Merge remote-tracking branch 'origin/main' into remove-skopt-learner

.github/workflows/auto-changelog-generator.yml

@@ -0,0 +1,58 @@
+name: Generate Changelog
+
+on:
+  # Manual trigger only
+  workflow_dispatch:
+    inputs:
+      branch:
+        description: 'Branch name'
+        required: true
+
+jobs:
+  generate-changelog:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Setup Ruby
+        uses: ruby/setup-ruby@v1
+        with:
+          ruby-version: 3.0
+
+      - name: Install github-changelog-generator
+        run: gem install github_changelog_generator
+
+      - name: Generate Changelog
+        run: |
+          github_changelog_generator \
+            -u ${{ github.repository_owner }} \
+            -p ${{ github.event.repository.name }} \
+            --token ${{ secrets.GITHUB_TOKEN }} \
+            --output CHANGELOG.md
+
+      - name: Commit updated CHANGELOG.md
+        id: commit
+        run: |
+          git add CHANGELOG.md
+          git config --local user.email "github-actions[bot]@users.noreply.github.com"
+          git config --local user.name "github-actions[bot]"
+          if git diff --quiet && git diff --staged --quiet; then
+            echo "No changes in CHANGELOG.md, skipping commit."
+            echo "commit_status=skipped" >> $GITHUB_ENV
+          else
+            git commit -m "Update CHANGELOG.md"
+            echo "commit_status=committed" >> $GITHUB_ENV
+          fi
+
+      - name: Echo CHANGELOG.md
+        run: cat CHANGELOG.md
+
+      - name: Push changes
+        if: env.commit_status == 'committed'
+        uses: ad-m/github-push-action@master
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          branch: ${{ github.event.inputs.branch }}

.github/workflows/coverage.yml

@@ -7,14 +7,14 @@ jobs:
   coverage:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v1
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
-        python-version: 3.7
+        python-version: 3.11
     - name: Install dependencies
-      run: pip install nox codecov
+      run: pip install nox
     - name: Test with nox
       run: nox -e coverage
-    - name: Upload test coverage
-      run: codecov -t ${{ secrets.CODECOV_TOKEN }} -f .coverage.xml
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action@v4

.github/workflows/nox.yml

@@ -12,24 +12,19 @@ jobs:
       fail-fast: false
       matrix:
         platform: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
 
     steps:
-    - uses: actions/checkout@v1
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
-    - name: Set Python version for nox
-      run: echo "PY_VERSION=$(echo ${version})" >> $GITHUB_ENV
-      shell: bash
-      env:
-        version: ${{ matrix.python-version }}
     - name: Register Python problem matcher
       run: echo "::add-matcher::.github/workflows/matchers/pytest.json"
     - name: Install dependencies
       run: pip install nox pytest-github-actions-annotate-failures
     - name: Test with nox using minimal dependencies
-      run: nox -e "pytest-${{ env.PY_VERSION }}(all_deps=False)"
+      run: nox -e "pytest-${{ matrix.python-version }}(all_deps=False)"
     - name: Test with nox with all dependencies
-      run: nox -e "pytest-${{ env.PY_VERSION }}(all_deps=True)"
+      run: nox -e "pytest-${{ matrix.python-version }}(all_deps=True)"

.github/workflows/pythonpublish.yml

@@ -13,19 +13,19 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Set up Python
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: '3.x'
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install setuptools wheel twine
+        pip install setuptools wheel twine build
     - name: Build and publish
       env:
         TWINE_USERNAME: __token__
         TWINE_PASSWORD: ${{ secrets.PYPI_TOKEN }}
       run: |
-        python setup.py sdist bdist_wheel
+        python -m build
         twine upload dist/*

.github/workflows/toc.yaml

@@ -0,0 +1,10 @@
+on: push
+name: TOC Generator
+jobs:
+  generateTOC:
+    name: TOC Generator
+    runs-on: ubuntu-latest
+    steps:
+      - uses: technote-space/toc-generator@v4
+        with:
+          TOC_TITLE: ""

.github/workflows/typeguard.yml

@@ -1,15 +1,16 @@
 name: typeguard
 
-on:
-  - push
+# TODO: enable this once typeguard=4 is released and issues are fixed.
+# on:
+#   - push
 
 jobs:
   typeguard:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v1
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: "3.11"
     - name: Install dependencies

.pre-commit-config.yaml

@@ -1,19 +1,29 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.6.0
     hooks:
       - id: trailing-whitespace
       - id: end-of-file-fixer
       - id: check-docstring-first
       - id: check-yaml
       - id: debug-statements
       - id: check-ast
-  - repo: https://github.com/psf/black
-    rev: 23.3.0
-    hooks:
-      - id: black
-  - repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: "v0.0.261"
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: "v0.3.5"
     hooks:
       - id: ruff
         args: ["--fix"]
+      - id: ruff-format
+  - repo: https://github.com/nbQA-dev/nbQA
+    rev: 1.8.5
+    hooks:
+      - id: nbqa-black
+        additional_dependencies: [jupytext, black]
+      - id: nbqa
+        args: ["ruff", "--fix", "--ignore=E402,B018,F704"]
+        additional_dependencies: [jupytext, ruff]
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: "v1.9.0"
+    hooks:
+      - id: mypy
+        exclude: ipynb_filter.py|docs/source/conf.py

AUTHORS.md

@@ -1,4 +1,4 @@
-## Authors
+## 👥 Authors
 
 The current maintainers of Adaptive are:
 

CHANGELOG.md

@@ -1,19 +1,101 @@
-# Changelog
+# 🗞️ Changelog
 
-## [v0.15.0](https://github.com/python-adaptive/adaptive/tree/v0.15.0) (2022-11-30)
+## [v.1.2.0](https://github.com/python-adaptive/adaptive/tree/v1.2.0) (2024-04-10)
 
-[Full Changelog](https://github.com/python-adaptive/adaptive/compare/v0.14.2...v0.15.0)
+[Full Changelog](https://github.com/python-adaptive/adaptive/compare/v1.1.0...HEAD)
+
+**Closed issues:**
+
+-  Issues with Multiprocess and AsyncRunner in adaptive for Phase Diagram Illustration [\#449](https://github.com/python-adaptive/adaptive/issues/449)
+- Create API for just signle process \(No pickle\) [\#442](https://github.com/python-adaptive/adaptive/issues/442)
+- Handling with regions unreachable inside the `ConvexHull` in `LearnerND` [\#438](https://github.com/python-adaptive/adaptive/issues/438)
+- Use in script with BlockingRunner: get log and/or feedback on progress [\#436](https://github.com/python-adaptive/adaptive/issues/436)
+
+**Merged pull requests:**
+
+- Test Python 3.12 and fix its installation [\#453](https://github.com/python-adaptive/adaptive/pull/453) ([basnijholt](https://github.com/basnijholt))
+- \[pre-commit.ci\] pre-commit autoupdate [\#447](https://github.com/python-adaptive/adaptive/pull/447) ([pre-commit-ci[bot]](https://github.com/apps/pre-commit-ci))
+- Use ruff-format instead of black [\#446](https://github.com/python-adaptive/adaptive/pull/446) ([basnijholt](https://github.com/basnijholt))
+- Bump versions to compatible packages in `docs/environment.yml` [\#445](https://github.com/python-adaptive/adaptive/pull/445) ([basnijholt](https://github.com/basnijholt))
+- Add `AsyncRunner.block_until_done` [\#444](https://github.com/python-adaptive/adaptive/pull/444) ([basnijholt](https://github.com/basnijholt))
+- Add `live_info_terminal`, closes \#436 [\#441](https://github.com/python-adaptive/adaptive/pull/441) ([basnijholt](https://github.com/basnijholt))
+- \[pre-commit.ci\] pre-commit autoupdate [\#434](https://github.com/python-adaptive/adaptive/pull/434) ([pre-commit-ci[bot]](https://github.com/apps/pre-commit-ci))
+- Add benchmarks page for Learner1D and Learner2D functions [\#405](https://github.com/python-adaptive/adaptive/pull/405) ([basnijholt](https://github.com/basnijholt))
+
+## [v1.1.0](https://github.com/python-adaptive/adaptive/tree/v1.1.0) (2023-08-14)
+
+[Full Changelog](https://github.com/python-adaptive/adaptive/compare/v1.0.0...v1.1.0)
+
+**Closed issues:**
+
+- large delay when using start\_periodic\_saving  [\#439](https://github.com/python-adaptive/adaptive/issues/439)
+- Target function returns NaN [\#435](https://github.com/python-adaptive/adaptive/issues/435)
+
+**Merged pull requests:**
+
+- Ensure periodic saving fires immediately after runner task is finished [\#440](https://github.com/python-adaptive/adaptive/pull/440) ([jbweston](https://github.com/jbweston))
+- Add Learner2D loss function 'thresholded\_loss\_factory' [\#437](https://github.com/python-adaptive/adaptive/pull/437) ([basnijholt](https://github.com/basnijholt))
+- \[pre-commit.ci\] pre-commit autoupdate [\#433](https://github.com/python-adaptive/adaptive/pull/433) ([pre-commit-ci[bot]](https://github.com/apps/pre-commit-ci))
+- \[pre-commit.ci\] pre-commit autoupdate [\#431](https://github.com/python-adaptive/adaptive/pull/431) ([pre-commit-ci[bot]](https://github.com/apps/pre-commit-ci))
+- Add adaptive.utils.daskify [\#422](https://github.com/python-adaptive/adaptive/pull/422) ([basnijholt](https://github.com/basnijholt))
+
+## [v1.0.0](https://github.com/python-adaptive/adaptive/tree/v1.0.0) (2023-05-15)
+
+[Full Changelog](https://github.com/python-adaptive/adaptive/compare/v0.15.0...v1.0.0)
+
+**Closed issues:**
+
+- No module named 'typing\_extensions'" [\#394](https://github.com/python-adaptive/adaptive/issues/394)
+- Documentation: use cases of coroutine by Learner and Runner not properly explained [\#360](https://github.com/python-adaptive/adaptive/issues/360)
+
+**Merged pull requests:**
+
+- Update CHANGELOG for v1.0.0 [\#429](https://github.com/python-adaptive/adaptive/pull/429) ([basnijholt](https://github.com/basnijholt))
+- \[pre-commit.ci\] pre-commit autoupdate [\#426](https://github.com/python-adaptive/adaptive/pull/426) ([pre-commit-ci[bot]](https://github.com/apps/pre-commit-ci))
+- Allow storing the full sequence in SequenceLearner.to\_dataframe [\#425](https://github.com/python-adaptive/adaptive/pull/425) ([basnijholt](https://github.com/basnijholt))
+- \[pre-commit.ci\] pre-commit autoupdate [\#423](https://github.com/python-adaptive/adaptive/pull/423) ([pre-commit-ci[bot]](https://github.com/apps/pre-commit-ci))
+- Add github-changelog-generator CI workflow [\#421](https://github.com/python-adaptive/adaptive/pull/421) ([basnijholt](https://github.com/basnijholt))
+- Use versioningit to work with pyproject.toml and remove setup.py [\#420](https://github.com/python-adaptive/adaptive/pull/420) ([basnijholt](https://github.com/basnijholt))
+- Update Python version requirement to 3.9 in accordance with NEP 29 [\#418](https://github.com/python-adaptive/adaptive/pull/418) ([basnijholt](https://github.com/basnijholt))
+- Update GitHub Actions CI [\#416](https://github.com/python-adaptive/adaptive/pull/416) ([basnijholt](https://github.com/basnijholt))
+- Disable typeguard CI pipeline [\#415](https://github.com/python-adaptive/adaptive/pull/415) ([basnijholt](https://github.com/basnijholt))
+- Add mypy to pre-commit and fix all current typing issues [\#414](https://github.com/python-adaptive/adaptive/pull/414) ([basnijholt](https://github.com/basnijholt))
+- \[pre-commit.ci\] pre-commit autoupdate [\#413](https://github.com/python-adaptive/adaptive/pull/413) ([pre-commit-ci[bot]](https://github.com/apps/pre-commit-ci))
+- Use codecov/codecov-action instead of removed codecov package [\#412](https://github.com/python-adaptive/adaptive/pull/412) ([basnijholt](https://github.com/basnijholt))
+- Cache the loss of a SequenceLearner [\#411](https://github.com/python-adaptive/adaptive/pull/411) ([basnijholt](https://github.com/basnijholt))
+- Only really import packages when needed [\#410](https://github.com/python-adaptive/adaptive/pull/410) ([basnijholt](https://github.com/basnijholt))
+- Remove \_RequireAttrsABCMeta metaclass and replace with simple check [\#409](https://github.com/python-adaptive/adaptive/pull/409) ([basnijholt](https://github.com/basnijholt))
+- Use the build module [\#407](https://github.com/python-adaptive/adaptive/pull/407) ([basnijholt](https://github.com/basnijholt))
+- Avoid asyncio.coroutine error in Readthedocs.org builds [\#406](https://github.com/python-adaptive/adaptive/pull/406) ([basnijholt](https://github.com/basnijholt))
+- Bump scikit-optimize in environment.yml [\#403](https://github.com/python-adaptive/adaptive/pull/403) ([basnijholt](https://github.com/basnijholt))
+- Replace isort, flake8, and pyupgrade by ruff [\#402](https://github.com/python-adaptive/adaptive/pull/402) ([basnijholt](https://github.com/basnijholt))
+- Move to pyproject.toml based install [\#401](https://github.com/python-adaptive/adaptive/pull/401) ([basnijholt](https://github.com/basnijholt))
+- Rewrite parts of README, reorder sections, and add features section [\#400](https://github.com/python-adaptive/adaptive/pull/400) ([basnijholt](https://github.com/basnijholt))
+- \[pre-commit.ci\] pre-commit autoupdate [\#398](https://github.com/python-adaptive/adaptive/pull/398) ([pre-commit-ci[bot]](https://github.com/apps/pre-commit-ci))
+- \[pre-commit.ci\] pre-commit autoupdate [\#397](https://github.com/python-adaptive/adaptive/pull/397) ([pre-commit-ci[bot]](https://github.com/apps/pre-commit-ci))
+- Use nb\_execution\_raise\_on\_error Sphinx myst-nb option [\#396](https://github.com/python-adaptive/adaptive/pull/396) ([basnijholt](https://github.com/basnijholt))
+- \[pre-commit.ci\] pre-commit autoupdate [\#395](https://github.com/python-adaptive/adaptive/pull/395) ([pre-commit-ci[bot]](https://github.com/apps/pre-commit-ci))
+- \[pre-commit.ci\] pre-commit autoupdate [\#393](https://github.com/python-adaptive/adaptive/pull/393) ([pre-commit-ci[bot]](https://github.com/apps/pre-commit-ci))
+- \[pre-commit.ci\] pre-commit autoupdate [\#392](https://github.com/python-adaptive/adaptive/pull/392) ([pre-commit-ci[bot]](https://github.com/apps/pre-commit-ci))
+- Add nbQA for notebook and docs linting [\#361](https://github.com/python-adaptive/adaptive/pull/361) ([basnijholt](https://github.com/basnijholt))
+- Fix HoloViews opts deprecation warnings [\#357](https://github.com/python-adaptive/adaptive/pull/357) ([basnijholt](https://github.com/basnijholt))
+
+## [v0.15.0](https://github.com/python-adaptive/adaptive/tree/v0.15.0) (2022-12-02)
+
+[Full Changelog](https://github.com/python-adaptive/adaptive/compare/v0.15.1...v0.15.0)
+
+## [v0.15.1](https://github.com/python-adaptive/adaptive/tree/v0.15.1) (2022-12-02)
+
+[Full Changelog](https://github.com/python-adaptive/adaptive/compare/v0.14.2...v0.15.1)
 
 **Closed issues:**
 
 - Fix branch name \(master --\> main\) in binder link in readme [\#383](https://github.com/python-adaptive/adaptive/issues/383)
 
 **Merged pull requests:**
 
-- Add support for Python 3.11 and test on it [\#387](https://github.com/python-adaptive/adaptive/pull/387) ([basnijholt](https://github.com/basnijholt))
 - Rename master -\> main [\#384](https://github.com/python-adaptive/adaptive/pull/384) ([basnijholt](https://github.com/basnijholt))
 - Add loss\_goal, npoints\_goal, and an auto\_goal function and use it in the runners [\#382](https://github.com/python-adaptive/adaptive/pull/382) ([basnijholt](https://github.com/basnijholt))
-- Add type-hints to Runner [\#370](https://github.com/python-adaptive/adaptive/pull/370) ([basnijholt](https://github.com/basnijholt))
 - Add docs section about executing coroutines  [\#364](https://github.com/python-adaptive/adaptive/pull/364) ([juandaanieel](https://github.com/juandaanieel))
 
 ## [v0.14.2](https://github.com/python-adaptive/adaptive/tree/v0.14.2) (2022-10-14)
@@ -198,7 +280,7 @@
 - bump pre-commit filter dependencies [\#293](https://github.com/python-adaptive/adaptive/pull/293) ([basnijholt](https://github.com/basnijholt))
 - fix docs [\#291](https://github.com/python-adaptive/adaptive/pull/291) ([basnijholt](https://github.com/basnijholt))
 - update to miniver 0.7.0 [\#290](https://github.com/python-adaptive/adaptive/pull/290) ([basnijholt](https://github.com/basnijholt))
-- add `runner.live\_plot\(\)` in README example [\#288](https://github.com/python-adaptive/adaptive/pull/288) ([basnijholt](https://github.com/basnijholt))
+- add `runner.live_plot()` in README example [\#288](https://github.com/python-adaptive/adaptive/pull/288) ([basnijholt](https://github.com/basnijholt))
 - Update pre commit [\#287](https://github.com/python-adaptive/adaptive/pull/287) ([basnijholt](https://github.com/basnijholt))
 - Use m2r2 [\#286](https://github.com/python-adaptive/adaptive/pull/286) ([basnijholt](https://github.com/basnijholt))
 - temporarily pin scikit-learn\<=0.23.1 [\#285](https://github.com/python-adaptive/adaptive/pull/285) ([basnijholt](https://github.com/basnijholt))
@@ -243,7 +325,6 @@
 
 **Closed issues:**
 
-
 - add minimum number of points parameter to AverageLearner [\#273](https://github.com/python-adaptive/adaptive/issues/273)
 - Release v0.10 [\#258](https://github.com/python-adaptive/adaptive/issues/258)
 
@@ -433,7 +514,7 @@
 - Gracefully handle exceptions when evaluating the function to be learned [\#125](https://github.com/python-adaptive/adaptive/issues/125)
 - Allow BalancingLearner to return arbitrary number of points from 'choose\_points' [\#124](https://github.com/python-adaptive/adaptive/issues/124)
 - Increase the default refresh rate for 'live\_plot' [\#120](https://github.com/python-adaptive/adaptive/issues/120)
-- remove default number of points to choose in `choose\_points` [\#118](https://github.com/python-adaptive/adaptive/issues/118)
+- remove default number of points to choose in `choose_points` [\#118](https://github.com/python-adaptive/adaptive/issues/118)
 - Consider using Gaussian process optimization as a learner [\#115](https://github.com/python-adaptive/adaptive/issues/115)
 - Make `distributed.Client` work with automatic scaling of the cluster [\#104](https://github.com/python-adaptive/adaptive/issues/104)
 - Improve plotting for learners [\#83](https://github.com/python-adaptive/adaptive/issues/83)
@@ -520,7 +601,7 @@
 - Remove public 'fname' learner attribute [\#17](https://github.com/python-adaptive/adaptive/issues/17)
 - Release v0.7.0 [\#14](https://github.com/python-adaptive/adaptive/issues/14)
 - \(Learner1D\) improve time complexity [\#13](https://github.com/python-adaptive/adaptive/issues/13)
-- Typo in documentation for` adaptive.learner.learner2D.uniform\_loss\(ip\)` [\#12](https://github.com/python-adaptive/adaptive/issues/12)
+- Typo in documentation for` adaptive.learner.learner2D.uniform_loss(ip)` [\#12](https://github.com/python-adaptive/adaptive/issues/12)
 - \(LearnerND\) fix plotting of scaled domains [\#11](https://github.com/python-adaptive/adaptive/issues/11)
 - suggested points lie outside of domain [\#7](https://github.com/python-adaptive/adaptive/issues/7)
 - DEVELOPMENT IS ON GITLAB: https://gitlab.kwant-project.org/qt/adaptive [\#5](https://github.com/python-adaptive/adaptive/issues/5)

LICENSE

@@ -1,6 +1,6 @@
 BSD 3-Clause License
 
-Copyright (c) 2017-2021, Adaptive authors
+Copyright (c) 2017-2023, Adaptive authors
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without