Merge remote-tracking branch 'upstream/main' into bootstrap_weights

.github/ISSUE_TEMPLATE/enhancement.md

@@ -7,7 +7,7 @@ assignees: ''
 
 ---
 
-* estimagic version used, if any:
+* optimagic version used, if any:
 * Python version, if any:
 * Operating System:
 

.github/workflows/main.yml

@@ -21,7 +21,6 @@ jobs:
         os:
           - ubuntu-latest
         python-version:
-          - '3.9'
           - '3.10'
           - '3.11'
           - '3.12'
@@ -30,14 +29,14 @@ 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=${{ matrix.python-version }}
       - name: run pytest
         shell: bash -l {0}
         run: |
-          micromamba activate estimagic
+          micromamba activate optimagic
           pytest --cov-report=xml --cov=./
       - name: Upload coverage report.
         if: runner.os == 'Linux' && matrix.python-version == '3.10'
@@ -54,27 +53,26 @@ jobs:
           - macos-latest
           - windows-latest
         python-version:
-          - '3.9'
           - '3.10'
           - '3.11'
     steps:
       - uses: actions/checkout@v4
       - name: create build environment
         uses: mamba-org/setup-micromamba@v1
         with:
-          environment-file: ./.envs/testenv-others.yml
+          environment-file: ./.tools/envs/testenv-others.yml
           cache-environment: true
           create-args: |
             python=${{ matrix.python-version }}
       - name: run pytest
         shell: bash -l {0}
         run: |
-          micromamba activate estimagic
+          micromamba activate optimagic
           pytest -m "not slow and not jax"
   run-tests-with-old-pandas:
-    # This job is only for testing if estimagic works with older pandas versions, as
-    # many pandas functions we use will be deprecated in pandas 3. estimagic's behavior
-    # for older verions is handled in src/estimagic/compat.py.
+    # This job is only for testing if optimagic works with older pandas versions, 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.
     name: Run tests for ${{ matrix.os}} on ${{ matrix.python-version }} with pandas 1
     runs-on: ${{ matrix.os }}
     strategy:
@@ -83,23 +81,21 @@ jobs:
         os:
           - ubuntu-latest
         python-version:
-          - '3.11'
+          - '3.10'
     steps:
       - uses: actions/checkout@v4
       - name: create build environment
         uses: mamba-org/setup-micromamba@v1
         with:
-          environment-file: ./.envs/testenv-pandas.yml
+          environment-file: ./.tools/envs/testenv-pandas.yml
           cache-environment: true
           create-args: |
             python=${{ matrix.python-version }}
       - name: run pytest
         shell: bash -l {0}
         run: |
-          micromamba activate estimagic
-          pytest tests/visualization
-          pytest tests/parameters
-          pytest tests/inference
+          micromamba activate optimagic
+          pytest -m "not slow and not jax"
   code-in-docs:
     name: Run code snippets in documentation
     runs-on: ubuntu-latest
@@ -108,12 +104,34 @@ 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-environment: true
-          create-args: python=3.10
+          create-args: |
+            python=3.12
       - name: run sphinx
         shell: bash -l {0}
         run: |-
-          micromamba activate estimagic
+          micromamba activate optimagic
           cd docs/source
-          python -m doctest -v how_to_guides/optimization/how_to_specify_constraints.md
+          python -m doctest -v 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
+        with:
+          environment-file: ./.tools/envs/testenv-linux.yml
+          environment-name: optimagic
+          cache-environment: true
+          create-args: |
+            python=3.10
+      - name: Run mypy
+        shell: bash -l {0}
+        run: |-
+          micromamba activate optimagic
+          mypy

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

@@ -3,7 +3,7 @@ name: PyPI
 on: push
 jobs:
   build-n-publish:
-    name: Build and publish Python 🐍 distributions 📦 to PyPI
+    name: Build and publish optimagic Python 🐍 distributions 📦 to PyPI
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
@@ -28,4 +28,4 @@ jobs:
         if: startsWith(github.ref, 'refs/tags')
         uses: pypa/gh-action-pypi-publish@release/v1
         with:
-          password: ${{ secrets.PYPI_API_TOKEN }}
+          password: ${{ secrets.PYPI_API_TOKEN_OPTIMAGIC }}

.gitignore

@@ -132,5 +132,6 @@ venv.bak/
 
 
 src/estimagic/_version.py
+src/optimagic/_version.py
 
 *.~lock.*

.pre-commit-config.yaml

@@ -6,15 +6,15 @@ repos:
       - id: check-useless-excludes
         # - id: identity  # Prints all files passed to pre-commits. Debugging.
   - repo: https://github.com/lyz-code/yamlfix
-    rev: 1.16.0
+    rev: 1.17.0
     hooks:
       - id: yamlfix
-        exclude: tests/optimization/fixtures
+        exclude: tests/optimagic/optimizers/_pounders/fixtures
   - repo: local
     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
@@ -24,7 +24,7 @@ repos:
       - id: check-added-large-files
         args:
           - --maxkb=1300
-        exclude: tests/optimization/fixtures/
+        exclude: tests/optimagic/optimizers/_pounders/fixtures/
       - id: check-case-conflict
       - id: check-merge-conflict
       - id: check-vcs-permalinks
@@ -48,24 +48,13 @@ repos:
           - --branch
           - main
       - id: trailing-whitespace
+        exclude: docs/
       - id: check-ast
-      - id: check-docstring-first
-        exclude: src/estimagic/optimization/algo_options.py
   - repo: https://github.com/adrienverge/yamllint.git
     rev: v1.35.1
     hooks:
       - id: yamllint
-        exclude: tests/optimization/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_guides/optimization/how_to_specify_constraints.md
+        exclude: tests/optimagic/optimizers/_pounders/fixtures
   - repo: https://github.com/PyCQA/docformatter
     rev: v1.7.5
     hooks:
@@ -77,23 +66,32 @@ repos:
           - --wrap-descriptions
           - '88'
           - --blank
-        exclude: src/estimagic/optimization/algo_options.py
+        exclude: src/optimagic/optimization/algo_options.py
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.5.0
+    rev: v0.6.3
     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'
@@ -104,23 +102,36 @@ 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/kynan/nbstripout
+    rev: 0.7.1
     hooks:
-      - id: setup-cfg-fmt
-  - repo: https://github.com/mgedmin/check-manifest
-    rev: '0.49'
-    hooks:
-      - id: check-manifest
+      - id: nbstripout
+        exclude: |
+          (?x)^(
+            docs/source/estimagic/tutorials/estimation_tables_overview.ipynb|
+            docs/source/estimagic/explanation/bootstrap_montecarlo_comparison.ipynb|
+          )$
         args:
-          - --no-build-isolation
+          - --drop-empty-cells
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.11.2
+    hooks:
+      - id: mypy
+        files: src|tests
         additional_dependencies:
-          - setuptools-scm
-          - toml
+          - numpy<2.0
+          - 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

@@ -1,19 +1,19 @@
 ---
-name: estimagic
+name: optimagic
 channels:
   - conda-forge
   - nodefaults
 dependencies:
+  - petsc4py
   - jax
-  - pygmo
+  - cyipopt>=1.4.0  # dev, tests
+  - pygmo>=2.19.0  # dev, tests
   - nlopt  # dev, tests
   - pip  # dev, tests, docs
   - pytest  # dev, tests
   - pytest-cov  # tests
   - pytest-xdist  # dev, tests
   - statsmodels  # dev, tests
-  - bokeh<=2.4.3  # run, tests
-  - click  # run, tests
   - cloudpickle  # run, tests
   - joblib  # run, tests
   - numpy<2.0  # run, tests
@@ -22,12 +22,19 @@ dependencies:
   - pybaum >= 0.1.2  # run, tests
   - scipy>=1.2.1  # run, tests
   - sqlalchemy  # run, tests
-  - tranquilo>=0.0.4  # dev, tests
   - seaborn  # dev, tests
+  - mypy>=1.11  # dev, tests
+  - pyyaml  # dev, tests
+  - jinja2  # dev, tests
+  - annotated-types  # dev, tests
   - pip:  # dev, tests, docs
       - DFO-LS  # dev, tests
       - Py-BOBYQA  # dev, tests
       - fides==0.7.4  # dev, tests
       - kaleido  # dev, tests
-      - simoptlib==1.0.1  # dev, tests
-      - -e ../
+      - pandas-stubs  # dev, tests
+      - types-cffi  # dev, tests
+      - types-openpyxl  # dev, tests
+      - types-jinja2  # dev, tests
+      - sqlalchemy-stubs  # dev, tests
+      - -e ../../

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

@@ -1,18 +1,17 @@
 ---
-name: estimagic
+name: optimagic
 channels:
   - conda-forge
   - nodefaults
 dependencies:
-  - cyipopt<=1.2.0
+  - cyipopt>=1.4.0  # dev, tests
+  - pygmo>=2.19.0  # dev, tests
   - nlopt  # dev, tests
   - pip  # dev, tests, docs
   - pytest  # dev, tests
   - pytest-cov  # tests
   - pytest-xdist  # dev, tests
   - statsmodels  # dev, tests
-  - bokeh<=2.4.3  # run, tests
-  - click  # run, tests
   - cloudpickle  # run, tests
   - joblib  # run, tests
   - numpy<2.0  # run, tests
@@ -21,12 +20,19 @@ dependencies:
   - pybaum >= 0.1.2  # run, tests
   - scipy>=1.2.1  # run, tests
   - sqlalchemy  # run, tests
-  - tranquilo>=0.0.4  # dev, tests
   - seaborn  # dev, tests
+  - mypy>=1.11  # dev, tests
+  - pyyaml  # dev, tests
+  - jinja2  # dev, tests
+  - annotated-types  # dev, tests
   - pip:  # dev, tests, docs
       - DFO-LS  # dev, tests
       - Py-BOBYQA  # dev, tests
       - fides==0.7.4  # dev, tests
       - kaleido  # dev, tests
-      - simoptlib==1.0.1  # dev, tests
-      - -e ../
+      - pandas-stubs  # dev, tests
+      - types-cffi  # dev, tests
+      - types-openpyxl  # dev, tests
+      - types-jinja2  # dev, tests
+      - sqlalchemy-stubs  # dev, tests
+      - -e ../../