Merge pull request #167 from spacetelescope/phot_examples

Update flux conversion notebook
spacetelescope · Dec 18, 2023 · 3ce4645 · 3ce4645
2 parents 7b98bbc + b151c78
commit 3ce4645
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diff --git a/.github/workflows/ci_html_build.yml b/.github/workflows/ci_html_build.yml
@@ -7,11 +7,6 @@ on:
 
   workflow_dispatch:
 
-permissions:
-  contents: write
-  id-token: write
-
-
 jobs:
   Generate_HTML:
     if: github.event.pull_request.merged == true

diff --git a/.github/workflows/ci_nightly.yml b/.github/workflows/ci_nightly.yml
@@ -1,11 +1,11 @@
-name: Nightly Notebook Execution
+name: Scheduled Notebook Execution
 on:
   schedule:
     #- cron: '0 3 * * *' # run at 2 AM UTC
     - cron: '0 0 * * 0' # midnight sunday UTC
 
 jobs:
-  GenerateHTML:
+  Scheduled:
    uses: spacetelescope/notebook-ci-actions/.github/workflows/ci_scheduled.yml@v3
    with:
       python-version: ${{ vars.PYTHON_VERSION }}
diff --git a/.github/workflows/weekly_broken_link_finder.yml b/.github/workflows/weekly_broken_link_finder.yml
@@ -0,0 +1,8 @@
+name: Weekly broken link check
+on:
+  schedule:
+    - cron: '0 4 * * 0' # 0400 UTC every Sunday
+
+jobs:
+  Scheduled:
+   uses: spacetelescope/notebook-ci-actions/.github/workflows/broken_link_checker.yml@main
diff --git a/_config.yml b/_config.yml
@@ -24,6 +24,12 @@ latex:
 bibtex_bibfiles:
   - references.bib
 
+parse:
+  myst_enable_extensions:
+    # don't forget to list any other extensions you want enabled,
+    # including those that are enabled by default! See here: https://jupyterbook.org/en/stable/customize/config.html
+    - html_image
+
 launch_buttons:
   thebe                  : true
   colab                 : true
@@ -44,19 +50,11 @@ html:
 exclude_patterns: [notebooks/DrizzlePac/align_mosaics/align_mosaics.ipynb,
                    notebooks/DrizzlePac/sky_matching/sky_matching.ipynb,
                    notebooks/DrizzlePac/use_ds9_regions_in_tweakreg/use_ds9_regions_in_tweakreg.ipynb,
-                   notebooks/WFC3/calwf3_recalibration/calwf3_recal_tvb.ipynb,
-                   notebooks/WFC3/calwf3_v1.0_cte/calwf3_with_v1.0_PCTE.ipynb,
                    notebooks/WFC3/dash/dash.ipynb,
-                   notebooks/WFC3/exception_report/wfc3_exception_report.ipynb,
-                   notebooks/WFC3/filter_transformations/filter_transformations.ipynb,
                    notebooks/WFC3/image_displayer_analyzer/wfc3_image_displayer_analyzer.ipynb,
                    notebooks/WFC3/ir_ima_visualization/IR_IMA_Visualization_with_an_Example_of_Time_Variable_Background.ipynb,
                    notebooks/WFC3/ir_scattered_light_calwf3_corrections/Correcting_for_Scattered_Light_in_IR_Exposures_Using_calwf3_to_Mask_Bad_Reads.ipynb,
                    notebooks/WFC3/ir_scattered_light_manual_corrections/Correcting_for_Scattered_Light_in_IR_Exposures_by_Manually_Subtracting_Bad_Reads.ipynb,
-                   notebooks/WFC3/persistence/wfc3_ir_persistence.ipynb,
-                   notebooks/WFC3/photometry_examples/phot_examples.ipynb,
                    notebooks/WFC3/tvb_flattenramp/TVB_flattenramp_notebook.ipynb,
-                   notebooks/WFC3/uvis_pam_corrections/WFC3_UVIS_Pixel_Area_Map_Corrections_for_Subarrays.ipynb,
-                   notebooks/WFC3/uvis_time_dependent_photometry/uvis_timedep_phot.ipynb,
-                   notebooks/WFC3/zeropoints/zeropoints.ipynb]
+                   notebooks/WFC3/uvis_time_dependent_photometry/uvis_timedep_phot.ipynb]
 
diff --git a/_toc.yml b/_toc.yml
@@ -42,6 +42,9 @@ parts:
 #      - file: notebooks/DrizzlePac/sky_matching/sky_matching.ipynb
       - file: notebooks/DrizzlePac/use_ds9_regions_in_tweakreg/use_ds9_regions_in_tweakreg.ipynb
       - file: notebooks/DrizzlePac/using_updated_astrometry_solutions/using_updated_astrometry_solutions.ipynb
+  - caption: HASP
+    chapters:
+    - file: notebooks/HASP/Setup/Setup.ipynb
   - caption: NICMOS
     chapters:
     - file: notebooks/NICMOS/nicmos_unit_conversion/nicmos_unit_conversion.ipynb
@@ -59,19 +62,19 @@ parts:
   - caption: WFC3
     chapters:
       - file: notebooks/WFC3/README.md
-#      - file: notebooks/WFC3/calwf3_recalibration/calwf3_recal_tvb.ipynb
-#      - file: notebooks/WFC3/calwf3_v1.0_cte/calwf3_with_v1.0_PCTE.ipynb
+      - file: notebooks/WFC3/calwf3_recalibration/calwf3_recal_tvb.ipynb
+      - file: notebooks/WFC3/calwf3_v1.0_cte/calwf3_with_v1.0_PCTE.ipynb
 #      - file: notebooks/WFC3/dash/dash.ipynb
-#      - file: notebooks/WFC3/exception_report/wfc3_exception_report.ipynb
-#      - file: notebooks/WFC3/filter_transformations/filter_transformations.ipynb
+      - file: notebooks/WFC3/exception_report/wfc3_exception_report.ipynb
+      - file: notebooks/WFC3/filter_transformations/filter_transformations.ipynb
       - file: notebooks/WFC3/flux_conversion_tool/flux_conversion_tool.ipynb
-#      - file: notebooks/WFC3/image_displayer_analyzer/wfc3_image_displayer_analyzer.ipynb
-#      - file: notebooks/WFC3/ir_ima_visualization/IR_IMA_Visualization_with_an_Example_of_Time_Variable_Background.ipynb
+      - file: notebooks/WFC3/image_displayer_analyzer/wfc3_image_displayer_analyzer.ipynb
+      - file: notebooks/WFC3/ir_ima_visualization/IR_IMA_Visualization_with_an_Example_of_Time_Variable_Background.ipynb
 #      - file: notebooks/WFC3/ir_scattered_light_calwf3_corrections/Correcting_for_Scattered_Light_in_IR_Exposures_Using_calwf3_to_Mask_Bad_Reads.ipynb
 #      - file: notebooks/WFC3/ir_scattered_light_manual_corrections/Correcting_for_Scattered_Light_in_IR_Exposures_by_Manually_Subtracting_Bad_Reads.ipynb
-#      - file: notebooks/WFC3/persistence/wfc3_ir_persistence.ipynb
-#      - file: notebooks/WFC3/photometry_examples/phot_examples.ipynb
+      - file: notebooks/WFC3/persistence/wfc3_ir_persistence.ipynb
+      - file: notebooks/WFC3/photometry_examples/phot_examples.ipynb
 #      - file: notebooks/WFC3/tvb_flattenramp/TVB_flattenramp_notebook.ipynb
-#      - file: notebooks/WFC3/uvis_pam_corrections/WFC3_UVIS_Pixel_Area_Map_Corrections_for_Subarrays.ipynb
+      - file: notebooks/WFC3/uvis_pam_corrections/WFC3_UVIS_Pixel_Area_Map_Corrections_for_Subarrays.ipynb
 #      - file: notebooks/WFC3/uvis_time_dependent_photometry/uvis_timedep_phot.ipynb
-#      - file: notebooks/WFC3/zeropoints/zeropoints.ipynb
+      - file: notebooks/WFC3/zeropoints/zeropoints.ipynb
diff --git a/index.md b/index.md
@@ -1,13 +1,28 @@
-# STScI Notebook Repository HQ
-This page provides links to notebooks created by various Hubble Space
-Telescope instrument teams and software groups, including:
 
-[Advanced Camera for Surveys (ACS)](https://www.stsci.edu/hst/instrumentation/acs);
+## STScI HST Notebook Repository HQ
+Welcome to the STScI HST Notebook Repository
+This resource provides comprehensive documentation and interactive notebooks created by the Hubble Space Telescope instruments teams.
 
-[Cosmic Origins Spectrograph (COS)](https://www.stsci.edu/hst/instrumentation/cos);
+### Interactive Notebooks
+Explore our interactive notebooks for hands-on experience with HST data.
+- [ACS notebooks](./notebooks/ACS/README.md)
+- [COS notebooks](./notebooks/COS/README.md)
+- [DrizzlePac notebooks](./notebooks/DrizzlePac/README.md)
+- [NICMOS notebooks](./notebooks/NICMOS/nicmos_unit_conversion/nicmos_unit_conversion.ipynb)
+- [STIS notebooks](./notebooks/STIS/README.md)
+- [WFC3 notebooks](./notebooks/WFC3/README.md)
 
-[DrizzlePac](https://www.stsci.edu/scientific-community/software/drizzlepac);
+### Instrument Documentation
+Here, you can find detailed documentation for each instrument the Hubble Space Telescope uses.
 
-[Near Infrared Camera and Multi-Object Spectrometer (NICMOS)](https://www.stsci.edu/hst/instrumentation/legacy/nicmos);
+- [Advanced Camera for Surveys (ACS)](https://www.stsci.edu/hst/instrumentation/acs)
 
-[Space Telescope Imaging Spectrograph (STIS)](https://www.stsci.edu/hst/instrumentation/stis);
+- [Cosmic Origins Spectrograph (COS)](https://www.stsci.edu/hst/instrumentation/cos)
+
+- [DrizzlePac](https://www.stsci.edu/scientific-community/software/drizzlepac)
+
+- [Near Infrared Camera and Multi-Object Spectrometer (NICMOS)](https://www.stsci.edu/hst/instrumentation/legacy/nicmos)
+
+- [Space Telescope Imaging Spectrograph (STIS)](https://www.stsci.edu/hst/instrumentation/stis)
+
+- [Wide Field Camera 3 (WFC3)](https://www.stsci.edu/hst/instrumentation/wfc3)
diff --git a/notebooks/ACS/acs_cte_forward_model/requirements.txt b/notebooks/ACS/acs_cte_forward_model/requirements.txt
@@ -4,3 +4,5 @@ astroquery==0.4.6
 matplotlib==3.7.0
 numpy==1.23.4
 photutils==1.6.0
+crds==11.17.7
+stsci.tools==4.1.0
diff --git a/notebooks/ACS/acs_findsat_mrt/requirements.txt b/notebooks/ACS/acs_findsat_mrt/requirements.txt
@@ -1,5 +1,7 @@
-acstools==3.5.0
-astropy==5.2.1
+acstools==3.7.0
+astropy==5.3.4
 astroquery==0.4.6
-matplotlib==3.7.0
-numpy==1.23.4
+matplotlib==3.8.1
+numpy==1.26.2
+scikit-image==0.22.0
+photutils==1.9.0
diff --git a/notebooks/ACS/acs_pixel_area_maps/requirements.txt b/notebooks/ACS/acs_pixel_area_maps/requirements.txt
@@ -5,3 +5,4 @@ stsci.imagestats==1.6.3
 stsci.skypac==1.0.9
 stsci.stimage==0.2.6
 stsci.tools==4.0.1
+matplotlib==3.7.0
diff --git a/notebooks/ACS/acs_reduction/requirements.txt b/notebooks/ACS/acs_reduction/requirements.txt
@@ -1,3 +1,5 @@
 astropy==5.2.1
 astroquery==0.4.6
 stwcs==1.7.2
+crds==11.17.0
+matplotlib==3.7.0
diff --git a/notebooks/ACS/acs_saturation_trails/requirements.txt b/notebooks/ACS/acs_saturation_trails/requirements.txt
@@ -3,7 +3,7 @@ astroquery==0.4.6
 matplotlib==3.7.0
 numpy==1.23.4
 photutils==1.6.0
-scipy==1.9.1
+scipy==1.11.3
 stsci.image==2.3.5
 stsci.imagestats==1.6.3
 stsci.skypac==1.0.9

diff --git a/notebooks/ACS/acs_subarrays/requirements.txt b/notebooks/ACS/acs_subarrays/requirements.txt
@@ -2,3 +2,4 @@ acstools==3.5.0
 astropy==5.2.1
 astroquery==0.4.6
 stwcs==1.7.2
+crds==11.17.0