P-winds

This is the beta release of `p-winds` version 2.0. The newest addition is the brand new module `fluid`, which calculates self-consistent hydrodynamic simulations instead of assuming an isothermal Parker wind model. This version contains a wrapper for the [ATES code](https://github.com/AndreaCaldiroli/ATES-Code), originally developed by Andrea Caldiroli. Please follow the installation instructions and documentation for details on how to use the new module.

Change log:

- Implemented the new module `fluid`, which contains a wrapper for the hydrodynamic escape code ATES
- General improvements in code comments and documentation

This is an important update to `p-winds` that corrects bugs and implement a cool new algorithm that has been requested in the past. Updating to this version is highly recommended.

Change log:

- Corrected a bug in the calculation of the Gaussian width of Voigt profiles in the `transit` module.
- Added the option to pass `gas_temperature` as an array (in function of radius from planet) instead of only a `float` or `int`. This is useful if you have a model with self-consistently calculated temperatures and do not need to assume an isothermal profile.
- Other small improvements to documentation and code reading.

This is a fairly small, but useful update to `p-winds`. We added a new function in the `tools` module that generates a "generic" standard spectrum (`standard_spectrum()`) based on the stellar type and semi-major axis. The available stellar types are:
- ``'mid-A'`` (based on HR 8799)
- ``'early-F'`` (based on WASP-17)
- ``'late-F'`` (based on HD 108147)
- ``'early-G'`` (based on HD 149026)
- ``'solar'`` (based on the Sun)
- ``'young-sun'`` (based on iota Horologii)
- ``'late-G'`` (based on TOI-193)
- ``'active-K'`` (based on epsilon Eridanii)
- ``'early-K'`` (based on HD 97658)
- ``'late-k'`` (based on WASP-43)
- ``'active-M'`` (based on Proxima Centauri)
- ``'early-M'`` (based on GJ 436)
- ``'late-M'`` (based on TRAPPIST-1)

Another important change: the environment variable that defines the location of the MUSCLES spectra is now `$PWINDS_REFSPEC_DIR`. Please modify your workflow accordingly.

If you use any of these, please cite the papers that produced the spectra.
Enjoy it!

- Added almost all MUSCLES, Mega-MUSCLES and MUSCLES Extension stellar spectra are now supported in `tools.generate_muscles_spectrum()` function. See the documentation for details.
- Since there are many more spectra, starting on this version the MUSCLES fits files are not included in the `p-winds` package. Now the user needs to manually download them (either from the [survey website](https://archive.stsci.edu/prepds/muscles/) or from this [convenience Box link](https://stsci.box.com/s/f2u1gp6b4i7yqxmt1h70pwb9cz9rmup7)), and then set a `$MUSCLES_DIR` environment variable pointing to the location of the fits files. See installation instructions.
- General bug fixes.

- New module: `carbon.py` is used to calculate the distribution of neutral, singly-ionized and doubly-ionized carbon in an exoplanet's upper atmosphere.
- New module: `oxygen.py` is used to calculate the distribution of neutral and singly-ionized oxygen in an exoplanet's upper atmosphere.
- New module: `lines.py` stores spectral line information. This information was previously stored in `microphysics.py`, but was moved to avoid bloating the latter module. **Please pay attention to this new usage of `microphysics.py`! As always, check the documentation to learn more.**
- `helium.py` now includes a function `ion_fraction()` that calculates the ion fraction of helium more quickly than the `population_fraction()` function.
- The function `make_spectrum_from_file()` now has an option to scale an input spectrum by systemic distance and the semi-major axis of a planet around it.
- New examples in the documentation: Roche lobe effects and exospheric metals.
- General bug fixes and updates to docstrings.

A paper describing the `carbon` and `oxygen` modules is being submitted for refereed publication soon. As always, please check the documentation of the code for guidance on the functions parameters!

This is a beta test of the version 1.4.1 of `p-winds`. There is quite a bit of new features. The code now calculates the density profiles of exospheric metals! Here is the changelog:

- New module: `carbon.py` is used to calculate the distribution of neutral, singly-ionized and doubly-ionized carbon in an exoplanet's upper atmosphere.
- New module: `oxygen.py` is used to calculate the distribution of neutral and singly-ionized oxygen in an exoplanet's upper atmosphere.
- New module: `lines.py` stores spectral line information. This information was previously stored in `microphysics.py`, but was moved to avoid bloating the latter module. **Please pay attention to this new usage of `microphysics.py`! As always, check the documentation to learn more.**
- `helium.py` now includes a function `ion_fraction()` that calculates the ion fraction of helium more quickly than the `population_fraction()` function.
- New examples in the documentation: Roche lobe effects and exospheric metals.
- General bug fixes and updates to docstrings.

We encourage users to test this beta version and report bugs in the [GitHub issues](https://github.com/ladsantos/p-winds/issues). As always, please check the documentation of the code for guidance on the functions parameters!