Merge pull request #526 from automl/development

Release SMAC 0.11
automl · Aug 14, 2019 · 81eba54 · 81eba54
2 parents b5c3986 + aef02f3
commit 81eba54
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Showing 163 changed files with 4,983 additions and 3,264 deletions.
diff --git a/.gitignore b/.gitignore
@@ -32,3 +32,4 @@ target_algo_runs.json
 doc/main_options.rst
 doc/scenario_options.rst
 doc/smac_options.rst
+doc/apidoc
diff --git a/.travis.yml b/.travis.yml
@@ -60,7 +60,7 @@ before_install:
 install:
   - pip install pep8 codecov mypy flake8
   - cat requirements.txt | xargs -n 1 -L 1 pip install
-  - python setup.py install
+  - pip install .[all]
 
 script:
   - ci_scripts/$TESTSUITE

diff --git a/MANIFEST.in b/MANIFEST.in
@@ -1 +1,2 @@
-include requirements.txt
+include requirements.txt
+include extras_require.json
diff --git a/README.md b/README.md
@@ -54,7 +54,7 @@ used in SMAC3 requires SWIG (>= 3.0).
 
 ## Installation via pip
 
-SMAC3 is available on pipy.
+SMAC3 is available on PyPI.
 
 ```pip install smac```
 
@@ -63,7 +63,7 @@ SMAC3 is available on pipy.
 ```
 git clone https://github.com/automl/SMAC3.git && cd SMAC3
 cat requirements.txt | xargs -n 1 -L 1 pip install
-python setup.py install
+pip install .
 ```
 
 ## Installation in Anaconda
@@ -73,6 +73,29 @@ packages **before** you can install SMAC:
 
 ```conda install gxx_linux-64 gcc_linux-64 swig```
 
+## Optional dependencies
+
+SMAC3 comes with a set of optional dependencies that can be installed using
+[setuptools extras](https://setuptools.readthedocs.io/en/latest/setuptools.html#declaring-extras-optional-features-with-their-own-dependencies):
+
+- `lhd`: Latin hypercube design
+- `gp`: Gaussian process models
+
+These can be installed from PyPI or manually:
+
+```
+# from PyPI
+pip install smac[gp]
+
+# manually
+pip install .[gp,lhd]
+```
+
+For convenience there is also an `all` meta-dependency that installs all optional dependencies:
+```
+pip install smac[all]
+```
+
 # License
 
 This program is free software: you can redistribute it and/or modify

diff --git a/changelog.md b/changelog.md
@@ -1,3 +1,30 @@
+# 0.11.0
+
+## Major changes
+
+* Local search now starts from observed configurations with high acquisition function values, low cost and the from 
+  unobserved configurations with high acquisition function values found by random search (#509)
+* Reduces the number of mandatory requirements (#516)
+* Make Gaussian processes more resilient to linalg error by more aggressively adding noise to the diagonal (#511)
+* Inactive hyperparameters are now imputed with a value outside of the modeled range (-1) (#508)
+* Replace the GP library George by scikit-learn (#505)
+* Renames facades to better reflect their use cases (#492), and adds a table to help deciding which facade to use (#495)
+* SMAC facades now accept class arguments instead of object arguments (#486)
+
+## Minor changes
+
+* Vectorize local search for improved speed (#500)
+* Extend the Sobol and LHD initial design to work for non-continuous hyperparameters as well applying an idea similar
+  to inverse transform sampling (#494)
+
+
+## Bug fixes
+
+* Fixes a regression in the validation scripts (#519)
+* Fixes a unit test regression with numpy 1.17 (#523)
+* Fixes an error message (#510)
+* Fixes an error making random search behave identical for all seeds
+
 # 0.10.0
 
 ## Major changes

diff --git a/ci_scripts/circle_install.sh b/ci_scripts/circle_install.sh
@@ -8,12 +8,9 @@ source activate testenv
 
 # install documentation building dependencies
 pip install --upgrade numpy
-pip install --upgrade matplotlib setuptools nose coverage sphinx pillow sphinx-gallery sphinx_bootstrap_theme cython numpydoc
-# And finally, all other dependencies
-cat requirements.txt | xargs -n 1 -L 1 pip install
+pip install --upgrade matplotlib setuptools nose coverage sphinx pillow sphinx-gallery sphinx_bootstrap_theme numpydoc
 
-python setup.py clean
-python setup.py develop
+pip install -e .[all]
 
 # pipefail is necessary to propagate exit codes
 set -o pipefail && cd doc && make html 2>&1 | tee ~/log.txt
diff --git a/ci_scripts/create_doc.sh b/ci_scripts/create_doc.sh
@@ -9,7 +9,7 @@ if ! [[ -z ${DOCPUSH+x} ]]; then
     if [[ "$DOCPUSH" == "true" ]]; then
 
         # install documentation building dependencies
-        pip install --upgrade matplotlib seaborn setuptools nose coverage sphinx pillow sphinx-gallery sphinx_bootstrap_theme cython numpydoc nbformat nbconvert mock
+        pip install --upgrade sphinx_rtd_theme
 
         # $1 is the branch name
         # $2 is the global variable where we set the script status
@@ -20,7 +20,7 @@ if ! [[ -z ${DOCPUSH+x} ]]; then
         fi
 
         # create the documentation
-        cd doc && make html 2>&1
+        cd doc && make buildapi && make html 2>&1
 
         # create directory with branch name
         # the documentation for dev/stable from git will be stored here

diff --git a/ci_scripts/run_examples.sh b/ci_scripts/run_examples.sh
@@ -1,6 +1,6 @@
 cd examples
 
-for script in rf.py rosenbrock.py svm.py
+for script in fmin_rosenbrock.py SMAC4BO_rosenbrock.py SMAC4HPO_acq_rosenbrock.py SMAC4HPO_rf.py SMAC4HPO_rosenbrock.py SMAC4HPO_svm.py
 do
     python $script
     rval=$?
@@ -17,3 +17,19 @@ if [ "$rval" != 0 ]; then
     echo "Error running example QCP"
     exit $rval
 fi
+cd ..
+
+cd branin
+python branin_fmin.py
+rval=$?
+if [ "$rval" != 0 ]; then
+    echo "Error running example QCP"
+    exit $rval
+fi
+
+python ../../scripts/smac --scenario scenario.txt
+rval=$?
+if [ "$rval" != 0 ]; then
+    echo "Error running example QCP"
+    exit $rval
+fi
diff --git a/ci_scripts/run_unittests.sh b/ci_scripts/run_unittests.sh
@@ -1,2 +1,4 @@
 echo Testing revision $(git rev-parse HEAD) ...
-make test && bash scripts/test_no_files_left.sh
+echo Testing from directory `pwd`
+conda list
+make test && bash scripts/test_no_files_left.sh
diff --git a/doc/apidoc/smac.configspace.rst b/doc/apidoc/smac.configspace.rst
diff --git a/doc/apidoc/smac.configspace.util.rst b/doc/apidoc/smac.configspace.util.rst
diff --git a/doc/apidoc/smac.epm.base_epm.rst b/doc/apidoc/smac.epm.base_epm.rst
diff --git a/doc/apidoc/smac.epm.base_imputor.rst b/doc/apidoc/smac.epm.base_imputor.rst
diff --git a/doc/apidoc/smac.epm.random_epm.rst b/doc/apidoc/smac.epm.random_epm.rst
diff --git a/doc/apidoc/smac.epm.rf_with_instances.rst b/doc/apidoc/smac.epm.rf_with_instances.rst
diff --git a/doc/apidoc/smac.epm.rfr_imputator.rst b/doc/apidoc/smac.epm.rfr_imputator.rst
diff --git a/doc/apidoc/smac.epm.rst b/doc/apidoc/smac.epm.rst
diff --git a/doc/apidoc/smac.epm.uncorrelated_mo_rf_with_instances.rst b/doc/apidoc/smac.epm.uncorrelated_mo_rf_with_instances.rst
diff --git a/doc/apidoc/smac.facade.epils_facade.rst b/doc/apidoc/smac.facade.epils_facade.rst
diff --git a/doc/apidoc/smac.facade.func_facade.rst b/doc/apidoc/smac.facade.func_facade.rst
diff --git a/doc/apidoc/smac.facade.roar_facade.rst b/doc/apidoc/smac.facade.roar_facade.rst
diff --git a/doc/apidoc/smac.facade.rst b/doc/apidoc/smac.facade.rst
diff --git a/doc/apidoc/smac.facade.smac_facade.rst b/doc/apidoc/smac.facade.smac_facade.rst
diff --git a/doc/apidoc/smac.initial_design.default_configuration_design.rst b/doc/apidoc/smac.initial_design.default_configuration_design.rst
diff --git a/doc/apidoc/smac.initial_design.initial_design.rst b/doc/apidoc/smac.initial_design.initial_design.rst
diff --git a/doc/apidoc/smac.initial_design.multi_config_initial_design.rst b/doc/apidoc/smac.initial_design.multi_config_initial_design.rst
diff --git a/doc/apidoc/smac.initial_design.random_configuration_design.rst b/doc/apidoc/smac.initial_design.random_configuration_design.rst
diff --git a/doc/apidoc/smac.initial_design.rst b/doc/apidoc/smac.initial_design.rst
diff --git a/doc/apidoc/smac.initial_design.single_config_initial_design.rst b/doc/apidoc/smac.initial_design.single_config_initial_design.rst
diff --git a/doc/apidoc/smac.intensification.intensification.rst b/doc/apidoc/smac.intensification.intensification.rst