Merge dev (#26)

jbussemaker · web-flow · commit 08915b3a386e · 2024-06-20T08:26:28.000+02:00
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -37,8 +37,7 @@ jobs:
         python -m pip install --upgrade pip setuptools
         pip install -r requirements-tests.txt
         pip install -r requirements-assignment.txt
-        pip install -r requirements-hebo.txt
         pip install -e .[arch_sbo,botorch,trieste,tpe,rocket,egor]
 
     - name: Test with pytest
-      run: pytest sb_arch_opt --durations=0
+      run: pytest -v sb_arch_opt --durations=10
diff --git a/.github/workflows/tests_basic.yml b/.github/workflows/tests_basic.yml
@@ -49,4 +49,4 @@ jobs:
       run: echo "${{ steps.license_check_report.outputs.report }}"
 
     - name: Test with pytest
-      run: pytest sb_arch_opt --durations=0
+      run: pytest -v sb_arch_opt --durations=10
diff --git a/.github/workflows/tests_slow.yml b/.github/workflows/tests_slow.yml
@@ -34,7 +34,6 @@ jobs:
         python -m pip install --upgrade pip setuptools
         pip install -r requirements-tests.txt
         pip install -r requirements-assignment.txt
-        pip install -r requirements-hebo.txt
         pip install -r requirements-ota.txt
         pip install -e .[arch_sbo,botorch,trieste,tpe,rocket,egor]
         pip install jupyter ipython ipykernel
@@ -54,4 +53,4 @@ jobs:
       run: echo "${{ steps.license_check_report.outputs.report }}"
 
     - name: Test with pytest
-      run: RUN_SLOW_TESTS=1 pytest sb_arch_opt --durations=0
+      run: RUN_SLOW_TESTS=1 pytest -v sb_arch_opt --durations=20
diff --git a/README.md b/README.md
@@ -1,3 +1,5 @@
+![SBArchOpt Logo](https://github.com/jbussemaker/SBArchOpt/blob/main/docs/logo.svg)
+
 # SBArchOpt: Surrogate-Based Architecture Optimization
 
 [![Tests](https://github.com/jbussemaker/SBArchOpt/workflows/Tests/badge.svg)](https://github.com/jbussemaker/SBArchOpt/actions/workflows/tests.yml?query=workflow%3ATests)
diff --git a/docs/algo/hebo.md b/docs/algo/hebo.md
@@ -12,7 +12,7 @@ Artificial Intelligence Research, 74, pp.1269-1349, DOI: [10.1613/jair.1.13643](
 ## Installation
 
 ```
-pip install -r requirements-hebo.txt
+pip install sb-arch-opt[hebo]
 ```
 
 ## Usage
diff --git a/docs/icon.png b/docs/icon.png
diff --git a/docs/index.md b/docs/index.md
@@ -1,3 +1,5 @@
+![SBArchOpt Logo](logo.svg)
+
 # SBArchOpt: Surrogate-Based Architecture Optimization
 
 SBArchOpt (es-bee-ARK-opt) provides a set of classes and interfaces for applying Surrogate-Based Optimization (SBO)
@@ -25,6 +27,23 @@ The library provides:
   - Connectors to various external SBO libraries
 - Analytical and realistic test problems that exhibit one or more of the architecture optimization challenges
 
+## Installation
+
+First, create a conda environment (skip if you already have one):
+```
+conda create --name opt python=3.9
+conda activate opt
+```
+
+Then install the package:
+```
+conda install numpy
+pip install sb-arch-opt
+```
+
+Note: there are optional dependencies for the connected optimization frameworks and test problems.
+Refer to their documentation for dedicated installation instructions.
+
 ## Citing
 
 If you use SBArchOpt in your work, please cite it:
diff --git a/docs/logo.svg b/docs/logo.svg
diff --git a/docs/overrides/partials/copyright.html b/docs/overrides/partials/copyright.html
@@ -0,0 +1,8 @@
+<div class="md-copyright">
+    <p><img src="{{ 'logo.svg' | url }}" alt="logo" style="height: 50px" /></p>
+  {% if config.copyright %}
+    <div class="md-copyright__highlight">
+      {{ config.copyright }}
+    </div>
+  {% endif %}
+</div>
diff --git a/docs/style.css b/docs/style.css
@@ -0,0 +1,3 @@
+:root {
+  --md-primary-fg-color: #330a5e;
+}
diff --git a/docs/tutorial.ipynb b/docs/tutorial.ipynb
diff --git a/mkdocs.yml b/mkdocs.yml
@@ -2,10 +2,19 @@ site_name: SBArchOpt
 site_url: https://sbarchopt.readthedocs.io/
 repo_url: https://github.com/jbussemaker/SBArchOpt
 docs_dir: docs
+copyright: © 2024, Deutsches Zentrum für Luft- und Raumfahrt e.V.
 theme:
   name: material
+  logo: icon.png
+  favicon: icon.png
+  palette:
+    scheme: default
+    primary: custom
   features:
     - navigation.tabs
+  custom_dir: docs/overrides
+extra_css:
+  - style.css
 
 nav:
   - 'Overview': index.md
diff --git a/requirements-hebo.txt b/requirements-hebo.txt
diff --git a/sb_arch_opt/__init__.py b/sb_arch_opt/__init__.py
@@ -1 +1 @@
-__version__ = '1.5.1'
+__version__ = '1.5.2'
diff --git a/sb_arch_opt/algo/pymoo_interface/storage_restart.py b/sb_arch_opt/algo/pymoo_interface/storage_restart.py
@@ -206,6 +206,10 @@ def initialize_cumulative(self, cumulative_pop: Population):
         self._cumulative_pop = cumulative_pop
         self.n_eval = len(self._get_idx_evaluated(cumulative_pop))
 
+    @property
+    def cumulative_pop(self) -> Optional[Population]:
+        return self._cumulative_pop
+
     def eval(self, problem, pop: Population, skip_already_evaluated: bool = None, evaluate_values_of: list = None,
              count_evals: bool = True, **kwargs):
 
@@ -249,6 +253,7 @@ def eval_post(self, problem, pop, advance_n_eval=True, evaluate_values_of: list
         self._apply_extreme_barrier(pop, evaluate_values_of=evaluate_values_of)
 
         # Post-evaluation storage
+        self._update_cumulative_pop(pop)
         if self.results_folder is not None:
             self._store_intermediate(problem, pop)
         self._non_eval_cumulative_pop = None
@@ -304,6 +309,7 @@ def eval_batch_post(self, problem, pop: Population, batch_pop: Population, evalu
         self._apply_extreme_barrier(batch_pop, evaluate_values_of=evaluate_values_of)
         intermediate_pop = self._normalize_pop(pop, evaluate_values_of, evaluated_pop=self._evaluated_pop)
 
+        self._update_cumulative_pop(intermediate_pop)
         if self.results_folder is not None:
             self._store_intermediate(problem, intermediate_pop)
         return intermediate_pop
@@ -348,16 +354,18 @@ def _normalize_pop(pop: Population, evaluate_values_of, evaluated_pop: Populatio
             normalized_pop = Population.merge(evaluated_pop, normalized_pop)
         return normalized_pop
 
-    def _store_intermediate(self, problem, pop: Population):
-        # Store pymoo population
-        self.store_pop(pop)
-
-        # Store cumulative pymoo population
+    def _update_cumulative_pop(self, pop: Population):
         if self._non_eval_cumulative_pop is not None:
             unique_non_eval_pop = LargeDuplicateElimination().do(self._non_eval_cumulative_pop, pop, to_itself=False)
             self._cumulative_pop = Population.merge(unique_non_eval_pop, pop)
         else:
             self._cumulative_pop = pop
+
+    def _store_intermediate(self, problem, pop: Population):
+        # Store pymoo population
+        self.store_pop(pop)
+
+        # Store cumulative pymoo population
         self.store_pop(self._cumulative_pop, cumulative=True)
 
         # Store problem-specific results
diff --git a/sb_arch_opt/tests/algo/test_hebo.py b/sb_arch_opt/tests/algo/test_hebo.py
@@ -10,9 +10,9 @@ def check_dependency():
     return pytest.mark.skipif(not HAS_HEBO, reason='HEBO dependencies not installed')
 
 
-@pytest.mark.skipif(int(os.getenv('RUN_SLOW_TESTS', 0)) != 1, reason='Set RUN_SLOW_TESTS=1 to run slow tests')
-def test_slow_tests():
-    assert HAS_HEBO
+# @pytest.mark.skipif(int(os.getenv('RUN_SLOW_TESTS', 0)) != 1, reason='Set RUN_SLOW_TESTS=1 to run slow tests')
+# def test_slow_tests():
+#     assert HAS_HEBO
 
 
 @check_dependency()
diff --git a/sb_arch_opt/tests/test_tutorials.py b/sb_arch_opt/tests/test_tutorials.py
@@ -1,15 +1,30 @@
 import os
 import pytest
 import testbook
+from testbook.client import TestbookNotebookClient
 
 _docs_path = f'{os.path.dirname(__file__)}/../../docs'
 _t = 60*20
 
 
 @pytest.mark.skipif(int(os.getenv('RUN_SLOW_TESTS', 0)) != 1, reason='Set RUN_SLOW_TESTS=1 to run slow tests')
-@testbook.testbook(f'{_docs_path}/tutorial.ipynb', execute=True, timeout=_t)
-def test_tutorial(tb):
-    pass
+@testbook.testbook(f'{_docs_path}/tutorial.ipynb', execute=False, timeout=_t)
+def test_tutorial(tb: TestbookNotebookClient):
+    code_cells = []
+    for cell in tb.cells:
+        if cell.cell_type == 'code':
+            code_cells.append(cell)
+
+    # Set less infills to reduce testing time
+    sbo_example_cell = code_cells[1]
+    code = sbo_example_cell.source.split('\n')
+    for i, line in enumerate(code):
+        if line.startswith('n_infill'):
+            code[i] = 'n_infill = 2'
+            break
+    sbo_example_cell.source = '\n'.join(code)
+
+    tb.execute()
 
 
 @pytest.mark.skipif(int(os.getenv('RUN_SLOW_TESTS', 0)) != 1, reason='Set RUN_SLOW_TESTS=1 to run slow tests')
diff --git a/setup.py b/setup.py
@@ -51,7 +51,7 @@ def _get_readme():
         ],
         license='MIT',
         install_requires=[
-            'numpy',
+            'numpy<2.0',
             'pymoo~=0.6.1',
             'scipy',
             'deprecated',
@@ -85,9 +85,9 @@ def _get_readme():
             'tpe': [
                 'tpe==0.0.8',
             ],
-            # 'hebo': [  # pip install -r requirements-hebo.txt
-            #     'HEBO',  # Disabled until commit f050865fd2f554b5ca94642667257b365c753f29 has been released on PyPI
-            # ],
+            'hebo': [
+                'HEBO',
+            ],
             'rocket': [
                 'ambiance',
             ],

Original file line number	Diff line number	Diff line change
`@@ -1,3 +1,5 @@`
	`1`	`+![SBArchOpt Logo](https://github.com/jbussemaker/SBArchOpt/blob/main/docs/logo.svg)`
	`2`	`+`
`1`	`3`	`# SBArchOpt: Surrogate-Based Architecture Optimization`
`2`	`4`
`3`	`5`	`[![Tests](https://github.com/jbussemaker/SBArchOpt/workflows/Tests/badge.svg)](https://github.com/jbussemaker/SBArchOpt/actions/workflows/tests.yml?query=workflow%3ATests)`
Original file line number	Diff line number	Diff line change
`@@ -0,0 +1,3 @@`
	`1`	`+:root {`
	`2`	`+ --md-primary-fg-color: #330a5e;`
	`3`	`+}`