Version 1.1 [Docs]

* Documentation was updated thoroughly. A new theme with a new structure is provided and all pages have been updated. Also, the examples revised and up-to-date. * Option to use an own stopping strategy using `IncorporateRunResultCallback`. * Changed `scripts/smac` to `scripts/smac.py`. * `README.md` updated. * `CITATION.cff` added. * Made `smac-validate.py` consistent with runhistory and tae. (#762) * `minR`, `maxR` and `use_ta_time` can now be initialized by the scenario. (#775) * `ConfigSpace.util.get_one_exchange_neighborhood`'s invalid configurations are ignored. (#773) * Fixed an incorrect adaptive capping behaviour. (#749) * Avoid the potential `ValueError` raised by `LocalSearch._do_search`. (#773) Co-authored-by: dengdifan <33290713+dengdifan@users.noreply.github.com> Co-authored-by: Filip Bártek <Filip.Bartek@hotmail.com> Co-authored-by: Thomas Holvoet <tholvoet@telenet.be> Co-authored-by: benjamc <75323339+benjamc@users.noreply.github.com> Co-authored-by: Carolin Benjamins <benjamins@tnt.uni-hannover.de> Co-authored-by: Marius Lindauer <marius.rks@googlemail.com> Co-authored-by: eddiebergman <eddiebergmanhs@gmail.com> Co-authored-by: Difan Deng <deng@dengster.tnt.uni-hannover.de> Co-authored-by: dengdifan <difandeng@gmail.com> Co-authored-by: Tim Ruhkopf <timruhkopf@gmail.com>
automl · Oct 20, 2021 · b2e0a65 · b2e0a65
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diff --git a/.github/workflows/terminal_examples.yml → ...ub/unused_workflows/terminal_examples.yml b/.github/workflows/terminal_examples.yml → ...ub/unused_workflows/terminal_examples.yml
@@ -8,7 +8,7 @@ jobs:
     runs-on: ubuntu-18.04
     strategy:
       matrix:
-        python-version: [3.8]
+        python-version: [3.9]
       fail-fast:  false
 
     steps:
@@ -28,26 +28,26 @@ jobs:
       run: |
         # Activate anaconda so default python is from conda
         export PATH="$CONDA/envs/testenv/bin:$PATH"
-        cd examples/quickstart/spear_qcp
+        cd examples/commandline
         bash run_SMAC.sh
     - name: Spear QCP ROAR
       timeout-minutes: 20
       run: |
         # Activate anaconda so default python is from conda
         export PATH="$CONDA/envs/testenv/bin:$PATH"
-        cd examples/quickstart/spear_qcp
+        cd examples/commandline
         bash run_ROAR.sh
     - name: Spear QCP Successive halving
       timeout-minutes: 20
       run: |
         # Activate anaconda so default python is from conda
         export PATH="$CONDA/envs/testenv/bin:$PATH"
-        cd examples/quickstart/spear_qcp
-        python SMAC4AC_SH_spear_qcp.py
+        cd examples/python
+        python spear_mf_instances.py
     - name:  Branin from the command line
       timeout-minutes: 20
       run: |
         # Activate anaconda so default python is from conda
         export PATH="$CONDA/envs/testenv/bin:$PATH"
-        cd examples/quickstart/branin
-        python ../../../scripts/smac --scenario scenario.txt
+        cd examples/commandline
+        python ../../scripts/smac.py --scenario branin/scenario.txt
diff --git a/.github/workflows/dist.yml b/.github/workflows/dist.yml
@@ -7,23 +7,28 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v2
+
     - name: Setup Python
       uses: actions/setup-python@v2
       with:
-        python-version: 3.8
+        python-version: 3.9
+
     - name: Build dist
       run: |
         python setup.py sdist
+
     - name: Twine check
       run: |
         pip install twine
         last_dist=$(ls -t dist/smac-*.tar.gz | head -n 1)
         twine_output=`twine check "$last_dist"`
         if [[ "$twine_output" != "Checking $last_dist: PASSED" ]]; then echo $twine_output && exit 1;fi
+
     - name: Install dist
       run: |
         last_dist=$(ls -t dist/smac-*.tar.gz | head -n 1)
         pip install $last_dist
+        
     - name: PEP 561 Compliance
       run: |
         pip install mypy

diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
@@ -6,30 +6,36 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v2
+
     - name: Setup Python
       uses: actions/setup-python@v2
       with:
-        python-version: 3.8
+        python-version: 3.9
+
     - name: Install dependencies
       run: |
         pip install -e .[all]
+
     - name: Make docs
       run: |
-        cd doc
+        cd docs
         make buildapi
         make html
+
     - name: Pull latest gh-pages
       if: (contains(github.ref, 'develop') || contains(github.ref, 'master')) && github.event_name == 'push'
       run: |
         cd ..
         git clone https://github.com/automl/SMAC3.git --branch gh-pages --single-branch gh-pages
-    - name: Copy new doc into gh-pages
+
+    - name: Copy new docs into gh-pages
       if: (contains(github.ref, 'develop') || contains(github.ref, 'master')) && github.event_name == 'push'
       run: |
         branch_name=${GITHUB_REF##*/}
         cd ../gh-pages
         rm -rf $branch_name
-        cp -r ../SMAC3/doc/build/html $branch_name
+        cp -r ../SMAC3/docs/html $branch_name
+
     - name: Push to gh-pages
       if: (contains(github.ref, 'develop') || contains(github.ref, 'master')) && github.event_name == 'push'
       run: |

diff --git a/.github/workflows/examples.yml b/.github/workflows/examples.yml
@@ -0,0 +1,25 @@
+name: Examples
+
+on: [push, pull_request]
+
+jobs:
+  ubuntu:
+
+    runs-on: ubuntu-18.04
+    strategy:
+      matrix:
+        python-version: [3.9]
+      fail-fast:  false
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Setup Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Conda Install test dependencies
+      run: |
+        # Miniconda is available in $CONDA env var
+        $CONDA/bin/conda create -n testenv --yes pip wheel gxx_linux-64 gcc_linux-64 swig python=${{ matrix.python-version }}
+        $CONDA/envs/testenv/bin/python3 -m pip install --upgrade pip
+        $CONDA/envs/testenv/bin/pip3 install -e .[all]
diff --git a/.github/workflows/pre-commit.yaml b/.github/workflows/pre-commit.yaml
@@ -7,14 +7,17 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v2
+
     - name: Setup Python 3.7
       uses: actions/setup-python@v2
       with:
         python-version: 3.7
+
     - name: Install pre-commit
       run: |
         pip install pre-commit
         pre-commit install
+        
     - name: Run pre-commit
       run: |
         pre-commit run --all-files
diff --git a/.gitignore b/.gitignore
@@ -15,6 +15,10 @@ dist
 runhistory.json
 target_algo_runs.json
 
+# Example outputs
+examples/*restored
+examples/*restore_me
+
 # Other
 .tox
 .pypirc
@@ -23,18 +27,20 @@ target_algo_runs.json
 *~
 .html/
 .mypy_cache/
+.DS_Store
+docs/html
 
 #eclipse files
 .pydevproject
 .project
 
 # generated by doc
-doc/main_options.rst
-doc/scenario_options.rst
-doc/smac_options.rst
-doc/apidoc
-doc/examples
-doc/quickstart
+docs/main_options*
+docs/scenario_options*
+docs/smac_options*
+docs/html
+docs/apidoc
+docs/pages/examples
 
 # Generated from running Sphinx-Gallery
 *smac3-output_*

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -3,20 +3,10 @@ repos:
     rev: v0.761
     hooks:
       - id: mypy
-        # We would like to have the following options set, 
-        # but for now we have to use the ones above to get started
-        # --ignore-missing-imports --strict"
-        # --disallow-any-unimported"
-        # --disallow-any-expr"
-        # --disallow-any-decorated"
-        # --disallow-any-explicit"
-        # --disallow-any-generics"
-        # Add the following once the scenario is removed from the main code or typed
-        # https://mypy.readthedocs.io/en/stable/command_line.html#configuring-warnings
-        # --warn-unused-ignores"
         args: [--show-error-codes, --ignore-missing-imports, --disallow-untyped-decorators, --disallow-incomplete-defs, --disallow-untyped-defs, --follow-imports, skip]
         name: mypy SMAC
         files: smac/.*
+
   - repo: https://gitlab.com/pycqa/flake8
     rev: 3.8.3
     hooks:

diff --git a/CITATION.cff b/CITATION.cff
@@ -0,0 +1,108 @@
+---
+cff-version: 1.2.0
+
+message: "If you used SMAC in one of your research projects, please cite us:"
+
+title: "SMAC3"
+date-released: "2016-08-17"
+
+url: "https://automl.github.io/SMAC3/master/index.html"
+repository-code: "https://github.com/automl/SMAC3"
+
+version: "1.0.1"
+
+type: "software"
+keywords:
+  - "blackbox optimization"
+  - "optimization"
+  - "bayesian optimization"
+  - "algorithm configuration"
+  - "machine learning"
+  - "algorithms"
+
+license: "BSD-3-Clause"
+
+authors:
+  - family-names: "Lindauer"
+    given-names: "Marius"
+    affiliation: "Leibniz Universität Hannover"
+
+  - family-names: "Eggensperger"
+    given-names: "Katharina" 
+    orcid: "https://orcid.org/0000-0002-0309-401X"
+    affiliation: "University of Freiburg, Germany"
+
+  - family-names: "Feurer"
+    given-names: "Matthias"
+    orcid: "https://orcid.org/0000-0001-9611-8588"
+    affiliation: "University of Freiburg, Germany"
+
+  - family-names: "Biedenkapp"
+    given-names: "André"
+    orcid: "https://orcid.org/0000-0002-8703-8559"
+    affiliation: "University of Freiburg, Germany"
+
+  - family-names: "Deng"
+    given-names: "Difan"
+    affiliation: "Leibniz Universität Hannover"
+
+  - family-names: "Benjamins"
+    given-names: "Carolin"
+    affiliation: "Leibniz Universität Hannover"
+
+  - family-names: "Sass"
+    given-names: "René"
+    affiliation: "Leibniz Universität Hannover"
+
+  - family-names: "Hutter"
+    given-names: "Frank"
+    affiliation: "University of Freiburg, Germany"
+
+  - family-names: "Falkner"
+    given-names: "Stefan"
+    orcid: "https://orcid.org/0000-0002-6303-9418"
+    affiliation: "Bosch Center for Artificial Intelligence, Rennigen, Germany"
+
+preferred-citation:
+  type: "article"
+  title: "SMAC3: A Versatile Bayesian Optimization Package for Hyperparameter Optimization"
+  month: "9"
+  year: "2021"
+  url: "https://arxiv.org/abs/2109.09831"
+
+  authors:
+    - family-names: "Lindauer"
+      given-names: "Marius"
+      affiliation: "Leibniz Universität Hannover"
+
+    - family-names: "Eggensperger"
+      given-names: "Katharina" 
+      orcid: "https://orcid.org/0000-0002-0309-401X"
+      affiliation: "University of Freiburg, Germany"
+
+    - family-names: "Feurer"
+      given-names: "Matthias"
+      orcid: "https://orcid.org/0000-0001-9611-8588"
+      affiliation: "University of Freiburg, Germany"
+
+    - family-names: "Biedenkapp"
+      given-names: "André "
+      orcid: "https://orcid.org/0000-0002-8703-8559"
+      affiliation: "University of Freiburg, Germany"
+
+    - family-names: "Deng"
+      given-names: "Difan"
+      affiliation: "Leibniz Universität Hannover"
+
+    - family-names: "Benjamins"
+      given-names: "Carolin"
+      affiliation: "Leibniz Universität Hannover"
+
+    - family-names: "Sass"
+      given-names: "René"
+      affiliation: "Leibniz Universität Hannover"
+
+    - family-names: "Hutter"
+      given-names: "Frank"
+      affiliation: "University of Freiburg, Germany"
+...
diff --git a/.github/CONTRIBUTING.md → CONTRIBUTING.md b/.github/CONTRIBUTING.md → CONTRIBUTING.md
@@ -1,8 +1,8 @@
-### Contributing to SMAC3
+# Contributing to SMAC3
 
 You are interested in developing a new feature or have found a bug? Awesome, feel welcome and read this guide in order to find out how to best report your ideas so that we can include them as quickly as possible.
 
-### General Notes
+## General Notes
 We are always happy to read about your experiences and ideas on how to improve SMAC3. We use the issue tracker as our main communication platform, so please open an issue to
 
 * report bugs (label as `bug`)
@@ -12,7 +12,7 @@ We are always happy to read about your experiences and ideas on how to improve S
 
 NOTE: Before working on a new feature please first create an issue. If the relevant issue already exists, please  comment that issue to let us know that you are going to work on it. Through that, we can ensure that there is no duplicated effort.
 
-### New Features
+## New Features
 
 If you are looking for feature that does not yet exist in SMAC3, we are happy to hear about it. Open an issue on our [issues list on GitHub](https://github.com/automl/SMAC3/issues), and describe 
 - the feature you would like to see
@@ -21,7 +21,7 @@ If you are looking for feature that does not yet exist in SMAC3, we are happy to
 
 If you already know how to implement the feature, please create a pull request. Please see the [Pull request](#pull-requests) section, to read further details on pull requests.
 
-### <a name="report-bugs"></a> Report Bugs
+## <a name="report-bugs"></a> Report Bugs
 
 Open an issue in our [issue list on GitHub](https://github.com/automl/SMAC3/issues).
 
@@ -37,12 +37,12 @@ If you found a bug, please provide us the following information:
 - Any information about your setup that could be helpful to resolve the bug (such as installed python packages)
 - Feel free, to add a screenshot showing the issue, if it helps.
 
-### Work on New Features
+## Work on New Features
 
 To work on new features, create a fork of the original repository and implement the feature there. When you are happy with the final result you can create a pull request which we will review.
 A good tutorial on how to do this is in the Github Guide: [Fork a repo](https://help.github.com/articles/fork-a-repo/).
 
-### <a name="pull-requests"></a> Pull Requests
+## <a name="pull-requests"></a> Pull Requests
 
 The target branch for your pull request has to be the development branch. If you have not worked with pull requests, please take a look at [how to Contribute to an Open Source Project on GitHub](https://egghead.io/series/how-to-contribute-to-an-open-source-project-on-github) or read more about it in the official github documentation <https://help.github.com/articles/about-pull-requests/>
 
@@ -56,6 +56,6 @@ If you know how to fix a bug or implement your own feature, follow this small gu
 
 We try to react as fast as possible to your pull request.
 
-### Reporting Security Issues
+## Reporting Security Issues
 
 If you find security related issues, vulnerabilities or bugs including sensitive information, please do *not* report this to the issue tracker, or elsewhere public. Instead, please let us know via security@automl.org