Merge pull request #85 from noaa-oar-arl/update-ci

Update CI

.github/workflows/ci.yml

@@ -22,19 +22,19 @@ jobs:
         shell: bash -l {0}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Install dependencies
         run: |
           sudo apt-get update
           sudo apt-get install libnetcdff-dev
 
       - name: Set up Python (micromamba)
-        uses: mamba-org/provision-with-micromamba@v15
+        uses: mamba-org/setup-micromamba@v1
         with:
           environment-file: python/environment.yml
-          cache-env: true
-          extra-specs: |
+          cache-environment: true
+          create-args: |
             python=3.10
 
       - name: Check that default input is nc

.github/workflows/lint.yml

@@ -19,5 +19,5 @@ jobs:
       - uses: actions/checkout@v3
       - uses: actions/setup-python@v4
         with:
-          python-version: "3.9"
+          python-version: "3.10"
       - uses: pre-commit/action@v3.0.0

README.md

@@ -22,7 +22,7 @@ See [the included Makefile](./src/Makefile), which detects NetCDF using `nf-conf
 Compilation options can be controlled with environment variables:
 
 - `FC=gfortran` (default) or compiler name/path (e.g. `FC=ifort`, `FC=gfortran-11`, `FC=/usr/bin/gfortran-11`)
-- `DEBUG=0` (off; default) or `DEBUG=1` (on)
+- `DEBUG=0` (off; default) or `DEBUG=1` (on) or `DEBUG=2` (more flags, including FPE traps and traceback)
 - `NC=0` (off) or `NC=1` (on; default)
 
 Example:

src/Makefile

@@ -18,19 +18,28 @@ NC ?= 1
 
 # Compile flags
 $(info DEBUG setting: '$(DEBUG)')
-ifeq ($(DEBUG), 1)
+ifeq ($(DEBUG), 0)
+  FCFLAGS := -O3
+else ifeq ($(DEBUG), 1)
   ifeq ($(findstring gfortran,$(notdir $(FC))),gfortran)
-    FCFLAGS := -g -Wall -Wextra -Wconversion -Og -pedantic -fcheck=bounds -fmax-errors=5 -std=f2003 -fall-intrinsics
-# More Debug Flags
-#      FCFLAGS := -g -Og -Wall -Wextra -pedantic -fcheck=all -fmax-errors=5 -std=f2003 \
-#      -fall-intrinsics -fbacktrace -ffpe-trap=invalid,zero,overflow
+    FCFLAGS := -g -Og -Wall -Wextra -Wconversion -pedantic \
+      -fcheck=bounds -fall-intrinsics -fmax-errors=5 \
+      -std=f2003
   else ifeq ($(FC),ifort)
-    FCFLAGS := -g -warn all -check bounds -implicitnone -O0 -error-limit 5
+    FCFLAGS := -g -O0 -warn all -check bounds -implicitnone -error-limit 5
+  endif
+else ifeq ($(DEBUG), 2)
+  ifeq ($(findstring gfortran,$(notdir $(FC))),gfortran)
+    FCFLAGS := -g -Og -Wall -Wextra -Wconversion -pedantic \
+      -fcheck=all -fall-intrinsics -fmax-errors=0 \
+      -fbacktrace -ffpe-trap=invalid,zero,overflow -finit-real=snan -finit-integer=-99999999 \
+      -std=f2003
+  else ifeq ($(FC),ifort)
+    FCFLAGS := -g  -O0 -warn all -check all -implicitnone -error-limit 0 \
+      -fpe0 -traceback
   endif
-else ifeq ($(DEBUG), 0)
-  FCFLAGS := -O3
 else
-  $(error invalid setting for DEBUG, should be 0 or 1 but is '$(DEBUG)')
+  $(error invalid setting for DEBUG, should be 0, 1 or 2 but is '$(DEBUG)')
 endif
 $(info FCFLAGS: '$(FCFLAGS)')
 
@@ -54,37 +63,37 @@ $(info LIBS: '$(LIBS)')
 $(info INC:  '$(INC)')
 
 # Source objects
-OBJS :=\
- canopy_const_mod.o \
- canopy_date_mod.o \
- canopy_coord_mod.o \
- canopy_canopts_mod.o \
- canopy_canmet_mod.o \
- canopy_canvars_mod.o \
- canopy_utils_mod.o \
- canopy_files_mod.o \
- canopy_readnml.o \
- canopy_alloc.o \
- canopy_init.o \
- canopy_txt_io_mod.o \
- canopy_ncf_io_mod.o \
- canopy_check_input.o \
- canopy_read_txt.o \
- canopy_dxcalc_mod.o \
- canopy_profile_mod.o \
- canopy_var3din_mod.o \
- canopy_phot_mod.o \
- canopy_rad_mod.o \
- canopy_tleaf_mod.o \
- canopy_wind_mod.o \
- canopy_fire_mod.o \
- canopy_eddy_mod.o \
- canopy_bioparm_mod.o \
- canopy_bioemi_mod.o \
- canopy_calcs.o \
- canopy_write_txt.o \
- canopy_dealloc.o \
- canopy_app.o
+OBJS := \
+  canopy_const_mod.o \
+  canopy_date_mod.o \
+  canopy_coord_mod.o \
+  canopy_canopts_mod.o \
+  canopy_canmet_mod.o \
+  canopy_canvars_mod.o \
+  canopy_utils_mod.o \
+  canopy_files_mod.o \
+  canopy_readnml.o \
+  canopy_alloc.o \
+  canopy_init.o \
+  canopy_txt_io_mod.o \
+  canopy_ncf_io_mod.o \
+  canopy_check_input.o \
+  canopy_read_txt.o \
+  canopy_dxcalc_mod.o \
+  canopy_profile_mod.o \
+  canopy_var3din_mod.o \
+  canopy_phot_mod.o \
+  canopy_rad_mod.o \
+  canopy_tleaf_mod.o \
+  canopy_wind_mod.o \
+  canopy_fire_mod.o \
+  canopy_eddy_mod.o \
+  canopy_bioparm_mod.o \
+  canopy_bioemi_mod.o \
+  canopy_calcs.o \
+  canopy_write_txt.o \
+  canopy_dealloc.o \
+  canopy_app.o
 
 ifeq ($(NC), 0)
   _ncf_objs := canopy_check_input.o canopy_ncf_io_mod.o

src/canopy_utils_mod.F90

@@ -658,56 +658,51 @@ function GET_GAMMA_LEAFAGE(leafage_opt,LAIpast,LAIcurrent,tsteplai,TABOVE,Anew,A
         !------------------------------------------------------------------------------
         !BOC
 
-        !-----------------------
-        ! Compute GAMMA_LEAFAGE
-        !-----------------------
-
-
         !TABOVE (Tt in MEGAN code) -> Above Canopy TEMP (tmp2mref or temp2)
 
         ! Calculate foliage fraction
         !-----------------------
         !Also, Compute ti and tm
         ! ti: number of days after budbreak required to induce emissions
         ! tm: number of days after budbreak required to reach peak emissions
-        IF (LAIcurrent - LAIpast > LAIdelta) THEN !(i.e. LAI has Increased)
-            IF (TABOVE .le. 303.0_rk) THEN
-                ti = 5.0_rk + 0.7_rk*(300.0_rk-TABOVE)
-            ELSE
-                ti = 2.9_rk
-            ENDIF
-            tm = 2.3_rk*ti
-            !Fnew calculated
-            IF (ti .ge. tsteplai) THEN
-                Fnew = 1.0_rk - (LAIpast/LAIcurrent)
-            ELSE
-                Fnew = (ti/tsteplai) * ( 1.0_rk-(LAIpast/LAIcurrent) )
-            ENDIF
-            !Fmat calculated
-            IF (tm .ge. tsteplai) THEN
-                Fmat = LAIpast/LAIcurrent
-            ELSE
-                Fmat = (LAIpast/LAIcurrent) + ( (tsteplai-tm)/tsteplai ) * ( 1.0_rk-(LAIpast/LAIcurrent) )
-            ENDIF
-
-            Fgro = 1.0_rk - Fnew - Fmat
-            Fold = 0.0_rk
-        ELSEIF (LAIpast - LAIcurrent > LAIdelta) THEN !(i.e. LAI has decreased)
-            Fnew = 0.0_rk
-            Fgro = 0.0_rk
-            Fold = ( LAIpast-LAIcurrent ) / LAIpast
-            Fmat = 1.0_rk-Fold
-        ELSE !(LAIpast == LAIcurrent) THEN !If LAI remains same
-            Fnew = 0.0_rk
-            Fgro = 0.1_rk
-            Fmat = 0.8_rk
-            Fold = 0.1_rk
-        ENDIF
 
         !-----------------------
         ! Compute GAMMA_AGE
         !-----------------------
         IF (leafage_opt .eq. 0) THEN
+            IF (LAIcurrent - LAIpast > LAIdelta) THEN !(i.e. LAI has Increased)
+                IF (TABOVE .le. 303.0_rk) THEN
+                    ti = 5.0_rk + 0.7_rk*(300.0_rk-TABOVE)
+                ELSE
+                    ti = 2.9_rk
+                ENDIF
+                tm = 2.3_rk*ti
+                !Fnew calculated
+                IF (ti .ge. tsteplai) THEN
+                    Fnew = 1.0_rk - (LAIpast/LAIcurrent)
+                ELSE
+                    Fnew = (ti/tsteplai) * ( 1.0_rk-(LAIpast/LAIcurrent) )
+                ENDIF
+                !Fmat calculated
+                IF (tm .ge. tsteplai) THEN
+                    Fmat = LAIpast/LAIcurrent
+                ELSE
+                    Fmat = (LAIpast/LAIcurrent) + ( (tsteplai-tm)/tsteplai ) * ( 1.0_rk-(LAIpast/LAIcurrent) )
+                ENDIF
+
+                Fgro = 1.0_rk - Fnew - Fmat
+                Fold = 0.0_rk
+            ELSEIF (LAIpast - LAIcurrent > LAIdelta) THEN !(i.e. LAI has decreased)
+                Fnew = 0.0_rk
+                Fgro = 0.0_rk
+                Fold = ( LAIpast-LAIcurrent ) / LAIpast
+                Fmat = 1.0_rk-Fold
+            ELSE !(LAIpast == LAIcurrent) THEN !If LAI remains same
+                Fnew = 0.0_rk
+                Fgro = 0.1_rk
+                Fmat = 0.8_rk
+                Fold = 0.1_rk
+            ENDIF
             ! Compute GAMMA_LEAFAGE
             GAMMA_LEAFAGE = Fnew*Anew + Fgro*Agro + Fmat*Amat + Fold*Aold
             ! Prevent negative values