Rename files for clarity

Author: troyraen

deploy_to_fornax_manifest.in

@@ -18,19 +18,19 @@ tutorials/simulated-data/roman_hlss_number_density.md
 tutorials/spherex/spherex_cutouts.md
 tutorials/spherex/spherex_intro.md
 tutorials/spherex/spherex_psf.md
-tutorials/spherex/spherex_sdt/conda-sdt_env.yml
-tutorials/spherex/spherex_sdt/README.md
-tutorials/spherex/spherex_sdt/sdt_irsa.md
-tutorials/spherex/spherex_sdt/spx_sdt/__init__.py
-tutorials/spherex/spherex_sdt/spx_sdt/aperture_photometry.py
-tutorials/spherex/spherex_sdt/spx_sdt/bokeh_viz.py
-tutorials/spherex/spherex_sdt/spx_sdt/default_sdt.param
-tutorials/spherex/spherex_sdt/spx_sdt/default_sdt.sex
-tutorials/spherex/spherex_sdt/spx_sdt/default.conv
-tutorials/spherex/spherex_sdt/spx_sdt/default.nnw
-tutorials/spherex/spherex_sdt/spx_sdt/firefly_viz.py
-tutorials/spherex/spherex_sdt/spx_sdt/sdt_utils.py
-tutorials/spherex/spherex_sdt/spx_sdt/source_extraction.py
+tutorials/spherex/spherex_source_discovery/conda-spherex_sdt.yml
+tutorials/spherex/spherex_source_discovery/README.md
+tutorials/spherex/spherex_source_discovery/spherex_source_discovery_tool_demo.md
+tutorials/spherex/spherex_source_discovery/spherex_source_discovery_tool/__init__.py
+tutorials/spherex/spherex_source_discovery/spherex_source_discovery_tool/aperture_photometry.py
+tutorials/spherex/spherex_source_discovery/spherex_source_discovery_tool/bokeh_viz.py
+tutorials/spherex/spherex_source_discovery/spherex_source_discovery_tool/default_sdt.param
+tutorials/spherex/spherex_source_discovery/spherex_source_discovery_tool/default_sdt.sex
+tutorials/spherex/spherex_source_discovery/spherex_source_discovery_tool/default.conv
+tutorials/spherex/spherex_source_discovery/spherex_source_discovery_tool/default.nnw
+tutorials/spherex/spherex_source_discovery/spherex_source_discovery_tool/firefly_viz.py
+tutorials/spherex/spherex_source_discovery/spherex_source_discovery_tool/sdt_utils.py
+tutorials/spherex/spherex_source_discovery/spherex_source_discovery_tool/source_extraction.py
 tutorials/spitzer/siav2_seip.md
 tutorials/techniques-and-tools/cloud-access-intro.md
 tutorials/techniques-and-tools/Parallelize_Convolution.md

ignore_tutorials/ignore_rendering_execution

@@ -3,4 +3,4 @@ tutorials/techniques-and-tools/Parallelize_Convolution
 # Uses about 10G of memory which doesn't leave enough for other notebooks
 tutorials/wise/wise-allwise-catalog-demo
 # Requires source extractor, which requires a conda install
-tutorials/spherex/spherex_sdt/sdt_irsa.md
+tutorials/spherex/spherex_source_discovery/spherex_source_discovery_tool_demo.md

notebook_metadata.yml

@@ -77,7 +77,7 @@
   file: tutorials/euclid/3_Euclid_intro_1D_spectra.md
   description: Load a galaxy spectrum and plot it. Understand the wavelength, flux, and mask values.
 - title: Source Discovery Tool
-  file: tutorials/spherex/spherex_sdt/sdt_irsa.md
+  file: tutorials/spherex/spherex_source_discovery/spherex_source_discovery_tool_demo.md
   description: Discover, extract, and visualize sources from SPHEREx Spectral Images.
 - title: Spectral Image Cutouts
   file: tutorials/spherex/spherex_cutouts.md

toc.yml

@@ -13,7 +13,7 @@ project:
         - title: PSF Models
           file: tutorials/spherex/spherex_psf.md
         - title: Source Discovery Tool
-          file: tutorials/spherex/spherex_sdt/sdt_irsa.md
+          file: tutorials/spherex/spherex_source_discovery/spherex_source_discovery_tool_demo.md
     - title: Euclid
       file: tutorials/euclid/euclid.md
       children:

tutorials/spherex/spherex.md

@@ -12,4 +12,4 @@ SPHEREx data releases include weekly [Quick Release spectral image products](htt
 
 - [PSF Models](spherex_psf.md) - Understand how SPHEREx point spread function (PSF) information is organized and accessed.
 
-- [Source Discovery Tool](spherex_sdt/sdt_irsa.md) - Discover, extract, and visualize sources from SPHEREx Spectral Images.
+- [Source Discovery Tool](spherex_source_discovery/spherex_source_discovery_tool_demo.md) - Discover, extract, and visualize sources from SPHEREx Spectral Images.

tutorials/spherex/spherex_sdt/README.md …herex/spherex_source_discovery/README.mdtutorials/spherex/spherex_sdt/README.md renamed to tutorials/spherex/spherex_source_discovery/README.md tutorials/spherex/spherex_sdt/README.md renamed to tutorials/spherex/spherex_source_discovery/README.md

@@ -2,14 +2,14 @@
 
 ## Overview
 
-The SPHEREx Source Discovery Tool is the Python package `spx_sdt` (included in this directory), which is used to discover and extract sources from SPHEREx Spectral Images and visualize their spectra.
-The notebook [](sdt_irsa.md) demonstrates how to use it.
+The SPHEREx Source Discovery Tool is the Python package `spherex_source_discovery_tool` (included in this directory), which is used to discover and extract sources from SPHEREx Spectral Images and visualize their spectra.
+The notebook [](spherex_source_discovery_tool_demo.md) demonstrates how to use it.
 
 ### Directory Contents
 
-- `sdt_irsa.md`: Demo notebook.
-- `conda-sdt_env.yml`: Conda environment definition file.
-- `spx_sdt/`: Python package, including functions and configuration files to extract and visualize sources.
+- `spherex_source_discovery_tool_demo.md`: Demo notebook.
+- `conda-spherex_sdt.yml`: Conda environment definition file.
+- `spherex_source_discovery_tool/`: Python package, including functions and configuration files to extract and visualize sources.
   - Python modules
     - `aperture_photometry.py`: Functions adapted from Zafar Rustamkulov to perform aperture photometry.
     - `bokeh_viz.py`: Functions for dynamic `bokeh` visualizations.
@@ -26,37 +26,37 @@ The notebook [](sdt_irsa.md) demonstrates how to use it.
 
 ### On local machine
 
-All necessary packages and tools (SExtractor) are included in the `conda-sdt_env.yml` file.
+All necessary packages and tools (SExtractor) are listed in the `conda-spherex_sdt.yml` file.
 
 To create a conda environment with the dependencies on your local machine use:
   ```
-  conda env create --f conda-sdt_conda.yml
+  conda env create --f conda-spherex_sdt.yml
   ```
 
 Then, make the environment available in the list of kernels for your JupyterLab:
   ```
-  conda activate sdt_env
-  python -m ipykernel install --user --name=sdt_env
+  conda activate spherex_sdt
+  python -m ipykernel install --user --name=spherex_sdt
   ```
 
 To use the environment in your Jupyter notebooks, either start JupyterLab in that environment by typing
 
 ```
-conda activate std_env
+conda activate spherex_sdt
 jupyter-lab
 ```
 
-or select the environment `sdt_env` in your Jupyter Notebook using the dropdown on the upper left.
+or select the environment `spherex_sdt` in your Jupyter Notebook using the dropdown on the upper left.
 
 ### On Fornax
 
 Installing the conda environment on the [NASA Fornax Science Console](https://science.nasa.gov/astrophysics/programs/physics-of-the-cosmos/community/the-fornax-initiative/) needs slightly different steps. These can be reviewed in the documentation [create a new environment](https://docs.fornax.sciencecloud.nasa.gov/compute-environments/#create-new-env).
 
-In order to install this specific conda environment on Fornax, the file name of the `yml` file specifically needs to be in the following format `conda-*.yml`. The `yml` file distributed here is already in that format (`conda-sdt_env.yml`). Once this is set, open a new terminal (click on the large "+" button right under the "File" menu tab) and type to following command _inside_ the same directory where the `yml` file is located:
+In order to install this specific conda environment on Fornax, the file name of the `yml` file specifically needs to be in the following format `conda-*.yml`. The `yml` file distributed here is already in that format (`conda-spherex_sdt.yml`). Once this is set, open a new terminal (click on the large "+" button right under the "File" menu tab) and type to following command _inside_ the same directory where the `yml` file is located:
   ```
   setup-conda-env --user
   ```
 
 Note that we use the `--user` option here, which will keep the environment available for subsequent Fornax sessions.
 
-To use the environment in your Jupyter notebooks on Fornax, directly select the environment `sdt_env` in your Jupyter Notebook using the dropdown on the upper left.
+To use the environment in your Jupyter notebooks on Fornax, directly select the environment `spherex_sdt` in your Jupyter Notebook using the dropdown on the upper left.

…ls/spherex/spherex_sdt/conda-sdt_env.yml …x_source_discovery/conda-spherex_sdt.ymltutorials/spherex/spherex_sdt/conda-sdt_env.yml renamed to tutorials/spherex/spherex_source_discovery/conda-spherex_sdt.yml tutorials/spherex/spherex_sdt/conda-sdt_env.yml renamed to tutorials/spherex/spherex_source_discovery/conda-spherex_sdt.yml

@@ -1,4 +1,4 @@
-name: sdt_env
+name: spherex_sdt
 channels:
   - conda-forge
   - defaults

…/spherex/spherex_sdt/spx_sdt/__init__.py …pherex_source_discovery_tool/__init__.pytutorials/spherex/spherex_sdt/spx_sdt/__init__.py renamed to tutorials/spherex/spherex_source_discovery/spherex_source_discovery_tool/__init__.py tutorials/spherex/spherex_sdt/spx_sdt/__init__.py renamed to tutorials/spherex/spherex_source_discovery/spherex_source_discovery_tool/__init__.py

@@ -19,7 +19,7 @@
 from tqdm import tqdm
 
 # Local
-from spx_sdt.sdt_utils import get_exp_id
+from spherex_source_discovery_tool.sdt_utils import get_exp_id
 
 
 # Constants