Merge pull request #228 from robelgeda/pyos

Clean up README and Citation

.github/ISSUE_TEMPLATE/01-bug-report.yml

@@ -7,7 +7,7 @@ body:
     attributes:
       label: Problem description
       description: |
-        A concise description of what you're experiencing.
+        Please provide a concise description of what you're experiencing.
 
         Please explain:
 
@@ -21,7 +21,7 @@ body:
     attributes:
       label: Code sample
       description: >
-        Create a [minimal, complete, verifiable example](https://stackoverflow.com/help/mcve).
+        Please create a [minimal, complete, verifiable example](https://stackoverflow.com/help/mcve).
         Please, paste your code between the ``` tickmarks below or link to a [gist](https://gist.github.com/).
       value: |
         Code run:

.github/ISSUE_TEMPLATE/03-feature-request.yml

@@ -7,7 +7,7 @@ body:
     attributes:
       label: Feature or Problem
       description: >
-        A clear and concise description of what you are trying to achieve.
+        Please provide a clear and concise description of what you are trying to achieve.
       placeholder: >
         "I want to be able to [...] but I can't because [...]".
     validations:

.github/SUPPORT.md

@@ -1,4 +1,3 @@
 # Support
 
 * Start a [discussion topic](https://github.com/PetroFit/petrofit/discussions)
-* Email the authors or maintainers

CITATION.rst

@@ -5,7 +5,7 @@ Citing and Credits
 Publications
 ============
 
-|AJ tag| |zonodo tag| |ascl tag|
+|AJ tag| |zonodo tag| |ads tag|  |ascl tag|
 
 If you would like to cite PetroFit for a publication, please use the acknowledgments below.
 Given the close relationship between PetroFit and Photutils, we ask that you also cite
@@ -94,10 +94,16 @@ HTML (.html):
     :target: https://arxiv.org/abs/2202.13493
     :alt: PetroFit arxiv
 
+
+.. |ads tag| image:: https://img.shields.io/badge/ADS-2022AJ....163..202G-blue.svg?style=flat&color=3484e0
+    :target: https://ui.adsabs.harvard.edu/abs/2022AJ....163..202G/abstract
+    :alt: ADS PetroFit
+
 .. |ascl tag| image:: https://img.shields.io/badge/ascl-2203.013-black.svg?colorB=262255
     :target: https://ascl.net/2203.013
     :alt: ascl:2203.013
 
 .. |petrofit tag| image:: https://img.shields.io/badge/powered%20by-PetroFit-blue.svg?style=flat&color=00B0F0
     :target: https://github.com/PetroFit/petrofit
     :alt: PetroFit
+

README.rst

@@ -4,7 +4,7 @@
 
 PetroFit
 --------
-|repostatus tag| |CI tag| |rtd tag| |PyPI tag| |AJ tag| |zonodo tag| |python version tag| |astropy tag| |photutils tag| 
+|repostatus tag| |CI tag| |rtd tag| |PyPI tag| |AJ tag| |zonodo tag| |python version tag| |CodeCov| |astropy tag| |photutils tag| 
 
 PetroFit is a package for calculating Petrosian properties, such as radii and concentration indices, as well as fitting
 galaxy light profiles. In particular, PetroFit includes tools for performing accurate photometry, segmentations,
@@ -17,9 +17,23 @@ for installation instructions and a guide to the ``petrofit`` module.
 Installation
 ------------
 
-You can install PetroFit using ``pip install petrofit``. Please see
+You can install PetroFit using pip or build a `jupyter lab <https://jupyter.org/>`_ environment using `hatch <https://jupyter.org/>`_ . Please see
 the `petrofit documentation <https://petrofit.readthedocs.io/en/latest/>`_ for detailed installation instructions.
 
+**pip Install**: 
+
+.. code-block:: bash
+
+    pip install petrofit
+
+**hatch  Jupyter Lab**:
+
+cd into the dir you want to launch jupyter lab in, and then run:
+
+.. code-block:: bash
+    
+    hatch run jupyter:lab
+
 Examples
 --------
 
@@ -88,8 +102,8 @@ Given a 2D image (``image``) the following code snippet demonstrates how to crea
 Citation
 --------
 
-Please see the `petrofit documentation <https://petrofit.readthedocs.io/en/latest/>`_
-for citation instructions. This information is also available in the `CITATION.rst`` 
+Please see the `PetroFit citation documentation <https://petrofit.readthedocs.io/en/latest/citing.html>`_
+for citation instructions. This information is also available in the ``CITATION.rst`` 
 file in the PetroFit repo.
 
 License
@@ -170,3 +184,7 @@ petrofit based on its use in the README file for the
 .. |python version tag| image:: https://img.shields.io/python/required-version-toml?tomlFilePath=https%3A%2F%2Fraw.githubusercontent.com%2Fpetrofit%2Fpetrofit%2Fmain%2Fpyproject.toml
    :alt: Python Version from PEP 621 TOML
    :target: https://www.python.org/downloads/
+
+.. |CodeCov| image:: https://codecov.io/gh/petrofit/petrofit/graph/badge.svg
+   :alt: Tests code coverage
+   :target: https://codecov.io/gh/petrofit/petrofit

docs/installation.rst

@@ -3,9 +3,7 @@ Installation
 ############
 
 There are multiple ways to install the PetroFit package. The latest release of PetroFit can be installed from `PyPi <https://pypi.org/project/petrofit>`_ using the ``pip install petrofit`` command (see the `<pip_>`_ section below). To install the latest developer version of `PetroFit`, please clone the `PetroFit GitHub repository <https://github.com/PetroFit/petrofit>`_
-and install the package (see the `<For Developers_>`_ section below). There are two recommended ways to install the requirements needed to run the PetroFit package, through
-`Conda <https://docs.conda.io/projects/conda/en/latest/user-guide/getting-started.html>`_ and
-`Docker <https://docs.docker.com/get-docker/>`_.
+and install the package (see the `<For Developers_>`_ section below).
 
 pip
 ****
@@ -15,6 +13,17 @@ PetroFit can be installed using pip as follows:
 
     pip install petrofit
 
+hatch
+******
+PetroFit is comaptible with ``hatch``. If you would like to create a jupyter lab instance with PetroFit installed, 
+you can use the following command: 
+
+ .. code-block:: bash
+    
+    cd <dir you want to launch jupyter lab in>
+    hatch run jupyter:lab
+
+
 Conda
 *****
 
@@ -37,73 +46,14 @@ environment as follows:
 
     conda env create -f environment.yml
 
-**Step 3:** Activate the `petrofit` environment.
-
-.. code-block:: bash
-
-    source activate petrofit
-
-**Step 4:** Install PetroFit.
-
-.. code-block:: bash
-
-    python setup.py install
-
-or if installing from pip:
-
-.. code-block:: bash
-
-    pip install petrofit
-
-Docker
-******
-
-We have included a Docker file as well as a helper script to make the installation of the package as easy as possible.
-The docker file will create a Jupyter Notebook image which makes creating and running Notebooks possible.
-To install using the helper script, please follow the instructions below.
-
-
-**Step 1:** Clone the PetroFit repo and ``cd`` into the cloned repo.
-
-.. code-block:: bash
-
-    git clone https://github.com/PetroFit/petrofit.git
-
-    cd petrofit
-
-**Step 2:** Use the helper script to create the new docker image.
-
-.. code-block:: bash
-
-    python docker.py build
-
-
-.. Note::
-
-    The cloned repo will be mounted when running using the helper script and any changes to the host code will
-    become available in the docker image (notebook restart may be required to import changed version).
-
-**Step 3:** Start the notebook using the helper script. You can mount a host directory or a list of directories
-(separated by space) by adding their paths at the end of the command. The host directories will be mounted under
-the `mount` directory in the docker image.
+**Step 3:** Install and activate the `petrofit` environment.
 
 .. code-block:: bash
 
-    python docker.py run [extra_mount_paths]
-
-.. important::
-
-    Please note that this type of mounting is called a ``bind`` which means the changes you make to the mounted virtual
-    directory will also apply in the host directory on your hard drive.
-
-**Step 4:** Copy and paste the notebook URL into your internet browser. The link to the notebook home should look like this:
-
-.. code-block:: bash
+    conda env create -f environment.yml
 
-    http://127.0.0.1:8888/?token=d020c13d029013c20d0329e6913c5df076d0a4a14e63dc77
+    source activate petrofit
 
-**Step 5:** You can close the server like any other Jupyter notebook server by hitting ``Ctrl + C``
-(make sure to have saved your notebook before shutting down the server).
 
 For Developers
 **************
@@ -122,13 +72,5 @@ For developers, we recommend setting up a conda environment and then using the f
 If you will be contributing to the software, we recommend forking the repository on GitHub first, cloning your forked repository,
 and then installing the developer version.
 
-Before installing PetroFit, you may need to install the required dependencies.
-You can do this using the requirements file located in the top directory of the repository. To do so, navigate to the
-top directory of the PetroFit repository (where the requirements.txt file is located). Then run:
-
-.. code-block:: bash
-
-    pip install -r requirements.txt
-
 Frozen versions of conda environment files are provided via the `petrofit_environments repository <https://github.com/PetroFit/petrofit_environments>`_.