xopt 2.3.0__tar.gz → 2.4.2__tar.gz

xopt-2.4.2/.flake8

@@ -0,0 +1,11 @@
+[flake8]
+extend-ignore = E203
+exclude =
+    .git,
+    __pycache__,
+    build,
+    dist,
+    versioneer.py,
+    xopt/_version.py
+    .ipynb_checkpoints
+max-line-length = 115

xopt-2.4.2/.pre-commit-config.yaml

@@ -0,0 +1,36 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks.git
+    rev: v4.6.0
+    hooks:
+      - id: no-commit-to-branch
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-ast
+      - id: check-case-conflict
+      - id: check-json
+      - id: check-merge-conflict
+      - id: check-symlinks
+      - id: check-xml
+      - id: check-yaml
+        exclude: "^(python/versioneer.py|python/xopt/_version.py)$"
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.5.0
+    hooks:
+      - id: ruff
+        args: [--fix]
+        types_or: [python, pyi, jupyter]
+      - id: ruff-format
+        types_or: [python, pyi, jupyter]
+
+  - repo: local
+    hooks:
+      - id: jupyter-notebook-clear-output
+        name: jupyter-notebook-jupyter-clear
+        files: \.ipynb$
+        stages: [commit]
+        language: system
+        entry: jupyter nbconvert --ClearOutputPreprocessor.enabled=True --inplace
+        exclude: "^.*(TODO|TODO2).ipynb$"

xopt-2.4.2/MANIFEST.in

@@ -0,0 +1 @@
+include LICENSE

xopt-2.4.2/PKG-INFO

@@ -0,0 +1,496 @@
+Metadata-Version: 2.1
+Name: xopt
+Version: 2.4.2
+Summary: Flexible optimization of arbitrary problems in Python.
+Author: Christopher Mayes, Ryan Roussel
+License:                                  Apache License
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+Project-URL: Homepage, https://github.com/xopt-org/xopt
+Classifier: Development Status :: 4 - Beta
+Classifier: Natural Language :: English
+Classifier: Programming Language :: Python :: 3
+Classifier: Topic :: Scientific/Engineering
+Requires-Python: >=3.9
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+Requires-Dist: botorch<=0.10.0,>=0.9.2
+Requires-Dist: scipy>=1.10.1
+Requires-Dist: pandas
+Requires-Dist: ipywidgets
+Requires-Dist: tqdm
+Requires-Dist: orjson
+Requires-Dist: matplotlib
+Provides-Extra: dev
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: pytest-cov; extra == "dev"
+Requires-Dist: ffmpeg; extra == "dev"
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: pytest-cov; extra == "dev"
+Requires-Dist: jupyterlab>=3; extra == "dev"
+Requires-Dist: jupyterlab-lsp; extra == "dev"
+Requires-Dist: python-lsp-server; extra == "dev"
+Requires-Dist: pygments; extra == "dev"
+Requires-Dist: dask; extra == "dev"
+Requires-Dist: mpi4py; extra == "dev"
+Provides-Extra: doc
+Requires-Dist: mkdocs; extra == "doc"
+Requires-Dist: mkdocs-jupyter; extra == "doc"
+Requires-Dist: mkdocs-macros-plugin; extra == "doc"
+Requires-Dist: mkdocs-material; extra == "doc"
+Requires-Dist: mkdocstrings; extra == "doc"
+Requires-Dist: mkdocstrings-python; extra == "doc"
+
+<div align="center">
+  <img src="docs/assets/Xopt-logo.png", width="200">
+</div>
+
+
+
+
+Xopt
+====
+
+
+| **`Documentation`**                                                                                                              |
+|----------------------------------------------------------------------------------------------------------------------------------|
+| [![Documentation](https://img.shields.io/badge/Xopt-documentation-blue.svg)](https://xopt-org.github.io/Xopt/index.html) |
+
+| Name | Downloads | Version | Platforms |
+| --- | --- | --- | --- |
+| [![Conda Recipe](https://img.shields.io/badge/recipe-xopt-green.svg)](https://anaconda.org/conda-forge/xopt) | [![Conda Downloads](https://img.shields.io/conda/dn/conda-forge/xopt.svg)](https://anaconda.org/conda-forge/xopt) | [![Conda Version](https://img.shields.io/conda/vn/conda-forge/xopt.svg)](https://anaconda.org/conda-forge/xopt) | [![Conda Platforms](https://img.shields.io/conda/pn/conda-forge/xopt.svg)](https://anaconda.org/conda-forge/xopt) |
+
+
+
+
+Flexible optimization of arbitrary problems in Python.
+
+The goal of this package is to provide advanced algorithmic support for arbitrary
+optimization problems (simulations/control systems) with minimal required coding. Users
+can easily connect
+arbitrary evaluation functions to advanced algorithms with minimal coding with
+support for multi-threaded or MPI-enabled execution.
+
+Currenty **Xopt** provides:
+
+- Optimization algorithms:
+  - Genetic algorithms
+    - `cnsga` Continuous NSGA-II with constraints
+  - Bayesian optimization (BO) algorithms:
+    - `upper_confidence_bound` BO using Upper Confidence Bound acquisition function
+      (w/ or w/o constraints, serial or parallel)
+    - `expected_improvement` BO using Expected Improvement acquisition function
+      (w/ or w/o constraints, serial or parallel)
+    - `mobo` Multi-objective BO (w/ or w/o constraints, serial or parallel)
+    - `bayesian_exploration` Autonomous function characterization using Bayesian
+      Exploration
+    - `mggpo` Parallelized hybrid Multi-Generation Multi-Objective Bayesian
+      optimization
+    - `multi_fidelity` Multi-fidelity single or multi objective optimization
+    - `BAX` Bayesian algorithm execution using virtual measurements
+    - BO customization:
+      - Trust region BO
+      - Heteroskedastic noise specification
+      - Multiple acquisition function optimization stratigies
+  - `extremum_seeking` Extremum seeking time-dependent optimization
+  - `rcds` Robust Conjugate Direction Search (RCDS)
+  - `neldermead` Nelder-Mead Simplex
+- Sampling algorithms:
+  - `random` Uniform random sampling
+- Convenient YAML/JSON based input format
+- Driver programs:
+  - `xopt.mpi.run` Parallel MPI execution using this input format
+
+Xopt does **not** provide:
+- your custom simulation or experimental measurement via an `evaluate` function.
+
+
+Installing Xopt
+===============
+
+Installing `xopt` from the `conda-forge` channel can be achieved by adding `conda-forge` to your channels with:
+
+```shell
+conda config --add channels conda-forge
+```
+
+Once the `conda-forge` channel has been enabled, `xopt` can be installed with:
+
+```shell
+conda install xopt
+```
+
+It is possible to list all of the versions of `xopt` available on your platform with:
+
+```shell
+conda search xopt --channel conda-forge
+```
+
+
+Configuring an Xopt run
+===============
+Xopt runs can be specified via a YAML file or dictonary input. This requires `generator`, `evaluator`, and `vocs` to be specified, along with optional general options such as `max_evaluations`. An example to run a multi-objective optimiation of a user-defined function `my_function` is:
+```yaml
+generator:
+    name: cnsga
+    population_size: 64
+    population_file: test.csv
+    output_path: .
+
+evaluator:
+    function: my_function
+    function_kwargs:
+      my_arguments: 42
+
+vocs:
+    variables:
+        x1: [0, 3.14159]
+        x2: [0, 3.14159]
+    objectives:
+        y1: MINIMIZE
+        y2: MINIMIZE
+    constraints:
+        c1: [GREATER_THAN, 0]
+        c2: [LESS_THAN, 0.5]
+    constants: {a: dummy_constant}
+
+max_evaluations: 6400
+```
+
+Xopt can also be used through a simple Python interface.
+```python
+import math
+
+from xopt.vocs import VOCS
+from xopt.evaluator import Evaluator
+from xopt.generators.bayesian import UpperConfidenceBoundGenerator
+from xopt import Xopt
+
+# define variables and function objectives
+vocs = VOCS(
+    variables={"x": [0, 2 * math.pi]},
+    objectives={"f": "MINIMIZE"},
+)
+
+# define the function to optimize
+def sin_function(input_dict):
+    return {"f": math.sin(input_dict["x"])}
+
+# create Xopt evaluator, generator, and Xopt objects
+evaluator = Evaluator(function=sin_function)
+generator = UpperConfidenceBoundGenerator(vocs=vocs)
+X = Xopt(evaluator=evaluator, generator=generator, vocs=vocs)
+
+# call X.random_evaluate() to generate + evaluate 3 initial points
+X.random_evaluate(3)
+
+# run optimization for 10 steps
+for i in range(10):
+    X.step()
+
+# view collected data
+print(X.data)
+```
+
+Defining an evaluation function
+===============
+Xopt can interface with arbitrary evaluate functions (defined in Python) with the
+following form:
+```python
+def evaluate(inputs: dict) -> dict:
+    """ your code here """
+```
+Evaluate functions must accept a dictionary object that **at least** has the keys
+specified in `variables, constants` and returns a dictionary
+containing **at least** the
+keys contained in `objectives, constraints`. Extra dictionary keys are tracked and
+used in the evaluate function but are not modified by xopt.
+
+Using MPI
+===============
+Example MPI run, with `xopt.yaml` as the only user-defined file:
+```b
+mpirun -n 64 python -m mpi4py.futures -m xopt.mpi.run xopt.yaml
+```
+
+
+Citing Xopt
+==========
+If you use ```Xopt``` for your research, please consider adding the following
+citation to your publications.
+```
+R. Roussel., et al., "Xopt: A simplified framework for optimization of accelerator problems using advanced algorithms",
+in Proc. IPAC'23, Venezia.doi:https://doi.org/10.18429/JACoW-14th International Particle Accelerator Conference-THPL164
+```
+
+BibTex entry:
+```bibtex
+@inproceedings{Xopt,
+	title        = {Xopt: A simplified framework for optimization of accelerator problems using advanced algorithms},
+	author       = {R. Roussel and A. Edelen and A. Bartnik and C. Mayes},
+	year         = 2023,
+	month        = {05},
+	booktitle    = {Proc. IPAC'23},
+	publisher    = {JACoW Publishing, Geneva, Switzerland},
+	series       = {IPAC'23 - 14th International Particle Accelerator Conference},
+	number       = 14,
+	pages        = {4796--4799},
+	doi          = {doi:10.18429/jacow-ipac2023-thpl164},
+	isbn         = {978-3-95450-231-8},
+	issn         = {2673-5490},
+	url          = {https://indico.jacow.org/event/41/contributions/2556},
+	paper        = {THPL164},
+	venue        = {Venezia},
+	language     = {english}
+}
+```
+
+Particular versions of Xopt can be cited from [Zenodo](https://zenodo.org/record/7983779)
+
+
+Developers
+==========
+
+Clone this repository with a truncated git history (recommended):
+```shell
+git clone --depth=1 https://github.com/xopt-org/xopt.git
+```
+
+Or, clone this repository with the full git history (> 970 MB):
+```shell
+git clone https://github.com/xopt-org/xopt.git
+```
+
+Create an environment `xopt-dev` with all the dependencies:
+```shell
+conda env create -f environment.yml
+```
+
+
+Install as editable:
+```shell
+conda activate xopt-dev
+pip install --no-dependencies -e .
+```
+
+Install pre-commit hooks:
+```
+pre-commit install
+```
+
+The pre-commit hooks perform autoformatting and report style-compliance errors.
+* [ufmt](https://pypi.org/project/ufmt/) formats files w.r.t. [black](https://github.com/psf/black) a strict style enforcer, and [μsort](https://usort.readthedocs.io/en/stable/), which sorts imports in Python modules.
+* [flake8](https://flake8.pycqa.org/en/latest/) confirms compliance. Occasionally black misses long-line comments/docstrings and they require manual format.
+
+Pre-commit runs the hooks against your files. If the commit fails, correct the reported errors and then re-add the file with `git add my_file.py`.
+
+### VSCode
+The source control integration packaged with VSCode requires additional configuration. Git commands are run in the integrated terminal, which does not inherit the Python interpreter configured with the VSCode project thus breaking the pre-commit hooks. The integration terminal can be configured to use the conda Python environment by including a `.env` file in your project repository:
+
+```
+#!/usr/bin/bash
+source /path/to/xopt-dev/bin/activate
+```

{xopt-2.3.0 → xopt-2.4.2}/README.md

@@ -11,7 +11,7 @@ Xopt
 
 | **`Documentation`**                                                                                                              |
 |----------------------------------------------------------------------------------------------------------------------------------|
-| [![Documentation](https://img.shields.io/badge/Xopt-documentation-blue.svg)](https://ChristopherMayes.github.io/Xopt/index.html) |
+| [![Documentation](https://img.shields.io/badge/Xopt-documentation-blue.svg)](https://xopt-org.github.io/Xopt/index.html) |
 
 | Name | Downloads | Version | Platforms |
 | --- | --- | --- | --- |
@@ -22,10 +22,10 @@ Xopt
 
 Flexible optimization of arbitrary problems in Python.
 
-The goal of this package is to provide advanced algorithmic support for arbitrary 
-optimization problems (simulations/control systems) with minimal required coding. Users 
-can easily connect 
-arbitrary evaluation functions to advanced algorithms with minimal coding with 
+The goal of this package is to provide advanced algorithmic support for arbitrary
+optimization problems (simulations/control systems) with minimal required coding. Users
+can easily connect
+arbitrary evaluation functions to advanced algorithms with minimal coding with
 support for multi-threaded or MPI-enabled execution.
 
 Currenty **Xopt** provides:
@@ -34,14 +34,14 @@ Currenty **Xopt** provides:
   - Genetic algorithms
     - `cnsga` Continuous NSGA-II with constraints
   - Bayesian optimization (BO) algorithms:
-    - `upper_confidence_bound` BO using Upper Confidence Bound acquisition function 
+    - `upper_confidence_bound` BO using Upper Confidence Bound acquisition function
       (w/ or w/o constraints, serial or parallel)
-    - `expected_improvement` BO using Expected Improvement acquisition function 
+    - `expected_improvement` BO using Expected Improvement acquisition function
       (w/ or w/o constraints, serial or parallel)
     - `mobo` Multi-objective BO (w/ or w/o constraints, serial or parallel)
-    - `bayesian_exploration` Autonomous function characterization using Bayesian 
+    - `bayesian_exploration` Autonomous function characterization using Bayesian
       Exploration
-    - `mggpo` Parallelized hybrid Multi-Generation Multi-Objective Bayesian 
+    - `mggpo` Parallelized hybrid Multi-Generation Multi-Objective Bayesian
       optimization
     - `multi_fidelity` Multi-fidelity single or multi objective optimization
     - `BAX` Bayesian algorithm execution using virtual measurements
@@ -58,7 +58,7 @@ Currenty **Xopt** provides:
 - Driver programs:
   - `xopt.mpi.run` Parallel MPI execution using this input format
 
-Xopt does **not** provide: 
+Xopt does **not** provide:
 - your custom simulation or experimental measurement via an `evaluate` function.
 
 
@@ -103,7 +103,7 @@ vocs:
     variables:
         x1: [0, 3.14159]
         x2: [0, 3.14159]
-    objectives: 
+    objectives:
         y1: MINIMIZE
         y2: MINIMIZE
     constraints:
@@ -111,7 +111,7 @@ vocs:
         c2: [LESS_THAN, 0.5]
     constants: {a: dummy_constant}
 
-max_evaluations: 6400    
+max_evaluations: 6400
 ```
 
 Xopt can also be used through a simple Python interface.
@@ -151,16 +151,16 @@ print(X.data)
 
 Defining an evaluation function
 ===============
-Xopt can interface with arbitrary evaluate functions (defined in Python) with the 
+Xopt can interface with arbitrary evaluate functions (defined in Python) with the
 following form:
 ```python
 def evaluate(inputs: dict) -> dict:
     """ your code here """
 ```
-Evaluate functions must accept a dictionary object that **at least** has the keys 
-specified in `variables, constants` and returns a dictionary 
-containing **at least** the 
-keys contained in `objectives, constraints`. Extra dictionary keys are tracked and 
+Evaluate functions must accept a dictionary object that **at least** has the keys
+specified in `variables, constants` and returns a dictionary
+containing **at least** the
+keys contained in `objectives, constraints`. Extra dictionary keys are tracked and
 used in the evaluate function but are not modified by xopt.
 
 Using MPI
@@ -173,10 +173,10 @@ mpirun -n 64 python -m mpi4py.futures -m xopt.mpi.run xopt.yaml
 
 Citing Xopt
 ==========
-If you use ```Xopt``` for your research, please consider adding the following 
+If you use ```Xopt``` for your research, please consider adding the following
 citation to your publications.
 ```
-R. Roussel., et al., "Xopt: A simplified framework for optimization of accelerator problems using advanced algorithms", 
+R. Roussel., et al., "Xopt: A simplified framework for optimization of accelerator problems using advanced algorithms",
 in Proc. IPAC'23, Venezia.doi:https://doi.org/10.18429/JACoW-14th International Particle Accelerator Conference-THPL164
 ```
 
@@ -210,12 +210,12 @@ Developers
 
 Clone this repository with a truncated git history (recommended):
 ```shell
-git clone --depth=1 https://github.com/ChristopherMayes/Xopt.git
+git clone --depth=1 https://github.com/xopt-org/xopt.git
 ```
 
 Or, clone this repository with the full git history (> 970 MB):
 ```shell
-git clone https://github.com/ChristopherMayes/Xopt.git
+git clone https://github.com/xopt-org/xopt.git
 ```
 
 Create an environment `xopt-dev` with all the dependencies:
@@ -235,7 +235,7 @@ Install pre-commit hooks:
 pre-commit install
 ```
 
-The pre-commit hooks perform autoformatting and report style-compliance errors. 
+The pre-commit hooks perform autoformatting and report style-compliance errors.
 * [ufmt](https://pypi.org/project/ufmt/) formats files w.r.t. [black](https://github.com/psf/black) a strict style enforcer, and [μsort](https://usort.readthedocs.io/en/stable/), which sorts imports in Python modules.
 * [flake8](https://flake8.pycqa.org/en/latest/) confirms compliance. Occasionally black misses long-line comments/docstrings and they require manual format.
 
@@ -245,6 +245,6 @@ Pre-commit runs the hooks against your files. If the commit fails, correct the r
 The source control integration packaged with VSCode requires additional configuration. Git commands are run in the integrated terminal, which does not inherit the Python interpreter configured with the VSCode project thus breaking the pre-commit hooks. The integration terminal can be configured to use the conda Python environment by including a `.env` file in your project repository:
 
 ```
-#!/usr/bin/bash 
+#!/usr/bin/bash
 source /path/to/xopt-dev/bin/activate
-```
+```