ipynb notebooks generated

docs/source/apidocs/index.ipynb

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+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# API docs\n",
+    "\n",
+    "This is an overview over all classes available in pyopenms\n",
+    "\n",
+    "pyopenms\n",
+    "\n",
+    "pyopenms.Constants pyopenms.plotting"
+   ],
+   "id": "d3f6ae10-03f0-4130-8602-acb1c88e5be6"
+  }
+ ],
+ "nbformat": 4,
+ "nbformat_minor": 5,
+ "metadata": {}
+}

docs/source/community/adding_pure_python.ipynb

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+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Adding pure python classes/functionality\n",
+    "\n",
+    "Pure python modules can be found <span class=\"title-ref\">here\n",
+    "\\<https://github.com/OpenMS/OpenMS/tree/develop/src/pyOpenMS/pyopenms\\></span>.\n",
+    "Just add a new <span class=\"title-ref\">.py</span> file and a new\n",
+    "submodule will appear that can be imported with\n",
+    "<span class=\"title-ref\">import pyopenms.submodule</span>.\n",
+    "\n",
+    "Remember to add additional requirements in the setup.py but try to avoid\n",
+    "large dependencies unless absolutely necessary.\n",
+    "\n",
+    "Testing is done via pytest. Every new module, class, function, member\n",
+    "should be documented with Sphinx reStructuredText docstrings. See the\n",
+    "<span class=\"title-ref\">Sphinx-RTD-Tutorial\n",
+    "\\<https://sphinx-rtd-tutorial.readthedocs.io/en/latest/docstrings.html\\></span>\n",
+    "and the <span class=\"title-ref\">Python Developers Guide\n",
+    "\\<https://devguide.python.org/documentation/start-documenting/index.html\\></span>."
+   ],
+   "id": "b8f40e49-2d27-4ef1-bef5-f0b3f19795ba"
+  }
+ ],
+ "nbformat": 4,
+ "nbformat_minor": 5,
+ "metadata": {}
+}

docs/source/community/build_from_source.ipynb

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+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Build from Source\n",
+    "\n",
+    "To install pyOpenMS from `source`, you will first have to compile OpenMS\n",
+    "successfully on your platform of choice (note that for MS Windows you\n",
+    "will need to match your compiler and Python version). Please follow the\n",
+    "[official\n",
+    "documentation](https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/release/latest/html/index.html)\n",
+    "in order to compile OpenMS for your platform. Next you will need to\n",
+    "install the following software packages\n",
+    "\n",
+    "On Microsoft Windows: you need the 64 bit C++ compiler from Visual\n",
+    "Studio 2015 to compile the newest pyOpenMS for Python 3.5, 3.6 or 3.7.\n",
+    "This is important, else you get a clib that is different than the one\n",
+    "used for building the Python executable, and pyOpenMS will crash on\n",
+    "import. The OpenMS wiki has [detailed\n",
+    "information](https://github.com/OpenMS/OpenMS/wiki/Build-pyOpenMS-on-Windows)\n",
+    "on building pyOpenMS on Windows.\n",
+    "\n",
+    "You can install all necessary Python packages on which pyOpenMS depends\n",
+    "through\n",
+    "\n",
+    "``` bash\n",
+    "pip install -U setuptools\n",
+    "pip install -U pip\n",
+    "pip install -U autowrap\n",
+    "pip install -U pytest\n",
+    "pip install -U numpy\n",
+    "pip install -U wheel\n",
+    "```\n",
+    "\n",
+    "Depending on your systems setup, it may make sense to do this inside a\n",
+    "virtual environment\n",
+    "\n",
+    "``` bash\n",
+    "virtualenv pyopenms_venv\n",
+    "source pyopenms_venv/bin/activate\n",
+    "```\n",
+    "\n",
+    "Next, configure OpenMS with pyOpenMS: execute `cmake` as usual, but with\n",
+    "parameters `DPYOPENMS=ON`. Also, if using virtualenv or using a specific\n",
+    "Python version, add `-DPYTHON_EXECUTABLE:FILEPATH=/path/to/python` to\n",
+    "ensure that the correct Python executable is used. Compiling pyOpenMS\n",
+    "can use a lot of memory and take some time, however you can reduce the\n",
+    "memory consumption by breaking up the compilation into multiple units\n",
+    "and compiling in parallel, for example\n",
+    "`-DPY_NUM_THREADS=2 -DPY_NUM_MODULES=4` will build 4 modules with 2\n",
+    "threads. You can then configure pyOpenMS:\n",
+    "\n",
+    "``` bash\n",
+    "cmake -DPYOPENMS=ON\n",
+    "make pyopenms\n",
+    "```\n",
+    "\n",
+    "Build pyOpenMS (now there should be pyOpenMS specific build targets).\n",
+    "Afterwards, test that all went well by running the tests:\n",
+    "\n",
+    "``` bash\n",
+    "ctest -R pyopenms\n",
+    "```\n",
+    "\n",
+    "Which should execute all the tests and return with all tests passing.\n",
+    "\n",
+    "## Further Questions\n",
+    "\n",
+    "In case the above instructions did not work, please refer to the [Wiki\n",
+    "Page](https://github.com/OpenMS/OpenMS/wiki/pyOpenMS), contact the\n",
+    "development team on github or send an email to the OpenMS mailing list."
+   ],
+   "id": "e07ef770-88bc-452d-a541-fb2ce383dc43"
+  }
+ ],
+ "nbformat": 4,
+ "nbformat_minor": 5,
+ "metadata": {}
+}

docs/source/community/index.ipynb

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+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Contribute\n",
+    "\n",
+    "## pyopenms docs\n",
+    "\n",
+    "Contribution to the pyOpenMS documentation is easy and we would love to\n",
+    "expand it with you. To edit a tutorial page you can click on the \"Edit\n",
+    "on GitHub\" link at the top right of each page. Once you changed (or\n",
+    "added new) .rst files you can and open a pull request.\n",
+    "\n",
+    "(Note that edits you perform on binder don't get stored in this\n",
+    "repository. Thus, binder and the displayed jupyter notebooks can not be\n",
+    "used to edit the existing documentation. All edits need to happen\n",
+    "through the .rst files in the OpenMS/pyopenms-docs repository.)\n",
+    "\n",
+    "If you are unsure how to do that or want to discuss questions (e.g. your\n",
+    "example workflow can be included on this webpage) contact us via the\n",
+    "[OpenMS Gitter chat channel](https://gitter.im/OpenMS/OpenMS/).\n",
+    "\n",
+    "## pyopenms sources\n",
+    "\n",
+    "pyopenms mostly consists of Cython wrappers around the OpenMS C++\n",
+    "library. Below you will find information on how to build pyopenms from\n",
+    "source and how to wrap new classes. You can of course also contribute\n",
+    "classesa and functionality in pure python.\n",
+    "\n",
+    "build_from_source wrapping_workflows_new_classes adding_pure_python"
+   ],
+   "id": "df9a79cd-fef3-499f-8cd1-2dc449fc0046"
+  }
+ ],
+ "nbformat": 4,
+ "nbformat_minor": 5,
+ "metadata": {}
+}