spacetelescope · mgough-970 · May 14, 2024 · May 14, 2024 · May 14, 2024 · May 21, 2024
diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -0,0 +1,11 @@
+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for all configuration options:
+# dsd
+
+version: 2
+updates:
+  - package-ecosystem: "" # See documentation for possible values
+    directory: "/notebooks/" # Location of package manifests
+    schedule:
+      interval: "weekly"
diff --git a/_toc.yml b/_toc.yml
@@ -12,99 +12,98 @@ parts:
     - file: install.rst
       title: Installation
     - file: docs/notebook_development_workflow.rst
-      title: Notebook Development Workflow   
+      title: Notebook Development Workflow
   - caption: Development
     chapters:
     - file: docs/submitting_notebooks.rst
       title: Submitting Notebooks
     - file: docs/requirements.rst
-      title: Requirements file 
+      title: Requirements file
     - file: docs/notebooks.rst
       title: Jupyter Notebooks
     - file: docs/data_files.rst
-      title: Data Files 
+      title: Data Files
   - caption: GitHub Guidelines
     chapters:
     - file: docs/github_setup.rst
       title: GitHub Setup
     - file: docs/github_workflow.rst
       title: GitHub Workflow
     - file: docs/github_pr.rst
-      title: GitHub PR        
+      title: GitHub PR
   #- caption: Developers and Staff
-    # chapters:     
-    # - file : docs/stsci_notebook_leads.rst     
-    #   title: STScI Notebook Leads     
+    # chapters:
+    # - file : docs/stsci_notebook_leads.rst
+    #   title: STScI Notebook Leads
   - caption: Cross-Instrument
     chapters:
-    - file: notebooks/asdf_example/asdf_example.ipynb
+    - file: notebooks/cross_instrument/asdf_example/asdf_example.ipynb
       title: ASDF Example
-    - file: notebooks/background_estimation_imaging/Imaging_Sky_Background_Estimation.ipynb
+    - file: notebooks/cross_instrument/background_estimation_imaging/Imaging_Sky_Background_Estimation.ipynb
       title: Complex 2D Background
-    - file: notebooks/composite_model_fitting/specfit_demo_3.ipynb
+    - file: notebooks/cross_instrument/composite_model_fitting/specfit_demo_3.ipynb
       title: Composite Model Spectral Fitting
-    - file: notebooks/NIRSpec_MAST_Query/NIRSpec_MAST_Query.ipynb
+    - file: notebooks/cross_instrument/NIRSpec_MAST_Query/NIRSpec_MAST_Query.ipynb
       title: MAST Query
-    - file: notebooks/rgb_imviz/imviz_rgb_carina.ipynb
+    - file: notebooks/cross_instrument/rgb_imviz/imviz_rgb_carina.ipynb
       title: RGB images with Imviz
-    - file: notebooks/specviz_notebookGUI_interaction/specviz_notebook_gui_interaction_redshift.ipynb
+    - file: notebooks/cross_instrument/specviz_notebookGUI_interaction/specviz_notebook_gui_interaction_redshift.ipynb
       title: Specviz Simple Demo
   - caption: MIRI
     chapters:
-    - file: notebooks/MRS_Mstar_analysis/JWST_Mstar_dataAnalysis_runpipeline.ipynb
+    - file: notebooks/MIRI/MRS_Mstar_analysis/JWST_Mstar_dataAnalysis_runpipeline.ipynb
       title: MRS Mstar - Run Pipeline
-    - file: notebooks/MRS_Mstar_analysis/JWST_Mstar_dataAnalysis_PointSourceDetectorBasedExtraction.ipynb
+    - file: notebooks/MIRI/MRS_Mstar_analysis/JWST_Mstar_dataAnalysis_PointSourceDetectorBasedExtraction.ipynb
       title: MRS Mstar - Optimal Extraction
-    - file: notebooks/MRS_Mstar_analysis/JWST_Mstar_dataAnalysis_analysis.ipynb
+    - file: notebooks/MIRI/MRS_Mstar_analysis/JWST_Mstar_dataAnalysis_analysis.ipynb
       title: MRS Mstar - Data Analysis
-    - file: notebooks/MIRI_IFU_YSOs_in_the_LMC/isha_nayak_ysos_in_the_lmc.ipynb
+    - file: notebooks/MIRI/MIRI_IFU_YSOs_in_the_LMC/isha_nayak_ysos_in_the_lmc.ipynb
       title: IFU of YSOs in LMC
-    - file: notebooks/MIRI_LRS_spectral_extraction/miri_lrs_advanced_extraction_part1.ipynb
+    - file: notebooks/MIRI/MIRI_LRS_spectral_extraction/miri_lrs_advanced_extraction_part1.ipynb
       title: LRS Optimal Spectral Extraction
   - caption: NIRCam
     chapters:
-    - file: notebooks/aperture_photometry/NIRCam_Aperture_Photometry_Example.ipynb
+    - file: notebooks/NIRCam/aperture_photometry/NIRCam_Aperture_Photometry_Example.ipynb
       title: Point Source Aperture Photometry
-    - file: notebooks/NIRCam_photometry/NIRCam_multiband_photometry.ipynb
+    - file: notebooks/NIRCam/NIRCam_photometry/NIRCam_multiband_photometry.ipynb
       title: Extended Aperture Photometry
-    - file: notebooks/NIRCam_PSF-matched_photometry/NIRCam_PSF_matched_multiband_photometry.ipynb
+    - file: notebooks/NIRCam/NIRCam_PSF-matched_photometry/NIRCam_PSF_matched_multiband_photometry.ipynb
       title: Cross-Filter PSF Matching
-    - file: notebooks/psf_photometry/NIRCam_PSF_Photometry_Example.ipynb
+    - file: notebooks/NIRCam/psf_photometry/NIRCam_PSF_Photometry_Example.ipynb
       title: PSF Photometry
   - caption: NIRISS
     chapters:
-    - file: notebooks/NIRISS_WFSS_postpipeline/00_Optimal_extraction.ipynb
+    - file: notebooks/NIRISS/NIRISS_WFSS_postpipeline/00_Optimal_extraction.ipynb
       title: WFSS Spectra - Optimal Extraction
-    - file: notebooks/NIRISS_WFSS_postpipeline/01_Combine_and_normalize_1D_spectra.ipynb
+    - file: notebooks/NIRISS/NIRISS_WFSS_postpipeline/01_Combine_and_normalize_1D_spectra.ipynb
       title: WFSS Spectra - Combine and Normalize 1D Spectra
-    - file: notebooks/NIRISS_WFSS_postpipeline/02_Cross_correlation_template.ipynb 
+    - file: notebooks/NIRISS/NIRISS_WFSS_postpipeline/02_Cross_correlation_template.ipynb
       title: WFSS Spectra - Cross-Correlation Template
-    - file: notebooks/NIRISS_WFSS_postpipeline/03_Spatially_resolved_emission_line_map.ipynb
+    - file: notebooks/NIRISS/NIRISS_WFSS_postpipeline/03_Spatially_resolved_emission_line_map.ipynb
       title: WFSS Spectra - Emission Line Map
-    - file: notebooks/niriss_imaging/niriss-imaging-tutorial.ipynb
+    - file: notebooks/NIRISS/niriss_imaging/niriss-imaging-tutorial.ipynb
       title: NIRISS Imaging Tutorial
-
   - caption: NIRSpec
     chapters:
-    - file: notebooks/IFU_cube_continuum_fit/NGC4151_FeII_ContinuumFit.ipynb
+    - file: notebooks/NIRSpec/IFU_cube_continuum_fit/NGC4151_FeII_ContinuumFit.ipynb
       title: IFU Background Subtraction
-    - file: notebooks/cube_fitting/cube_fitting.ipynb
+    - file: notebooks/NIRSpec/cube_fitting/cube_fitting.ipynb
       title: IFU Cube Modeling
-    - file: notebooks/ifu_optimal/ifu_optimal.ipynb
+    - file: notebooks/NIRSpec/ifu_optimal/ifu_optimal.ipynb
       title: IFU Optimal Spectral Extraction
-    - file: notebooks/optimal_extraction/Spectral_Extraction-static.ipynb
+    - file: notebooks/NIRSpec/optimal_extraction/Spectral_Extraction-static.ipynb
       title: MOS Optimal Extraction
-    - file: notebooks/mos_spectroscopy_advanced/MOSspec_advanced.ipynb
+    - file: notebooks/NIRSpec/mos_spectroscopy_advanced/MOSspec_advanced.ipynb
       title: MOS Spectroscopy of Extragalactic Field
-    - file: notebooks/transit_spectroscopy_notebook/Exoplanet_Transmission_Spectra_JWST.ipynb
+    - file: notebooks/NIRSpec/transit_spectroscopy_notebook/Exoplanet_Transmission_Spectra_JWST.ipynb
       title: BOTS Time Series Observations
-    - file: notebooks/galaxy_redshift/redshift_fitting.ipynb
+    - file: notebooks/NIRSpec/galaxy_redshift/redshift_fitting.ipynb
       title: Redshift and Template Fitting
-    - file: notebooks/NIRSpec_NSClean/FS_NSClean_example.ipynb
+    - file: notebooks/NIRSpec/NIRSpec_NSClean/FS_NSClean_example.ipynb
       title: FS Products with NSClean
-    - file: notebooks/NIRSpec_NSClean/IFU_NSClean_example.ipynb
+    - file: notebooks/NIRSpec/NIRSpec_NSClean/IFU_NSClean_example.ipynb
       title: IFU Products with NSClean
-    - file: notebooks/NIRSpec_NSClean/MOS_NSClean_example.ipynb
+    - file: notebooks/NIRSpec/NIRSpec_NSClean/MOS_NSClean_example.ipynb
       title: MOS Products with NSClean
-    - file: notebooks/NIRSpec_NSClean/BOTS_NSClean_example.ipynb
-      title: BOTS Products with NSClean
+    - file: notebooks/NIRSpec/NIRSpec_NSClean/BOTS_NSClean_example.ipynb
+      title: BOTS Products with NSClean
diff --git a/..._the_LMC/isha_nayak_ysos_in_the_lmc.ipynb → ..._the_LMC/isha_nayak_ysos_in_the_lmc.ipynb b/..._the_LMC/isha_nayak_ysos_in_the_lmc.ipynb → ..._the_LMC/isha_nayak_ysos_in_the_lmc.ipynb
diff --git a/...MIRI_IFU_YSOs_in_the_LMC/requirements.txt → ...MIRI_IFU_YSOs_in_the_LMC/requirements.txt b/...MIRI_IFU_YSOs_in_the_LMC/requirements.txt → ...MIRI_IFU_YSOs_in_the_LMC/requirements.txt
diff --git a/.../miri_lrs_advanced_extraction_part1.ipynb → .../miri_lrs_advanced_extraction_part1.ipynb b/.../miri_lrs_advanced_extraction_part1.ipynb → .../miri_lrs_advanced_extraction_part1.ipynb
diff --git a/..._LRS_spectral_extraction/requirements.txt → ..._LRS_spectral_extraction/requirements.txt b/..._LRS_spectral_extraction/requirements.txt → ..._LRS_spectral_extraction/requirements.txt
diff --git a/..._PointSourceDetectorBasedExtraction.ipynb → ..._PointSourceDetectorBasedExtraction.ipynb b/..._PointSourceDetectorBasedExtraction.ipynb → ..._PointSourceDetectorBasedExtraction.ipynb
diff --git a/...is/JWST_Mstar_dataAnalysis_analysis.ipynb → ...is/JWST_Mstar_dataAnalysis_analysis.ipynb b/...is/JWST_Mstar_dataAnalysis_analysis.ipynb → ...is/JWST_Mstar_dataAnalysis_analysis.ipynb
diff --git a/...JWST_Mstar_dataAnalysis_runpipeline.ipynb → ...JWST_Mstar_dataAnalysis_runpipeline.ipynb b/...JWST_Mstar_dataAnalysis_runpipeline.ipynb → ...JWST_Mstar_dataAnalysis_runpipeline.ipynb
diff --git a/...ointSourceDetectorBasedExtractionFuncs.py → ...ointSourceDetectorBasedExtractionFuncs.py b/...ointSourceDetectorBasedExtractionFuncs.py → ...ointSourceDetectorBasedExtractionFuncs.py
diff --git a/...S_Mstar_analysis/create_distortionMaps.py → ...S_Mstar_analysis/create_distortionMaps.py b/...S_Mstar_analysis/create_distortionMaps.py → ...S_Mstar_analysis/create_distortionMaps.py
diff --git a/...books/MRS_Mstar_analysis/requirements.txt → .../MIRI/MRS_Mstar_analysis/requirements.txt b/...books/MRS_Mstar_analysis/requirements.txt → .../MIRI/MRS_Mstar_analysis/requirements.txt
diff --git a/notebooks/MRS_Mstar_analysis/stpipe-log.cfg → ...ks/MIRI/MRS_Mstar_analysis/stpipe-log.cfg b/notebooks/MRS_Mstar_analysis/stpipe-log.cfg → ...ks/MIRI/MRS_Mstar_analysis/stpipe-log.cfg
diff --git a/...am_PSF_matched_multiband_photometry.ipynb → ...am_PSF_matched_multiband_photometry.ipynb b/...am_PSF_matched_multiband_photometry.ipynb → ...am_PSF_matched_multiband_photometry.ipynb
diff --git a/...m_PSF-matched_photometry/requirements.txt → ...m_PSF-matched_photometry/requirements.txt b/...m_PSF-matched_photometry/requirements.txt → ...m_PSF-matched_photometry/requirements.txt
diff --git a/notebooks/NIRCam_photometry/.gitignore → ...books/NIRCam/NIRCam_photometry/.gitignore b/notebooks/NIRCam_photometry/.gitignore → ...books/NIRCam/NIRCam_photometry/.gitignore
diff --git a/...tometry/NIRCam_multiband_photometry.ipynb → ...tometry/NIRCam_multiband_photometry.ipynb b/...tometry/NIRCam_multiband_photometry.ipynb → ...tometry/NIRCam_multiband_photometry.ipynb
diff --git a/notebooks/NIRCam_photometry/requirements.txt → ...NIRCam/NIRCam_photometry/requirements.txt b/notebooks/NIRCam_photometry/requirements.txt → ...NIRCam/NIRCam_photometry/requirements.txt
diff --git a/.../NIRCam_Aperture_Photometry_Example.ipynb → .../NIRCam_Aperture_Photometry_Example.ipynb b/.../NIRCam_Aperture_Photometry_Example.ipynb → .../NIRCam_Aperture_Photometry_Example.ipynb
diff --git a/...ooks/aperture_photometry/requirements.txt → ...RCam/aperture_photometry/requirements.txt b/...ooks/aperture_photometry/requirements.txt → ...RCam/aperture_photometry/requirements.txt
diff --git a/notebooks/psf_photometry/.gitignore → notebooks/NIRCam/psf_photometry/.gitignore b/notebooks/psf_photometry/.gitignore → notebooks/NIRCam/psf_photometry/.gitignore
diff --git a/...metry/NIRCam_PSF_Photometry_Example.ipynb → ...metry/NIRCam_PSF_Photometry_Example.ipynb b/...metry/NIRCam_PSF_Photometry_Example.ipynb → ...metry/NIRCam_PSF_Photometry_Example.ipynb
diff --git a/notebooks/psf_photometry/requirements.txt → ...ks/NIRCam/psf_photometry/requirements.txt b/notebooks/psf_photometry/requirements.txt → ...ks/NIRCam/psf_photometry/requirements.txt
diff --git a/...books/NIRISS_WFSS_postpipeline/.gitignore → ...IRISS/NIRISS_WFSS_postpipeline/.gitignore b/...books/NIRISS_WFSS_postpipeline/.gitignore → ...IRISS/NIRISS_WFSS_postpipeline/.gitignore
diff --git a/..._postpipeline/00_Optimal_extraction.ipynb → ..._postpipeline/00_Optimal_extraction.ipynb b/..._postpipeline/00_Optimal_extraction.ipynb → ..._postpipeline/00_Optimal_extraction.ipynb
diff --git a/...01_Combine_and_normalize_1D_spectra.ipynb → ...01_Combine_and_normalize_1D_spectra.ipynb b/...01_Combine_and_normalize_1D_spectra.ipynb → ...01_Combine_and_normalize_1D_spectra.ipynb
diff --git a/...eline/02_Cross_correlation_template.ipynb → ...eline/02_Cross_correlation_template.ipynb b/...eline/02_Cross_correlation_template.ipynb → ...eline/02_Cross_correlation_template.ipynb
diff --git a/...patially_resolved_emission_line_map.ipynb → ...patially_resolved_emission_line_map.ipynb b/...patially_resolved_emission_line_map.ipynb → ...patially_resolved_emission_line_map.ipynb