Merge pull request #170 from NOAA-EDAB/dev

sync `dev` and `main`

Author: BBeltz1

.github/workflows/verify_pr.yml

@@ -0,0 +1,15 @@
+name: Run PR Checks
+on:
+  pull_request:
+    branches:
+    - master
+
+jobs:
+  check_description:
+    runs-on: ubuntu-latest
+    name: Verify DESCRIPTION Updated
+    steps:
+    - name: Verify DESCRIPTION Updated
+      uses: takanuva15/verify-file-updated@v1
+      with:
+        filename_to_check: DESCRIPTION

DESCRIPTION

@@ -2,7 +2,7 @@ Package: placeholder
 Type: Book
 Title: Technical Documentation, State of the Ecosystem Report
 Description: Technical documentation for State of the Ecosystem Reporting.
-Version: 2026.0.0
+Version: 7.0.0
 Depends: 
   bookdown, 
   rmarkdown,
@@ -14,9 +14,11 @@ Depends:
   kableExtra,
   ecodata,
   stocksmart,
-  DT
+  DT, 
+  formatR
 Remotes:
   NOAA-EDAB/ecodata@dev,
   NOAA-EDAB/stocksmart
 
 
+

README.md

@@ -1,7 +1,8 @@
 # tech-doc
 
 [![build-book](https://github.com/NOAA-EDAB/tech-doc/actions/workflows/bookdown.yaml/badge.svg)](https://github.com/NOAA-EDAB/tech-doc/actions/workflows/bookdown.yaml)
-![gitleaks](https://github.com/NOAA-EDAB/tech-doc/workflows/gitleaks/badge.svg)
+[![gitleaks](https://github.com/NOAA-EDAB/tech-doc/workflows/gitleaks/badge.svg)
+[![Run PR Checks](https://github.com/NOAA-EDAB/tech-doc/actions/workflows/verify_pr.yml/badge.svg)](https://github.com/NOAA-EDAB/tech-doc/actions/workflows/verify_pr.yml)
 
 Technical documentation for State of the Ecosystem indicators and general methods. 
 

_404.Rmd

@@ -3,11 +3,13 @@
 
 **The following pages have been moved or renamed**
 
-- [Bottom Temperature - in situ](https://noaa-edab.github.io/catalog/bottom_temp_insitu.html)
-- [Bottom Temperature - Seasonal Anomaly](https://noaa-edab.github.io/catalog/bottom_temp_model_anom.html)
-- [Bottom Temperature - Seasonal Gridded](https://noaa-edab.github.io/catalog/bottom_temp_model_gridded.html)
-- [Cetacean Distribution Shifts](https://noaa-edab.github.io/catalog/cetacean_dist.html)
-- [Thermal Habitat Persistence](https://noaa-edab.github.io/catalog/thermal_habitat_gridded.html)
-- [Seasonal OISST Anomaly Map](https://noaa-edab.github.io/catalog/seasonal_oisst_anom_gridded.html)
+- [Bottom Temperature - in situ](https://noaa-edab.github.io/tech-doc/bottom_temp_insitu.html)
+- [Bottom Temperature - Seasonal Anomaly](https://noaa-edab.github.io/tech-doc/bottom_temp_model_anom.html)
+- [Bottom Temperature - Seasonal Gridded](https://noaa-edab.github.io/tech-doc/bottom_temp_model_gridded.html)
+- [Calanus Variation - WBTS](https://noaa-edab.github.io/tech-doc/wbts_zoo.html)
+- [Cetacean Distribution Shifts](https://noaa-edab.github.io/tech-doc/cetacean_dist.html)
+- [Mesozooplankton Biomass - WBTS](https://noaa-edab.github.io/tech-doc/wbts_zoo.html)
+- [Thermal Habitat Persistence](https://noaa-edab.github.io/tech-doc/thermal_habitat_gridded.html)
+- [Seasonal OISST Anomaly Map](https://noaa-edab.github.io/tech-doc/seasonal_oisst_anom_gridded.html)
 
 **If the page you are looking for is not listed above, please refer to the Table of Contents to the left. If you are having trouble finding something, please email Brandon Beltz (brandon.beltz@noaa.gov) for assistance.**

_bookdown.yml

@@ -23,8 +23,8 @@ rmd_files:
     -   "chapters/habs.Rmd"
     -   "chapters/SAV.Rmd"
     -   "chapters/zooplankton_index.Rmd"
-    -   "chapters/calanus_variation.Rmd"
-    -   "chapters/wbts_mesozooplankton.Rmd"
+    -   "chapters/wbts_zoo.Rmd"
+    -   "chapters/preyfield_energy.Rmd"
     -   "chapters/zoo_abundance_anom.Rmd"
     #-   "chapters/zoo_diversity.Rmd" *Missing tech doc page
 #
@@ -34,8 +34,8 @@ rmd_files:
     -   "chapters/aggregate_biomass.rmd" 
     -   "chapters/survey_shannon.rmd" 
     -   "chapters/mab_inshore_survey.Rmd"
-    #-   "chapters/mass_inshore_survey.Rmd" *Shares tech doc page with mab_inshore_survey
-    #-   "chapters/ne_inshore_survey.Rmd" *Shares tech doc page with mab_inshore_survey
+    -   "chapters/ne_inshore_survey.Rmd"
+    -   "chapters/mass_inshore_survey.Rmd" 
     #-   "chapters/osw_survey_impact.Rmd" *Missing tech doc page
     -   "chapters/condition.Rmd"
     -   "chapters/finfish_traits.Rmd"
@@ -44,6 +44,7 @@ rmd_files:
     -   "chapters/energy_density.Rmd"
     -   "chapters/spawn_timing.Rmd"
     -   "chapters/exp_n.Rmd"
+    -   "chapters/effective_sweptarea.Rmd"
     -   "chapters/forage_index.Rmd"
     -   "chapters/benthos_index.Rmd"
     -   "chapters/harborporpoise.Rmd"
@@ -65,7 +66,7 @@ rmd_files:
 # #################### OCEANOGRAPHIC ##################
     -   "chapters/sectionHeaders/oceanographic.rmd" 
     -   "chapters/bottom_temp_insitu.Rmd"
-    #-   "chapters/bottom_temp_model_anom.Rmd" *Missing tech doc page
+    -   "chapters/bottom_temp_model_anom.Rmd"
     -   "chapters/bottom_temp_model_gridded.Rmd"
     -   "chapters/seasonal_oisst_anom_gridded.Rmd"
     #-   "chapters/seasonal_oisst_anom.Rmd" *Missing tech doc page
@@ -77,13 +78,16 @@ rmd_files:
     -   "chapters/slopewater.Rmd"
     -   "chapters/persistent_hotspots.Rmd"
     -   "chapters/wcr.Rmd"
-    #-   "chapters/thermal_habitat_area.Rmd" *Missing tech doc page
-    #-   "chapters/thermal_habitat_persistence.Rmd" *Missing tech doc page
+    -   "chapters/advection.Rmd"
+    -   "chapters/thermal_habitat_area.Rmd"
+    -   "chapters/thermal_habitat_gridded.Rmd"
     -   "chapters/ch_bay_sal.Rmd"
     -   "chapters/ch_bay_temp.Rmd"
     -   "chapters/ches_bay_sst.Rmd"
     #-   "chapters/ches_bay_synthesis.Rmd" *Missing tech doc page
     -   "chapters/heatwave.Rmd"
+    -   "chapters/cold_spell.Rmd"
+    -   "chapters/MOM6_forecasts.Rmd"
     #-   "chapters/heatwave_year.Rmd" *Shares tech doc page with heatwave
     #-   "chapters/timing_shifts.Rmd" *Missing tech doc page
     #-   "chapters/observation_synthesis.Rmd" *Missing tech doc page
@@ -94,6 +98,7 @@ rmd_files:
 # ######################## ECONOMIC ##################
     -   "chapters/sectionHeaders/economic.rmd"
     -   "chapters/comdat.Rmd"
+    -   "chapters/comdat_profit.Rmd"
     -   "chapters/commercial_div.Rmd"
     -   "chapters/ppr.Rmd"
     -   "chapters/recdat.Rmd"
@@ -103,6 +108,7 @@ rmd_files:
     -   "chapters/stock_status.Rmd"
     -   "chapters/engagement.Rmd"
     #-   "chapters/community_climate_vulnerability.Rmd" *Missing tech doc page
+    -   "chapters/crew_survey.Rmd"
     -   "chapters/aquaculture.Rmd"
     -   "chapters/Wind_dev_speed.Rmd"
     -   "chapters/wind_port.Rmd"
@@ -113,7 +119,6 @@ rmd_files:
     -   "chapters/sectionHeaders/legacy.rmd"
     -   "chapters/regime_shift_analysis.Rmd" 
     -   "chapters/Annual_SST_cycle_indicator.Rmd"
-    -   "chapters/bottom_temperature_GLORYS.Rmd"
     -   "chapters/calanus_stage.Rmd"
     #-   "chapters/forage_anomaly.Rmd"
     -   "chapters/occupancy_indicator.Rmd"
@@ -135,6 +140,11 @@ rmd_files:
     -   "chapters/observer_data_indicator.Rmd"
     -   "chapters/Seabird_MAB.Rmd"
     -   "chapters/wind_habitat_occupancy.Rmd"
+#
+#
+# #################### RESOURCES ##################
+    -   "chapters/sectionHeaders/resources.rmd"
+    -   "chapters/changelog.Rmd"
     -   "chapters/references.Rmd"
 before_chapter_script: _common.R
 delete_merged_file: true