iniabu

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---
# iniabu: Getting Solar System Abundances in Python
 
Reto Trappitsch

October 27, 2020

.footnote[Go to: [source code](https://github.com/galactic-forensics/iniabu), [documentation](https://iniabu.readthedocs.io/en/latest/)]

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## What does it provide?
---

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.left-column[
## `iniabu`
### - Goal
]
.right-column[
  **A simple API to retrieve solar abundances in python
  and perform simple calculations useful for astrophysics.**

- Compatible with Python 3.6+

- Open source

- Maintainable

- Well documented

- Simple mechanism to add databases later on and extend capabilities
]
---

- Load / switch various databases

- Retrieve element and isotope information

- Calculate commonly used comparisons with measurements / observations / models:

- δ-, ε-, µ-values

- bracket notation

- Internal normalization*

- All values / calculations are either returned as `floats` or `numpy.ndarrays`

---

.left-column[
## `iniabu`
### - Goal
### - Functionality
### - Current state
]
.right-column[
- [Previous project](https://github.com/llnl/iniabu) will be replaced since not easily extendable

- This package: testing / extending phase

- Source code available on [GitHub](https://github.com/galactic-forensics/iniabu)

- Not yet on PyPi, but will be released when testing is completed as `iniabu` v1.0.0*

- Full documentation with examples and auto-generated API docs available on
  [iniabu.readthedocs.io](https://iniabu.readthedocs.io/)

---

.left-column[
## `iniabu`
### - Goal
### - Functionality
### - Current state
### - Development
]
.right-column[
- Developer reference [available in docs](https://iniabu.readthedocs.io/en/latest/dev/index.html)

- Use `nox` for automation:

- Testing using `pytest`*

- Linting with `flake8`*

- Documentation tests with `xdoctest`*

- Local documentation generation with `sphinx`

- Auto formatting with `black`

- Build and release with `flit`

-  [Pre-commit](https://pre-commit.com/) hook setup available

- CI via GithubActions and [coveralls.io](https://coveralls.io/github/galactic-forensics/iniabu)

---

# Getting started

## Installation

Currently:

```bash
$ pip install git+https://github.com/galactic-forensics/iniabu.git
```

.red[Attention:] Currently the old package (v0.3.1) would be installed
if you try to install `iniabu` directly from PyPi.

## The standard import

Using Lodders et al. (2009) database

```python
>>> from iniabu import ini
```

---

# Exploring databases

## Loading and testing another database

```python
>>> ini.database = "asplund09"  # load
>>> ini.database  # query
'asplund09'
```

## Simultaneous usage of multiple databases

```python
>>> import iniabu
>>> db1 = iniabu.IniAbu(database="lodders09")
>>> db2 = iniabu.IniAbu(database="asplund09")
```

---

# Units used to return information

- **Default**: Linear, number abundance

- Normed to abundance of silicon: Si = 106.

- Used, e.g., in Lodders et al. (2009)
--

- Can easily switch to logarithmic abundance
  ```python
  >>> ini.abundance_unit == "log"
  ```

- Now, abundance of element *X* normed to hydrogen:
  `$$\log_{10}(\epsilon_{X}) = \log_{10} \left( \frac{\mathrm{N}_X}{\mathrm{N}_\mathrm{H}} \right) + 12$$`

- Query the currently set abundance unit:
  ```python
  >>> ini.abundance_unit
  'log'
```

---

# Querying an element or isotope

## Load the element / isotope into a variable

```python
>>> ele = ini.element['Fe']
>>> iso = ini.isotope['Ne-20']
```
--

## Query solar abundance

```python
>>> ele.solar_abundance
847990.0
>>> iso.solar_abundance
3060000.0
```

## Query the isotopes of an element
```python
>>> ele.isotopes_a
*array([54, 56, 57, 58])
>>> ele.isotopes_solar_abundance
*array([ 49600., 778000.,  18000.,   2390.])
```

---

# Calculate δ-value for your measurements

## What is the δ-value?

`$$\delta\left( \frac{^{i}X}{^{j}X}\right) = 
\left( \frac{\left(\frac{^{i}X}{^{j}X}\right)_\mathrm{msr}}
{\left(\frac{^{i}X}{^{j}X}\right)_\odot} - 1 \right) \times f$$`

- Deviation of an isotope ratio from solar ratio

- Generally expressed in parts per thousand (‰)

- Achieve retrieving δ-value in ‰ by setting \$f=1000\$ (set by default)

---

# Calculate δ-value for your measurements

- Assume silicon isotope ratios have been measured with respect to 28Si

- Three ways to calculate the δ-values:
  ```python
  >>> msr = [1., 0.01, 0.04]  # measurements
  ```
--
  - Manual:
    ```python
    >>> ini.delta_isotope(['Si-28', 'Si-29', 'Si-30'], 'Si-28', msr)
    array([   0.        , -803.05359812,  195.07612569])
    ```
--
  - Automatically select all isotopes in nominator:
    ```python
    >>> ini.delta_isotope('Si', 'Si-28', msr)
    array([   0.        , -803.05359812,  195.07612569])
    ```
--
  - Also set denominator automatically to most abundant isotope:
  ```python
  >>> ini.delta_isotope('Si', 'Si', msr)
  array([   0.        , -803.05359812,  195.07612569])
  ```

---

# Get help by calling `ini.delta_isotope?`

```python
Signature:
ini.delta_isotope(
    nominator,
    denominator,
    value,
    mass_fraction=False,
    delta_factor=1000.0,
)
Docstring:
Calculate the delta-value for a given isotope ratio and a value.

The delta-value is defined as:

result = (measured value / solar ratio - 1)

By default, the delta-value is multiplied by 1000, thus, expressing it in
permil. Other factors can be chosen.

Nominator and denominator have the same restrictions as for the
``ratio_element`` method.
The same number of values must be supplied as there are isotope ratios defined.

:param nominator: Isotope(s) in nominator.
:type nominator: str,list
:
```

---

---

# The next steps...

- User testing and feature proposals

- Your chance to take direct influence

- Voice your opinion on bugs / enhancements by raising an [issue on GitHub](https://github.com/galactic-forensics/iniabu/issues) (preferred)

- .gray[Send me an e-mail with your request (I will raise the issue)]

- Improve test suite

- Release v1.0.0 as `iniabu` on PyPi (hopefully end of 2020)

**Feel free to contribute!**
]

---

## Questions?