Update infrastructure

.github/workflows/main.yml

@@ -29,7 +29,7 @@ jobs:
       - name: create build environment
         uses: mamba-org/setup-micromamba@v1
         with:
-          environment-file: ./.envs/testenv-linux.yml
+          environment-file: ./.tools/envs/testenv-linux.yml
           cache-environment: true
           create-args: |
             python=${{ matrix.python-version }}
@@ -60,7 +60,7 @@ jobs:
       - name: create build environment
         uses: mamba-org/setup-micromamba@v1
         with:
-          environment-file: ./.envs/testenv-others.yml
+          environment-file: ./.tools/envs/testenv-others.yml
           cache-environment: true
           create-args: |
             python=${{ matrix.python-version }}
@@ -87,7 +87,7 @@ jobs:
       - name: create build environment
         uses: mamba-org/setup-micromamba@v1
         with:
-          environment-file: ./.envs/testenv-pandas.yml
+          environment-file: ./.tools/envs/testenv-pandas.yml
           cache-environment: true
           create-args: |
             python=${{ matrix.python-version }}
@@ -104,10 +104,11 @@ jobs:
       - name: create build environment
         uses: mamba-org/setup-micromamba@v1
         with:
-          environment-file: ./.envs/testenv-linux.yml
+          environment-file: ./.tools/envs/testenv-linux.yml
           environment-name: optimagic
-          cache-env: true
-          extra-specs: python=3.12
+          cache-environment: true
+          create-args: |
+            python=3.12
       - name: run sphinx
         shell: bash -l {0}
         run: |-
@@ -124,10 +125,10 @@ jobs:
       - name: create build environment
         uses: mamba-org/setup-micromamba@v1
         with:
-          environment-file: ./.envs/testenv-linux.yml
+          environment-file: ./.tools/envs/testenv-linux.yml
           environment-name: optimagic
-          cache-env: true
-          extra-specs: |
+          cache-environment: true
+          create-args: |
             python=3.10
       - name: Run mypy
         shell: bash -l {0}

.github/workflows/publish-to-pypi.yml

@@ -2,8 +2,8 @@
 name: PyPI
 on: push
 jobs:
-  build-n-publish:
-    name: Build and publish Python 🐍 distributions 📦 to PyPI
+  build-n-publish-optimagic:
+    name: Build and publish optimagic Python 🐍 distributions 📦 to PyPI
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
@@ -24,6 +24,40 @@ jobs:
           --sdist
           --wheel
           --outdir dist/
+      - name: Publish distribution 📦 to PyPI
+        if: startsWith(github.ref, 'refs/tags')
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          password: ${{ secrets.PYPI_API_TOKEN_OPTIMAGIC }}
+  build-n-publish-estimagic:
+    name: Build and publish estimagic Python 🐍 distributions 📦 to PyPI
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.10'
+      - name: Install pypa/build
+        run: >-
+          python -m
+          pip install
+          build
+          toml
+          --user
+      - name: Set name entry in pyproject.toml to estimagic
+        run: >-
+          python .tools/update_name_pyproject.py
+      - name: Add FutureWarning to init files
+        run: >-
+          python .tools/update_init_files.py
+      - name: Build a binary wheel and a source tarball
+        run: >-
+          python -m
+          build
+          --sdist
+          --wheel
+          --outdir dist/
       - name: Publish distribution 📦 to PyPI
         if: startsWith(github.ref, 'refs/tags')
         uses: pypa/gh-action-pypi-publish@release/v1

.pre-commit-config.yaml

@@ -14,7 +14,7 @@ repos:
     hooks:
       - id: update-environment-files
         name: check environment file updates
-        entry: python .envs/update_envs.py
+        entry: python .tools/update_envs.py
         language: python
         always_run: true
         require_serial: true
@@ -55,16 +55,6 @@ repos:
     hooks:
       - id: yamllint
         exclude: tests/optimagic/optimizers/_pounders/fixtures
-  - repo: https://github.com/psf/black
-    rev: 24.4.2
-    hooks:
-      - id: black
-        language_version: python3.10
-  - repo: https://github.com/asottile/blacken-docs
-    rev: 1.18.0
-    hooks:
-      - id: blacken-docs
-        exclude: docs/source/how_to/how_to_constraints.md
   - repo: https://github.com/PyCQA/docformatter
     rev: v1.7.5
     hooks:
@@ -78,21 +68,30 @@ repos:
           - --blank
         exclude: src/optimagic/optimization/algo_options.py
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.5.0
+    rev: v0.5.4
     hooks:
+      # Run the linter.
       - id: ruff
-  - repo: https://github.com/nbQA-dev/nbQA
-    rev: 1.8.5
-    hooks:
-      - id: nbqa-black
-      - id: nbqa-ruff
+        types_or:
+          - python
+          - pyi
+          - jupyter
+        args:
+          - --fix
+      # Run the formatter.
+      - id: ruff-format
+        types_or:
+          - python
+          - pyi
+          - jupyter
   - repo: https://github.com/executablebooks/mdformat
     rev: 0.7.17
     hooks:
       - id: mdformat
         additional_dependencies:
           - mdformat-gfm
-          - mdformat-black
+          - mdformat-gfm-alerts
+          - mdformat-ruff
         args:
           - --wrap
           - '88'
@@ -103,23 +102,24 @@ repos:
       - id: mdformat
         additional_dependencies:
           - mdformat-myst
-          - mdformat-black
+          - mdformat-ruff
         args:
           - --wrap
           - '88'
         files: (docs/.)
-  - repo: https://github.com/asottile/setup-cfg-fmt
-    rev: v2.5.0
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.10.0
     hooks:
-      - id: setup-cfg-fmt
-  - repo: https://github.com/mgedmin/check-manifest
-    rev: '0.49'
-    hooks:
-      - id: check-manifest
-        args:
-          - --no-build-isolation
+      - id: mypy
+        files: src|tests
         additional_dependencies:
-          - setuptools-scm
-          - toml
+          - packaging
+          - pandas-stubs
+          - sqlalchemy-stubs
+          - types-cffi
+          - types-openpyxl
+          - types-jinja2
+        args:
+          - --config=pyproject.toml
 ci:
   autoupdate_schedule: monthly

.envs/testenv-linux.yml → .tools/envs/testenv-linux.yml

@@ -21,7 +21,7 @@ dependencies:
   - scipy>=1.2.1  # run, tests
   - sqlalchemy  # run, tests
   - seaborn  # dev, tests
-  - mypy  # dev, tests
+  - mypy>=1.10  # dev, tests
   - pyyaml  # dev, tests
   - jinja2  # dev, tests
   - pip:  # dev, tests, docs
@@ -33,4 +33,4 @@ dependencies:
       - types-cffi  # dev, tests
       - types-openpyxl  # dev, tests
       - types-jinja2  # dev, tests
-      - -e ../
+      - -e ../../

.envs/testenv-others.yml → .tools/envs/testenv-others.yml

@@ -20,7 +20,7 @@ dependencies:
   - scipy>=1.2.1  # run, tests
   - sqlalchemy  # run, tests
   - seaborn  # dev, tests
-  - mypy  # dev, tests
+  - mypy>=1.10  # dev, tests
   - pyyaml  # dev, tests
   - jinja2  # dev, tests
   - pip:  # dev, tests, docs
@@ -32,4 +32,4 @@ dependencies:
       - types-cffi  # dev, tests
       - types-openpyxl  # dev, tests
       - types-jinja2  # dev, tests
-      - -e ../
+      - -e ../../

.envs/testenv-pandas.yml → .tools/envs/testenv-pandas.yml

@@ -19,7 +19,7 @@ dependencies:
   - scipy>=1.2.1  # run, tests
   - sqlalchemy  # run, tests
   - seaborn  # dev, tests
-  - mypy  # dev, tests
+  - mypy>=1.10  # dev, tests
   - pyyaml  # dev, tests
   - jinja2  # dev, tests
   - pip:  # dev, tests, docs
@@ -30,4 +30,4 @@ dependencies:
       - types-cffi  # dev, tests
       - types-openpyxl  # dev, tests
       - types-jinja2  # dev, tests
-      - -e ../
+      - -e ../../

.envs/update_envs.py → .tools/update_envs.py

@@ -20,7 +20,7 @@ def main():
     # create standard testing environments
 
     test_env = [line for line in lines if _keep_line(line, "tests")]
-    test_env.append("      - -e ../")  # add local installation
+    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
@@ -42,16 +42,17 @@ def main():
     # create docs testing environment
 
     docs_env = [line for line in lines if _keep_line(line, "docs")]
-    docs_env.append("      - -e ../")  # add local installation
+    docs_env.append("      - -e ../../")  # add local installation
 
     # write environments
     for name, env in zip(
         ["linux", "others", "pandas"],
         [test_env_linux, test_env_others, test_env_pandas],
+        strict=False,
     ):
         # Specify newline to avoid wrong line endings on Windows.
         # See: https://stackoverflow.com/a/69869641
-        Path(f".envs/testenv-{name}.yml").write_text(
+        Path(f".tools/envs/testenv-{name}.yml").write_text(
             "\n".join(env) + "\n", newline="\n"
         )
 

.tools/update_init_files.py

@@ -0,0 +1,29 @@
+from pathlib import Path
+
+SRC = Path(__file__).parent.parent.resolve() / "src"
+
+
+to_append = r"""
+import warnings
+warnings.warn(
+    "estimagic has been renamed to optimagic. Please uninstall estimagic and install "
+    "optimagic instead. Don't worry, your estimagic imports will still work if you "
+    "install optimagic, and simple warnings will help you to adjust them for future "
+    "releases.\n\n"
+    "To make these changes using pip, run:\n"
+    "-------------------------------------\n"
+    "$ pip uninstall estimagic\n"
+    "$ pip install optimagic\n\n"
+    "For conda users, use:\n"
+    "---------------------\n"
+    "$ conda remove estimagic\n"
+    "$ conda install -c conda-forge optimagic\n",
+    FutureWarning,
+)
+"""
+
+for package in ("estimagic", "optimagic"):
+    init_file = SRC / package / "__init__.py"
+    current_content = init_file.read_text()
+    new_content = current_content + to_append
+    init_file.write_text(new_content)

.tools/update_name_pyproject.py

@@ -0,0 +1,12 @@
+import toml
+from pathlib import Path
+
+file_path = Path(__file__).parent.parent.resolve() / "pyproject.toml"
+
+with file_path.open("r") as f:
+    config = toml.load(f)
+
+config["project"]["name"] = "estimagic"
+
+with file_path.open("w") as f:
+    toml.dump(config, f)

docs/rtd_environment.yml

@@ -8,7 +8,6 @@ dependencies:
   - pip
   - setuptools_scm
   - toml
-  - black
   - sphinx
   - sphinxcontrib-bibtex
   - sphinx-copybutton

docs/source/development/ep-02-typing.md

@@ -1222,7 +1222,6 @@ class ScipyNelderMead(Algorithm):
     def _solve_internal_problem(
         self, problem: InternalProblem, x0: NDArray[float]
     ) -> InternalOptimizeResult:
-
         options = {
             "maxiter": self.stopping_max_iterations,
             "maxfev": self.stopping_max_criterion_evaluations,
@@ -1540,7 +1539,6 @@ FvalType = TypeVar("FvalType", bound=float | NDArray[float])
 
 
 class BenchmarkNoise(ABC):
-
     @abstractmethod
     def draw_noise(
         self, fval: FvalType, params: NDArray, size: int, rng: np.random.Generator