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Builds automatic documentation of the API (#103)
* Scaffolds automatic documentation of the API * Adds links to class implementations * Removes colons from attribute, raises, returns titles in docstrings * Fixes a colon in docstrings, to follow numpy standards * Adds documentation to the core module * Adds documentation to the objective factory module * Documents the objective script * Documents most functions inside the objective repository * Documents the remaining objective functions inside the repository * Adds several packages to the mock imports of autodoc * Removes the autogenerated rst files from git tracking
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‎.github/workflows/python-tox-testing-including-conda.yml

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python -m pip install tox
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- name: Test linting with tox
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run: |
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tox -c tox.dev.ini -e lint
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tox -c tox.ini -e lint
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- name: Test poli-base with tox (ignoring RaSP)
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run: |
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tox -c tox.dev.ini -e poli-base-py39 -- --ignore=src/poli/tests/registry/proteins/test_rasp.py
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tox -c tox.ini -e poli-base-py39 -- --ignore=src/poli/tests/registry/proteins/test_rasp.py

‎.gitignore

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2020

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# Ignore temporary files
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tmp/
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src/poli/objective_repository/rasp/101m.pdb
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src/poli/objective_repository/rasp/101m.pdb
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# Documentation
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docs/build/
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docs/source/generated/

‎README.MD

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print(f"f({x}) = {f(x)}")
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```
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## Where can I find the documentation?
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### Building the documentation locally
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If you install the `requirements-dev.txt` via
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```bash
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pip install -r requirements-dev.txt
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```
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then you will have access to `sphinx`. You should be able to build the documentation by going to the docs folder and building it:
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```bash
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cd docs/
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make html
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```
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Afterwards, you can enter the `build` folder and open `index.html`.

‎docs/Makefile

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# Minimal makefile for Sphinx documentation
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#
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# You can set these variables from the command line, and also
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# from the environment for the first two.
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SPHINXOPTS ?=
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SPHINXBUILD ?= sphinx-build
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SOURCEDIR = source
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BUILDDIR = build
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# Put it first so that "make" without argument is like "make help".
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help:
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@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
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.PHONY: help Makefile
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# Catch-all target: route all unknown targets to Sphinx using the new
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# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).
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%: Makefile
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@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

‎docs/make.bat

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@ECHO OFF
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pushd %~dp0
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REM Command file for Sphinx documentation
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if "%SPHINXBUILD%" == "" (
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set SPHINXBUILD=sphinx-build
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)
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set SOURCEDIR=source
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set BUILDDIR=build
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%SPHINXBUILD% >NUL 2>NUL
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if errorlevel 9009 (
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echo.
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echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
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echo.installed, then set the SPHINXBUILD environment variable to point
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echo.to the full path of the 'sphinx-build' executable. Alternatively you
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echo.may add the Sphinx directory to PATH.
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echo.
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echo.If you don't have Sphinx installed, grab it from
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echo.https://www.sphinx-doc.org/
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exit /b 1
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)
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if "%1" == "" goto help
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%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
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goto end
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:help
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%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
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:end
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popd

‎docs/source/_templates/custom-class-template.rst

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{{ fullname | escape | underline}}
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.. currentmodule:: {{ module }}
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.. autoclass:: {{ objname }}
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:members:
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:show-inheritance:
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:inherited-members:
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{% block methods %}
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.. automethod:: __init__
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{% if methods %}
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.. rubric:: {{ _('Methods') }}
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.. autosummary::
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{% for item in methods %}
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~{{ name }}.{{ item }}
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{%- endfor %}
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{% endif %}
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{% endblock %}
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{% block attributes %}
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{% if attributes %}
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.. rubric:: {{ _('Attributes') }}
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.. autosummary::
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{% for item in attributes %}
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~{{ name }}.{{ item }}
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{%- endfor %}
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{% endif %}
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{% endblock %}

‎docs/source/_templates/custom-module-template.rst

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{{ fullname | escape | underline}}
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.. automodule:: {{ fullname }}
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{% block attributes %}
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{% if attributes %}
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.. rubric:: {{ _('Module Attributes') }}
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.. autosummary::
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:toctree:
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{% for item in attributes %}
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{{ item }}
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{%- endfor %}
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{% endif %}
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{% endblock %}
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{% block functions %}
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{% if functions %}
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.. rubric:: {{ _('Functions') }}
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.. autosummary::
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:toctree:
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{% for item in functions %}
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{{ item }}
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{%- endfor %}
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{% endif %}
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{% endblock %}
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{% block classes %}
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{% if classes %}
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.. rubric:: {{ _('Classes') }}
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.. autosummary::
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:toctree:
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{% for item in classes %}
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{{ item }}
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{%- endfor %}
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{% endif %}
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{% endblock %}
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{% block exceptions %}
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{% if exceptions %}
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.. rubric:: {{ _('Exceptions') }}
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.. autosummary::
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:toctree:
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{% for item in exceptions %}
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{{ item }}
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{%- endfor %}
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{% endif %}
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{% endblock %}
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{% block modules %}
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{% if modules %}
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.. rubric:: Modules
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.. autosummary::
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:toctree:
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:template: custom-module-template.rst
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:recursive:
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{% for item in modules %}
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{{ item }}
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{%- endfor %}
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{% endif %}
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{% endblock %}

‎docs/source/conf.py

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# Configuration file for the Sphinx documentation builder.
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#
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# This file only contains a selection of the most common options. For a full
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# list see the documentation:
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# https://www.sphinx-doc.org/en/master/usage/configuration.html
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# -- Path setup --------------------------------------------------------------
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# If extensions (or modules to document with autodoc) are in another directory,
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# add these directories to sys.path here. If the directory is relative to the
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# documentation root, use os.path.abspath to make it absolute, like shown here.
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#
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import os
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# import sys
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# sys.path.insert(0, os.path.abspath('.'))
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import pathlib
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import sys
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path_to_poli = (pathlib.Path(__file__).parents[2].resolve() / "src").as_posix()
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sys.path.insert(0, path_to_poli)
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for x in os.walk(path_to_poli):
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sys.path.insert(0, x[0])
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# -- Project information -----------------------------------------------------
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project = "poli"
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copyright = "2023, MLLS"
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author = "MLLS"
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# The full version, including alpha/beta/rc tags
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release = "0.0.1"
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# -- General configuration ---------------------------------------------------
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# Add any Sphinx extension module names here, as strings. They can be
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# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
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# ones.
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extensions = [
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"sphinx.ext.autodoc",
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"sphinx.ext.autosummary",
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"sphinx.ext.napoleon",
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]
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autosummary_generate = True # Turn on sphinx.ext.autosummary
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autodoc_mock_imports = [
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"biopython",
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"Bio",
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"tdc",
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"pdbtools",
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"torch",
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"pandas",
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"rdkit",
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"lambo",
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"selfies",
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"github",
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"yaml",
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"pytz",
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"matplotlib",
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"scipy",
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"sklearn",
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"tensorflow",
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"hydra",
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"ptitprince",
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"seaborn",
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"pdbfixer",
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"openmm",
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"simtk",
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"dockstring",
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]
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# Add any paths that contain templates here, relative to this directory.
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templates_path = ["_templates"]
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# List of patterns, relative to source directory, that match files and
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# directories to ignore when looking for source files.
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# This pattern also affects html_static_path and html_extra_path.
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exclude_patterns = []
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# -- Options for HTML output -------------------------------------------------
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# The theme to use for HTML and HTML Help pages. See the documentation for
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# a list of builtin themes.
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#
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html_theme = "furo"
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# Add any paths that contain custom static files (such as style sheets) here,
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# relative to this directory. They are copied after the builtin static files,
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# so a file named "default.css" will overwrite the builtin "default.css".
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html_static_path = ["_static"]

‎docs/source/index.rst

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.. poli documentation master file, created by
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sphinx-quickstart on Thu Dec 21 10:41:44 2023.
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You can adapt this file completely to your liking, but it should at least
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contain the root `toctree` directive.
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Contents
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========
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.. currentmodule:: poli
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.. autosummary::
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:toctree: generated
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:template: custom-module-template.rst
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:recursive:
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core
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objective_factory
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objective_repository
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Indices and tables
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==================
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* :ref:`genindex`
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* :ref:`modindex`
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* :ref:`search`

‎requirements-dev.txt

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black
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tox
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setuptools
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setuptools
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sphinx
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furo

‎src/poli/__init__.py

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"""poli, a library for black-box optimization of discrete sequences."""
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__author__ = "Simon Bartels"

‎src/poli/core/__init__.py

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"""Core classes and utilities inside poli
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"""

‎src/poli/core/abstract_black_box.py

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-------
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set_observer(observer)
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Set the observer object for recording observations during evaluation.
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reset_evaluation_budget()
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Reset the evaluation budget by setting the number of evaluations made to 0.
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__call__(x, context=None)
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Evaluate the black box function for the given input.
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_black_box(x, context=None)
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self.observer = observer
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def reset_evaluation_budget(self):
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"""Resets the evaluation budget by setting the number of evaluations made to 0."""
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self._num_evaluations = 0
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def __call__(self, x: np.array, context=None):
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class NegativeBlackBox(AbstractBlackBox):
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"""A wrapper for a black box that negates the objective function.
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If you construct a black-box function f for maximizing, then -f is
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a black-box function for minimizing. This class is a wrapper for
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implementing the latter.
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The only difference is that the __call__ method returns -f(x) instead
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of f(x). The _black_box method is the same as the original black box.
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"""
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def __init__(self, f: AbstractBlackBox):
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self.f = f
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super().__init__(info=f.info, batch_size=f.batch_size)

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