pykoala-ifs 0.18.1__tar.gz

pykoala_ifs-0.18.1/LICENSE

@@ -0,0 +1,29 @@
+BSD 3-Clause License
+
+Copyright (c) 2020, pykoala
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

pykoala_ifs-0.18.1/MANIFEST.in

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+include versioneer.py
+include src/pykoala/_version.py
+include src/pykoala/plotting/pykoala.mplstyle
+
+include *.toml
+include LICENSE
+include tox.ini
+recursive-include src *.dat
+recursive-include src *.txt
+recursive-include src *.fits
+recursive-include src *.tfits
+recursive-include src *.ctio
+
+recursive-include docs *.bat
+recursive-include docs *.py
+recursive-include docs *.rst
+recursive-include docs Makefile
+recursive-include tests *.py
+include *.txt
+recursive-include * .empty
+
+recursive-exclude .circleci *
+exclude .circleci
+exclude codecov.yml
+recursive-exclude ci *
+exclude azure-pipelines.yml

pykoala_ifs-0.18.1/PKG-INFO

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+Metadata-Version: 2.4
+Name: pykoala-ifs
+Version: 0.18.1
+Summary: Data reduction tools for IFS data.
+Author-email: Pablo Corcho-Caballero <p.corcho.caballero@rug.nl>, "Ángel R. López-Sánchez" <angel.lopez-sanchez@mq.edu.au>, Yago Ascasibar <yago.ascasibar@uam.es>
+License: BSD-3-Clause
+Project-URL: Homepage, https://github.com/pykoala/koala
+Project-URL: Issues, https://github.com/pykoala/koala/issues
+Keywords: astronomy,IFS,data reduction
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Topic :: Scientific/Engineering
+Classifier: Programming Language :: Python :: 3
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Dynamic: license-file
+
+# PyKOALA
+
+> A multi-instrument tool for reducing Integral Field Spectroscopic Data
+
+---
+
+**PyKOALA** is a Python package to reduce KOALA+AAOmega integral field spectroscopy (IFS) data creating a data cube. It produces full calibrated (wavelength, flux and astrometry) data cubes ready for science.
+
+[KOALA][koala_website], the Kilofibre Optical AAT Lenslet Array, is a wide-field, high efficiency, integral field unit used by the 
+AAOmega spectrograph on the 3.9m AAT ([Anglo-Australian Telescope][aat_website]) at Siding Spring Observatory. **PyKOALA** is the forthcoming data reduction pipeline for creating science-ready 3D data cubes using Raw Stacked Spectra (RSS) images created with [2dfdr][2dfdr_website].
+
+[koala_website]: https://aat.anu.edu.au/science/instruments/current/koala/overview
+[aat_website]: https://aat.anu.edu.au/about-us/AAT
+[2dfdr_website]: https://aat.anu.edu.au/science/instruments/current/AAOmega/reduction
+
+---
+## Status
+[![Documentation Status](https://readthedocs.org/projects/pykoala/badge/?version=latest)](https://pykoala.readthedocs.io/en/latest/?badge=latest)
+[![test](https://github.com/pykoala/pykoala/actions/workflows/test.yml/badge.svg)](https://github.com/pykoala/pykoala/actions/workflows/test.yml)
+[![Coverage Status](https://codecov.io/github/pykoala/koala/coverage.svg?branch=master)](https://codecov.io/github/pykoala/koala?branch=master)
+[![License](https://img.shields.io/pypi/l/pykoala-ifs.svg)](https://pypi.python.org/pypi/pykoala-ifs/)
+[![Supported versions](https://img.shields.io/pypi/pyversions/pykoala-ifs.svg)](https://pypi.python.org/pypi/pykoala-ifs/)
+[![PyPI](https://img.shields.io/pypi/status/pykoala-ifs.svg)](https://pypi.python.org/pypi/pykoala-ifs/)
+
+---
+## Documentation
+
+**PyKOALA** full documentation can be found here: https://pykoala.readthedocs.io/en/latest/index.html
+
+---
+## Download
+
+**PyKOALA** can be obtained by cloning the repository, using git:
+
+```bash
+git clone https://github.com/pykoala/pykoala.git
+```
+
+## Installation (recommended)
+
+We recommend the use of Python environments for the installation of **PyKOALA**. First, from the terminal enter in the downloaded **PyKOALA** package and create the Python environment:
+
+```bash
+cd pykoala
+python3 -m venv venv_koala
+```
+
+To activate the environment, use:
+
+```bash
+source venv_koala/bin/activate
+```
+
+then install all required packages with:
+
+```bash
+pip install -r requirements.txt
+pip install .
+```
+
+The second command will also install **PyKOALA** in the virtual environment. Once you are finished with your **PyKOALA** session, use:
+
+```bash
+deactivate
+```
+
+to deactivate the Python environment.
+
+For more information about installation and usage of Python virtual environment, check the [documentation](https://pykoala.readthedocs.io/en/latest/getting-started/virtual-environment.html) or the oficial [Python documentation](https://docs.python.org/3/library/venv.html).
+
+
+## Tutorials
+---
+
+See the list of available [tutorials](https://github.com/pykoala/pykoala-tutorials)
+
+## License and Acknowledgements
+
+BSD 3-Clause License
+
+Copyright (c) 2020, pykoala All rights reserved.
+
+Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
+    
+2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
+    
+3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
+    
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS “AS IS” AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

pykoala_ifs-0.18.1/README.md

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+# PyKOALA
+
+> A multi-instrument tool for reducing Integral Field Spectroscopic Data
+
+---
+
+**PyKOALA** is a Python package to reduce KOALA+AAOmega integral field spectroscopy (IFS) data creating a data cube. It produces full calibrated (wavelength, flux and astrometry) data cubes ready for science.
+
+[KOALA][koala_website], the Kilofibre Optical AAT Lenslet Array, is a wide-field, high efficiency, integral field unit used by the 
+AAOmega spectrograph on the 3.9m AAT ([Anglo-Australian Telescope][aat_website]) at Siding Spring Observatory. **PyKOALA** is the forthcoming data reduction pipeline for creating science-ready 3D data cubes using Raw Stacked Spectra (RSS) images created with [2dfdr][2dfdr_website].
+
+[koala_website]: https://aat.anu.edu.au/science/instruments/current/koala/overview
+[aat_website]: https://aat.anu.edu.au/about-us/AAT
+[2dfdr_website]: https://aat.anu.edu.au/science/instruments/current/AAOmega/reduction
+
+---
+## Status
+[![Documentation Status](https://readthedocs.org/projects/pykoala/badge/?version=latest)](https://pykoala.readthedocs.io/en/latest/?badge=latest)
+[![test](https://github.com/pykoala/pykoala/actions/workflows/test.yml/badge.svg)](https://github.com/pykoala/pykoala/actions/workflows/test.yml)
+[![Coverage Status](https://codecov.io/github/pykoala/koala/coverage.svg?branch=master)](https://codecov.io/github/pykoala/koala?branch=master)
+[![License](https://img.shields.io/pypi/l/pykoala-ifs.svg)](https://pypi.python.org/pypi/pykoala-ifs/)
+[![Supported versions](https://img.shields.io/pypi/pyversions/pykoala-ifs.svg)](https://pypi.python.org/pypi/pykoala-ifs/)
+[![PyPI](https://img.shields.io/pypi/status/pykoala-ifs.svg)](https://pypi.python.org/pypi/pykoala-ifs/)
+
+---
+## Documentation
+
+**PyKOALA** full documentation can be found here: https://pykoala.readthedocs.io/en/latest/index.html
+
+---
+## Download
+
+**PyKOALA** can be obtained by cloning the repository, using git:
+
+```bash
+git clone https://github.com/pykoala/pykoala.git
+```
+
+## Installation (recommended)
+
+We recommend the use of Python environments for the installation of **PyKOALA**. First, from the terminal enter in the downloaded **PyKOALA** package and create the Python environment:
+
+```bash
+cd pykoala
+python3 -m venv venv_koala
+```
+
+To activate the environment, use:
+
+```bash
+source venv_koala/bin/activate
+```
+
+then install all required packages with:
+
+```bash
+pip install -r requirements.txt
+pip install .
+```
+
+The second command will also install **PyKOALA** in the virtual environment. Once you are finished with your **PyKOALA** session, use:
+
+```bash
+deactivate
+```
+
+to deactivate the Python environment.
+
+For more information about installation and usage of Python virtual environment, check the [documentation](https://pykoala.readthedocs.io/en/latest/getting-started/virtual-environment.html) or the oficial [Python documentation](https://docs.python.org/3/library/venv.html).
+
+
+## Tutorials
+---
+
+See the list of available [tutorials](https://github.com/pykoala/pykoala-tutorials)
+
+## License and Acknowledgements
+
+BSD 3-Clause License
+
+Copyright (c) 2020, pykoala All rights reserved.
+
+Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
+    
+2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
+    
+3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
+    
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS “AS IS” AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

pykoala_ifs-0.18.1/bors.toml

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+status = [
+#  "continuous-integration/travis-ci/push",
+#  "continuous-integration/appveyor/branch",
+  "pykoala.pykoala",
+#  "codecov/patch",
+#  "codecov/project",
+]
+

pykoala_ifs-0.18.1/dev_requirements.txt

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+pytest
+nbval

pykoala_ifs-0.18.1/doc-requirements.txt

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+astropy>=5.3.4
+matplotlib>=3.7.2
+mock==4.0.3
+nbsphinx==0.9.3
+photutils>=1.9.0
+sphinx_rtd_theme>=3.0.0
+sphinx>=5.0.0

pykoala_ifs-0.18.1/docs/Makefile

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

pykoala_ifs-0.18.1/docs/api.rst

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+API Documentation
+=================
+
+The Documentation is divided into four main categories:
+
+- Data Structures
+   How `pykoala` deals with different sorts of data.
+- Data Corrections
+   What corrections does `pykoala` perform on the data.
+- 1D Spectra manipulation
+   Tools for manipulating one dimensional spectra.
+- Plotting facilities
+   Quick visualization and quality control plots.
+
+Data Structures
+---------------
+
+.. toctree:: pykoala.data_container
+   :maxdepth: 1
+   :caption: Available modules
+
+
+Supported IFS Instruments
+^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The currently available instrument modules in `pykoala` are:
+
+- :class:`pykoala.instruments.koala_ifu`
+
+
+Data Corrections
+----------------
+ 
+This section contains the different correction modules included in `pykoala`.
+
+.. toctree:: pykoala.corrections
+   :maxdepth: 1
+   :caption: Available modules
+
+
+Cubing
+------
+
+.. toctree:: pykoala.cubing
+   :maxdepth: 1
+
+Manipulating Spectra
+--------------------
+
+Tools for manipulating 1D spectra.
+
+
+Plotting tools
+--------------
+
+Useful methods for plotting and performing quality control tests.
+
+.. toctree:: pykoala.plotting
+   :maxdepth: 1

pykoala_ifs-0.18.1/docs/conf.py

@@ -0,0 +1,138 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+import os
+import sys
+sys.path.insert(0, os.path.abspath('../src'))
+
+
+# Avoid build failures on read the docs
+try:
+    import numpy
+except ImportError:
+    from mock import MagicMock
+
+    MOCK_MODULES = [
+        'numpy',
+        'astropy',
+        'astropy.convolution',
+        'astropy.io',
+        'astropy.wcs',
+        'matplotlib',
+        'matplotlib.colors',
+        'matplotlib.pyplot',
+        'synphot',
+        'scipy',
+        'scipy.ndimage',
+        'scipy.ndimage.interpolation',
+        'scipy.optimize',
+        'scipy.signal',
+        "past",
+        "past.utils"
+    ]
+    sys.modules.update((mod_name, MagicMock()) for mod_name in MOCK_MODULES)
+
+
+# -- Project information -----------------------------------------------------
+
+project = 'pykoala'
+copyright = u'2024, Pablo Corcho-Caballero'
+author = u'Pablo Corcho-Caballero'
+
+# The full version, including alpha/beta/rc tags
+import pykoala
+version = '.'.join(pykoala.__version__.split(".")[0:2])
+# The full version, including alpha/beta/rc tags.
+release = pykoala.__version__
+
+
+
+source_suffix = '.rst'
+
+# The encoding of source files.
+#source_encoding = 'utf-8-sig'
+
+# The master toctree document.
+master_doc = 'index'
+
+
+
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+    'sphinx.ext.autodoc',
+    'sphinx.ext.doctest',
+    'sphinx.ext.intersphinx',
+    'sphinx.ext.todo',
+    'sphinx.ext.coverage',
+    'sphinx.ext.imgmath',
+    'sphinx.ext.viewcode',
+    'sphinx.ext.napoleon',
+
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = 'sphinx_rtd_theme'
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']
+
+
+# -- Extension configuration -------------------------------------------------
+
+# -- Options for intersphinx extension ---------------------------------------
+
+# Example configuration for intersphinx: refer to the Python standard library.
+intersphinx_mapping = {'python': ('https://docs.python.org/3/', None),
+                       'astropy': ('https://docs.astropy.org/en/stable/', None),
+                       'numpy': ('https://numpy.org/doc/stable/', None),
+                       'scipy': ('https://docs.scipy.org/doc/scipy/', None)}
+
+# -- Options for todo extension ----------------------------------------------
+
+# If true, `todo` and `todoList` produce output, else they produce nothing.
+todo_include_todos = False
+autodoc_member_order = 'bysource'
+
+# Napoleon settings
+napoleon_google_docstring = False
+napoleon_numpy_docstring = True
+napoleon_include_init_with_doc = True
+napoleon_include_private_with_doc = True
+napoleon_include_special_with_doc = True
+napoleon_use_admonition_for_examples = False
+napoleon_use_admonition_for_notes = False
+napoleon_use_admonition_for_references = False
+napoleon_use_ivar = False
+napoleon_use_param = False
+napoleon_use_rtype = False
+napoleon_preprocess_types = False
+napoleon_type_aliases = None
+napoleon_attr_annotations = True

pykoala_ifs-0.18.1/docs/developer-guide/fork.rst

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+Forking PyKOALA
+===============
+
+Working on a fork enables you to develop your own copy of PyKOALA, contributing your code back to the main repository through a "pull request."
+
+How to fork
+-----------
+First, click “Fork this repository” on the main PyKOALA repository in github. You then have your own copy of PyKOALA in github.com/USERNAME/koala
+
+.. figure:: ../_static/figures/fork_buttom.png
+
+How to work on your fork
+------------------------
+Clone a copy of your fork onto a local machine:
+::
+
+    git clone git@github.com:USERNAME/koala
+
+This gets a copy of the entire repository. Here replace USERNAME with your GitHub username.
+
+
+How to update your fork from the main PyKOALA repo
+--------------------------------------------------
+
+Make a

pykoala_ifs-0.18.1/docs/developer-guide/index.rst

@@ -0,0 +1,13 @@
+Developer guide
+===============
+
+Here is the PyKOALA developer guide.
+
+Contents
+--------
+
+.. toctree::
+    :maxdepth: 1
+
+
+    fork

pykoala_ifs-0.18.1/docs/getting-started/get-copy.rst

@@ -0,0 +1,55 @@
+Working with PyKOALA and git
+=============================
+
+Getting a copy
+--------------
+
+To get PyKOALA, clone the repository, using git:
+
+::
+    
+    git clone https://github.com/pykoala/koala.git
+
+
+Setting username and email address
+----------------------------------
+
+Before pushing changes, make sure your name and email address are set as follows:
+
+::
+
+    cd koala
+    git config --global user.name "Ben Kenobi"
+    git config --global user.email "obi.wan@mq.edu.au"
+
+
+
+Please use your full name in the specified format, as it will appear in the commit logs and the AUTHORS file.
+
+Getting updates from your fork 
+------------------------------
+
+If the main repository has been updated, you may want to get those in your local version of the code. If so, your version will be in on of these cases:
+
+- If you have not made changes in your local version, enter in the ``koala`` directory and use:
+
+::
+
+    git pull
+
+- If you have made modifications that you do not wish to keep, use this instead:
+
+::
+
+    git stash 
+    git pull
+    
+- In the case you want to keep the changes, type:
+
+::
+
+    git stash 
+    git pull
+    git stash pop
+
+

pykoala_ifs-0.18.1/docs/getting-started/index.rst

@@ -0,0 +1,21 @@
+Getting started
+===============
+
+Quickstart
+-----------
+
+1. :doc:`Get a copy <get-copy>` of the code.
+
+2. Installation of a :doc:`Python environment <virtual-environment>` for PyKoala.
+
+3. Running jupyter tutorials in a Python environment.
+
+
+Contents
+--------
+
+.. toctree::
+    :maxdepth: 1
+
+    get-copy
+    virtual-environment