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Feature/documentation #20

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Jun 3, 2022
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Feature/documentation #20

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b712cbd
JJ: Updating glossary
joohlz May 13, 2022
0576aaf
JJ: added github link
joohlz May 27, 2022
416c217
Update link in contact info.
May 27, 2022
4c3f40b
Fill out glossary entries, except zero-point luminosity
May 27, 2022
c886de1
[JB] fixed table to wrap text
juditbergfalk May 27, 2022
1f80c09
[JB] table format..trying it again
juditbergfalk May 27, 2022
4012aac
Get table to be narrower by inserting line breaks.
May 27, 2022
6150d2e
Updating links, badges, and working on unifying reference labels.
May 27, 2022
3b4cdce
[JB] added more definitions, changed citation, changed references titles
juditbergfalk May 28, 2022
37bdc31
Fix formatting issues on links, set up release notes.
Jun 2, 2022
9be8fe3
Fix more link formatting and add blurb about offline work.
Jun 2, 2022
598a553
Add installation instructions.
Jun 2, 2022
1baae99
Merge branch 'develop' into feature/documentation
Jun 2, 2022
f6845c6
Add glossary entries
Jun 2, 2022
032a1f5
JJ: added term
joohlz Jun 2, 2022
d8e7df4
Merge branch 'develop' into feature/documentation
Jun 3, 2022
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17 changes: 9 additions & 8 deletions RELEASE_CHECKLIST.md
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Expand Up @@ -8,11 +8,12 @@ Please be sure to do the following when making a release.
5. Update release notes `RELEASENOTES.md`.
6. Update `docs/source/index.rst` if badges changed.
7. Restore fail-on-warning on .readthedocs.yaml if it was turned off.
8. Make a release on github.
9. Be sure the `stable` build of readthedocs points to the new release.
10. Be sure to create a version on readthedocs of the new release.
11. If the version is a patch, deactivate the docs version for the previous patch of the same minor version. (Only one docs version for each minor version should be active at a time.)
12. Be sure codecov website is switched to default to master branch.
13. Update Zenodo.
14. Move readthedocs latest to master branch.
15. Remove items 14 and 15 from this list.
8. Update all binder links in `docs/source/02_Modules.rst` to point to the upcoming version.
9. Make a release on github.
10. Be sure the `stable` build of readthedocs points to the new release.
11. Be sure to create a version on readthedocs of the new release.
12. If the version is a patch, deactivate the docs version for the previous patch of the same minor version. (Only one docs version for each minor version should be active at a time.)
13. Be sure codecov website is switched to default to master branch.
14. Update Zenodo.
15. Move readthedocs latest to master branch.
16. Remove items 14 and 15 from this list.
33 changes: 27 additions & 6 deletions docs/source/01_Getting_Started.rst
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1. Getting started
==================


------
Binder
------
======

.. image:: https://mybinder.org/badge_logo.svg
:target: https://mybinder.org/v2/gh/villano-lab/galactic-spin-W1/master?labpath=binder

Binder is a website that hosts jupyter notebooks and allows users to run them on the web without any download or installation required
from the user. If you only wish to run the notebooks, you can click on the binder button above to run them from your browser.

------------
Installation
------------
============

Installation of this workshop is not needed.
Binder Project provides an easy access to Jupyter notebooks and their environments without the hassle of installation. Upon clicking on the provided Binder URLs, the modules of the workshop open in your browser.
Binder Project provides an easy access to Jupyter notebooks and their environments without the hassle of installation.
Upon clicking on the provided Binder URLs, the modules of the workshop open in your browser.

If you wish to work offline, you can run these notebooks in Jupyter Lab or Jupyter Notebooks.

Requirements
------------

1. **Jupyter Lab** or **Jupyter Notebooks**, which are both included with `Anaconda Python <https://www.anaconda.com/>`_.
2. The ability to install python modules, either through **pip**, **conda**, or `Anaconda Python <https://www.anaconda.com/>`_.

Instructions
------------

These instructions will assume that you will use Anaconda.
For experienced users with other setups,
please install the environment found in `binder/environment.yml` to run our notebooks.

0. Install `Anaconda Python <https://www.anaconda.com/>`_.
1. `Download <https://github.com/villano-lab/galactic-spin-W1/archive/refs/heads/master.zip>`_ and unzip the repository somewhere inside your user directory, such as the "Documents" folder.
2. In Anaconda Navigator, go to "Environments," then select "Import."
3. Import from "Local drive" and select the file `binder/environment.yml` from the repository. Name the environment `galactic-spin`. Anaconda will start installing all other necessary dependencies; please be patient, as this will take some time.
4. Once the environment is finished building, from the "Home" menu of Anaconda Navigator, launch a prompt. The prompt will depend on your system -- for example, in Windows, you can choose "CMD.exe Prompt."
5. In the prompt, run the following command: `ipython kernel install --user --name=galactic-spin`
6. In Anaconda Navigator, launch "JupyterLab" and browse to your local copy of the repository, then enter the `binder` subdirectory. Enjoy!
67 changes: 44 additions & 23 deletions docs/source/02_Modules.rst
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2. Modules
==========

.. role:: raw-html(raw)
:format: html

--------
Overview
--------

Description of the learning modules


+------------------------------------------+----------------------------------------------------------------------------------------------------------------+
| **File Name** | **Short Description** |
+------------------------------------------+----------------------------------------------------------------------------------------------------------------+
| `01_DM_Rotation_Curve_Intro.ipynb` | Animations and rotation curve plots demonstrating three types of rotational motion. |
+------------------------------------------+----------------------------------------------------------------------------------------------------------------+
| `02_Widget_NGC5533_DMonly.ipynb` | An interactive introduction to Dark Matter. |
+------------------------------------------+----------------------------------------------------------------------------------------------------------------+
| `03_Measured_Data_Plotting.ipynb` | Rotation curve plotting of measured velocities to visualize star and gas motions in a galaxy. |
+------------------------------------------+----------------------------------------------------------------------------------------------------------------+
| `04_Plotting_Rotation_Curves.ipynb` | Choose between 4 galaxies and plot the rotation curve of each component and their total velocity. |
+------------------------------------------+----------------------------------------------------------------------------------------------------------------+
| `05_Widget_NGC5533_All_Components.ipynb` | Interactive widget to adjust the components of the galaxy NGC 5533 and see how velocity changes. |
+------------------------------------------+----------------------------------------------------------------------------------------------------------------+
| `06_Plotting_SPARC_Data.ipynb` | Plotting the components of galactic rotation curves using the SPARC database of 175 galaxies. |
+------------------------------------------+----------------------------------------------------------------------------------------------------------------+
| `07_Bonus_Bulge_Rotation_Curve.ipynb` | Calculate the theoretical rotation curve of the bulge component using empirically derived parameters. |
+------------------------------------------+----------------------------------------------------------------------------------------------------------------+
| `08_Interactive_Fitting.ipynb` | Calculate the fitting parameters of the rotation curve to determine the amount of Dark Matter needed. |
+------------------------------------------+----------------------------------------------------------------------------------------------------------------+
| `09_Widget_SPARC_Galaxies.ipynb` | Interactive widget to visualize the components of multiple galaxies using the SPARC database of 175 galaxies. |
+------------------------------------------+----------------------------------------------------------------------------------------------------------------+
| `10_Bonus_Black_Holes_as_DM.ipynb` | Considering tiny black holes as Dark Matter candidates. |
+------------------------------------------+----------------------------------------------------------------------------------------------------------------+
+------------------------------------------+--------------------------------------------------------+
| **File Name** | **Short Description** |
+------------------------------------------+--------------------------------------------------------+
| `01_DM_Rotation_Curve_Intro.ipynb` | Animations and rotation curve plots demonstrating |
| | :raw-html:`<br />` |
| | three types of rotational motion. |
+------------------------------------------+--------------------------------------------------------+
| `02_Widget_NGC5533_DMonly.ipynb` | An interactive introduction to Dark Matter. |
+------------------------------------------+--------------------------------------------------------+
| `03_Measured_Data_Plotting.ipynb` | Rotation curve plotting of measured velocities to |
| | :raw-html:`<br />` |
| | visualize star and gas motions in a galaxy. |
+------------------------------------------+--------------------------------------------------------+
| `04_Plotting_Rotation_Curves.ipynb` | Choose between 4 galaxies and plot the rotation curve |
| | :raw-html:`<br />` |
| | of each component and their total velocity. |
+------------------------------------------+--------------------------------------------------------+
| `05_Widget_NGC5533_All_Components.ipynb` | Interactive widget to adjust the components of the |
| | :raw-html:`<br />` |
| | galaxy NGC 5533 and see how velocity changes. |
+------------------------------------------+--------------------------------------------------------+
| `06_Plotting_SPARC_Data.ipynb` | Plotting the components of galactic rotation curves |
| | :raw-html:`<br />` |
| | using the SPARC database of 175 galaxies. |
+------------------------------------------+--------------------------------------------------------+
| `07_Bonus_Bulge_Rotation_Curve.ipynb` | Calculate the theoretical rotation curve of the bulge |
| | :raw-html:`<br />` |
| | component using empirically derived parameters. |
+------------------------------------------+--------------------------------------------------------+
| `08_Interactive_Fitting.ipynb` | Calculate the fitting parameters of the rotation curve |
| | :raw-html:`<br />` |
| | to determine the amount of Dark Matter needed. |
+------------------------------------------+--------------------------------------------------------+
| `09_Widget_SPARC_Galaxies.ipynb` | Interactive widget to visualize the components of |
| | :raw-html:`<br />` |
| | multiple galaxies using the SPARC database of 175 |
| | :raw-html:`<br />` |
| | galaxies. |
+------------------------------------------+--------------------------------------------------------+
| `10_Bonus_Black_Holes_as_DM.ipynb` | Considering tiny black holes as Dark Matter candidates.|
+------------------------------------------+--------------------------------------------------------+

--------------------------
01_DM_Rotation_Curve_Intro
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101 changes: 69 additions & 32 deletions docs/source/03_Glossary.rst
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Expand Up @@ -5,88 +5,125 @@ Glossary
.. glossary::

Arcsecond
Unit of an angle of how large something appears in the sky.
Unit of an angle denoting how large something appears in the sky.

Bulge
Dense spherical core of the galaxy.
Dense, spherical core of the galaxy.

Central mass density
The central mass density is the density at the center of the galaxy, changing this value changes the magnitude of the Dark Matter curve.
The density of dark matter at the center of the galaxy. Changing this value changes the magnitude of the dark matter curve.

Centripetal force
A force that causes circular motion.

Concentration parameter
Also known as the bulge Sersic parameter "describes the curvature of the profile in a radius-magnitude plot" (Noordermeer 2008).
Also known as the bulge Sersic parameter. "Describes the curvature of the profile in a radius-magnitude plot" [Noordermeer2008]_.

Core radius
The core radius indicates where the density falls off by a factor of e (~2.7). Adjusting this factor changes where the "bump" of the curve is located. Related words: cutoff radius, scale radius.
Indicates the distance from the galactic center where the density falls off by a factor of *e* (~2.7). Adjusting this factor changes where the "bump" of the curve is located. Synonyms: cutoff radius, scale radius.

Dark matter
Dark matter is a placeholder to account for the matter in spiral galaxies that is `missing` ... Related words: Dark Matter halo.
A placeholder to account for the matter in spiral galaxies that is `missing` based on our observations of galactic motion. Related words: Dark Matter halo, Halo.

Dark matter halo
A disk-shaped distribution of Dark Matter that is most dense at some distance from the galactic center.

Density profile
The mass distribution of matter in the galaxy.

Disk
The stellar disk of the galaxy is a relatively flat component of the galaxy.

Inclination angle
The angle of the galaxy from the horizontal.

A large, relatively flat component of the galaxy.

Enclosed mass
The total mass of the area between the center of the galaxy or other body and the specified radius.

Edge-on spiral galaxy
A galaxy which lies in the same plane as our viewing direction which results in us only seeing the outer edge of the galaxy and part of the central bulge. Alternatively, a face-on galaxy is perpendicular to our line of sight revealing its spiral structure.

Fitting
...
The process of adjusting unknown parameters in order to match a theoretical equation to measured data.

Flat Rotation
Rotation whose curve plateaus at large radii.

Gravitational constant (G)
...

The constant of proportionality used to calculate effects of gravity.
In SI units, G = 6.67e-11 m^3 kg^-1 s^-2

Inclination angle
The angle of the galaxy from the horizontal, as viewed from Earth. For example, a face-on galaxy has an inclination angle of 0, and an edge-on galaxy has an inclination angle of 90°.

Interstellar gas
Gas between stars and galaxies.
Gas between stars and galaxies -- mostly Hydrogen. Synonyms: atomic gas.

Isothermal
...

Luminous matter
All matter that we are able to `see` in galaxies. Related words: light matter, visible matter, baryonic matter.
Having a constant temperature. In thermal physics, this affects the behavior of temperature-related properties, such as density.
Keplerian model
A model of the orbital motion of planets in solar systems such that the orbital velocity is inversely proportional to the square root of the radius. Related words: planet-like motion.

kpc
Unit of distance. kiloparsec: 1 kpc = 3262 light years = 3.086e+19 meters = 1.917e+16 miles.
Unit of distance; kiloparsec. 1 kpc = 3262 light years = 3.086e+19 meters = 1.917e+16 miles.

Luminous matter
All matter that emits visible light in galaxies. Synonyms: light matter, visible matter, baryonic matter.

MACHO
Massive Compact Halo Object.
MAssive Compact Halo Object. A type of object that emits little to no light, such as brown dwarfs, rogue planets, or black holes.

Mass-to-light ratio
The ratio of how much mass there is compared to how much it is visible. How much mass it is expected from the light source. The variation in the mass-to-light ratio means there is a wider range of masses that are plausible for the stellar component. Related words: M/L
Mass-to-light ratio (M/L ratio)
The ratio of how much mass there is compared to how much light the body emits; how much mass it is expected from the light source. Variation in the mass-to-light ratio means there is a wider range of masses that are plausible for the stellar component.

Measured datapoints
Measured velocities of stars and gas in a galaxy. Related words: measured velocities.
Measured velocities of stars and gas in a galaxy. Synonyms: measured velocities.

Mpc
Unit of distance. Megaparsec: 1 Mpc = 1000 kpc.
Unit of distance; megaparsec: 1 Mpc = 1000 kpc.

NGC
New General Catalogue of galaxies.

Photometry
...
The measurement of light emitted from astronomical objects.

Planet-like rotation
Rotation whose curve resembles that of planets orbiting a star. Related words: Keplerian model.

Prefactor
... Related words: scaling parameter, M/L ratio
A parameter that multiplies/directly scales the other information in an equation. Synonyms: scaling parameter. Related words: M/L ratio

Radial velocity
The speed stars and gas are moving at different distances from the center of the galaxy.

Reduced chi-squared value
In a strictly statistical sense, a reduced chi-squared of zero represents a perfect fit. However, a reduced chi-squared much less than 1 often indicates that more parameters were used than represented by the physical system. We would be simply connecting the measured data points.
A measure of how close the data and theory are to one another. In a strictly statistical sense, a reduced chi-squared of zero represents a perfect fit. However, a reduced chi-squared much less than 1 often indicates that more parameters were used than represented by the physical system, and we may be simply connecting the measured data points.

Rigid body rotation
Rotation whose curve resembles that of a rigid object. Synonyms: frisbee rotation

Rotation curve
A plot of a galaxy's radial velocity versus the radius or distance from the center.

Solar mass
Mass of the Sun. Approximately equal to 1.989e30 kilograms
Mass of the Sun, equal to 1.989e30 kilograms.

Spiral arms
In a spiral galaxy, these are the long parts protruding from the disc's otherwise elliptical shape. Related words: spiral galaxy.

Spiral galaxy
Galaxies that have spiral structures. Components are bulge, disk, gas, and Dark Matter halo. Spiral galaxies are less luminous than elliptical galaxies on average and have active star formation. Related words: spiral arms.

Surface brightness
The amount of flux from the galaxy per square arcsecond on the sky.

Theoretical rotation curve
...
A rotation curve that has been modeled from known parameters that is then used to match observed data.

UGC
Uppsala General Catalogue of galaxies.

Uncertainty
A value representing what range of values a data point might differ from what we measured. Synonyms: error.

Zero-point luminosity
...
A reference luminosity for a star that has a zero absolute bolometric magnitude [Mamajek2015]_.
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