Migrate from conda/micromamba to pixi

.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 +12,34 @@ 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'
+          - '312'
+          - '313'
+          - '314'
     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: ${{ github.event_name == 'push' && github.ref_name == 'main' }}
+          frozen: true
+          environments: tests-linux-py${{ matrix.python-version }}
+      - name: Run pytest
+        shell: bash -el {0}
+        run: pixi run -e tests-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 == '312'
         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: ${{ matrix.os }}
     strategy:
       fail-fast: false
@@ -54,163 +48,89 @@ jobs:
           - macos-latest
           - windows-latest
         python-version:
-          - '3.10'
-          - '3.11'
-          - '3.12'
-          - '3.13'
-    steps:
-      - uses: actions/checkout@v4
-      - name: create build environment
-        uses: mamba-org/setup-micromamba@v1
-        with:
-          micromamba-version: 1.5.6-0
-          environment-file: ./.tools/envs/testenv-others.yml
-          cache-environment: true
-          create-args: |
-            python=${{ matrix.python-version }}
-      - name: run pytest
-        shell: bash -l {0}
-        run: |
-          micromamba activate optimagic
-          pytest -m "not slow and not jax"
-  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: ${{ matrix.os }}
-    strategy:
-      fail-fast: false
-      matrix:
-        os:
-          - ubuntu-latest
-        python-version:
-          - '3.10'
-    steps:
-      - uses: actions/checkout@v4
-      - name: create build environment
-        uses: mamba-org/setup-micromamba@v1
-        with:
-          environment-file: ./.tools/envs/testenv-pandas.yml
-          cache-environment: true
-          create-args: |
-            python=${{ matrix.python-version }}
-      - name: run pytest
-        shell: bash -l {0}
-        run: |
-          micromamba activate optimagic
-          pytest -m "not slow and not jax"
-  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: ${{ matrix.os }}
-    strategy:
-      fail-fast: false
-      matrix:
-        os:
-          - ubuntu-latest
-        python-version:
-          - '3.10'
+          - '312'
+          - '313'
+          - '314'
     steps:
       - uses: actions/checkout@v4
-      - name: create build environment
-        uses: mamba-org/setup-micromamba@v1
+      - uses: prefix-dev/setup-pixi@v0.9.4
         with:
-          environment-file: ./.tools/envs/testenv-numpy.yml
-          cache-environment: true
-          create-args: |
-            python=${{ 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: ${{ github.event_name == 'push' && github.ref_name == 'main' }}
+          frozen: true
+          environments: tests-py${{ matrix.python-version }}
+      - name: Run pytest
+        shell: bash -el {0}
+        run: pixi run -e tests-py${{ matrix.python-version }} 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: tests-old-plotly
+      - name: Run pytest
+        shell: bash -el {0}
+        run: pixi run -e tests-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'
+          - '312'
+          - '313'
+          - '314'
     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: ${{ github.event_name == 'push' && github.ref_name == 'main' }}
+          frozen: true
+          environments: tests-nevergrad-py${{ matrix.python-version }}
+      - name: Run pytest
+        shell: bash -el {0}
+        run: >-
+          pixi run -e tests-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: tests-linux-py314
+      - name: Run doctest
+        shell: bash -el {0}
+        run: >-
+          pixi run -e tests-linux-py314
+          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: type-checking
       - name: Run mypy
-        shell: bash -l {0}
-        run: |-
-          micromamba activate optimagic
-          mypy
+        shell: bash -el {0}
+        run: pixi run -e type-checking mypy

.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

.gitignore

@@ -104,6 +104,7 @@ venv/
 ENV/
 env.bak/
 venv.bak/
+.pixi/
 
 # Spyder project settings
 .spyderproject

.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

.readthedocs.yml

@@ -1,12 +1,15 @@
 ---
 version: 2
 build:
-  os: ubuntu-22.04
+  os: ubuntu-24.04
   tools:
-    python: mambaforge-4.10
-conda:
-  environment: docs/rtd_environment.yml
-sphinx:
-  builder: html
-  configuration: docs/source/conf.py
-  fail_on_warning: false
+    python: '3.14'
+  jobs:
+    create_environment:
+      - asdf plugin add pixi
+      - asdf install pixi latest
+      - asdf global pixi latest
+    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

.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)