PecanProject · dlebauer · Aug 25, 2025 · Aug 25, 2025 · Aug 26, 2025 · Aug 26, 2025
diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml
@@ -1,31 +1,37 @@
-name: Publish Documentation
-
+name: Deploy production docs
 on:
   push:
-    branches:
-      - "master"
+    branches: [master]
+
+permissions:
+  contents: write
 
 jobs:
-  build:
+  build-and-deploy:
     runs-on: ubuntu-latest
-
     steps:
-      - name: Checkout repository
-        uses: actions/checkout@v4
+      - uses: actions/checkout@v4
 
-      - name: Install Dependencies
-        run: sudo apt-get update && sudo apt-get install -y doxygen graphviz python3-pip
+      - name: Install system deps
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y doxygen graphviz
+          python3 -m pip install --upgrade pip
+          python3 -m pip install mkdocs mkdocs-material pymdown-extensions
 
-      - name: Install MkDocs
+      - name: Build docs
         run: |
-          pip install mkdocs mkdocs-material pymdown-extensions
+          make clean document
 
-      - name: Generate Documentation
-        run: make document
+      - name: Ensure .nojekyll in site root
+        run: touch site/.nojekyll
 
-      - name: Deploy to GitHub Pages
-        uses: peaceiris/actions-gh-pages@v3
+      - name: Deploy to gh-pages
+        uses: JamesIves/github-pages-deploy-action@v4
         with:
-          github_token: ${{ secrets.GITHUB_TOKEN }}
-          publish_branch: gh-pages
-          publish_dir: site  
+          branch: gh-pages
+          folder: site
+          # Keep PR previews published under pr-preview/
+          clean: true
+          clean-exclude: pr-preview/
+          force: false
diff --git a/.github/workflows/link-check.yml b/.github/workflows/link-check.yml
@@ -0,0 +1,42 @@
+name: Broken Link Check
+
+on:
+  pull_request:
+  schedule:
+    - cron: '0 5 * * 1' # Weekly, Mondays at 05:00 UTC
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+jobs:
+  link-check:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Run lychee
+        uses: lycheeverse/lychee-action@v2
+        with:
+          args: >-
+            --include-fragments
+            --no-progress
+            --verbose
+            --timeout 20
+            --max-redirects 10
+            --max-retries 3
+            --retry-wait-time 2
+            --format markdown
+            --exclude https://doi.org/*
+            .
+          fail: true
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Upload lychee report
+        if: ${{ always() }}
+        uses: actions/upload-artifact@v4
+        with:
+          name: lychee-report
+          path: lychee
diff --git a/.gitignore b/.gitignore
@@ -7,6 +7,7 @@ transpose
 .doxygen.stamp
 .mkdocs.stamp
 site/*
+site_preview/*
 
 # documentation
 docs/api

diff --git a/CITATION.cff b/CITATION.cff
@@ -1,17 +1,20 @@
 cff-version: 1.2.0
 title: "SIPNET: Simple Photosynthesis and Evapotranspiration Model"
-version: 2.0..0
+version: 2.0.0
 abstract: >
   SIPNET (Simple Photosynthesis and Evapotranspiration Model) is a process-based
   ecosystem model designed to simulate carbon and water fluxes and (optionally) agricultural management
   events in terrestrial ecosystems.
-  SIPNET is used for research in ecosystem ecology, carbon and greenhouse gas accounting,
+  SIPNET is used for research in ecosystem ecology, agriculture, carbon and greenhouse gas accounting,
   data assimilation, and model benchmarking.
   Model development and recent features are detailed in the CHANGELOG and relevant literature.
 license: BSD-3-Clause
 message: "Please cite SIPNET using the metadata from 'preferred-citation'."
 type: software
 authors:
+  - family-names: Michael
+    given-names: Longfritz
+    orcid: "https://orcid.org/0009-0009-6024-8116"
   - family-names: Sacks
     given-names: William J.
     orcid: "https://orcid.org/0000-0003-2902-5263"
@@ -27,9 +30,6 @@ authors:
   - family-names: Schimel
     given-names: David S.
     orcid: "https://orcid.org/0000-0003-3473-8065"
-  - family-names: LeBauer
-    given-names: David S.
-    orcid: "https://orcid.org/0000-0001-7228-053X"
   - family-names: Kooper
     given-names: Rob
     orcid: "https://orcid.org/0000-0002-5781-7287"
@@ -39,10 +39,11 @@ authors:
   - family-names: Fer
     given-names: Istem
     orcid: "https://orcid.org/0000-0001-8236-303X"
-  - family-names: (other contributors)
-    given-names: See https://github.com/PecanProject/sipnet/graphs/contributors
-  - family-names: Michael
-    given-names: Longfritz
+  - family-names: Black
+    given-names: Chris
+  - family-names: LeBauer
+    given-names: David S.
+    orcid: "https://orcid.org/0000-0001-7228-053X"
 
 repository-code: https://github.com/PecanProject/sipnet
 keywords:
@@ -55,9 +56,11 @@ keywords:
 preferred-citation:
   type: software
   title: "SIPNET: Simple Photosynthesis and Evapotranspiration Model"
-  version: 1.3.0
+  version: 2.0.0
   url: https://github.com/PecanProject/sipnet
   authors:
+    - family-names: Michael
+      given-names: Longfritz
     - family-names: Sacks
       given-names: William J.
     - family-names: Moore
@@ -68,18 +71,14 @@ preferred-citation:
       given-names: Bobby H.
     - family-names: Schimel
       given-names: David S.
-    - family-names: LeBauer
-      given-names: David S.
     - family-names: Kooper
       given-names: Rob
     - family-names: Dietze
       given-names: Michael C.
     - family-names: Fer
       given-names: Istem
-    - family-names: Michael
-      given-names: Longfritz
-    - family-names: (other contributors)
-      given-names: See https://github.com/PecanProject/sipnet/graphs/contributors
+    - family-names: LeBauer
+      given-names: David S.
 
 references:
   - type: article

diff --git a/Makefile b/Makefile
@@ -85,7 +85,8 @@ SIPNET_TEST_DIRS:=$(shell find tests/sipnet -type d -mindepth 1 -maxdepth 1)
 SIPNET_TEST_DIRS_RUN:= $(addsuffix .run, $(SIPNET_TEST_DIRS))
 SIPNET_TEST_DIRS_CLEAN:= $(addsuffix .clean, $(SIPNET_TEST_DIRS))
 
-test: $(SIPNET_TEST_DIRS) $(COMMON_LIB) $(SIPNET_LIB)
+# Build unit test executables (does not run them)
+testbuild: $(SIPNET_TEST_DIRS) $(COMMON_LIB) $(SIPNET_LIB)
 
 # The dash in the build command tells make to continue if there are errors, allowing cleanup
 $(SIPNET_TEST_DIRS): $(SIPNET_LIB) $(COMMON_LIB)
@@ -105,7 +106,7 @@ $(SIPNET_TEST_DIRS_CLEAN):
 cleanall: clean testclean
 
 .PHONY: all clean help document exec cleanall \
-		test $(SIPNET_TEST_DIRS) $(SIPNET_TEST_DIRS_RUN) testclean $(SIPNET_TEST_DIRS_CLEAN) testrun
+		test testbuild $(SIPNET_TEST_DIRS) $(SIPNET_TEST_DIRS_RUN) testclean $(SIPNET_TEST_DIRS_CLEAN) testrun smoke unit
 
 help:
 	@echo "Available make targets:"
@@ -118,11 +119,24 @@ help:
 	@echo "  clean        - Remove compiled files, executables, and documentation"
 	@echo "  depend       - Generate build dependency information for source files and append to Makefile"
 	@echo "  === Tests ==="
-	@echo "  test         - Build the unit tests"
-	@echo "  testrun      - Run the unit tests"
+	@echo "  test         - Build + run unit tests, then smoke tests"
+	@echo "  testbuild    - Build the unit tests (does not run)"
+	@echo "  testrun      - Run the unit tests (per-directory runners)"
+	@echo "  unit         - Build and run unit tests (wrapper with summary)"
+	@echo "  smoke        - Run smoke tests (end-to-end diffs)"
 	@echo "  testclean    - Clean build artifacts and executables from the unit tests"
 	@echo "  cleanall     - Run both clean and testclean"
 
+# Convenience test targets
+unit: sipnet testbuild
+	./tools/run_unit_tests.sh
+
+smoke: sipnet
+	./tests/smoke/run_smoke.sh
+
+# Combined verification target
+test: sipnet testbuild
+	./tools/run_unit_tests.sh && ./tests/smoke/run_smoke.sh
 
 # Make sure this target and subsequent comment remain at the bottom of this file
 depend::

diff --git a/docs/.alternate-model-structure-ideas.md b/docs/.alternate-model-structure-ideas.md
@@ -17,7 +17,16 @@ $$
 
 Heterotrophic respiration ($R_h$) is a function of soil carbon content ($C_S$), a scaling factor ($K_h$), the $Q_{10}$ factor, and the ratio of soil moisture ($W$) to water holding capacity ($W_e$).
 
-## Flooding
+## Irrigation
+
+### Moisture based irrigation
+
+Currently, irrigation is specified as an amount.
+
+Additional approach based on farmer behavior:
+To represent an irrigation program that sets a moisture range and turns irrigation on at a lower moisture threshold and of at an upper threshold. This could be done internally by directly changing the soil moisture content - while keeping track of the amount of water added to report in events.out.
+
+### Flooding
 
 There are multiple options for representing flooding.
 
@@ -42,17 +51,17 @@ K could be a fixed value like 2 or 10. Or a site level parameter if warranted (e
 
 ### Variables (Pools, Fluxes, and Parameters)
 
-| Symbol         | Description                                                                 |
-|----------------|-----------------------------------------------------------------------------|
-| $$ R_{\text{leach,NO3}} $$ | Rate of nitrate leaching                                        |
-| $$ R_{\text{NH4,fert}} $$ | Rate of ammonium fertilization input                              |
-| $$ R_{\text{NO3,fert}} $$ | Rate of nitrate fertilization input    
+| Symbol                     | Description                          |
+| -------------------------- | ------------------------------------ |
+| $$ R_{\text{leach,NO3}} $$ | Rate of nitrate leaching             |
+| $$ R_{\text{NH4,fert}} $$  | Rate of ammonium fertilization input |
+| $$ R_{\text{NO3,fert}} $$  | Rate of nitrate fertilization input  |
 
 ### Subscripts (Temporal, Spatial, or Contextual Identifiers) 
-| Subscript      | Description                                                                 |
-|--------------- |----------------------------------------------------------------------------- |
-| $$ _\text{nitr} $$ | nitrification                                             |
-| $$ _\text{denitr} $$ | denitrification       
+| Subscript            | Description     |
+| -------------------- | --------------- |
+| $$ _\text{nitr} $$   | nitrification   |
+| $$ _\text{denitr} $$ | denitrification |
 
 
 ### Soil Ammonium
@@ -363,15 +372,15 @@ Some options considered:
 - Adapt the parabolic $D_\text{temp, A}$ from SIPNET (Braswell et al 2005)
 
 
-| Function                            | Formula                                                                                 | Parameters                          | Notes                                                                                          |
-|-------------------------------------|-----------------------------------------------------------------------------------------|-------------------------------------|------------------------------------------------------------------------------------------------|
-| **Beta Function**                   | $\left( \frac{f_{\text{WHC}} - f_{\text{WHC,min}}}{f_{\text{WHC,max}} - f_{\text{WHC,min}}} \right)^\beta \cdot \left( 1 - \frac{f_{\text{WHC}} - f_{\text{WHC,min}}}{f_{\text{WHC,max}} - f_{\text{WHC,min}}} \right)^\gamma$ | 4 ($\beta, \gamma, f_{\text{WHC,min}}, f_{\text{WHC,max}}$) | Scaled to [0, 1] within $f_{\text{WHC,min}}$ and $f_{\text{WHC,max}}$. Peak shape controlled by $\beta$ and $\gamma$. |
-| **Gaussian Function**               | $e^{-\frac{\left( \frac{f_{\text{WHC}} - \mu}{f_{\text{WHC,max}} - f_{\text{WHC,min}}} \right)^2}{2\sigma^2}}$       | 3 ($\mu, \sigma, f_{\text{WHC,max}}, f_{\text{WHC,min}}$) | Fixed maximum of 1. Centered at $\mu$, scaled to $f_{\text{WHC,min}}$ and $f_{\text{WHC,max}}$. Symmetric around $\mu$. |
-| **Piecewise Linear Function**       | $\begin{cases} m_1 \left( \frac{f_{\text{WHC}} - f_{\text{WHC,min}}}{f_{\text{WHC,max}} - f_{\text{WHC,min}}} \right) + c_1, & f_{\text{WHC}} \leq f_{\text{WHC,mid}} \\ m_2 \left( \frac{f_{\text{WHC}} - f_{\text{WHC,min}}}{f_{\text{WHC,max}} - f_{\text{WHC,min}}} \right) + c_2, & f_{\text{WHC}} > f_{\text{WHC,mid}} \end{cases}$ | 6 ($m_1, c_1, m_2, c_2, f_{\text{WHC,min}}, f_{\text{WHC,max}}$) | Two linear segments split at $f_{\text{WHC,mid}}$. Scaled to $f_{\text{WHC,min}}$ and $f_{\text{WHC,max}}$.                 |
-| **Double Exponential Function**     | $a_1 e^{b_1 \left( \frac{f_{\text{WHC}} - f_{\text{WHC,min}}}{f_{\text{WHC,max}} - f_{\text{WHC,min}}} \right)} + a_2 e^{b_2 \left( \frac{f_{\text{WHC}} - f_{\text{WHC,min}}}{f_{\text{WHC,max}} - f_{\text{WHC,min}}} \right)}$      | 4 ($a_1, b_1, a_2, b_2$)           | Scaled exponential components to $f_{\text{WHC,min}}$ and $f_{\text{WHC,max}}$.                                                  |
-| **Piecewise Double Exponential**    | $\begin{cases} (1 - e^{-k_1(f_{\text{WHC}} - f_{\text{WHC,min}})}), & f_{\text{WHC}} \leq f_{\text{WHC,opt}} \\ e^{-k_2(f_{\text{WHC}} - f_{\text{WHC,opt}})}, & f_{\text{WHC}} > f_{\text{WHC,opt}} \end{cases}$ | 4 ($k_1, k_2, f_{\text{WHC,opt}}, f_{\text{WHC,min}}$) | Piecewise rise (left of $f_{\text{WHC,opt}}$) and asymmetric exponential decay (right). Scaled to range.         |
-| **Double Logistic Function**        | $\frac{1}{1 + e^{-k_1 \left( \frac{f_{\text{WHC}} - x_1}{f_{\text{WHC,max}} - f_{\text{WHC,min}}} \right)}} + \frac{1}{1 + e^{-k_2 \left( \frac{f_{\text{WHC}} - x_2}{f_{\text{WHC,max}} - f_{\text{WHC,min}}} \right)}}$ | 6 ($k_1, x_1, k_2, x_2, f_{\text{WHC,min}}, f_{\text{WHC,max}}$) | Scaled logistic transitions split at $x_1$ and $x_2$. Scaled to $f_{\text{WHC,min}}$ and $f_{\text{WHC,max}}$.          |
-| **Parabolic (SIPNET)**              | $a \left( \frac{f_{\text{WHC}} - f_{\text{WHC,min}}}{f_{\text{WHC,max}} - f_{\text{WHC,min}}} - b \right)^2 + c$                                 | 5 ($a, b, c, f_{\text{WHC,min}}, f_{\text{WHC,max}}$) | Scaled to $f_{\text{WHC,min}}$ and $f_{\text{WHC,max}}$. Derived from SIPNET temperature-response function.             |
+| Function                         | Formula                                                                                                                                                                                                                                                                                                                                   | Parameters                                                       | Notes                                                                                                                   |
+| -------------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ---------------------------------------------------------------- | ----------------------------------------------------------------------------------------------------------------------- |
+| **Beta Function**                | $\left( \frac{f_{\text{WHC}} - f_{\text{WHC,min}}}{f_{\text{WHC,max}} - f_{\text{WHC,min}}} \right)^\beta \cdot \left( 1 - \frac{f_{\text{WHC}} - f_{\text{WHC,min}}}{f_{\text{WHC,max}} - f_{\text{WHC,min}}} \right)^\gamma$                                                                                                            | 4 ($\beta, \gamma, f_{\text{WHC,min}}, f_{\text{WHC,max}}$)      | Scaled to [0, 1] within $f_{\text{WHC,min}}$ and $f_{\text{WHC,max}}$. Peak shape controlled by $\beta$ and $\gamma$.   |
+| **Gaussian Function**            | $e^{-\frac{\left( \frac{f_{\text{WHC}} - \mu}{f_{\text{WHC,max}} - f_{\text{WHC,min}}} \right)^2}{2\sigma^2}}$                                                                                                                                                                                                                            | 3 ($\mu, \sigma, f_{\text{WHC,max}}, f_{\text{WHC,min}}$)        | Fixed maximum of 1. Centered at $\mu$, scaled to $f_{\text{WHC,min}}$ and $f_{\text{WHC,max}}$. Symmetric around $\mu$. |
+| **Piecewise Linear Function**    | $\begin{cases} m_1 \left( \frac{f_{\text{WHC}} - f_{\text{WHC,min}}}{f_{\text{WHC,max}} - f_{\text{WHC,min}}} \right) + c_1, & f_{\text{WHC}} \leq f_{\text{WHC,mid}} \\ m_2 \left( \frac{f_{\text{WHC}} - f_{\text{WHC,min}}}{f_{\text{WHC,max}} - f_{\text{WHC,min}}} \right) + c_2, & f_{\text{WHC}} > f_{\text{WHC,mid}} \end{cases}$ | 6 ($m_1, c_1, m_2, c_2, f_{\text{WHC,min}}, f_{\text{WHC,max}}$) | Two linear segments split at $f_{\text{WHC,mid}}$. Scaled to $f_{\text{WHC,min}}$ and $f_{\text{WHC,max}}$.             |
+| **Double Exponential Function**  | $a_1 e^{b_1 \left( \frac{f_{\text{WHC}} - f_{\text{WHC,min}}}{f_{\text{WHC,max}} - f_{\text{WHC,min}}} \right)} + a_2 e^{b_2 \left( \frac{f_{\text{WHC}} - f_{\text{WHC,min}}}{f_{\text{WHC,max}} - f_{\text{WHC,min}}} \right)}$                                                                                                         | 4 ($a_1, b_1, a_2, b_2$)                                         | Scaled exponential components to $f_{\text{WHC,min}}$ and $f_{\text{WHC,max}}$.                                         |
+| **Piecewise Double Exponential** | $\begin{cases} (1 - e^{-k_1(f_{\text{WHC}} - f_{\text{WHC,min}})}), & f_{\text{WHC}} \leq f_{\text{WHC,opt}} \\ e^{-k_2(f_{\text{WHC}} - f_{\text{WHC,opt}})}, & f_{\text{WHC}} > f_{\text{WHC,opt}} \end{cases}$                                                                                                                         | 4 ($k_1, k_2, f_{\text{WHC,opt}}, f_{\text{WHC,min}}$)           | Piecewise rise (left of $f_{\text{WHC,opt}}$) and asymmetric exponential decay (right). Scaled to range.                |
+| **Double Logistic Function**     | $\frac{1}{1 + e^{-k_1 \left( \frac{f_{\text{WHC}} - x_1}{f_{\text{WHC,max}} - f_{\text{WHC,min}}} \right)}} + \frac{1}{1 + e^{-k_2 \left( \frac{f_{\text{WHC}} - x_2}{f_{\text{WHC,max}} - f_{\text{WHC,min}}} \right)}}$                                                                                                                 | 6 ($k_1, x_1, k_2, x_2, f_{\text{WHC,min}}, f_{\text{WHC,max}}$) | Scaled logistic transitions split at $x_1$ and $x_2$. Scaled to $f_{\text{WHC,min}}$ and $f_{\text{WHC,max}}$.          |
+| **Parabolic (SIPNET)**           | $a \left( \frac{f_{\text{WHC}} - f_{\text{WHC,min}}}{f_{\text{WHC,max}} - f_{\text{WHC,min}}} - b \right)^2 + c$                                                                                                                                                                                                                          | 5 ($a, b, c, f_{\text{WHC,min}}, f_{\text{WHC,max}}$)            | Scaled to $f_{\text{WHC,min}}$ and $f_{\text{WHC,max}}$. Derived from SIPNET temperature-response function.             |
 
 ## Effect of SOM on Soil Water Dynamics