symfluence 0.7.4__tar.gz → 0.7.6__tar.gz

{symfluence-0.7.4 → symfluence-0.7.6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: symfluence
-Version: 0.7.4
+Version: 0.7.6
 Summary: SYnergistic Modelling Framework for Linking and Unifying Earth-system Nexii for Computational Exploration
 Project-URL: Homepage, https://symfluence.org
 Project-URL: Source, https://github.com/DarriEy/SYMFLUENCE

{symfluence-0.7.4 → symfluence-0.7.6}/symfluence/coupling/adapters/jax_adapters.py

@@ -93,7 +93,6 @@ class Snow17JAXComponent(JAXComponent):
 
         def step_wrapper(inputs, state, params, dt):
             import jax.numpy as jnp
-
             from jsnow17.parameters import (
                 DEFAULT_ADC,
                 Snow17State,
@@ -186,7 +185,6 @@ class XAJJAXComponent(JAXComponent):
 
         def step_wrapper(inputs, state, params, dt):
             import jax.numpy as jnp
-
             from jxaj.parameters import (
                 XinanjiangParams,
                 XinanjiangState,
@@ -273,7 +271,6 @@ class SacSmaJAXComponent(JAXComponent):
 
         def step_wrapper(inputs, state, params, dt):
             import jax.numpy as jnp
-
             from jsacsma.parameters import SacSmaParameters
             from jsacsma.sacsma import SacSmaState
             # Unpack flat array → SacSmaState namedtuple

{symfluence-0.7.4 → symfluence-0.7.6}/symfluence/models/gsflow/build_instructions.py

@@ -54,8 +54,8 @@ echo "gfortran version: $(gfortran --version | head -1)"
 GFORT_VER=$(gfortran -dumpversion | cut -d. -f1)
 COMPAT_FLAGS=""
 if [ "$GFORT_VER" -ge 10 ] 2>/dev/null; then
-    COMPAT_FLAGS="-fallow-argument-mismatch"
-    echo "Adding -fallow-argument-mismatch for gfortran >= 10"
+    COMPAT_FLAGS="-fallow-argument-mismatch -ffree-line-length-none -ffixed-line-length-none -Wno-error=line-truncation"
+    echo "Adding gfortran >= 10 compat flags: $COMPAT_FLAGS"
 fi
 
 UNAME_S=$(uname -s)
@@ -196,18 +196,31 @@ rm -f /tmp/_gsflow_patch.py
 
 mkdir -p lib
 
+# Use absolute paths to avoid cd issues with make changing CWD
+_BUILD_BASE=$(pwd)
+
+# Verify expected subdirectories exist
+for subdir in modflow prms gsflow; do
+    if [ ! -d "$_BUILD_BASE/$subdir" ]; then
+        echo "WARNING: $subdir directory not found in $_BUILD_BASE"
+        ls -la "$_BUILD_BASE" || true
+        echo "ERROR: GSFLOW source directory layout does not match expected structure"
+        exit 1
+    fi
+done
+
 echo "Step 1/3: Building MODFLOW-NWT..."
-cd modflow && make -j1 FC=gfortran 2>&1 && cd ..
+cd "$_BUILD_BASE/modflow" && make -j1 FC=gfortran 2>&1
 
 echo "Step 2/3: Building PRMS..."
-cp modflow/*.mod prms/ 2>/dev/null || true
-cp gsflow/*.mod prms/ 2>/dev/null || true
-cd prms && make -j1 FC=gfortran 2>&1 && cd ..
+cp "$_BUILD_BASE"/modflow/*.mod "$_BUILD_BASE/prms/" 2>/dev/null || true
+cp "$_BUILD_BASE"/gsflow/*.mod "$_BUILD_BASE/prms/" 2>/dev/null || true
+cd "$_BUILD_BASE/prms" && make -j1 FC=gfortran 2>&1
 
 echo "Step 3/3: Building GSFLOW..."
-cp modflow/*.mod gsflow/ 2>/dev/null || true
-cp prms/*.mod gsflow/ 2>/dev/null || true
-cd gsflow && make -j1 FC=gfortran 2>&1 && cd ..
+cp "$_BUILD_BASE"/modflow/*.mod "$_BUILD_BASE/gsflow/" 2>/dev/null || true
+cp "$_BUILD_BASE"/prms/*.mod "$_BUILD_BASE/gsflow/" 2>/dev/null || true
+cd "$_BUILD_BASE/gsflow" && make -j1 FC=gfortran 2>&1
 
 cd "$GSFLOW_INSTALL_ROOT"
 

{symfluence-0.7.4 → symfluence-0.7.6}/symfluence/models/ngen/build_instructions.py

@@ -275,7 +275,18 @@ if [ -n "${UDUNITS2_INCLUDE_DIR:-}" ] && [ -n "${UDUNITS2_LIBRARY:-}" ]; then
   _U2_LIB=$(echo "$UDUNITS2_LIBRARY" | sed 's/\\/\//g')
   CMAKE_ARGS="$CMAKE_ARGS -DUDUNITS2_ROOT=$_U2_DIR"
   CMAKE_ARGS="$CMAKE_ARGS -DUDUNITS2_INCLUDE_DIR=$_U2_INC"
-  CMAKE_ARGS="$CMAKE_ARGS -DUDUNITS2_LIBRARY=$_U2_LIB"
+  # When UDUNITS2 is a static archive, GNU ld needs transitive dependencies
+  # (expat, dl, m) AFTER the archive on the link line.  Shell quoting cannot
+  # reliably pass CMake semicolon-lists through bash variables, so write them
+  # to an initial-cache file that cmake processes directly.
+  if echo "$_U2_LIB" | grep -q '\.a$'; then
+    _U2_CACHE="/tmp/_ngen_u2_cache.cmake"
+    echo "set(UDUNITS2_LIBRARY \"$_U2_LIB;expat;dl;m\" CACHE STRING \"UDUNITS2 with transitive deps\" FORCE)" > "$_U2_CACHE"
+    CMAKE_ARGS="$CMAKE_ARGS -C $_U2_CACHE"
+    echo "Wrote UDUNITS2 cmake cache: $_U2_CACHE"
+  else
+    CMAKE_ARGS="$CMAKE_ARGS -DUDUNITS2_LIBRARY=$_U2_LIB"
+  fi
 
   # Also add to compiler flags (use forward-slash path)
   export CXXFLAGS="${CXXFLAGS:-} -I${_U2_INC}"
@@ -407,7 +418,13 @@ else
   if [ -n "${UDUNITS2_INCLUDE_DIR:-}" ] && [ -n "${UDUNITS2_LIBRARY:-}" ]; then
     FALLBACK_ARGS="$FALLBACK_ARGS -DUDUNITS2_ROOT=$UDUNITS2_DIR"
     FALLBACK_ARGS="$FALLBACK_ARGS -DUDUNITS2_INCLUDE_DIR=$UDUNITS2_INCLUDE_DIR"
-    FALLBACK_ARGS="$FALLBACK_ARGS -DUDUNITS2_LIBRARY=$UDUNITS2_LIBRARY"
+    if echo "$UDUNITS2_LIBRARY" | grep -q '\.a$'; then
+      _U2_CACHE="/tmp/_ngen_u2_cache.cmake"
+      echo "set(UDUNITS2_LIBRARY \"$UDUNITS2_LIBRARY;expat;dl;m\" CACHE STRING \"UDUNITS2 with transitive deps\" FORCE)" > "$_U2_CACHE"
+      FALLBACK_ARGS="$FALLBACK_ARGS -C $_U2_CACHE"
+    else
+      FALLBACK_ARGS="$FALLBACK_ARGS -DUDUNITS2_LIBRARY=$UDUNITS2_LIBRARY"
+    fi
   fi
   # Note: LIBRARY_PATH and CMAKE_PREFIX_PATH are already set in environment for expat
 

{symfluence-0.7.4 → symfluence-0.7.6}/symfluence/models/watflood/build_instructions.py

@@ -143,6 +143,47 @@ for f in "${SRC_DIR}/model/write_tb0.f" "${SRC_DIR}/model/write_diversion_tb0.f"
     fi
 done
 
+# Fix EF_Module.f: CountDataLinesAfterHeader is placed after END MODULE
+# which confuses gfortran.  Extract it into a separate source file instead
+# of trying to squeeze it into CONTAINS (which causes host-association errors).
+EF_MOD="${SRC_DIR}/common/EF_Module.f"
+if [ -f "$EF_MOD" ]; then
+    python3 -c "
+import re
+with open('$EF_MOD') as f:
+    txt = f.read()
+if 'CountDataLinesAfterHeader' in txt:
+    # Find END MODULE and everything after it
+    m = re.search(r'^(\s*END\s+MODULE\s+\w+\s*\n)(.*)', txt, re.DOTALL | re.MULTILINE | re.IGNORECASE)
+    if m:
+        end_mod = m.group(1)
+        after = m.group(2).strip()
+        if after:
+            # Write the trailing function(s) to a separate file
+            with open('${SRC_DIR}/common/EF_Extra.f90', 'w') as ef:
+                ef.write('! Extracted from EF_Module.f for gfortran compatibility\n')
+                ef.write(after + '\n')
+            # Remove the trailing code from the original file
+            txt = txt[:m.start()] + end_mod
+            with open('$EF_MOD', 'w') as f:
+                f.write(txt)
+            print('  EF_Module.f: extracted trailing function to EF_Extra.f90')
+        else:
+            print('  EF_Module.f: no trailing code after END MODULE')
+    else:
+        print('  EF_Module.f: no END MODULE found')
+else:
+    print('  EF_Module.f: no CountDataLinesAfterHeader found')
+" 2>/dev/null || echo "  WARNING: EF_Module.f patch failed (non-fatal)"
+fi
+
+# Fix WRITE statements with misquoted format strings
+# e.g. write(un,3020)':SourceFile         ',source_file_name
+# The colon inside the string confuses some compilers.  Ensure proper quoting.
+find "${SRC_DIR}" -name "*.f" -o -name "*.f90" | while read -r f; do
+    perl -pi -e "s/write\(([^)]+)\)'/write(\$1) '/gi" "$f"
+done
+
 # === Create compatibility source files ===
 echo "Creating compatibility stubs..."
 

{symfluence-0.7.4 → symfluence-0.7.6}/symfluence/models/wrfhydro/build_instructions.py

@@ -191,6 +191,25 @@ fi
 # Return to source dir for compilation
 cd "$SRC_DIR"
 
+# Pre-compile MPP module — needed by Routing/Reservoirs but may not be ready
+# in time during a parallel make (race condition on macOS especially).
+echo "Pre-compiling MPP modules..."
+MPP_DIR="$SRC_DIR/MPP"
+if [ -d "$MPP_DIR" ]; then
+    cd "$MPP_DIR"
+    MPPFLAGS="-O2 -ffree-form -ffree-line-length-none -fallow-argument-mismatch"
+    for src in module_mpp_land.F CPL_WRF.F; do
+        if [ -f "$src" ]; then
+            echo "  Compiling $src..."
+            $MPIFORT -c $MPPFLAGS "$src" 2>&1 || true
+        fi
+    done
+    # Copy .mod files to where they're expected
+    cp -f *.mod "$SRC_DIR/mod/" 2>/dev/null || true
+    echo "MPP modules pre-compiled"
+    cd "$SRC_DIR"
+fi
+
 # Compile with compile_offline_NoahMP.sh (the standard WRF-Hydro build method)
 # WRF-Hydro's SURFEX modules have circular Makefile deps (ini_csts needs modd_csts,
 # mode_surf_coefs needs mode_thermos, module_snowcro needs mode_surf_coefs, etc.)
@@ -212,14 +231,44 @@ if [ -f "$SRC_DIR/compile_offline_NoahMP.sh" ]; then
     if [ -f "$SRC_DIR/Run/wrf_hydro.exe" ] || [ -f "$SRC_DIR/Run/wrf_hydro_NoahMP.exe" ]; then
         echo "Build succeeded on first pass"
     else
+        # Pass 1's make clean wiped pre-compiled .mod files.
+        # Re-compile MPP and SURFEX modules before pass 2.
+        echo "=== Re-compiling MPP/SURFEX modules for pass 2 ==="
+        if [ -d "$MPP_DIR" ]; then
+            cd "$MPP_DIR"
+            for src in module_mpp_land.F CPL_WRF.F; do
+                [ -f "$src" ] && $MPIFORT -c $MPPFLAGS "$src" 2>&1 || true
+            done
+            cp -f *.mod "$SRC_DIR/mod/" 2>/dev/null || true
+            # Also copy to where Routing Makefiles expect them via relative path
+            for rdir in "$SRC_DIR/Routing/Reservoirs/Level_Pool" \
+                        "$SRC_DIR/Routing/Reservoirs/RFC_Forecasts" \
+                        "$SRC_DIR/Routing/Reservoirs"; do
+                [ -d "$rdir" ] && cp -f *.mod "$rdir/../../MPP/" 2>/dev/null || true
+            done
+            cd "$SRC_DIR"
+        fi
+        if [ -d "$SURFEX_DIR" ]; then
+            cd "$SURFEX_DIR"
+            for src in modd_csts.F modd_snow_par.F modd_snow_metamo.F modd_surf_atm.F \
+                       ini_csts.F mode_thermos.F mode_snow3l.F mode_surf_coefs.F \
+                       module_snowcro.F module_snowcro_intercept.F; do
+                [ -f "$src" ] && $MPIFORT -c $SFFLAGS "$src" 2>&1 || true
+            done
+            cp -f *.mod "$SRC_DIR/Land_models/NoahMP/phys/" 2>/dev/null || true
+            cp -f *.o "$SRC_DIR/Land_models/NoahMP/phys/" 2>/dev/null || true
+            cp -f *.mod "$SRC_DIR/mod/" 2>/dev/null || true
+            cd "$SRC_DIR"
+        fi
+
         # Pass 2: Create a patched compile script that skips `make clean`
-        # so that .mod files from pass 1 persist for dependency resolution
-        echo "=== Compile Pass 2 (with .mod files from pass 1) ==="
+        # so that .mod files from re-compilation persist
+        echo "=== Compile Pass 2 (with .mod files restored) ==="
         cd "$SRC_DIR"
         python3 -c "
 with open('compile_offline_NoahMP.sh') as f:
     content = f.read()
-# Remove make clean line to preserve .mod files from pass 1
+# Remove make clean line to preserve .mod files
 content = content.replace(
     'make clean; rm -f Run/wrf_hydro_NoahMP ; rm -f Run/*TBL ; rm -f Run/*namelist*',
     '# Skipping make clean to preserve .mod files')

{symfluence-0.7.4 → symfluence-0.7.6}/symfluence/optimization/parameter_managers/__init__.py

@@ -58,21 +58,22 @@ _register_parameter_managers()
 
 # Re-export from canonical locations (avoids deprecation warnings for internal use)
 # Users who import directly from the stub modules will still see deprecation warnings
+from jhbv.calibration.parameter_manager import HBVParameterManager
+from jsacsma.calibration.parameter_manager import SacSmaParameterManager
+from jxaj.calibration.parameter_manager import XinanjiangParameterManager
+
 from symfluence.models.fuse.calibration.parameter_manager import FUSEParameterManager
 from symfluence.models.gnn.calibration.parameter_manager import MLParameterManager
 from symfluence.models.gr.calibration.parameter_manager import GRParameterManager
 from symfluence.models.gsflow.calibration.parameter_manager import GSFLOWParameterManager
-from jhbv.calibration.parameter_manager import HBVParameterManager
 from symfluence.models.hype.calibration.parameter_manager import HYPEParameterManager
 from symfluence.models.mesh.calibration.parameter_manager import MESHParameterManager
 from symfluence.models.modflow.calibration.parameter_manager import CoupledGWParameterManager
 from symfluence.models.ngen.calibration.parameter_manager import NgenParameterManager
 from symfluence.models.pihm.calibration.parameter_manager import PIHMParameterManager
 from symfluence.models.rhessys.calibration.parameter_manager import RHESSysParameterManager
-from jsacsma.calibration.parameter_manager import SacSmaParameterManager
 from symfluence.models.summa.calibration.parameter_manager import SUMMAParameterManager
 from symfluence.models.watflood.calibration.parameter_manager import WATFLOODParameterManager
-from jxaj.calibration.parameter_manager import XinanjiangParameterManager
 
 __all__ = [
     'FUSEParameterManager',

{symfluence-0.7.4 → symfluence-0.7.6}/symfluence/symfluence_version.py

@@ -6,4 +6,4 @@ Single source of truth for the SYMFLUENCE version.
 Update this when cutting a release.
 """
 # Semantic version (PEP 440-friendly)
-__version__ = "0.7.4"
+__version__ = "0.7.6"