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pull/406/.buildinfo

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+# Sphinx build info version 1
+# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: a17da35968bb3c2fc3ccd7a4309ac208
+tags: 645f666f9bcd5a90fca523b33c5a78b7

pull/406/_sources/development/index.rst.txt

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+***************
+Developer Notes
+***************
+
+The following pages contain useful information for developers about 
+testing, debugging, the actual state of the code, etc.
+
+.. toctree::
+    :maxdepth: 1
+
+    notation.rst
+    units.rst
+    testing.rst
+    compare_atomic_files

pull/406/_sources/development/notation.rst.txt

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+******************
+Notation in Carsus
+******************
+
+* **Use "0" for neutral elements.** 
+    Example: ``Si 0``  is equivalent to :math:`\text{Si I}`, ``Si 1`` to :math:`\text{Si II}`, etc.
+
+* **Use "-" to grab intervals of consecsutive elements or species.**
+    Example: ``H-He`` selects  :math:`\text{H I}` and :math:`\text{H II}` plus :math:`\text{He I}`,  :math:`\text{He II}` and  :math:`\text{He III}`, while ``C 0-2`` selects  :math:`\text{C I}`,  :math:`\text{C II}` and :math:`\text{C III}`. 
+
+* **Use "," to grab non-consecutive species.** 
+    Example: ``Si 0, 2`` selects :math:`\text{Si I}` and :math:`\text{Si III}`.
+
+* **Use ";" to grab non-consecutive elements.**
+    Example: ``H; Li`` selects  :math:`\text{H I}` and :math:`\text{H II}` plus :math:`\text{Li I}`,  :math:`\text{Li II}`, :math:`\text{Li III}` and :math:`\text{Li IV}`.
+
+* **Finally, mix all the above syntax as needed.**
+    Example: ``H; C-Si; Fe 1,3``.

pull/406/_sources/development/testing.rst.txt

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+*************
+Running Tests
+*************
+
+Carsus's tests are based on the 
+`AstroPy Package Template <https://docs.astropy.org/projects/package-template/en/latest/index.html>`_ 
+and `pytest <https://pytest.org/en/latest>`_. Then, running simple tests on your machine is 
+straightforward:
+
+.. code ::
+
+    $ pytest carsus
+
+==============
+Optional Flags
+==============
+
+A set of flags can be appended to the above command to run different kinds of tests:
+
+- `--remote-data`
+    Run tests marked with the ``@pytest.mark.remote_data`` decorator. Requires an internet connection.
+
+- `--refdata=/path/to/carsus-refdata`
+    Run tests marked with the ``@with_refdata`` decorator. Requires the
+    `tardis-sn/carsus-refdata <https://github.com/tardis-sn/carsus-refdata>`_ repository.
+
+- `--cov=carsus --cov-report=xml --cov-report=html`
+    Get code coverage results using the `pytest-cov <https://pytest-cov.readthedocs.io/en/latest/>`_ plugin.
+
+- `--arraydiff-generate-path=carsus-refdata/arraydiff`
+    Generate reference files for tests marked with ``@pytest.mark.array_compare`` decorator and save them in the 
+    refdata folder.
+
+- `--arraydiff --arraydiff-reference-path=carsus-refdata/arraydiff`
+    Run tests marked with ``@pytest.mark.array_compare`` decorator. 
+    The tests would look for reference files in the refdata folder which can be generated using the above option.
+

pull/406/_sources/development/units.rst.txt

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+***************
+Units in Carsus
+***************
+
+In the recent years, much effort has been made to make Carsus easier to use and develop.
+A large piece of code was rewritten to avoid using an intermediate SQL database between
+the readers and the final atomic data. 
+
+This resulted in an simpler, faster and more maintainable Carsus codebase. But we lost
+some features in the process, being the most important one the tracking of physical
+quantities. Currently, we couldn't solve the management of units in a sensible way.
+
+We need to design and implement a new unit tracking system as soon as possible. In the
+meantime, should be enough to document the units used by the GFALL/CHIANTI/CMFGEN readers
+and the output module.

pull/406/_sources/index.rst.txt

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+**********************************
+Welcome to Carsus's Documentation!
+**********************************
+
+Carsus is a package to manage atomic datasets. It can read data from a variety of sources and output them to file formats readable by radiative transfer codes.
+
+.. toctree::
+    :maxdepth: 1
+    :caption: Getting Started
+
+    installation.rst
+    quickstart
+    development/compare_atomic_files
+
+.. toctree::
+    :maxdepth: 2
+    :caption: Datasets
+    :hidden:
+
+    io/nist
+    io/gfall
+    io/chianti
+    io/cmfgen
+    io/zeta
+    io/nndc
+    io/vald
+    io/barklem2016
+
+.. toctree::
+    :maxdepth: 2
+    :caption: Research with Carsus
+    :hidden:
+
+    research/publications.rst
+    research/references.rst
+
+
+.. toctree::
+    :maxdepth: 2
+    :caption: Contributing to Carsus
+    :hidden:
+
+    physics/index.rst
+    development/index.rst
+
+.. toctree::
+    :maxdepth: 2
+    :caption: API
+    :hidden:
+
+    api/modules
+
+.. toctree::
+    :maxdepth: 2
+    :caption: Legacy Code
+    :hidden:
+
+    legacy/index.rst
+
+
+.. seealso::
+    Need help? Contact us `on Gitter <https://gitter.im/tardis-sn/carsus/>`_.

pull/406/_sources/installation.rst.txt

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+************
+Installation
+************
+
+=============
+Prerequisites
+=============
+
+#. Requires a valid Anaconda `or Miniconda <https://docs.conda.io/projects/conda/en/latest/user-guide/install/download.html>`_ installation.
+#. *(optional)*. Download and extract the `Chianti Atomic Database <https://download.chiantidatabase.org/>`_ **v9.0.1** and set the following environment variable in your shell configuration file:
+
+    .. code ::
+
+        export XUVTOP=/path/to/chianti/root
+
+#. *(optional)*. Download and extract the `CMFGEN Atomic Data <http://kookaburra.phyast.pitt.edu/hillier/web/CMFGEN.htm>`_.  
+
+====================
+Clone the Repository
+====================
+
+.. code ::
+
+    $ git clone https://github.com/tardis-sn/carsus.git
+
+
+=====================
+Setup the Environment
+=====================
+
+.. code ::
+
+    $ cd carsus
+
+
+If you're using GNU/Linux or Intel-based Mac installation then directly create the environment using the below command:
+
+.. code ::
+
+    $ conda env create -f carsus_env3.yml
+
+
+However, if you're using M1-based Mac (Apple Silicon), then force conda to install Intel-based packages:
+
+.. code ::
+
+    $ CONDA_SUBDIR=osx-64 conda env create -f carsus_env3.yml
+
+
+===================
+Install the Package
+===================
+
+.. code ::
+
+    $ conda activate carsus
+    $ pip install -e .
+
+
+You are ready! Follow the `Quickstart for Carsus <quickstart.html>`_ guide to continue.