write_text( - "\n".join(env) + "\n", newline="\n" - ) - - -if __name__ == "__main__": - main() diff --git a/docs/rtd_environment.yml b/docs/rtd_environment.yml deleted file mode 100644 index b7e969bff..000000000 --- a/docs/rtd_environment.yml +++ /dev/null @@ -1,49 +0,0 @@ ---- -name: optimagic-docs -channels: - - conda-forge - - nodefaults -dependencies: - - python=3.12 - - typing-extensions - - pip - - setuptools_scm - - toml - - sphinx>=8.2.3 - - sphinxcontrib-bibtex - - sphinx-copybutton - - sphinx-design - - sphinx-llm - - sphinx-llms-txt - - ipython - - ipython_genutils - - myst-nb - - furo - - pybaum - - matplotlib - - bokeh - - altair - - anywidget - - seaborn - - numpy - - pandas - - scipy - - patsy - - joblib - - plotly>=6.2 - - nlopt - - annotated-types - - pygmo>=2.19.0 - - pip: - - -e ../ - - Py-BOBYQA - - DFO-LS - - pandas-stubs # dev, tests - - types-cffi # dev, tests - - types-openpyxl # dev, tests - - types-jinja2 # dev, tests - - sqlalchemy-stubs # dev, tests - - sphinxcontrib-mermaid # dev, tests, docs - - intersphinx-registry # docs - - fides==0.7.4 # dev, tests - - bayesian-optimization # dev, tests diff --git a/docs/source/development/how_to_contribute.md b/docs/source/development/how_to_contribute.md index e32d1c309..bf441abe1 100644 --- a/docs/source/development/how_to_contribute.md +++ b/docs/source/development/how_to_contribute.md @@ -44,9 +44,8 @@ For regular contributors: **Clone** the [repository](https://github.com/optimagi local optimagic repository: ```console - $ conda env create -f environment.yml - $ conda activate optimagic - $ pre-commit install + $ pixi install + $ pixi run lint # verify pre-commit hooks work ``` These commands install optimagic in editable mode and activate pre-commit hooks for @@ -86,14 +85,7 @@ Skip the next paragraph if you haven't worked on the documentation. up the optimagic-docs environment: ```console - $ conda env create -f rtd_environment.yml - $ conda activate optimagic-docs - ``` - - Inside the `docs` folder, run: - - ```console - $ make html + $ pixi run -e docs docs ``` This command builds the HTML documentation, saving all files in the `build/html` diff --git a/docs/source/how_to/how_to_add_optimizers.ipynb b/docs/source/how_to/how_to_add_optimizers.ipynb index fd90a72e5..86f926743 100644 --- a/docs/source/how_to/how_to_add_optimizers.ipynb +++ b/docs/source/how_to/how_to_add_optimizers.ipynb @@ -620,33 +620,7 @@ { "cell_type": "markdown", "metadata": {}, - "source": [ - "## 6. Integrate your code into optimagic\n", - "\n", - "So far you could have worked in a Jupyter Notebook. Integrating your code into \n", - "optimagic only requires a few small changes:\n", - "\n", - "1. Add new dependencies to the `environment.yml` file and run \n", - "`pre-commit run --all-files`. This will trigger a script that adds the dependencies to \n", - "multiple environments we need for continuous integration. Then re-create the enviroment \n", - "to make sure that the environment is the same as we will use for continuous integration.\n", - "If your dependencies don't work on all platforms (e.g. linux only packages), skip this\n", - "entire step and reach out to a core contributor for help. \n", - "2. Save the code for your algorithm wrapper in a .py file in `optimagic.algorithms`. \n", - "Use an existing file if you wrap another algorithm from a library we already had. \n", - "Otherwise, create a new file. \n", - "3. Run `pre-commit run --all-files`. This will trigger an automatic code generation \n", - "that fully integrates your wrapper into our algorithm selection tool.\n", - "4. Run `pytest`. This will run at least a few tests for your new algorithm. Add more \n", - "tests for algorithm specific things (e.g. tests that make sure tuning parameters have \n", - "the intended effects). \n", - "5. Write documentation. The documentation should contain everything you figured out in \n", - "step 2. You can either write it into the docstring of your algorithm class (preferred, \n", - "as this is what we will do for all algorithms in the long run) or in `algorithms.md` \n", - "in the documentation. \n", - "6. Create a pull request [in the optimagic repository](https://github.com/optimagic-dev/optimagic)\n", - "and ask for a review. " - ] + "source": "## 6. Integrate your code into optimagic\n\nSo far you could have worked in a Jupyter Notebook. Integrating your code into\noptimagic only requires a few small changes:\n\n1. Add new dependencies to the `[tool.pixi.feature.test.dependencies]` section of\n`pyproject.toml` and run `pixi install` to update the lock file. Then re-create the\nenvironment to make sure that the environment is the same as we will use for continuous\nintegration. If your dependencies don't work on all platforms (e.g. linux only packages),\nskip this entire step and reach out to a core contributor for help.\n2. Save the code for your algorithm wrapper in a .py file in `optimagic.algorithms`.\nUse an existing file if you wrap another algorithm from a library we already had.\nOtherwise, create a new file.\n3. Run `pre-commit run --all-files`. This will trigger an automatic code generation\nthat fully integrates your wrapper into our algorithm selection tool.\n4. Run `pytest`. This will run at least a few tests for your new algorithm. Add more\ntests for algorithm specific things (e.g. tests that make sure tuning parameters have\nthe intended effects).\n5. Write documentation. The documentation should contain everything you figured out in\nstep 2. You can either write it into the docstring of your algorithm class (preferred,\nas this is what we will do for all algorithms in the long run) or in `algorithms.md`\nin the documentation.\n6. Create a pull request [in the optimagic repository](https://github.com/optimagic-dev/optimagic)\nand ask for a review." } ], "metadata": { diff --git a/environment.yml b/environment.yml deleted file mode 100644 index 7d855693a..000000000 --- a/environment.yml +++ /dev/null @@ -1,66 +0,0 @@ ---- -name: optimagic -channels: - - conda-forge - - nodefaults -dependencies: - - python=3.10 # dev - - cyipopt>=1.4.0 # dev, tests - - pygmo>=2.19.0 # dev, tests, docs - - jupyterlab # dev, docs - - nlopt # dev, tests, docs - - pip # dev, tests, docs - - pytest # dev, tests - - pytest-cov # tests - - pytest-xdist # dev, tests - - setuptools_scm # dev - - statsmodels # dev, tests - - toml # dev - - cloudpickle # run, tests - - joblib # run, tests - - numpy >= 2 # run, tests - - pandas # run, tests - - plotly>=6.2 # run, tests - - matplotlib # tests - - bokeh # tests - - altair # tests - - pybaum>=0.1.2 # run, tests - - scipy>=1.2.1 # run, tests - - sqlalchemy # run, tests - - myst-nb # docs - - sphinx # docs - - sphinx-copybutton # docs - - sphinx-design # docs - - sphinx-panels # docs - - sphinxcontrib-bibtex # docs - - intersphinx-registry # docs - - seaborn # dev, tests - - mypy=1.19.1 # dev, tests - - pyyaml # dev, tests - - jinja2 # dev, tests - - furo # dev, docs - - annotated-types # dev, tests - - tranquilo>=0.1.1 # tests - - iminuit # dev, tests - - cma # dev, tests - - pygad # dev, tests - - pytorch-cpu # dev, tests - - pip: # dev, tests, docs - - bayesian-optimization>=2.0.4 # dev, tests - # - nevergrad # incompatible with bayesian-optimization>=2.0.4 - - DFO-LS>=1.5.3 # dev, tests - - Py-BOBYQA # dev, tests - - fides==0.7.4 # dev, tests - - kaleido>=1.0 # dev, tests - - pre-commit>=4 # dev - - gradient_free_optimizers # dev, tests - - pyswarms # dev, tests - - -e . # dev - # type stubs - - pandas-stubs # dev, tests - - types-cffi # dev, tests - - types-openpyxl # dev, tests - - types-jinja2 # dev, tests - - sqlalchemy-stubs # dev, tests - - sphinxcontrib-mermaid # 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libzlib >=1.3.1,<2.0a0 + license: BSD-3-Clause + license_family: BSD + purls: [] + size: 388453 + timestamp: 1764777142545 diff --git a/pyproject.toml b/pyproject.toml index af2cf0e65..ac84ec1b9 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -392,3 +392,168 @@ module = [ "gradient_free_optimizers.optimizers.base_optimizer", ] ignore_missing_imports = true + + +# ====================================================================================== +# Pixi configuration +# ====================================================================================== +[tool.pixi.workspace] +channels = ["conda-forge"] +platforms = ["linux-64", "osx-arm64", "win-64"] + +# --- Base dependencies (all environments) ------------------------------------------- +[tool.pixi.dependencies] +python = ">=3.10,<3.14" +# Prefer conda-forge builds for compiled scientific packages +numpy = "*" +scipy = ">=1.2.1" +pandas = "*" +jupyterlab = "*" + +[tool.pixi.pypi-dependencies] +optimagic = { path = ".", editable = true } +pdbp = "*" +pre-commit = ">=4" + +# --- Python version features -------------------------------------------------------- +[tool.pixi.feature.py310.dependencies] +python = "~=3.10.0" +[tool.pixi.feature.py311.dependencies] +python = "~=3.11.0" +[tool.pixi.feature.py312.dependencies] +python = "~=3.12.0" +[tool.pixi.feature.py313.dependencies] +python = "~=3.13.0" + +# --- Feature: test (test infrastructure + optional optimizer backends) --------------- +[tool.pixi.feature.test.dependencies] +pytest = "*" +pytest-cov = "*" +pytest-xdist = "*" +cyipopt = ">=1.4.0" +pygmo = ">=2.19.0" +nlopt = "*" +statsmodels = "*" +matplotlib = "*" +bokeh = "*" +altair = "*" +seaborn = "*" +mypy = "==1.19.1" +pyyaml = "*" +jinja2 = "*" +tranquilo = ">=0.1.1" +iminuit = "*" +cma = "*" +pygad = "*" +pytorch-cpu = "*" + +[tool.pixi.feature.test.pypi-dependencies] +bayesian-optimization = "*" +dfo-ls = ">=1.5.3" +py-bobyqa = "*" +fides = "==0.7.4" +kaleido = "*" +gradient-free-optimizers = "*" +pyswarms = "*" +pandas-stubs = "*" +types-cffi = "*" +types-openpyxl = "*" +types-jinja2 = "*" +sqlalchemy-stubs = "*" +sphinxcontrib-mermaid = "*" + +[tool.pixi.feature.test.tasks] +tests = "pytest" +tests-fast = "pytest -m 'not slow and not jax'" +tests-with-cov = "pytest --cov-report=xml --cov=./" +mypy = "mypy" +lint = "pre-commit run --all-files" + +# --- Feature: linux (Linux-only test deps) ------------------------------------------ +[tool.pixi.feature.linux] +platforms = ["linux-64"] +[tool.pixi.feature.linux.dependencies] +jax = "*" +petsc4py = "<=3.23.4" + +# --- Feature: docs ------------------------------------------------------------------ +[tool.pixi.feature.docs.dependencies] +sphinx = ">=8.2.3" +sphinxcontrib-bibtex = "*" +sphinx-copybutton = "*" +sphinx-design = "*" +sphinx-llm = "*" +sphinx-llms-txt = "*" +ipython = "*" +ipython_genutils = "*" +myst-nb = "*" +furo = "*" +anywidget = "*" +patsy = "*" +nlopt = "*" +pygmo = ">=2.19.0" +matplotlib = "*" +bokeh = "*" +altair = "*" +seaborn = "*" + +[tool.pixi.feature.docs.pypi-dependencies] +py-bobyqa = "*" +dfo-ls = "*" +sphinxcontrib-mermaid = "*" +intersphinx-registry = "*" +fides = "==0.7.4" +bayesian-optimization = "*" +pandas-stubs = "*" +types-cffi = "*" +types-openpyxl = "*" +types-jinja2 = "*" +sqlalchemy-stubs = "*" + +[tool.pixi.feature.docs.tasks] +docs = { cmd = "make html", cwd = "docs" } + +# --- Compat features (version overrides for backward-compat CI) --------------------- +[tool.pixi.feature.old-pandas.dependencies] +numpy = "<2" +pandas = "<2" + +[tool.pixi.feature.old-numpy.dependencies] +numpy = "<2" +pandas = ">=2" + +[tool.pixi.feature.old-plotly.dependencies] +plotly = "<6" + +[tool.pixi.feature.old-plotly.pypi-dependencies] +kaleido = "<0.3" + +[tool.pixi.feature.nevergrad.pypi-dependencies] +bayesian-optimization = "==1.4.0" +nevergrad = "*" + +# --- Environments -------------------------------------------------------------------- +[tool.pixi.environments] +# Default dev environment (Python 3.12, everything) +default = { features = ["test", "docs", "py312"], solve-group = "py312" } +# Linux CI (with JAX + PETSc) +test-linux-py310 = { features = ["test", "linux", "py310"], solve-group = "linux-py310" } +test-linux-py311 = { features = ["test", "linux", "py311"], solve-group = "linux-py311" } +test-linux-py312 = { features = ["test", "linux", "py312"], solve-group = "linux-py312" } +test-linux-py313 = { features = ["test", "linux", "py313"], solve-group = "linux-py313" } +# macOS/Windows CI +test-py310 = { features = ["test", "py310"], solve-group = "py310" } +test-py311 = { features = ["test", "py311"], solve-group = "py311" } +test-py312 = { features = ["test", "py312"], solve-group = "py312" } +test-py313 = { features = ["test", "py313"], solve-group = "py313" } +# Backward-compat CI (Python 3.10 only) +test-old-pandas = { features = ["test", "old-pandas", "py310"] } +test-old-numpy = { features = ["test", "old-numpy", "py310"] } +test-old-plotly = { features = ["test", "old-plotly", "py310"] } +# Nevergrad CI (bayesian-optimization==1.4.0) +test-nevergrad-py310 = { features = ["test", "nevergrad", "py310"] } +test-nevergrad-py311 = { features = ["test", "nevergrad", "py311"] } +test-nevergrad-py312 = { features = ["test", "nevergrad", "py312"] } +test-nevergrad-py313 = { features = ["test", "nevergrad", "py313"] } +# Docs +docs = { features = ["docs", "py312"], solve-group = "py312" } diff --git a/src/optimagic/algorithms.py b/src/optimagic/algorithms.py index 795046950..ed68c9e34 100644 --- a/src/optimagic/algorithms.py +++ b/src/optimagic/algorithms.py @@ -214,7 +214,7 @@ class BoundedGlobalGradientFreeParallelScalarAlgorithms(AlgoSelection): nevergrad_eda: Type[NevergradEDA] = NevergradEDA nevergrad_emna: Type[NevergradEMNA] = NevergradEMNA nevergrad_meta: Type[NevergradMeta] = NevergradMeta - nevergrad_NGOpt: Type[NevergradNGOpt] = NevergradNGOpt + nevergrad_ngopt: Type[NevergradNGOpt] = NevergradNGOpt nevergrad_oneplusone: Type[NevergradOnePlusOne] = NevergradOnePlusOne nevergrad_pso: Type[NevergradPSO] = NevergradPSO nevergrad_randomsearch: Type[NevergradRandomSearch] = NevergradRandomSearch @@ -441,7 +441,7 @@ class BoundedGlobalGradientFreeScalarAlgorithms(AlgoSelection): nevergrad_eda: Type[NevergradEDA] = NevergradEDA nevergrad_emna: Type[NevergradEMNA] = NevergradEMNA nevergrad_meta: Type[NevergradMeta] = NevergradMeta - nevergrad_NGOpt: Type[NevergradNGOpt] = NevergradNGOpt + nevergrad_ngopt: Type[NevergradNGOpt] = NevergradNGOpt nevergrad_oneplusone: Type[NevergradOnePlusOne] = NevergradOnePlusOne nevergrad_pso: Type[NevergradPSO] = NevergradPSO nevergrad_randomsearch: Type[NevergradRandomSearch] = NevergradRandomSearch @@ -497,7 +497,7 @@ class BoundedGlobalGradientFreeParallelAlgorithms(AlgoSelection): nevergrad_eda: Type[NevergradEDA] = NevergradEDA nevergrad_emna: Type[NevergradEMNA] = NevergradEMNA nevergrad_meta: Type[NevergradMeta] = NevergradMeta - nevergrad_NGOpt: Type[NevergradNGOpt] = NevergradNGOpt + nevergrad_ngopt: Type[NevergradNGOpt] = NevergradNGOpt nevergrad_oneplusone: Type[NevergradOnePlusOne] = NevergradOnePlusOne nevergrad_pso: Type[NevergradPSO] = NevergradPSO nevergrad_randomsearch: Type[NevergradRandomSearch] = NevergradRandomSearch @@ -569,7 +569,7 @@ class GlobalGradientFreeParallelScalarAlgorithms(AlgoSelection): nevergrad_eda: Type[NevergradEDA] = NevergradEDA nevergrad_emna: Type[NevergradEMNA] = NevergradEMNA nevergrad_meta: Type[NevergradMeta] = NevergradMeta - nevergrad_NGOpt: Type[NevergradNGOpt] = NevergradNGOpt + nevergrad_ngopt: Type[NevergradNGOpt] = NevergradNGOpt nevergrad_oneplusone: Type[NevergradOnePlusOne] = NevergradOnePlusOne nevergrad_pso: Type[NevergradPSO] = NevergradPSO nevergrad_randomsearch: Type[NevergradRandomSearch] = NevergradRandomSearch @@ -733,7 +733,7 @@ class BoundedGradientFreeParallelScalarAlgorithms(AlgoSelection): nevergrad_eda: Type[NevergradEDA] = NevergradEDA nevergrad_emna: Type[NevergradEMNA] = NevergradEMNA nevergrad_meta: Type[NevergradMeta] = NevergradMeta - nevergrad_NGOpt: Type[NevergradNGOpt] = NevergradNGOpt + nevergrad_ngopt: Type[NevergradNGOpt] = NevergradNGOpt nevergrad_oneplusone: Type[NevergradOnePlusOne] = NevergradOnePlusOne nevergrad_pso: Type[NevergradPSO] = NevergradPSO nevergrad_randomsearch: Type[NevergradRandomSearch] = NevergradRandomSearch @@ -844,7 +844,7 @@ class BoundedGlobalParallelScalarAlgorithms(AlgoSelection): nevergrad_eda: Type[NevergradEDA] = NevergradEDA nevergrad_emna: Type[NevergradEMNA] = NevergradEMNA nevergrad_meta: Type[NevergradMeta] = NevergradMeta - nevergrad_NGOpt: Type[NevergradNGOpt] = NevergradNGOpt + nevergrad_ngopt: Type[NevergradNGOpt] = NevergradNGOpt nevergrad_oneplusone: Type[NevergradOnePlusOne] = NevergradOnePlusOne nevergrad_pso: Type[NevergradPSO] = NevergradPSO nevergrad_randomsearch: Type[NevergradRandomSearch] = NevergradRandomSearch @@ -1204,7 +1204,7 @@ class BoundedGlobalGradientFreeAlgorithms(AlgoSelection): nevergrad_eda: Type[NevergradEDA] = NevergradEDA nevergrad_emna: Type[NevergradEMNA] = NevergradEMNA nevergrad_meta: Type[NevergradMeta] = NevergradMeta - nevergrad_NGOpt: Type[NevergradNGOpt] = NevergradNGOpt + nevergrad_ngopt: Type[NevergradNGOpt] = NevergradNGOpt nevergrad_oneplusone: Type[NevergradOnePlusOne] = NevergradOnePlusOne nevergrad_pso: Type[NevergradPSO] = NevergradPSO nevergrad_randomsearch: Type[NevergradRandomSearch] = NevergradRandomSearch @@ -1301,7 +1301,7 @@ class GlobalGradientFreeScalarAlgorithms(AlgoSelection): nevergrad_eda: Type[NevergradEDA] = NevergradEDA nevergrad_emna: Type[NevergradEMNA] = NevergradEMNA nevergrad_meta: Type[NevergradMeta] = NevergradMeta - nevergrad_NGOpt: Type[NevergradNGOpt] = NevergradNGOpt + nevergrad_ngopt: Type[NevergradNGOpt] = NevergradNGOpt nevergrad_oneplusone: Type[NevergradOnePlusOne] = NevergradOnePlusOne nevergrad_pso: Type[NevergradPSO] = NevergradPSO nevergrad_randomsearch: Type[NevergradRandomSearch] = NevergradRandomSearch @@ -1361,7 +1361,7 @@ class GlobalGradientFreeParallelAlgorithms(AlgoSelection): nevergrad_eda: Type[NevergradEDA] = NevergradEDA nevergrad_emna: Type[NevergradEMNA] = NevergradEMNA nevergrad_meta: Type[NevergradMeta] = NevergradMeta - nevergrad_NGOpt: Type[NevergradNGOpt] = NevergradNGOpt + nevergrad_ngopt: Type[NevergradNGOpt] = NevergradNGOpt nevergrad_oneplusone: Type[NevergradOnePlusOne] = NevergradOnePlusOne nevergrad_pso: Type[NevergradPSO] = NevergradPSO nevergrad_randomsearch: Type[NevergradRandomSearch] = NevergradRandomSearch @@ -1560,7 +1560,7 @@ class BoundedGradientFreeScalarAlgorithms(AlgoSelection): nevergrad_eda: Type[NevergradEDA] = NevergradEDA nevergrad_emna: Type[NevergradEMNA] = NevergradEMNA nevergrad_meta: Type[NevergradMeta] = NevergradMeta - nevergrad_NGOpt: Type[NevergradNGOpt] = NevergradNGOpt + nevergrad_ngopt: Type[NevergradNGOpt] = NevergradNGOpt nevergrad_oneplusone: Type[NevergradOnePlusOne] = NevergradOnePlusOne nevergrad_pso: Type[NevergradPSO] = NevergradPSO nevergrad_randomsearch: Type[NevergradRandomSearch] = NevergradRandomSearch @@ -1648,7 +1648,7 @@ class BoundedGradientFreeParallelAlgorithms(AlgoSelection): nevergrad_eda: Type[NevergradEDA] = NevergradEDA nevergrad_emna: Type[NevergradEMNA] = NevergradEMNA nevergrad_meta: Type[NevergradMeta] = NevergradMeta - nevergrad_NGOpt: Type[NevergradNGOpt] = NevergradNGOpt + nevergrad_ngopt: Type[NevergradNGOpt] = NevergradNGOpt nevergrad_oneplusone: Type[NevergradOnePlusOne] = NevergradOnePlusOne nevergrad_pso: Type[NevergradPSO] = NevergradPSO nevergrad_randomsearch: Type[NevergradRandomSearch] = NevergradRandomSearch @@ -1746,7 +1746,7 @@ class GradientFreeParallelScalarAlgorithms(AlgoSelection): nevergrad_eda: Type[NevergradEDA] = NevergradEDA nevergrad_emna: Type[NevergradEMNA] = NevergradEMNA nevergrad_meta: Type[NevergradMeta] = NevergradMeta - nevergrad_NGOpt: Type[NevergradNGOpt] = NevergradNGOpt + nevergrad_ngopt: Type[NevergradNGOpt] = NevergradNGOpt nevergrad_oneplusone: Type[NevergradOnePlusOne] = NevergradOnePlusOne nevergrad_pso: Type[NevergradPSO] = NevergradPSO nevergrad_randomsearch: Type[NevergradRandomSearch] = NevergradRandomSearch @@ -1848,7 +1848,7 @@ class BoundedGlobalScalarAlgorithms(AlgoSelection): nevergrad_eda: Type[NevergradEDA] = NevergradEDA nevergrad_emna: Type[NevergradEMNA] = NevergradEMNA nevergrad_meta: Type[NevergradMeta] = NevergradMeta - nevergrad_NGOpt: Type[NevergradNGOpt] = NevergradNGOpt + nevergrad_ngopt: Type[NevergradNGOpt] = NevergradNGOpt nevergrad_oneplusone: Type[NevergradOnePlusOne] = NevergradOnePlusOne nevergrad_pso: Type[NevergradPSO] = NevergradPSO nevergrad_randomsearch: Type[NevergradRandomSearch] = NevergradRandomSearch @@ -1913,7 +1913,7 @@ class BoundedGlobalParallelAlgorithms(AlgoSelection): nevergrad_eda: Type[NevergradEDA] = NevergradEDA nevergrad_emna: Type[NevergradEMNA] = NevergradEMNA nevergrad_meta: Type[NevergradMeta] = NevergradMeta - nevergrad_NGOpt: Type[NevergradNGOpt] = NevergradNGOpt + nevergrad_ngopt: Type[NevergradNGOpt] = NevergradNGOpt nevergrad_oneplusone: Type[NevergradOnePlusOne] = NevergradOnePlusOne nevergrad_pso: Type[NevergradPSO] = NevergradPSO nevergrad_randomsearch: Type[NevergradRandomSearch] = NevergradRandomSearch @@ -1998,7 +1998,7 @@ class GlobalParallelScalarAlgorithms(AlgoSelection): nevergrad_eda: Type[NevergradEDA] = NevergradEDA nevergrad_emna: Type[NevergradEMNA] = NevergradEMNA nevergrad_meta: Type[NevergradMeta] = NevergradMeta - nevergrad_NGOpt: Type[NevergradNGOpt] = NevergradNGOpt + nevergrad_ngopt: Type[NevergradNGOpt] = NevergradNGOpt nevergrad_oneplusone: Type[NevergradOnePlusOne] = NevergradOnePlusOne nevergrad_pso: Type[NevergradPSO] = NevergradPSO nevergrad_randomsearch: Type[NevergradRandomSearch] = NevergradRandomSearch @@ -2249,7 +2249,7 @@ class BoundedParallelScalarAlgorithms(AlgoSelection): nevergrad_eda: Type[NevergradEDA] = NevergradEDA nevergrad_emna: Type[NevergradEMNA] = NevergradEMNA nevergrad_meta: Type[NevergradMeta] = NevergradMeta - nevergrad_NGOpt: Type[NevergradNGOpt] = NevergradNGOpt + nevergrad_ngopt: Type[NevergradNGOpt] = NevergradNGOpt nevergrad_oneplusone: Type[NevergradOnePlusOne] = NevergradOnePlusOne nevergrad_pso: Type[NevergradPSO] = NevergradPSO nevergrad_randomsearch: Type[NevergradRandomSearch] = NevergradRandomSearch @@ -2541,7 +2541,7 @@ class GlobalGradientFreeAlgorithms(AlgoSelection): nevergrad_eda: Type[NevergradEDA] = NevergradEDA nevergrad_emna: Type[NevergradEMNA] = NevergradEMNA nevergrad_meta: Type[NevergradMeta] = NevergradMeta - nevergrad_NGOpt: Type[NevergradNGOpt] = NevergradNGOpt + nevergrad_ngopt: Type[NevergradNGOpt] = NevergradNGOpt nevergrad_oneplusone: Type[NevergradOnePlusOne] = NevergradOnePlusOne nevergrad_pso: Type[NevergradPSO] = NevergradPSO nevergrad_randomsearch: Type[NevergradRandomSearch] = NevergradRandomSearch @@ -2662,7 +2662,7 @@ class BoundedGradientFreeAlgorithms(AlgoSelection): nevergrad_eda: Type[NevergradEDA] = NevergradEDA nevergrad_emna: Type[NevergradEMNA] = NevergradEMNA nevergrad_meta: Type[NevergradMeta] = NevergradMeta - nevergrad_NGOpt: Type[NevergradNGOpt] = NevergradNGOpt + nevergrad_ngopt: Type[NevergradNGOpt] = NevergradNGOpt nevergrad_oneplusone: Type[NevergradOnePlusOne] = NevergradOnePlusOne nevergrad_pso: Type[NevergradPSO] = NevergradPSO nevergrad_randomsearch: Type[NevergradRandomSearch] = NevergradRandomSearch @@ -2792,7 +2792,7 @@ class GradientFreeScalarAlgorithms(AlgoSelection): nevergrad_eda: Type[NevergradEDA] = NevergradEDA nevergrad_emna: Type[NevergradEMNA] = NevergradEMNA nevergrad_meta: Type[NevergradMeta] = NevergradMeta - nevergrad_NGOpt: Type[NevergradNGOpt] = NevergradNGOpt + nevergrad_ngopt: Type[NevergradNGOpt] = NevergradNGOpt nevergrad_oneplusone: Type[NevergradOnePlusOne] = NevergradOnePlusOne nevergrad_pso: Type[NevergradPSO] = NevergradPSO nevergrad_randomsearch: Type[NevergradRandomSearch] = NevergradRandomSearch @@ -2889,7 +2889,7 @@ class GradientFreeParallelAlgorithms(AlgoSelection): nevergrad_eda: Type[NevergradEDA] = NevergradEDA nevergrad_emna: Type[NevergradEMNA] = NevergradEMNA nevergrad_meta: Type[NevergradMeta] = NevergradMeta - nevergrad_NGOpt: Type[NevergradNGOpt] = NevergradNGOpt + nevergrad_ngopt: Type[NevergradNGOpt] = NevergradNGOpt nevergrad_oneplusone: Type[NevergradOnePlusOne] = NevergradOnePlusOne nevergrad_pso: Type[NevergradPSO] = NevergradPSO nevergrad_randomsearch: Type[NevergradRandomSearch] = NevergradRandomSearch @@ -2962,7 +2962,7 @@ class BoundedGlobalAlgorithms(AlgoSelection): nevergrad_eda: Type[NevergradEDA] = NevergradEDA nevergrad_emna: Type[NevergradEMNA] = NevergradEMNA nevergrad_meta: Type[NevergradMeta] = NevergradMeta - nevergrad_NGOpt: Type[NevergradNGOpt] = NevergradNGOpt + nevergrad_ngopt: Type[NevergradNGOpt] = NevergradNGOpt nevergrad_oneplusone: Type[NevergradOnePlusOne] = NevergradOnePlusOne nevergrad_pso: Type[NevergradPSO] = NevergradPSO nevergrad_randomsearch: Type[NevergradRandomSearch] = NevergradRandomSearch @@ -3077,7 +3077,7 @@ class GlobalScalarAlgorithms(AlgoSelection): nevergrad_eda: Type[NevergradEDA] = NevergradEDA nevergrad_emna: Type[NevergradEMNA] = NevergradEMNA nevergrad_meta: Type[NevergradMeta] = NevergradMeta - nevergrad_NGOpt: Type[NevergradNGOpt] = NevergradNGOpt + nevergrad_ngopt: Type[NevergradNGOpt] = NevergradNGOpt nevergrad_oneplusone: Type[NevergradOnePlusOne] = NevergradOnePlusOne nevergrad_pso: Type[NevergradPSO] = NevergradPSO nevergrad_randomsearch: Type[NevergradRandomSearch] = NevergradRandomSearch @@ -3146,7 +3146,7 @@ class GlobalParallelAlgorithms(AlgoSelection): nevergrad_eda: Type[NevergradEDA] = NevergradEDA nevergrad_emna: Type[NevergradEMNA] = NevergradEMNA nevergrad_meta: Type[NevergradMeta] = NevergradMeta - nevergrad_NGOpt: Type[NevergradNGOpt] = NevergradNGOpt + nevergrad_ngopt: Type[NevergradNGOpt] = NevergradNGOpt nevergrad_oneplusone: Type[NevergradOnePlusOne] = NevergradOnePlusOne nevergrad_pso: Type[NevergradPSO] = NevergradPSO nevergrad_randomsearch: Type[NevergradRandomSearch] = NevergradRandomSearch @@ -3444,7 +3444,7 @@ class BoundedScalarAlgorithms(AlgoSelection): nevergrad_eda: Type[NevergradEDA] = NevergradEDA nevergrad_emna: Type[NevergradEMNA] = NevergradEMNA nevergrad_meta: Type[NevergradMeta] = NevergradMeta - nevergrad_NGOpt: Type[NevergradNGOpt] = NevergradNGOpt + nevergrad_ngopt: Type[NevergradNGOpt] = NevergradNGOpt nevergrad_oneplusone: Type[NevergradOnePlusOne] = NevergradOnePlusOne nevergrad_pso: Type[NevergradPSO] = NevergradPSO nevergrad_randomsearch: Type[NevergradRandomSearch] = NevergradRandomSearch @@ -3561,7 +3561,7 @@ class BoundedParallelAlgorithms(AlgoSelection): nevergrad_eda: Type[NevergradEDA] = NevergradEDA nevergrad_emna: Type[NevergradEMNA] = NevergradEMNA nevergrad_meta: Type[NevergradMeta] = NevergradMeta - nevergrad_NGOpt: Type[NevergradNGOpt] = NevergradNGOpt + nevergrad_ngopt: Type[NevergradNGOpt] = NevergradNGOpt nevergrad_oneplusone: Type[NevergradOnePlusOne] = NevergradOnePlusOne nevergrad_pso: Type[NevergradPSO] = NevergradPSO nevergrad_randomsearch: Type[NevergradRandomSearch] = NevergradRandomSearch @@ -3679,7 +3679,7 @@ class ParallelScalarAlgorithms(AlgoSelection): nevergrad_eda: Type[NevergradEDA] = NevergradEDA nevergrad_emna: Type[NevergradEMNA] = NevergradEMNA nevergrad_meta: Type[NevergradMeta] = NevergradMeta - nevergrad_NGOpt: Type[NevergradNGOpt] = NevergradNGOpt + nevergrad_ngopt: Type[NevergradNGOpt] = NevergradNGOpt nevergrad_oneplusone: Type[NevergradOnePlusOne] = NevergradOnePlusOne nevergrad_pso: Type[NevergradPSO] = NevergradPSO nevergrad_randomsearch: Type[NevergradRandomSearch] = NevergradRandomSearch @@ -3820,7 +3820,7 @@ class GradientFreeAlgorithms(AlgoSelection): nevergrad_eda: Type[NevergradEDA] = NevergradEDA nevergrad_emna: Type[NevergradEMNA] = NevergradEMNA nevergrad_meta: Type[NevergradMeta] = NevergradMeta - nevergrad_NGOpt: Type[NevergradNGOpt] = NevergradNGOpt + nevergrad_ngopt: Type[NevergradNGOpt] = NevergradNGOpt nevergrad_oneplusone: Type[NevergradOnePlusOne] = NevergradOnePlusOne nevergrad_pso: Type[NevergradPSO] = NevergradPSO nevergrad_randomsearch: Type[NevergradRandomSearch] = NevergradRandomSearch @@ -3924,7 +3924,7 @@ class GlobalAlgorithms(AlgoSelection): nevergrad_eda: Type[NevergradEDA] = NevergradEDA nevergrad_emna: Type[NevergradEMNA] = NevergradEMNA nevergrad_meta: Type[NevergradMeta] = NevergradMeta - nevergrad_NGOpt: Type[NevergradNGOpt] = NevergradNGOpt + nevergrad_ngopt: Type[NevergradNGOpt] = NevergradNGOpt nevergrad_oneplusone: Type[NevergradOnePlusOne] = NevergradOnePlusOne nevergrad_pso: Type[NevergradPSO] = NevergradPSO nevergrad_randomsearch: Type[NevergradRandomSearch] = NevergradRandomSearch @@ -4091,7 +4091,7 @@ class BoundedAlgorithms(AlgoSelection): nevergrad_eda: Type[NevergradEDA] = NevergradEDA nevergrad_emna: Type[NevergradEMNA] = NevergradEMNA nevergrad_meta: Type[NevergradMeta] = NevergradMeta - nevergrad_NGOpt: Type[NevergradNGOpt] = NevergradNGOpt + nevergrad_ngopt: Type[NevergradNGOpt] = NevergradNGOpt nevergrad_oneplusone: Type[NevergradOnePlusOne] = NevergradOnePlusOne nevergrad_pso: Type[NevergradPSO] = NevergradPSO nevergrad_randomsearch: Type[NevergradRandomSearch] = NevergradRandomSearch @@ -4261,7 +4261,7 @@ class ScalarAlgorithms(AlgoSelection): nevergrad_eda: Type[NevergradEDA] = NevergradEDA nevergrad_emna: Type[NevergradEMNA] = NevergradEMNA nevergrad_meta: Type[NevergradMeta] = NevergradMeta - nevergrad_NGOpt: Type[NevergradNGOpt] = NevergradNGOpt + nevergrad_ngopt: Type[NevergradNGOpt] = NevergradNGOpt nevergrad_oneplusone: Type[NevergradOnePlusOne] = NevergradOnePlusOne nevergrad_pso: Type[NevergradPSO] = NevergradPSO nevergrad_randomsearch: Type[NevergradRandomSearch] = NevergradRandomSearch @@ -4406,7 +4406,7 @@ class ParallelAlgorithms(AlgoSelection): nevergrad_eda: Type[NevergradEDA] = NevergradEDA nevergrad_emna: Type[NevergradEMNA] = NevergradEMNA nevergrad_meta: Type[NevergradMeta] = NevergradMeta - nevergrad_NGOpt: Type[NevergradNGOpt] = NevergradNGOpt + nevergrad_ngopt: Type[NevergradNGOpt] = NevergradNGOpt nevergrad_oneplusone: Type[NevergradOnePlusOne] = NevergradOnePlusOne nevergrad_pso: Type[NevergradPSO] = NevergradPSO nevergrad_randomsearch: Type[NevergradRandomSearch] = NevergradRandomSearch @@ -4488,7 +4488,7 @@ class Algorithms(AlgoSelection): nevergrad_eda: Type[NevergradEDA] = NevergradEDA nevergrad_emna: Type[NevergradEMNA] = NevergradEMNA nevergrad_meta: Type[NevergradMeta] = NevergradMeta - nevergrad_NGOpt: Type[NevergradNGOpt] = NevergradNGOpt + nevergrad_ngopt: Type[NevergradNGOpt] = NevergradNGOpt nevergrad_oneplusone: Type[NevergradOnePlusOne] = NevergradOnePlusOne nevergrad_pso: Type[NevergradPSO] = NevergradPSO nevergrad_randomsearch: Type[NevergradRandomSearch] = NevergradRandomSearch From 0b4eca61bd8106a76754626c5a37c736c357abe7 Mon Sep 17 00:00:00 2001 From: timmens Date: Tue, 10 Mar 2026 13:32:26 +0100 Subject: [PATCH 02/18] Address PR review feedback - Move optimizer backends and viz libs from test feature to base deps - Create separate typecheck env with mypy + type stubs - Slim down docs feature to only sphinx tooling + doc-specific deps - Slim down default env to just base + test (no typecheck/docs) - Rename docs task to build-docs - Remove pixi install from RTD config (pixi run handles it) - Remove pre-commit/pdbp from pixi deps (install globally) - Update contributor guide: explain global pre-commit install - Fix two pre-existing mypy errors in history.py and slice_plot_3d.py Co-Authored-By: Claude Opus 4.6 --- .github/workflows/main.yml | 4 +- .readthedocs.yml | 4 +- docs/source/development/how_to_contribute.md | 19 +- pixi.lock | 3288 ++++++------------ pyproject.toml | 84 +- src/optimagic/optimization/history.py | 2 +- src/optimagic/visualization/slice_plot_3d.py | 2 +- 7 files changed, 1174 insertions(+), 2229 deletions(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 28a9added..5375941a8 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -163,7 +163,7 @@ jobs: cache: true cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }} frozen: true - environments: test-linux-py310 + environments: typecheck - name: Run mypy shell: bash -el {0} - run: pixi run -e test-linux-py310 mypy + run: pixi run -e typecheck mypy diff --git a/.readthedocs.yml b/.readthedocs.yml index ff31076ee..28e6b2aea 100644 --- a/.readthedocs.yml +++ b/.readthedocs.yml @@ -9,10 +9,8 @@ build: - asdf plugin add pixi - asdf install pixi latest - asdf global pixi latest - install: - - pixi install -e docs build: - - pixi run -e docs docs + - pixi run -e docs build-docs post_build: - mkdir --parents $READTHEDOCS_OUTPUT/html/ - cp -a docs/build/html/. "$READTHEDOCS_OUTPUT/html" && rm -r docs/build diff --git a/docs/source/development/how_to_contribute.md b/docs/source/development/how_to_contribute.md index bf441abe1..aa4f2d79d 100644 --- a/docs/source/development/how_to_contribute.md +++ b/docs/source/development/how_to_contribute.md @@ -44,12 +44,21 @@ For regular contributors: **Clone** the [repository](https://github.com/optimagi local optimagic repository: ```console - $ pixi install - $ pixi run lint # verify pre-commit hooks work + $ pre-commit install ``` - These commands install optimagic in editable mode and activate pre-commit hooks for - linting and style formatting. + This activates pre-commit hooks for linting and style formatting. + + ```{note} + `pre-commit` is not managed by pixi and must be installed globally. We recommend + installing it globally using pixi or uv. + ``` + + You can then run the test suite with: + + ```console + $ pixi run tests + ``` 1. Implement your fix or feature. Use git to add, commit, and push your changes to the remote repository. For more on git and how to stage and commit your work, refer to @@ -85,7 +94,7 @@ Skip the next paragraph if you haven't worked on the documentation. up the optimagic-docs environment: ```console - $ pixi run -e docs docs + $ pixi run build-docs ``` This command builds the HTML documentation, saving all files in the `build/html` diff --git a/pixi.lock b/pixi.lock index 960a580ec..e7310b77c 100644 --- a/pixi.lock +++ b/pixi.lock @@ -11,13 +11,10 @@ environments: linux-64: - conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-7_kmp_llvm.conda - conda: https://conda.anaconda.org/conda-forge/noarch/_python_abi3_support-1.0-hd8ed1ab_2.conda - - conda: https://conda.anaconda.org/conda-forge/noarch/accessible-pygments-0.0.5-pyhd8ed1ab_1.conda - - conda: https://conda.anaconda.org/conda-forge/noarch/alabaster-1.0.0-pyhd8ed1ab_1.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/alsa-lib-1.2.15.3-hb03c661_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/altair-6.0.0-pyhd8ed1ab_1.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/ampl-asl-1.0.0-h5888daf_2.conda - conda: https://conda.anaconda.org/conda-forge/noarch/anyio-4.12.1-pyhcf101f3_0.conda - - conda: https://conda.anaconda.org/conda-forge/noarch/anywidget-0.9.21-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/argon2-cffi-25.1.0-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/argon2-cffi-bindings-25.1.0-py312h4c3975b_2.conda - conda: https://conda.anaconda.org/conda-forge/noarch/arrow-1.4.0-pyhcf101f3_0.conda @@ -41,7 +38,6 @@ environments: - conda: https://conda.anaconda.org/conda-forge/noarch/certifi-2026.2.25-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/cffi-2.0.0-py312h460c074_1.conda - conda: https://conda.anaconda.org/conda-forge/noarch/charset-normalizer-3.4.5-pyhd8ed1ab_0.conda - - conda: https://conda.anaconda.org/conda-forge/noarch/click-8.3.1-pyh8f84b5b_1.conda - conda: https://conda.anaconda.org/conda-forge/noarch/cloudpickle-3.1.2-pyhcf101f3_1.conda - conda: https://conda.anaconda.org/conda-forge/noarch/cma-4.0.0-pyhecae5ae_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/colorama-0.4.6-pyhd8ed1ab_1.conda @@ -56,7 +52,6 @@ environments: - conda: https://conda.anaconda.org/conda-forge/linux-64/debugpy-1.8.20-py312h8285ef7_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/decorator-5.2.1-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/defusedxml-0.7.1-pyhd8ed1ab_0.tar.bz2 - - conda: https://conda.anaconda.org/conda-forge/noarch/docutils-0.22.4-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/double-conversion-3.4.0-hecca717_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/exceptiongroup-1.3.1-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/execnet-2.1.2-pyhd8ed1ab_0.conda @@ -74,7 +69,6 @@ environments: - conda: https://conda.anaconda.org/conda-forge/noarch/fqdn-1.5.1-pyhd8ed1ab_1.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/freetype-2.14.2-ha770c72_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/fsspec-2026.2.0-pyhd8ed1ab_0.conda - - conda: https://conda.anaconda.org/conda-forge/noarch/furo-2025.12.19-pyhd8ed1ab_1.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/gmp-6.3.0-hac33072_2.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/gmpy2-2.3.0-py312hcaba1f9_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/graphite2-1.3.14-hecca717_2.conda @@ -88,7 +82,6 @@ environments: - conda: https://conda.anaconda.org/conda-forge/noarch/hyperframe-6.1.0-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/icu-78.2-h33c6efd_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/idna-3.11-pyhd8ed1ab_0.conda - - conda: https://conda.anaconda.org/conda-forge/noarch/imagesize-1.4.1-pyhd8ed1ab_0.tar.bz2 - conda: https://conda.anaconda.org/conda-forge/linux-64/iminuit-2.32.0-py312h8285ef7_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/importlib-metadata-8.7.0-pyhe01879c_1.conda - conda: https://conda.anaconda.org/conda-forge/noarch/iniconfig-2.3.0-pyhd8ed1ab_0.conda @@ -96,9 +89,7 @@ environments: - conda: https://conda.anaconda.org/conda-forge/noarch/ipykernel-7.2.0-pyha191276_1.conda - conda: https://conda.anaconda.org/conda-forge/noarch/ipyparallel-9.0.2-pyhcf101f3_1.conda - conda: https://conda.anaconda.org/conda-forge/noarch/ipython-9.11.0-pyhecfbec7_0.conda - - conda: https://conda.anaconda.org/conda-forge/noarch/ipython_genutils-0.2.0-pyhd8ed1ab_2.conda - conda: https://conda.anaconda.org/conda-forge/noarch/ipython_pygments_lexers-1.1.1-pyhd8ed1ab_0.conda - - conda: https://conda.anaconda.org/conda-forge/noarch/ipywidgets-8.1.8-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/isoduration-20.11.0-pyhd8ed1ab_1.conda - conda: https://conda.anaconda.org/conda-forge/noarch/jedi-0.19.2-pyhd8ed1ab_1.conda - conda: https://conda.anaconda.org/conda-forge/noarch/jinja2-3.1.6-pyhcf101f3_1.conda @@ -108,7 +99,6 @@ environments: - conda: https://conda.anaconda.org/conda-forge/noarch/jsonschema-4.26.0-pyhcf101f3_0.conda - 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-[tool.pixi.pypi-dependencies] -optimagic = { path = ".", editable = true } -pdbp = "*" -pre-commit = ">=4" - -# --- Python version features -------------------------------------------------------- -[tool.pixi.feature.py310.dependencies] -python = "~=3.10.0" -[tool.pixi.feature.py311.dependencies] -python = "~=3.11.0" -[tool.pixi.feature.py312.dependencies] -python = "~=3.12.0" -[tool.pixi.feature.py313.dependencies] -python = "~=3.13.0" - -# --- Feature: test (test infrastructure + optional optimizer backends) --------------- -[tool.pixi.feature.test.dependencies] -pytest = "*" -pytest-cov = "*" -pytest-xdist = "*" cyipopt = ">=1.4.0" pygmo = ">=2.19.0" nlopt = "*" @@ -438,7 +417,6 @@ matplotlib = "*" bokeh = "*" altair = "*" seaborn = "*" -mypy = "==1.19.1" pyyaml = "*" jinja2 = "*" tranquilo = ">=0.1.1" @@ -447,7 +425,8 @@ cma = "*" pygad = "*" pytorch-cpu = "*" -[tool.pixi.feature.test.pypi-dependencies] +[tool.pixi.pypi-dependencies] +optimagic = { path = ".", editable = true } bayesian-optimization = "*" dfo-ls = ">=1.5.3" py-bobyqa = "*" @@ -455,28 +434,50 @@ fides = "==0.7.4" kaleido = "*" gradient-free-optimizers = "*" pyswarms = "*" + +# --- Python version features -------------------------------------------------------- +[tool.pixi.feature.py310.dependencies] +python = "~=3.10.0" +[tool.pixi.feature.py311.dependencies] +python = "~=3.11.0" +[tool.pixi.feature.py312.dependencies] +python = "~=3.12.0" +[tool.pixi.feature.py313.dependencies] +python = "~=3.13.0" + +# --- Feature: test (test infrastructure) --------------------------------------------- +[tool.pixi.feature.test.dependencies] +pytest = "*" +pytest-cov = "*" +pytest-xdist = "*" + +[tool.pixi.feature.test.tasks] +tests = "pytest" +tests-fast = "pytest -m 'not slow and not jax'" +tests-with-cov = "pytest --cov-report=xml --cov=./" + +# --- Feature: typecheck (mypy + type stubs) ------------------------------------------ +[tool.pixi.feature.typecheck.dependencies] +mypy = "==1.19.1" + +[tool.pixi.feature.typecheck.pypi-dependencies] pandas-stubs = "*" types-cffi = "*" types-openpyxl = "*" types-jinja2 = "*" sqlalchemy-stubs = "*" -sphinxcontrib-mermaid = "*" -[tool.pixi.feature.test.tasks] -tests = "pytest" -tests-fast = "pytest -m 'not slow and not jax'" -tests-with-cov = "pytest --cov-report=xml --cov=./" +[tool.pixi.feature.typecheck.tasks] mypy = "mypy" -lint = "pre-commit run --all-files" -# --- Feature: linux (Linux-only test deps) ------------------------------------------ +# --- Feature: linux (Linux-only deps) ------------------------------------------------ [tool.pixi.feature.linux] platforms = ["linux-64"] [tool.pixi.feature.linux.dependencies] jax = "*" petsc4py = "<=3.23.4" -# --- Feature: docs ------------------------------------------------------------------ +# --- Feature: docs ------------------------------------------------------------------- [tool.pixi.feature.docs.dependencies] sphinx = ">=8.2.3" sphinxcontrib-bibtex = "*" @@ -490,28 +491,13 @@ myst-nb = "*" furo = "*" anywidget = "*" patsy = "*" -nlopt = "*" -pygmo = ">=2.19.0" -matplotlib = "*" -bokeh = "*" -altair = "*" -seaborn = "*" [tool.pixi.feature.docs.pypi-dependencies] -py-bobyqa = "*" -dfo-ls = "*" sphinxcontrib-mermaid = "*" intersphinx-registry = "*" -fides = "==0.7.4" -bayesian-optimization = "*" -pandas-stubs = "*" -types-cffi = "*" -types-openpyxl = "*" -types-jinja2 = "*" -sqlalchemy-stubs = "*" [tool.pixi.feature.docs.tasks] -docs = { cmd = "make html", cwd = "docs" } +build-docs = { cmd = "make html", cwd = "docs" } # --- Compat features (version overrides for backward-compat CI) --------------------- [tool.pixi.feature.old-pandas.dependencies] @@ -535,7 +521,7 @@ nevergrad = "*" # --- Environments -------------------------------------------------------------------- [tool.pixi.environments] # Default dev environment (Python 3.12, everything) -default = { features = ["test", "docs", "py312"], solve-group = "py312" } +default = { features = ["test", "py312"], solve-group = "py312" } # Linux CI (with JAX + PETSc) test-linux-py310 = { features = ["test", "linux", "py310"], solve-group = "linux-py310" } test-linux-py311 = { features = ["test", "linux", "py311"], solve-group = "linux-py311" } @@ -555,5 +541,7 @@ test-nevergrad-py310 = { features = ["test", "nevergrad", "py310"] } test-nevergrad-py311 = { features = ["test", "nevergrad", "py311"] } test-nevergrad-py312 = { features = ["test", "nevergrad", "py312"] } test-nevergrad-py313 = { features = ["test", "nevergrad", "py313"] } +# Type checking +typecheck = { features = ["typecheck", "py310"], solve-group = "py310" } # Docs docs = { features = ["docs", "py312"], solve-group = "py312" } diff --git a/src/optimagic/optimization/history.py b/src/optimagic/optimization/history.py index b0b850dc2..48dedf7cc 100644 --- a/src/optimagic/optimization/history.py +++ b/src/optimagic/optimization/history.py @@ -517,7 +517,7 @@ def _apply_reduction_to_batches( ) raise ValueError(msg) - batch_results.append(reduced) + batch_results.append(float(reduced)) # type: ignore[arg-type] return np.array(batch_results, dtype=np.float64) diff --git a/src/optimagic/visualization/slice_plot_3d.py b/src/optimagic/visualization/slice_plot_3d.py index ce3be5615..1b6a7fc90 100644 --- a/src/optimagic/visualization/slice_plot_3d.py +++ b/src/optimagic/visualization/slice_plot_3d.py @@ -799,7 +799,7 @@ def combine_plots( # type: ignore[no-untyped-def] ) if shared_y and all_y: - y_range = compute_yaxis_range(np.concatenate(all_y), expand_yrange) + y_range = compute_yaxis_range(np.concatenate(all_y).tolist(), expand_yrange) fig.update_yaxes(range=y_range) if shared_x and all_x: x_all = np.concatenate(all_x) From 4415da0712ab95c7765c2bb9e865b5b60b10742f Mon Sep 17 00:00:00 2001 From: timmens Date: Tue, 10 Mar 2026 13:51:17 +0100 Subject: [PATCH 03/18] Address PR review feedback - Move optimizer backends and viz libs from test feature to base deps - Create separate typecheck env with mypy + type stubs - Slim down docs feature to only sphinx tooling + doc-specific deps - Slim down default env to just base + test (no typecheck/docs) - Rename docs task to build-docs - Remove pixi install from RTD config (pixi run handles it) - Remove pre-commit/pdbp from pixi deps (install globally) - Update contributor guide: explain global pre-commit install - Revert unrelated algorithms.py changes from pre-commit hook - Fix two pre-existing mypy errors in history.py and slice_plot_3d.py - Pin pandas<3 for gradient-free-optimizers compatibility - Pin gradient-free-optimizers>=1.6.0 Co-Authored-By: Claude Opus 4.6 --- pixi.lock | 916 +++++++++++++------------- pyproject.toml | 4 +- src/optimagic/optimization/history.py | 2 +- 3 files changed, 445 insertions(+), 477 deletions(-) diff --git a/pixi.lock b/pixi.lock index e7310b77c..fd13d9227 100644 --- a/pixi.lock +++ b/pixi.lock @@ -206,7 +206,7 @@ environments: - conda: https://conda.anaconda.org/conda-forge/noarch/overrides-7.7.0-pyhd8ed1ab_1.conda - conda: https://conda.anaconda.org/conda-forge/noarch/packaging-26.0-pyhcf101f3_0.conda - 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pypi: https://files.pythonhosted.org/packages/d1/c6/df1fe324248424f77b89371116dab5243db7f052c32cc9fe7442ad9c5f75/pandas_stubs-2.3.3.260113-py3-none-any.whl name: pandas-stubs version: 2.3.3.260113 diff --git a/pyproject.toml b/pyproject.toml index 3ed25662b..95fdf8352 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -407,7 +407,7 @@ python = ">=3.10,<3.14" # Prefer conda-forge builds for compiled scientific packages numpy = "*" scipy = ">=1.2.1" -pandas = "*" +pandas = "<3" jupyterlab = "*" cyipopt = ">=1.4.0" pygmo = ">=2.19.0" @@ -432,7 +432,7 @@ dfo-ls = ">=1.5.3" py-bobyqa = "*" fides = "==0.7.4" kaleido = "*" -gradient-free-optimizers = "*" +gradient-free-optimizers = ">=1.6.0" pyswarms = "*" # --- Python version features -------------------------------------------------------- diff --git a/src/optimagic/optimization/history.py b/src/optimagic/optimization/history.py index 48dedf7cc..73bea2d93 100644 --- a/src/optimagic/optimization/history.py +++ b/src/optimagic/optimization/history.py @@ -517,7 +517,7 @@ def _apply_reduction_to_batches( ) raise ValueError(msg) - batch_results.append(float(reduced)) # type: ignore[arg-type] + batch_results.append(float(reduced)) # type: ignore[arg-type,unused-ignore] return np.array(batch_results, dtype=np.float64) From 5ec8a8ff29a8ff286603227593736daed65bf4c9 Mon Sep 17 00:00:00 2001 From: timmens Date: Tue, 10 Mar 2026 13:55:24 +0100 Subject: [PATCH 04/18] Pin jax>=0.4.1 to fix scipy.linalg.tril AttributeError JAX 0.3.0 (resolved for py310) references scipy.linalg.tril which was removed in newer scipy. Pin to >=0.4.1 to ensure compatibility. Co-Authored-By: Claude Opus 4.6 --- pixi.lock | 381 ++++++++++++++++++++++++++++++++++++++++--------- pyproject.toml | 2 +- 2 files changed, 318 insertions(+), 65 deletions(-) diff --git a/pixi.lock b/pixi.lock index fd13d9227..4c01d31a1 100644 --- a/pixi.lock +++ b/pixi.lock @@ -1895,7 +1895,6 @@ environments: packages: linux-64: - conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-7_kmp_llvm.conda - - conda: https://conda.anaconda.org/conda-forge/noarch/absl-py-2.4.0-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/alsa-lib-1.2.15.3-hb03c661_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/altair-6.0.0-pyhd8ed1ab_1.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/ampl-asl-1.0.0-h5888daf_2.conda @@ -1945,7 +1944,6 @@ environments: - conda: https://conda.anaconda.org/conda-forge/noarch/executing-2.2.1-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/fftw-3.3.10-mpi_openmpi_h76e6d66_12.conda - 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Move the build to post_build (matching the dags pattern) and remove the sphinx section so RTD doesn't try to run its own sphinx build. Co-Authored-By: Claude Opus 4.6 --- .readthedocs.yml | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/.readthedocs.yml b/.readthedocs.yml index 28e6b2aea..0d995bf47 100644 --- a/.readthedocs.yml +++ b/.readthedocs.yml @@ -9,11 +9,7 @@ build: - asdf plugin add pixi - asdf install pixi latest - asdf global pixi latest - build: - - pixi run -e docs build-docs post_build: + - pixi run -e docs build-docs - mkdir --parents $READTHEDOCS_OUTPUT/html/ - cp -a docs/build/html/. "$READTHEDOCS_OUTPUT/html" && rm -r docs/build -sphinx: - configuration: docs/source/conf.py - fail_on_warning: false From 834fc6dbe130636f0a8e65e04bd67075aba5d59e Mon Sep 17 00:00:00 2001 From: timmens Date: Tue, 10 Mar 2026 14:26:05 +0100 Subject: [PATCH 06/18] Drop Python 3.10/3.11 support, add Python 3.14 - Update requires-python to >=3.12, add 3.14 classifier - Set Python 3.14 as default dev, typecheck, and docs version - Remove py310/py311 pixi features, CI matrix entries, and environments - Add py314 pixi feature and environments across linux, mac/win, nevergrad - Remove test-old-pandas env (pandas <2 incompatible with Python 3.12+) - Remove petsc4py upper bound pin (no 3.14 builds at <=3.23.4) - Update ruff target-version to py312 - Update publish workflow and RTD config Python versions Co-Authored-By: Claude Opus 4.6 --- .github/workflows/main.yml | 30 ++++-------------- .github/workflows/publish-to-pypi.yml | 4 +-- .readthedocs.yml | 2 +- pyproject.toml | 45 ++++++++++----------------- 4 files changed, 26 insertions(+), 55 deletions(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 5375941a8..226803f11 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -18,10 +18,9 @@ jobs: fail-fast: false matrix: python-version: - - '310' - - '311' - '312' - '313' + - '314' steps: - uses: actions/checkout@v4 - uses: prefix-dev/setup-pixi@v0.9.4 @@ -35,7 +34,7 @@ jobs: shell: bash -el {0} run: pixi run -e test-linux-py${{ matrix.python-version }} tests-with-cov - name: Upload coverage report. - if: matrix.python-version == '310' + if: matrix.python-version == '312' uses: codecov/codecov-action@v4 with: token: ${{ secrets.CODECOV_TOKEN }} @@ -49,10 +48,9 @@ jobs: - macos-latest - windows-latest python-version: - - '310' - - '311' - '312' - '313' + - '314' steps: - uses: actions/checkout@v4 - uses: prefix-dev/setup-pixi@v0.9.4 @@ -65,21 +63,6 @@ jobs: - name: Run pytest shell: bash -el {0} run: pixi run -e test-py${{ matrix.python-version }} tests-fast - run-tests-with-old-pandas: - name: Run tests on ubuntu-latest with pandas < 2 - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@v4 - - uses: prefix-dev/setup-pixi@v0.9.4 - with: - pixi-version: v0.65.0 - cache: true - cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }} - frozen: true - environments: test-old-pandas - - name: Run pytest - shell: bash -el {0} - run: pixi run -e test-old-pandas tests-fast run-tests-with-old-numpy: name: Run tests on ubuntu-latest with numpy < 2 runs-on: ubuntu-latest @@ -117,10 +100,9 @@ jobs: fail-fast: false matrix: python-version: - - '310' - - '311' - '312' - '313' + - '314' steps: - uses: actions/checkout@v4 - uses: prefix-dev/setup-pixi@v0.9.4 @@ -146,11 +128,11 @@ jobs: cache: true cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }} frozen: true - environments: test-linux-py312 + environments: test-linux-py314 - name: Run doctest shell: bash -el {0} run: >- - pixi run -e test-linux-py312 + pixi run -e test-linux-py314 python -m doctest -v docs/source/how_to/how_to_constraints.md run-mypy: name: Run mypy diff --git a/.github/workflows/publish-to-pypi.yml b/.github/workflows/publish-to-pypi.yml index c763cb682..0f5933a33 100644 --- a/.github/workflows/publish-to-pypi.yml +++ b/.github/workflows/publish-to-pypi.yml @@ -7,10 +7,10 @@ jobs: runs-on: ubuntu-latest steps: - uses: actions/checkout@v4 - - name: Set up Python 3.10 + - name: Set up Python 3.12 uses: actions/setup-python@v5 with: - python-version: '3.10' + python-version: '3.12' - name: Install pypa/build run: >- python -m diff --git a/.readthedocs.yml b/.readthedocs.yml index 0d995bf47..1ba5d0f4b 100644 --- a/.readthedocs.yml +++ b/.readthedocs.yml @@ -3,7 +3,7 @@ version: 2 build: os: ubuntu-24.04 tools: - python: '3.12' + python: '3.14' jobs: create_environment: - asdf plugin add pixi diff --git a/pyproject.toml b/pyproject.toml index 8e0d756cc..fbc762860 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -4,7 +4,7 @@ [project] name = "optimagic" description = "Tools to solve difficult numerical optimization problems." -requires-python = ">=3.10" +requires-python = ">=3.12" dependencies = [ "cloudpickle", "joblib", @@ -40,10 +40,9 @@ classifiers = [ "Operating System :: MacOS :: MacOS X", "Operating System :: Microsoft :: Windows", "Operating System :: POSIX", - "Programming Language :: Python :: 3.10", - "Programming Language :: Python :: 3.11", "Programming Language :: Python :: 3.12", "Programming Language :: Python :: 3.13", + "Programming Language :: Python :: 3.14", "Topic :: Scientific/Engineering", ] authors = [ @@ -96,7 +95,7 @@ allow-direct-references = true # Ruff configuration # ====================================================================================== [tool.ruff] -target-version = "py310" +target-version = "py312" fix = true [tool.ruff.lint] @@ -403,7 +402,7 @@ platforms = ["linux-64", "osx-arm64", "win-64"] # --- Base dependencies (all environments) ------------------------------------------- [tool.pixi.dependencies] -python = ">=3.10,<3.14" +python = ">=3.12,<3.15" # Prefer conda-forge builds for compiled scientific packages numpy = "*" scipy = ">=1.2.1" @@ -436,14 +435,12 @@ gradient-free-optimizers = ">=1.6.0" pyswarms = "*" # --- Python version features -------------------------------------------------------- -[tool.pixi.feature.py310.dependencies] -python = "~=3.10.0" -[tool.pixi.feature.py311.dependencies] -python = "~=3.11.0" [tool.pixi.feature.py312.dependencies] python = "~=3.12.0" [tool.pixi.feature.py313.dependencies] python = "~=3.13.0" +[tool.pixi.feature.py314.dependencies] +python = "~=3.14.0" # --- Feature: test (test infrastructure) --------------------------------------------- [tool.pixi.feature.test.dependencies] @@ -475,7 +472,7 @@ mypy = "mypy" platforms = ["linux-64"] [tool.pixi.feature.linux.dependencies] jax = ">=0.4.1" -petsc4py = "<=3.23.4" +petsc4py = "*" # --- Feature: docs ------------------------------------------------------------------- [tool.pixi.feature.docs.dependencies] @@ -500,10 +497,6 @@ intersphinx-registry = "*" build-docs = { cmd = "make html", cwd = "docs" } # --- Compat features (version overrides for backward-compat CI) --------------------- -[tool.pixi.feature.old-pandas.dependencies] -numpy = "<2" -pandas = "<2" - [tool.pixi.feature.old-numpy.dependencies] numpy = "<2" pandas = ">=2" @@ -520,28 +513,24 @@ nevergrad = "*" # --- Environments -------------------------------------------------------------------- [tool.pixi.environments] -# Default dev environment (Python 3.12, everything) -default = { features = ["test", "py312"], solve-group = "py312" } +# Default dev environment (Python 3.14, everything) +default = { features = ["test", "py314"], solve-group = "py314" } # Linux CI (with JAX + PETSc) -test-linux-py310 = { features = ["test", "linux", "py310"], solve-group = "linux-py310" } -test-linux-py311 = { features = ["test", "linux", "py311"], solve-group = "linux-py311" } test-linux-py312 = { features = ["test", "linux", "py312"], solve-group = "linux-py312" } test-linux-py313 = { features = ["test", "linux", "py313"], solve-group = "linux-py313" } +test-linux-py314 = { features = ["test", "linux", "py314"], solve-group = "linux-py314" } # macOS/Windows CI -test-py310 = { features = ["test", "py310"], solve-group = "py310" } -test-py311 = { features = ["test", "py311"], solve-group = "py311" } test-py312 = { features = ["test", "py312"], solve-group = "py312" } test-py313 = { features = ["test", "py313"], solve-group = "py313" } -# Backward-compat CI (Python 3.10 only) -test-old-pandas = { features = ["test", "old-pandas", "py310"] } -test-old-numpy = { features = ["test", "old-numpy", "py310"] } -test-old-plotly = { features = ["test", "old-plotly", "py310"] } +test-py314 = { features = ["test", "py314"], solve-group = "py314" } +# Backward-compat CI (Python 3.12, lowest supported) +test-old-numpy = { features = ["test", "old-numpy", "py312"] } +test-old-plotly = { features = ["test", "old-plotly", "py312"] } # Nevergrad CI (bayesian-optimization==1.4.0) -test-nevergrad-py310 = { features = ["test", "nevergrad", "py310"] } -test-nevergrad-py311 = { features = ["test", "nevergrad", "py311"] } test-nevergrad-py312 = { features = ["test", "nevergrad", "py312"] } test-nevergrad-py313 = { features = ["test", "nevergrad", "py313"] } +test-nevergrad-py314 = { features = ["test", "nevergrad", "py314"] } # Type checking -typecheck = { features = ["typecheck", "py310"], solve-group = "py310" } +typecheck = { features = ["typecheck", "py314"], solve-group = "py314" } # Docs -docs = { features = ["docs", "py312"], solve-group = "py312" } +docs = { features = ["docs", "py314"], solve-group = "py314" } From 4debf378c933a7e456b8bd67b39e1a3c014702b3 Mon Sep 17 00:00:00 2001 From: timmens Date: Tue, 10 Mar 2026 14:28:38 +0100 Subject: [PATCH 07/18] Update pixi.lock --- pixi.lock | 13424 +++++++++++++++++----------------------------------- 1 file changed, 4220 insertions(+), 9204 deletions(-) diff --git a/pixi.lock b/pixi.lock index 4c01d31a1..a087cfd48 100644 --- a/pixi.lock +++ b/pixi.lock @@ -16,40 +16,40 @@ environments: - 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Co-Authored-By: Claude Opus 4.6 --- .github/workflows/main.yml | 15 ------- pixi.lock | 22 +++++----- pyproject.toml | 73 ++++++++++++++++------------------ src/optimagic/config.py | 10 ----- src/optimagic/shared/compat.py | 8 +--- 5 files changed, 46 insertions(+), 82 deletions(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 226803f11..a80810013 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -63,21 +63,6 @@ jobs: - name: Run pytest shell: bash -el {0} run: pixi run -e test-py${{ matrix.python-version }} tests-fast - run-tests-with-old-numpy: - name: Run tests on ubuntu-latest with numpy < 2 - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@v4 - - uses: prefix-dev/setup-pixi@v0.9.4 - with: - pixi-version: v0.65.0 - cache: true - cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }} - frozen: true - environments: test-old-numpy - - name: Run pytest - shell: bash -el {0} - run: pixi run -e test-old-numpy tests-fast run-tests-with-old-plotly: name: Run tests on ubuntu-latest with plotly < 6 runs-on: ubuntu-latest diff --git a/pixi.lock b/pixi.lock index a087cfd48..a9c13e2f0 100644 --- a/pixi.lock +++ b/pixi.lock @@ -20427,19 +20427,19 @@ packages: timestamp: 1733688053334 - 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"cloudpickle", - "joblib", - "numpy", - "pandas", - "plotly", + "cloudpickle>=2.2", + "joblib>=1.1", + "numpy>=1.26", + "pandas>=2.1", + "plotly>=5.14", "pybaum>=0.1.2", - "scipy>=1.2.1", - "sqlalchemy>=1.3", - "annotated-types", - "typing-extensions", + "scipy>=1.11", + "sqlalchemy>=2.0", + "annotated-types>=0.4", + "typing-extensions>=4.5", ] dynamic = ["version"] keywords = [ @@ -404,35 +404,35 @@ platforms = ["linux-64", "osx-arm64", "win-64"] [tool.pixi.dependencies] python = ">=3.12,<3.15" # Prefer conda-forge builds for compiled scientific packages -numpy = "*" -scipy = ">=1.2.1" -pandas = "<3" -jupyterlab = "*" +numpy = ">=1.26" +scipy = ">=1.11" +pandas = ">=2.1,<3" +jupyterlab = ">=4.0" cyipopt = ">=1.4.0" pygmo = ">=2.19.0" -nlopt = "*" -statsmodels = "*" -matplotlib = "*" -bokeh = "*" -altair = "*" -seaborn = "*" -pyyaml = "*" -jinja2 = "*" +nlopt = ">=2.7" +statsmodels = ">=0.14" +matplotlib = ">=3.8" +bokeh = ">=3.2" +altair = ">=5.1" +seaborn = ">=0.13" +pyyaml = ">=6.0.1" +jinja2 = ">=3.1" tranquilo = ">=0.1.1" -iminuit = "*" -cma = "*" -pygad = "*" -pytorch-cpu = "*" +iminuit = ">=2.25" +cma = ">=3.3" +pygad = ">=3.2" +pytorch-cpu = ">=2.2" [tool.pixi.pypi-dependencies] optimagic = { path = ".", editable = true } -bayesian-optimization = "*" +bayesian-optimization = ">=1.4" dfo-ls = ">=1.5.3" -py-bobyqa = "*" +py-bobyqa = ">=1.3" fides = "==0.7.4" -kaleido = "*" +kaleido = ">=0.2.1" gradient-free-optimizers = ">=1.6.0" -pyswarms = "*" +pyswarms = ">=1.3" # --- Python version features -------------------------------------------------------- [tool.pixi.feature.py312.dependencies] @@ -444,9 +444,9 @@ python = "~=3.14.0" # --- Feature: test (test infrastructure) --------------------------------------------- [tool.pixi.feature.test.dependencies] -pytest = "*" -pytest-cov = "*" -pytest-xdist = "*" +pytest = ">=7.2" +pytest-cov = ">=4.0" +pytest-xdist = ">=3.2" [tool.pixi.feature.test.tasks] tests = "pytest" @@ -471,8 +471,8 @@ mypy = "mypy" [tool.pixi.feature.linux] platforms = ["linux-64"] [tool.pixi.feature.linux.dependencies] -jax = ">=0.4.1" -petsc4py = "*" +jax = ">=0.4.8" +petsc4py = ">=3.18" # --- Feature: docs ------------------------------------------------------------------- [tool.pixi.feature.docs.dependencies] @@ -497,10 +497,6 @@ intersphinx-registry = "*" build-docs = { cmd = "make html", cwd = "docs" } # --- Compat features (version overrides for backward-compat CI) --------------------- -[tool.pixi.feature.old-numpy.dependencies] -numpy = "<2" -pandas = ">=2" - [tool.pixi.feature.old-plotly.dependencies] plotly = "<6" @@ -524,7 +520,6 @@ test-py312 = { features = ["test", "py312"], solve-group = "py312" } test-py313 = { features = ["test", "py313"], solve-group = "py313" } test-py314 = { features = ["test", "py314"], solve-group = "py314" } # Backward-compat CI (Python 3.12, lowest supported) -test-old-numpy = { features = ["test", "old-numpy", "py312"] } test-old-plotly = { features = ["test", "old-plotly", "py312"] } # Nevergrad CI (bayesian-optimization==1.4.0) test-nevergrad-py312 = { features = ["test", "nevergrad", "py312"] } diff --git a/src/optimagic/config.py b/src/optimagic/config.py index e75f11f62..859ef3803 100644 --- a/src/optimagic/config.py +++ b/src/optimagic/config.py @@ -1,9 +1,7 @@ import importlib.util from pathlib import Path -import pandas as pd import plotly.express as px -from packaging import version DOCS_DIR = Path(__file__).parent.parent / "docs" OPTIMAGIC_ROOT = Path(__file__).parent @@ -74,11 +72,3 @@ def _is_installed(module_name: str) -> bool: IS_MATPLOTLIB_INSTALLED = _is_installed("matplotlib") IS_BOKEH_INSTALLED = _is_installed("bokeh") IS_ALTAIR_INSTALLED = _is_installed("altair") - -# ====================================================================================== -# Check if pandas version is newer or equal to version 2.1.0 -# ====================================================================================== - -IS_PANDAS_VERSION_NEWER_OR_EQUAL_TO_2_1_0 = version.parse( - pd.__version__ -) >= version.parse("2.1.0") diff --git a/src/optimagic/shared/compat.py b/src/optimagic/shared/compat.py index 324d2e511..9a561283d 100644 --- a/src/optimagic/shared/compat.py +++ b/src/optimagic/shared/compat.py @@ -5,8 +5,6 @@ """ -from optimagic.config import IS_PANDAS_VERSION_NEWER_OR_EQUAL_TO_2_1_0 - def pd_df_map(df, func, na_action=None, **kwargs): """Apply a function to a Dataframe elementwise. @@ -26,8 +24,4 @@ def pd_df_map(df, func, na_action=None, **kwargs): pd.DataFrame: Transformed DataFrame. """ - if IS_PANDAS_VERSION_NEWER_OR_EQUAL_TO_2_1_0: - out = df.map(func, na_action=na_action, **kwargs) - else: - out = df.applymap(func, na_action=na_action, **kwargs) - return out + return df.map(func, na_action=na_action, **kwargs) From 7313de4b107288badd81d98ca0065cd8f54753c2 Mon Sep 17 00:00:00 2001 From: timmens Date: Tue, 10 Mar 2026 14:50:19 +0100 Subject: [PATCH 09/18] Set minimum numpy version to 2.0.0 Co-Authored-By: Claude Opus 4.6 --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 182993771..1330cfc6b 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -404,7 +404,7 @@ platforms = ["linux-64", "osx-arm64", "win-64"] [tool.pixi.dependencies] python = ">=3.12,<3.15" # Prefer conda-forge builds for compiled scientific packages -numpy = ">=1.26" +numpy = ">=2.0.0" scipy = ">=1.11" pandas = ">=2.1,<3" jupyterlab = ">=4.0" From 1de4201cd46d92f0f4e1dc46c7ccb82dadc801e0 Mon Sep 17 00:00:00 2001 From: timmens Date: Tue, 10 Mar 2026 14:51:46 +0100 Subject: [PATCH 10/18] Update pixi.lock --- pixi.lock | 948 +----------------------------------------------------- 1 file changed, 2 insertions(+), 946 deletions(-) diff --git a/pixi.lock b/pixi.lock index a9c13e2f0..229c7a36d 100644 --- a/pixi.lock +++ b/pixi.lock @@ -5722,892 +5722,6 @@ environments: - 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- vc14_runtime >=14.29.30139 - constrains: - - numpy-base <0a0 - license: BSD-3-Clause - license_family: BSD - purls: - - pkg:pypi/numpy?source=hash-mapping - size: 6495445 - timestamp: 1707226412944 - conda: https://conda.anaconda.org/conda-forge/win-64/numpy-2.4.2-py312ha72d056_1.conda sha256: bae400995eed564cf68d3939d5b782680407b3e25dc7363687df19c6b2cf396f md5: 52254edfb993f9e61552c63813041689 @@ -20427,8 +19483,8 @@ packages: timestamp: 1733688053334 - pypi: ./ name: optimagic - version: 0.5.4.dev10+g4debf378c.d20260310 - sha256: a4c500ceab415140096168b0525f785260672f69c12d997e38c8bb08e0b52297 + version: 0.5.4.dev12+g7313de4b1.d20260310 + sha256: 0724a05c17f78b9ab3840839f59f9811fe3b6d1fe20baa718018289f72d587dc requires_dist: - annotated-types>=0.4 - cloudpickle>=2.2 From 7af637e583faa287dff36fb9ce39ff6ab590ecd9 Mon Sep 17 00:00:00 2001 From: timmens Date: Tue, 10 Mar 2026 15:05:25 +0100 Subject: [PATCH 11/18] Add descriptions to pixi tasks and document pixi task list Co-Authored-By: Claude Opus 4.6 --- docs/source/development/how_to_contribute.md | 6 ++++++ pyproject.toml | 10 +++++----- 2 files changed, 11 insertions(+), 5 deletions(-) diff --git a/docs/source/development/how_to_contribute.md b/docs/source/development/how_to_contribute.md index aa4f2d79d..0a12322dc 100644 --- a/docs/source/development/how_to_contribute.md +++ b/docs/source/development/how_to_contribute.md @@ -54,6 +54,12 @@ For regular contributors: **Clone** the [repository](https://github.com/optimagi installing it globally using pixi or uv. ``` + To see all available pixi tasks, run: + + ```console + $ pixi task list + ``` + You can then run the test suite with: ```console diff --git a/pyproject.toml b/pyproject.toml index 1330cfc6b..6b1cee6b3 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -449,9 +449,9 @@ pytest-cov = ">=4.0" pytest-xdist = ">=3.2" [tool.pixi.feature.test.tasks] -tests = "pytest" -tests-fast = "pytest -m 'not slow and not jax'" -tests-with-cov = "pytest --cov-report=xml --cov=./" +tests = { cmd = "pytest", description = "Run the full test suite" } +tests-fast = { cmd = "pytest -m 'not slow and not jax'", description = "Run tests excluding slow and jax tests" } +tests-with-cov = { cmd = "pytest --cov-report=xml --cov=./", description = "Run tests with XML coverage report" } # --- Feature: typecheck (mypy + type stubs) ------------------------------------------ [tool.pixi.feature.typecheck.dependencies] @@ -465,7 +465,7 @@ types-jinja2 = "*" sqlalchemy-stubs = "*" [tool.pixi.feature.typecheck.tasks] -mypy = "mypy" +mypy = { cmd = "mypy", description = "Run mypy type checker" } # --- Feature: linux (Linux-only deps) ------------------------------------------------ [tool.pixi.feature.linux] @@ -494,7 +494,7 @@ sphinxcontrib-mermaid = "*" intersphinx-registry = "*" [tool.pixi.feature.docs.tasks] -build-docs = { cmd = "make html", cwd = "docs" } +build-docs = { cmd = "make html", cwd = "docs", description = "Build the HTML documentation" } # --- Compat features (version overrides for backward-compat CI) --------------------- [tool.pixi.feature.old-plotly.dependencies] From 2a7b91239c1997d336cc1a248eaa80f1c659a399 Mon Sep 17 00:00:00 2001 From: timmens Date: Tue, 10 Mar 2026 15:05:57 +0100 Subject: [PATCH 12/18] Update pixi.lock --- pixi.lock | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pixi.lock b/pixi.lock index 229c7a36d..8f90c242f 100644 --- a/pixi.lock +++ b/pixi.lock @@ -19483,8 +19483,8 @@ packages: timestamp: 1733688053334 - pypi: ./ name: optimagic - version: 0.5.4.dev12+g7313de4b1.d20260310 - sha256: 0724a05c17f78b9ab3840839f59f9811fe3b6d1fe20baa718018289f72d587dc + version: 0.5.4.dev14+g7af637e58 + sha256: 6e9a1c1d5431af5665db8c9891263b9d43bcdbcf28078dec6b45730e18fe2729 requires_dist: - annotated-types>=0.4 - cloudpickle>=2.2 From 9d412494292adc6662d64d3b2078aa02d09ec99a Mon Sep 17 00:00:00 2001 From: timmens Date: Tue, 10 Mar 2026 15:40:40 +0100 Subject: [PATCH 13/18] Use relative codecov project target instead of absolute 90% Set target to auto (base branch coverage) with 1% threshold to avoid failing on infrastructure PRs that don't change code. Co-Authored-By: Claude Opus 4.6 --- codecov.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/codecov.yml b/codecov.yml index d25993136..ba856a08c 100644 --- a/codecov.yml +++ b/codecov.yml @@ -12,7 +12,8 @@ coverage: target: 80% project: default: - target: 90% + target: auto + threshold: 1% ignore: # Uses numba - src/optimagic/benchmarking/cartis_roberts.py From e6d04ecb9329f55c810fe5789f39bf2556bea9cf Mon Sep 17 00:00:00 2001 From: timmens Date: Tue, 10 Mar 2026 16:53:41 +0100 Subject: [PATCH 14/18] Fix coverage: scope --cov to src/optimagic instead of ./ --cov=./ measured coverage of the entire repo including .tools/ and other non-source files. Scoping to src/optimagic gives accurate results and restores the codecov/project check. Also reverts the codecov target change since the root cause is now fixed. Co-Authored-By: Claude Opus 4.6 --- codecov.yml | 3 +-- pyproject.toml | 2 +- 2 files changed, 2 insertions(+), 3 deletions(-) diff --git a/codecov.yml b/codecov.yml index ba856a08c..d25993136 100644 --- a/codecov.yml +++ b/codecov.yml @@ -12,8 +12,7 @@ coverage: target: 80% project: default: - target: auto - threshold: 1% + target: 90% ignore: # Uses numba - src/optimagic/benchmarking/cartis_roberts.py diff --git a/pyproject.toml b/pyproject.toml index 6b1cee6b3..3e3a6663e 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -451,7 +451,7 @@ pytest-xdist = ">=3.2" [tool.pixi.feature.test.tasks] tests = { cmd = "pytest", description = "Run the full test suite" } tests-fast = { cmd = "pytest -m 'not slow and not jax'", description = "Run tests excluding slow and jax tests" } -tests-with-cov = { cmd = "pytest --cov-report=xml --cov=./", description = "Run tests with XML coverage report" } +tests-with-cov = { cmd = "pytest --cov-report=xml --cov=src/optimagic", description = "Run tests with XML coverage report" } # --- Feature: typecheck (mypy + type stubs) ------------------------------------------ [tool.pixi.feature.typecheck.dependencies] From 835ad723d5baf5ef01b0a25d86f5dcce7e3c1854 Mon Sep 17 00:00:00 2001 From: timmens Date: Tue, 10 Mar 2026 17:07:57 +0100 Subject: [PATCH 15/18] Fix coverage scope: use --cov=src to include estimagic --cov=src/optimagic excluded src/estimagic from coverage. Using --cov=src captures both packages while still avoiding .pixi/envs/ contamination. Co-Authored-By: Claude Opus 4.6 --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 3e3a6663e..16b4520b4 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -451,7 +451,7 @@ pytest-xdist = ">=3.2" [tool.pixi.feature.test.tasks] tests = { cmd = "pytest", description = "Run the full test suite" } tests-fast = { cmd = "pytest -m 'not slow and not jax'", description = "Run tests excluding slow and jax tests" } -tests-with-cov = { cmd = "pytest --cov-report=xml --cov=src/optimagic", description = "Run tests with XML coverage report" } +tests-with-cov = { cmd = "pytest --cov-report=xml --cov=src", description = "Run tests with XML coverage report" } # --- Feature: typecheck (mypy + type stubs) ------------------------------------------ [tool.pixi.feature.typecheck.dependencies] From 3c5720e2557d579ffeb75514ec848a1289738719 Mon Sep 17 00:00:00 2001 From: timmens Date: Tue, 10 Mar 2026 17:14:52 +0100 Subject: [PATCH 16/18] Update pixi.lock --- pixi.lock | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pixi.lock b/pixi.lock index 8f90c242f..0f4e47f57 100644 --- a/pixi.lock +++ b/pixi.lock @@ -19483,8 +19483,8 @@ packages: timestamp: 1733688053334 - pypi: ./ name: optimagic - version: 0.5.4.dev14+g7af637e58 - sha256: 6e9a1c1d5431af5665db8c9891263b9d43bcdbcf28078dec6b45730e18fe2729 + version: 0.5.4.dev18+g835ad723d + sha256: 1cf23607e851a487eec134f359acb31bb979f572dc6955dfd3d210948deaecaa requires_dist: - annotated-types>=0.4 - cloudpickle>=2.2 From 4106914eb80d4b60491160bc51aa64abf37cf7d1 Mon Sep 17 00:00:00 2001 From: timmens Date: Wed, 11 Mar 2026 09:01:44 +0100 Subject: [PATCH 17/18] Apply manual edits to the how-to-contribute guide --- docs/source/development/how_to_contribute.md | 33 +++++++++----------- 1 file changed, 14 insertions(+), 19 deletions(-) diff --git a/docs/source/development/how_to_contribute.md b/docs/source/development/how_to_contribute.md index 0a12322dc..46c68c2b7 100644 --- a/docs/source/development/how_to_contribute.md +++ b/docs/source/development/how_to_contribute.md @@ -37,7 +37,7 @@ contribution process (see Notes below). For regular contributors: **Clone** the [repository](https://github.com/optimagic-dev/optimagic/) to your local machine and create a new branch for implementing your changes. You can push your branch directly to the remote optimagic repository and open a PR from there. ``` -2. Clone your forked repository to your disk. This is where you'll make all your +1. Clone your forked repository to your disk. This is where you'll make all your changes. 1. Open your terminal and execute the following commands from the root directory of your @@ -54,16 +54,17 @@ For regular contributors: **Clone** the [repository](https://github.com/optimagi installing it globally using pixi or uv. ``` - To see all available pixi tasks, run: + You can then run the test suite with: ```console - $ pixi task list + $ pixi run tests ``` - You can then run the test suite with: + which installs the development dependencies and runs pytest. To see all available + pixi tasks, run: ```console - $ pixi run tests + $ pixi task list ``` 1. Implement your fix or feature. Use git to add, commit, and push your changes to the @@ -74,18 +75,14 @@ For regular contributors: **Clone** the [repository](https://github.com/optimagi 1. Contributions are validated in two main ways. We run a comprehensive test suite to ensure compatibility with the existing codebase and employ [pre-commit hooks](https://effective-programming-practices.vercel.app/git/pre_commits/objectives_materials.html) - to maintain quality and adherence to our style guidelines. Opening a PR (see - paragraph 7 below) triggers optimagic's + to maintain quality and adherence to our style guidelines. Opening a PR (see below) + triggers optimagic's [Continuous Integration (CI)](https://docs.github.com/en/actions/automating-builds-and-tests/about-continuous-integration) - workflow, which runs the full `pytest` suite, pre-commit hooks, and other checks on a + workflow, which runs the full test suite, pre-commit hooks, and other checks on a remote server. You can also run the test suite locally for - [debugging](https://effective-programming-practices.vercel.app/debugging/pdbp/objectives_materials.html): - - ```console - $ pytest - ``` + [debugging](https://effective-programming-practices.vercel.app/debugging/pdbp/objectives_materials.html). With pre-commit installed, linters run before each commit. Commits are rejected if any checks fail. Note that some linters may automatically fix errors by modifying the @@ -95,18 +92,16 @@ For regular contributors: **Clone** the [repository](https://github.com/optimagi Skip the next paragraph if you haven't worked on the documentation. ``` -6. Assuming you have updated the documentation, verify that it builds correctly. From - the root directory of your local optimagic repo, navigate to the docs folder and set - up the optimagic-docs environment: +1. Assuming you have updated the documentation, verify that it builds correctly. Run: ```console $ pixi run build-docs ``` - This command builds the HTML documentation, saving all files in the `build/html` + This command builds the HTML documentation, saving all files in the `docs/build/html` directory. You can view the documentation with your preferred web browser by opening - `build/html/index.html` or any other file. Similar to the online documentation, you - can navigate to different pages simply by clicking on the links. + `docs/build/html/index.html` or any other file. Similar to the online documentation, + you can navigate to different pages simply by clicking on the links. 1. Once all tests and pre-commit hooks pass locally, push your changes to your forked repository and create a pull request through GitHub: Go to the Github repository of From 9210ff4f23f191fde36f6956da715b1def617b25 Mon Sep 17 00:00:00 2001 From: timmens Date: Thu, 12 Mar 2026 13:03:06 +0100 Subject: [PATCH 18/18] Align pixi section in pyproject.toml with ai-instructions repository --- .github/workflows/main.yml | 24 +- pixi.lock | 1972 ++++++++++++++---------------------- pyproject.toml | 39 +- 3 files changed, 814 insertions(+), 1221 deletions(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index a80810013..027bc75f5 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -29,10 +29,10 @@ jobs: cache: true cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }} frozen: true - environments: test-linux-py${{ matrix.python-version }} + environments: tests-linux-py${{ matrix.python-version }} - name: Run pytest shell: bash -el {0} - run: pixi run -e test-linux-py${{ matrix.python-version }} tests-with-cov + run: pixi run -e tests-linux-py${{ matrix.python-version }} tests-with-cov - name: Upload coverage report. if: matrix.python-version == '312' uses: codecov/codecov-action@v4 @@ -59,10 +59,10 @@ jobs: cache: true cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }} frozen: true - environments: test-py${{ matrix.python-version }} + environments: tests-py${{ matrix.python-version }} - name: Run pytest shell: bash -el {0} - run: pixi run -e test-py${{ matrix.python-version }} tests-fast + run: pixi run -e tests-py${{ matrix.python-version }} tests-fast run-tests-with-old-plotly: name: Run tests on ubuntu-latest with plotly < 6 runs-on: ubuntu-latest @@ -74,10 +74,10 @@ jobs: cache: true cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }} frozen: true - environments: test-old-plotly + environments: tests-old-plotly - name: Run pytest shell: bash -el {0} - run: pixi run -e test-old-plotly tests-fast + run: pixi run -e tests-old-plotly tests-fast run-tests-nevergrad: name: Run nevergrad tests py${{ matrix.python-version }} runs-on: ubuntu-latest @@ -96,11 +96,11 @@ jobs: cache: true cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }} frozen: true - 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