fix: Memory leak (#282)

* test: Add reproducing test

* fix: Make sampling neighbors form uniform Int stable

* fix: Memory leak with UniformIntegerHyperparameter

When querying a large range for a UniformIntegerHyperparameter with a
small std.deviation and log scale, this could cause an infinite loop as
the reachable neighbors would be quickly exhausted, yet rejection
sampling will continue sampling until some arbitrary termination
criterion. Why this was causing a memory leak, I'm not entirely sure.

The solution now is that is we have seen a sampled value before, we
simply take the one "next to it".

* fix: Memory issues with Normal and Beta dists

Replaced usages of arange with a chunked version to prevent memory
blowup. However this is still incredibly slow and needs a more refined
solution as a huge amount of values are required to be computed for what
can possibly be analytically derived.

* chore: Update flake8

* fix: flake8 version compatible with Python 3.7

* fix: Name generators properly

* fix: Test numbers

* doc: typo fixes

* perf: Generate all possible neighbors at once

* test: Add test for center_range and arange_chunked

* perf: Call transform on np vector from rvs

* perf: Use numpy `.astype(int)` instead of `int`

* doc: Document how to get flamegraphs for optimizing

* fix: Allow for negatives in arange_chunked again

* fix: Change build back to raw Extensions

* build: Properly set compiler_directives

* ci: Update makefile with helpful commands

* ci: Fix docs to install build

* perf: cython optimizations

* perf: Fix possible memory leak with UniformIntegerHyperparam

* fix: Duplicates as `list` instead of set

* fix: Convert to `long long` vector

* perf: Revert clip to truncnorm

This truncnorm has some slight overhead due to however
scipy generates its truncnorm distribution, however this
overhead is considered worth it for the sake of readability
and understanding

* test: Test values not match implementation

* Intermediate commit

* INtermediate commit 2

* Update neighborhood generation for UniformIntegerHyperparameter

* Update tests

* Make the benchmark sampling script more robust

* Revert small change in util function

* Improve readability

Co-authored-by: Matthias Feurer <[email protected]>

Author: eddiebergman

.github/workflows/docs.yml

@@ -36,6 +36,7 @@ jobs:
 
     - name: Install dependencies
       run: |
+        pip install build
         pip install ".[dev]"
 
     - name: Make docs

.github/workflows/pytest.yml

@@ -159,9 +159,9 @@ jobs:
     - name: Create sdist
       id: sdist
       run: |
-        python -m pip install --upgrade pip
-        python setup.py sdist
-        echo "sdist_name=$(ls -t dist/${{ env.package-name }}-*.tar.gz | head -n 1)" >> $GITHUB_ENV
+        python -m pip install --upgrade pip build
+        python -m build --sdist
+        echo "sdist_name=$(ls -t dist/${{ env.package-name }}-*.tar.gz | head -n 1)" >> "$GITHUB_ENV"
 
     - name: Install ${{ env.package-name }}
       run: |

.github/workflows/release.yml

@@ -184,9 +184,9 @@ jobs:
 
       - name: Build source distribution
         run: |
-          python -m pip install --upgrade pip
-          python setup.py sdist
-          echo "sdist_name=$(ls -t dist/${{ env.package-name }}-*.tar.gz | head -n 1)" >> $GITHUB_ENV
+          python -m pip install --upgrade pip build
+          python build --sdist
+          echo "sdist_name=$(ls -t dist/${{ env.package-name }}-*.tar.gz | head -n 1)" >> "$GITHUB_ENV"
 
       - name: Twine check ${{ env.package-name }}
         run: |

.pre-commit-config.yaml

@@ -7,8 +7,8 @@ repos:
         name: mypy ConfigSpace
         files: ConfigSpace
 
-  - repo: https://gitlab.com/pycqa/flake8
-    rev: 4.0.1
+  - repo: https://github.com/pycqa/flake8
+    rev: 5.0.4
     hooks:
       - id: flake8
         name: flake8 ConfigSpace

ConfigSpace/__init__.py

@@ -29,8 +29,6 @@
 from ConfigSpace.__version__ import __version__
 from ConfigSpace.__authors__ import __authors__
 
-import ConfigSpace.api.distributions as distributions
-import ConfigSpace.api.types as types
 from ConfigSpace.api import (Beta, Categorical, Distribution, Float, Integer,
                              Normal, Uniform)
 from ConfigSpace.conditions import (AndConjunction, EqualsCondition,
@@ -53,6 +51,8 @@
                                          UniformFloatHyperparameter,
                                          UniformIntegerHyperparameter,
                                          UnParametrizedHyperparameter)
+import ConfigSpace.api.distributions as distributions
+import ConfigSpace.api.types as types
 
 __all__ = [
     "__authors__",

ConfigSpace/c_util.pyx

@@ -1,5 +1,3 @@
-# cython: language_level=3
-
 from collections import deque
 
 import numpy as np

ConfigSpace/conditions.pxd

@@ -1,5 +1,3 @@
-# cython: language_level=3
-
 import numpy as np
 cimport numpy as np
 

ConfigSpace/conditions.pyx

@@ -26,8 +26,6 @@
 # (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
 # SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
-# cython: language_level=3
-
 import io
 from functools import reduce
 from abc import ABCMeta, abstractmethod

ConfigSpace/configuration_space.pyx

@@ -26,8 +26,6 @@
 # (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
 # SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
-# cython: language_level=3
-
 import collections.abc
 from collections import defaultdict, deque, OrderedDict
 import copy

ConfigSpace/forbidden.pxd

@@ -1,5 +1,3 @@
-# cython: language_level=3
-
 import numpy as np
 cimport numpy as np