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‎docs/source/apidocs/index.ipynb

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{
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"cells": [
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"# API docs\n",
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"\n",
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"This is an overview over all classes available in pyopenms\n",
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"\n",
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"pyopenms\n",
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"\n",
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"pyopenms.Constants pyopenms.plotting"
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],
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"id": "2de8ac6f-2c09-4bc3-9e0d-3ada8c1f8e49"
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}
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],
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"nbformat": 4,
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"nbformat_minor": 5,
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"metadata": {}
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}

‎docs/source/community/adding_pure_python.ipynb

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{
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"cells": [
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"# Adding pure python classes/functionality\n",
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"\n",
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"Pure python modules can be found <span class=\"title-ref\">here\n",
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"\\<https://github.com/OpenMS/OpenMS/tree/develop/src/pyOpenMS/pyopenms\\></span>.\n",
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"Just add a new <span class=\"title-ref\">.py</span> file and a new\n",
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"submodule will appear that can be imported with\n",
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"<span class=\"title-ref\">import pyopenms.submodule</span>.\n",
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"\n",
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"Remember to add additional requirements in the setup.py but try to avoid\n",
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"large dependencies unless absolutely necessary.\n",
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"\n",
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"Testing is done via pytest. Every new module, class, function, member\n",
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"should be documented with Sphinx reStructuredText docstrings. See the\n",
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"<span class=\"title-ref\">Sphinx-RTD-Tutorial\n",
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"\\<https://sphinx-rtd-tutorial.readthedocs.io/en/latest/docstrings.html\\></span>\n",
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"and the <span class=\"title-ref\">Python Developers Guide\n",
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"\\<https://devguide.python.org/documentation/start-documenting/index.html\\></span>."
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],
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"id": "a186626b-9aa3-4168-b6a7-f607cce3b8d1"
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}
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],
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"nbformat": 4,
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"nbformat_minor": 5,
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"metadata": {}
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}

‎docs/source/community/build_from_source.ipynb

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{
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"cells": [
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"# Build from Source\n",
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"\n",
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"To install pyOpenMS from `source`, you will first have to compile OpenMS\n",
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"successfully on your platform of choice (note that for MS Windows you\n",
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"will need to match your compiler and Python version). Please follow the\n",
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"[official\n",
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"documentation](https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/release/latest/html/index.html)\n",
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"in order to compile OpenMS for your platform. Next you will need to\n",
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"install the following software packages\n",
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"\n",
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"On Microsoft Windows: you need the 64 bit C++ compiler from Visual\n",
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"Studio 2015 to compile the newest pyOpenMS for Python 3.5, 3.6 or 3.7.\n",
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"This is important, else you get a clib that is different than the one\n",
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"used for building the Python executable, and pyOpenMS will crash on\n",
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"import. The OpenMS wiki has [detailed\n",
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"information](https://github.com/OpenMS/OpenMS/wiki/Build-pyOpenMS-on-Windows)\n",
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"on building pyOpenMS on Windows.\n",
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"\n",
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"You can install all necessary Python packages on which pyOpenMS depends\n",
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"through\n",
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"\n",
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"``` bash\n",
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"pip install -U setuptools\n",
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"pip install -U pip\n",
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"pip install -U autowrap\n",
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"pip install -U pytest\n",
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"pip install -U numpy\n",
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"pip install -U wheel\n",
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"```\n",
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"\n",
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"Depending on your systems setup, it may make sense to do this inside a\n",
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"virtual environment\n",
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"\n",
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"``` bash\n",
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"virtualenv pyopenms_venv\n",
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"source pyopenms_venv/bin/activate\n",
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"```\n",
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"\n",
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"Next, we will configure the CMake-based OpenMS build system to enable\n",
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"the pyOpenMS target with the configuration option `-DPYOPENMS=ON`. If\n",
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"your are using virtualenv or a specific Python version, add\n",
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"`-DPYTHON_EXECUTABLE:FILEPATH=/path/to/python` to ensure that the\n",
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"correct Python executable is used. Compiling pyOpenMS can use a lot of\n",
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"memory and take some time, however you can reduce the memory consumption\n",
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"by breaking up the compilation into multiple units and compiling in\n",
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"parallel, for example `-DPY_NUM_THREADS=2 -DPY_NUM_MODULES=4` will build\n",
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"4 modules with 2 threads. You can now configure pyOpenMS (inside your\n",
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"build folder) with:\n",
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"\n",
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"``` bash\n",
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"cmake -DPYOPENMS=ON\n",
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"```\n",
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"\n",
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"Remember, that you can pass the other options as described above to the\n",
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"first command by adding `-DOPTION=VALUE` statements if you need them.\n",
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"\n",
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"Now build pyOpenMS (now there should be pyOpenMS specific build\n",
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"targets). If you are still inside your build folder, you can use \".\" as\n",
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"the build folder parameter.\n",
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"\n",
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"``` bash\n",
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"cmake --build $YOURBUILDFOLDER --target pyopenms --config Release\n",
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"```\n",
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"\n",
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"Afterwards, test that all went well by running the tests:\n",
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"\n",
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"``` bash\n",
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"ctest -R pyopenms\n",
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"```\n",
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"\n",
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"Which should execute all the tests and return with all tests passing.\n",
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"\n",
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"## Further Questions\n",
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"\n",
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"In case the above instructions did not work, please refer to the [Wiki\n",
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"Page](https://github.com/OpenMS/OpenMS/wiki/pyOpenMS), contact the\n",
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"development team on github or send an email to the OpenMS mailing list."
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],
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"id": "e5f2f68e-5ff9-4895-9a2b-5877e0a98813"
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}
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],
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"nbformat": 4,
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"nbformat_minor": 5,
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"metadata": {}
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}

‎docs/source/community/index.ipynb

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{
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"cells": [
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"# Contribute\n",
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"\n",
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"## pyopenms docs\n",
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"\n",
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"Contribution to the pyOpenMS documentation is easy and we would love to\n",
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"expand it with you. To edit a tutorial page you can click on the \"Edit\n",
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"on GitHub\" link at the top right of each page. Once you changed (or\n",
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"added new) .rst files you can and open a pull request.\n",
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"\n",
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"(Note that edits you perform on binder don't get stored in this\n",
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"repository. Thus, binder and the displayed jupyter notebooks can not be\n",
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"used to edit the existing documentation. All edits need to happen\n",
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"through the .rst files in the OpenMS/pyopenms-docs repository.)\n",
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"\n",
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"If you are unsure how to do that or want to discuss questions (e.g. your\n",
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"example workflow can be included on this webpage) contact us via the\n",
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"[OpenMS Gitter chat channel](https://gitter.im/OpenMS/OpenMS/).\n",
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"\n",
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"## pyopenms sources\n",
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"\n",
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"pyopenms mostly consists of Cython wrappers around the OpenMS C++\n",
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"library. Below you will find information on how to build pyopenms from\n",
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"source and how to wrap new classes. You can of course also contribute\n",
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"classesa and functionality in pure python.\n",
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"\n",
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"build_from_source wrapping_workflows_new_classes adding_pure_python"
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],
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"id": "7985ac13-ebe6-4c84-825c-f04fa69fa439"
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}
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],
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"nbformat": 4,
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"nbformat_minor": 5,
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"metadata": {}
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}

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