initial

Author: bartzbeielstein

.gitignore

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+
+.DS_Store
+test/__pycache__/test_aggregate_mean_var.cpython-310-pytest-7.1.3.pyc
+test/__pycache__/test_build_Psi.cpython-310-pytest-7.1.3.pyc
+test/__pycache__/test_build_psi_vec.cpython-310-pytest-7.1.3.pyc
+test/__pycache__/test_build_U.cpython-310-pytest-7.1.3.pyc
+test/__pycache__/test_evaluate_new_solutions.cpython-310-pytest-7.1.3.pyc
+test/__pycache__/test_evaluate_new_X.cpython-310-pytest-7.1.3.pyc
+test/__pycache__/test_extract_from_bounds.cpython-310-pytest-7.1.3.pyc
+test/__pycache__/test_generate_design.cpython-310-pytest-7.1.3.pyc
+test/__pycache__/test_infill.cpython-310-pytest-7.1.3.pyc
+test/__pycache__/test_nat_to_cod.cpython-310-pytest-7.1.3.pyc
+test/__pycache__/test_nat_to_cod_init.cpython-310-pytest-7.1.3.pyc
+test/__pycache__/test_ocba.cpython-310-pytest-7.1.3.pyc
+test/__pycache__/test_repair_non_numeric.cpython-310-pytest-7.1.3.pyc
+test/__pycache__/test_set_de_bounds.cpython-310-pytest-7.1.3.pyc
+test/__pycache__/test_show_progress.cpython-310-pytest-7.1.3.pyc
+test/__pycache__/test_suggest_new_X.cpython-310-pytest-7.1.3.pyc
+test/__pycache__/test_update_surrogate.cpython-310-pytest-7.1.3.pyc

LICENSE.txt

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+include src/spotPython/data/*.rst
+include src/spotPython/data/*.tar
+include src/spotPython/data/*.c
+include src/spotPython/data/*.csv
+
+

MANIFEST.in

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+# spotPython
+
+# Development
+
+
+## Styleguide 
+
+Follow the Google Python Style Guide from [https://google.github.io/styleguide/pyguide.html]([https://google.github.io/styleguide/pyguide.html).
+
+## Pre commit checks
+
+Before you commit your code, please check that it is "clean". 
+To do so, first run [`black`](https://github.com/psf/black) from the projects root directory:
+
+```
+$ black .
+```
+
+Next, check if [`flake8`](https://flake8.pycqa.org/en/latest/) shows any errors:
+
+```
+$ flake8
+```
+
+Fix any shown errors before you commit.
+
+# Installation
+
+`pip install spotPython`
+
+
+## Python
+
+* Mac Users: Install [brew](https://brew.sh/index_de)
+  * `brew install python` and `brew install graphviz` etc.
+
+* Generate and activate a virtual environment, see [venv](https://docs.python.org/3/library/venv.html), e.g.,
+  * `cd ~; python3 -m venv .venv`
+  * `source ~/.venv/bin/activate`
+
+### Python mkdocs
+
+* `python -m pip install mkdocs mkdocs-gen-files mkdocs-literate-nav mkdocs-section-index mkdocs-material`
+* `mkdocs build`
+* `mkdocs serve`
+* `http://127.0.0.1:8000/`
+
+
+### Optimizing/Profiling Code
+
+* [scipy lecture notes: optimizing code](https://scipy-lectures.org/advanced/optimizing/index.html)
+
+https://scipy-lectures.org/advanced/optimizing/index.html
+
+## Editor/IDE
+
+* Optional: Install [visualstudio](https://code.visualstudio.com)
+* Optional: Install [quarto](https://quarto.org)
+
+
+## Package Installation
+
+### Configuration Files
+
+* This information is based on [https://packaging.python.org/en/latest/tutorials/packaging-projects/](https://packaging.python.org/en/latest/tutorials/packaging-projects/)
+* Information is stored in `pyproject.toml` (`setup.py` is not used anymore.)
+* A `src` folder is used for the package sources.
+* The following files are used for the package building:
+   * `pyproject.toml`: see [pyproject.toml](./pyproject.toml). 
+   * Important: Follow the instructions from [https://setuptools.pypa.io/en/latest/userguide/pyproject_config.html](https://setuptools.pypa.io/en/latest/userguide/pyproject_config.html) for including data files (like *.csv, *.tar, etc.). These files can be specified in the following `MANIFEST` file:
+     * `MANIFEST`: see [MANIFEST](MANIFEST.in). It describes the data files to be included, e.g.:
+       * `include src/spotPython/data/*.rst`
+    * `LICENSE`: see [LICENSE](./LICENSE)
+
+### Installation
+
+* Perform the following steps to install the package:
+  * Make sure you have the latest version of PyPA’s build installed:
+    * `python3 -m pip install --upgrade build`
+  * Start the package building process via:  `python3 -m build` 
+  * This command should output a lot of text and once completed should generate two files in the `dist` directory.
+  * You can use the local `spotPython*.tar.gz` file from the `dist` folder for your package installation with `pip`, e.g.;
+  * `python3 -m pip install ./dist/spotPython-0.0.1.tar.gz`
+
+

README.md

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+# Install spotPython
+
+    pip install spotPython

dist/spotPython-0.0.1-py3-none-any.whl

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+# SPOT Examples
+
+## Simple spotPython run
+
+import numpy as np
+from spotPython.fun.objectivefunctions import analytical
+from spotPython.spot import spot
+import numpy as np
+from math import inf
+# number of initial points:
+ni = 7
+# number of points
+n = 10
+
+fun = analytical().fun_sphere
+lower = np.array([-1])
+upper = np.array([1])
+design_control={"init_size": ni}
+
+spot_1 = spot.Spot(fun=fun,
+            lower = lower,
+            upper= upper,
+            fun_evals = n,
+            show_progress=True,
+            design_control=design_control,)
+spot_1.run()

dist/spotPython-0.0.1.tar.gz

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+"""Generate the code reference pages and navigation."""
+
+from pathlib import Path
+
+import mkdocs_gen_files
+
+nav = mkdocs_gen_files.Nav()
+
+for path in sorted(Path("src").rglob("*.py")):
+    module_path = path.relative_to("src").with_suffix("")
+    doc_path = path.relative_to("src").with_suffix(".md")
+    full_doc_path = Path("reference", doc_path)
+
+    parts = tuple(module_path.parts)
+
+    if parts[-1] == "__init__":
+        parts = parts[:-1]
+        doc_path = doc_path.with_name("index.md")
+        full_doc_path = full_doc_path.with_name("index.md")
+    elif parts[-1] == "__main__":
+        continue
+
+    nav[parts] = doc_path.as_posix()
+
+    with mkdocs_gen_files.open(full_doc_path, "w") as fd:
+        ident = ".".join(parts)
+        fd.write(f"::: {ident}")
+
+    mkdocs_gen_files.set_edit_path(full_doc_path, path)
+
+with mkdocs_gen_files.open("reference/SUMMARY.md", "w") as nav_file:
+    nav_file.writelines(nav.build_literate_nav())