symfluence 0.7.2__tar.gz → 0.7.4__tar.gz

{symfluence-0.7.2 → symfluence-0.7.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: symfluence
-Version: 0.7.2
+Version: 0.7.4
 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
@@ -697,6 +697,12 @@ Requires-Dist: geopandas<2.0.0,>=0.13.0
 Requires-Dist: h5netcdf<2.0.0,>=1.1.0
 Requires-Dist: hydrobm
 Requires-Dist: intake-xarray
+Requires-Dist: jhbv>=0.1.0
+Requires-Dist: jhechms>=0.1.0
+Requires-Dist: jsacsma>=0.1.0
+Requires-Dist: jsnow17>=0.1.0
+Requires-Dist: jtopmodel>=0.1.0
+Requires-Dist: jxaj>=0.1.0
 Requires-Dist: matplotlib<4.0.0,>=3.7.0
 Requires-Dist: netcdf4<2.0.0,>=1.6.0
 Requires-Dist: networkx<4.0.0,>=3.0.0

{symfluence-0.7.2 → symfluence-0.7.4}/pyproject.toml

@@ -74,6 +74,13 @@ dependencies = [
   "pydantic>=2.0.0,<3.0.0",
   # Differentiable coupling framework
   "dcoupler>=0.2.0",
+  # JAX-based model plugins
+  "jsnow17>=0.1.0",
+  "jsacsma>=0.1.0",
+  "jxaj>=0.1.0",
+  "jhbv>=0.1.0",
+  "jhechms>=0.1.0",
+  "jtopmodel>=0.1.0",
 ]
 
 [project.optional-dependencies]

{symfluence-0.7.2 → symfluence-0.7.4}/symfluence/__init__.py

@@ -144,7 +144,7 @@ __all__ = [
 ]
 
 # Suppress overly verbose external logging/warnings
-rpy2_logger = logging.getLogger("r2.rinterface_lib.embedded")
+rpy2_logger = logging.getLogger("rpy2.rinterface_lib.embedded")
 rpy2_logger.setLevel(logging.WARNING)
 rpy2_logger.addHandler(logging.NullHandler())
 rpy2_logger.propagate = False

symfluence-0.7.4/symfluence/__main__.py

@@ -0,0 +1,10 @@
+# SPDX-License-Identifier: GPL-3.0-or-later
+# Copyright (C) 2024-2026 SYMFLUENCE Team <dev@symfluence.org>
+
+"""Allow running SYMFLUENCE as ``python -m symfluence``."""
+
+import sys
+
+from symfluence.main_cli import main
+
+sys.exit(main())

{symfluence-0.7.2 → symfluence-0.7.4}/symfluence/cli/external_tools_config.py

@@ -232,10 +232,20 @@ else
   echo "Non-HPC environment detected; using NGIAB-CloudInfra"
 fi
 
-cd ..
-rm -rf ngiab
-git clone "$NGIAB_REPO" ngiab
-cd ngiab
+# Clone into a temp directory first, then move contents into the install dir.
+# We cannot do `cd .. && rm -rf ngiab` because _build.sh itself lives inside
+# the ngiab/ directory.  On HPC parallel filesystems (GPFS, Lustre) removing a
+# directory that still has an open file handle (the running script) fails with
+# "Directory not empty".
+TMPCLONE="$(mktemp -d "${TMPDIR:-/tmp}/ngiab_clone.XXXXXX")"
+git clone "$NGIAB_REPO" "$TMPCLONE/ngiab"
+
+# Wipe current contents (except _build.sh which is still running) and copy new
+# files in.  Using rsync-style approach: remove old files, copy new ones.
+find . -mindepth 1 -maxdepth 1 ! -name '_build.sh' -exec rm -rf {} + 2>/dev/null || true
+cp -a "$TMPCLONE/ngiab/." .
+rm -rf "$TMPCLONE"
+
 [ -f guide.sh ] && chmod +x guide.sh && bash -n guide.sh || true
             '''.strip()
         ],

{symfluence-0.7.2 → symfluence-0.7.4}/symfluence/cli/services/system_deps.py

@@ -216,6 +216,14 @@ class SystemDepsRegistry:
             if found:
                 path = f"(pkg-config: {pkg_config_name})"
 
+        # Conda prefix fallback: on Conda (especially Windows), CLI tools
+        # like nc-config are often absent.  Probe $CONDA_PREFIX for known
+        # header files to confirm the library is actually installed.
+        if not found and self._platform == Platform.CONDA:
+            conda_header = check.get("conda_header", "")
+            if conda_header:
+                found, path = self._check_conda_prefix(conda_header)
+
         # Homebrew keg-only fallback: on macOS, packages like openblas and
         # lapack are "keg-only" (not symlinked into the Homebrew prefix), so
         # their .pc files are invisible to pkg-config by default.  Probe the
@@ -377,6 +385,34 @@ class SystemDepsRegistry:
             pass
         return False, None
 
+    @staticmethod
+    def _check_conda_prefix(header_relpath: str) -> tuple:
+        """Probe ``$CONDA_PREFIX`` for a known header file.
+
+        On Windows Conda, CLI tools like ``nc-config`` are often absent, but
+        the libraries are installed under ``$CONDA_PREFIX/Library/`` (Windows)
+        or ``$CONDA_PREFIX/`` (Unix).
+
+        Args:
+            header_relpath: Relative path to check, e.g. ``"include/netcdf.h"``.
+
+        Returns:
+            ``(found, path_str)`` — *found* is True if the header exists.
+        """
+        prefix = os.environ.get("CONDA_PREFIX", "")
+        if not prefix:
+            return False, None
+
+        # Windows Conda puts headers in Library/include/, Unix in include/
+        candidates = [
+            os.path.join(prefix, "Library", header_relpath),
+            os.path.join(prefix, header_relpath),
+        ]
+        for candidate in candidates:
+            if os.path.isfile(candidate):
+                return True, f"(conda: {candidate})"
+        return False, None
+
     @staticmethod
     def _check_brew_keg_pkg_config(pkg_config_name: str, brew_formulas: List[str]) -> tuple:
         """Probe Homebrew keg-only packages for pkg-config metadata.

{symfluence-0.7.2 → symfluence-0.7.4}/symfluence/coupling/adapters/jax_adapters.py

@@ -24,25 +24,25 @@ logger = logging.getLogger(__name__)
 
 def _get_snow17_step():
     """Import Snow-17 step function."""
-    from symfluence.models.snow17.model import snow17_step
+    from jsnow17.model import snow17_step
     return snow17_step
 
 
 def _get_snow17_params():
     """Import Snow-17 parameter bounds."""
-    from symfluence.models.snow17.parameters import SNOW17_PARAM_BOUNDS
+    from jsnow17.parameters import SNOW17_PARAM_BOUNDS
     return SNOW17_PARAM_BOUNDS
 
 
 def _get_xaj_step():
     """Import XAJ step function."""
-    from symfluence.models.xinanjiang.model import step_jax
+    from jxaj.model import step_jax
     return step_jax
 
 
 def _get_sacsma_step():
     """Import SAC-SMA step function."""
-    from symfluence.models.sacsma.sacsma import sacsma_step
+    from jsacsma.sacsma import sacsma_step
     return sacsma_step
 
 
@@ -94,7 +94,7 @@ class Snow17JAXComponent(JAXComponent):
         def step_wrapper(inputs, state, params, dt):
             import jax.numpy as jnp
 
-            from symfluence.models.snow17.parameters import (
+            from jsnow17.parameters import (
                 DEFAULT_ADC,
                 Snow17State,
                 params_dict_to_namedtuple,
@@ -187,7 +187,7 @@ class XAJJAXComponent(JAXComponent):
         def step_wrapper(inputs, state, params, dt):
             import jax.numpy as jnp
 
-            from symfluence.models.xinanjiang.parameters import (
+            from jxaj.parameters import (
                 XinanjiangParams,
                 XinanjiangState,
             )
@@ -274,8 +274,8 @@ class SacSmaJAXComponent(JAXComponent):
         def step_wrapper(inputs, state, params, dt):
             import jax.numpy as jnp
 
-            from symfluence.models.sacsma.parameters import SacSmaParameters
-            from symfluence.models.sacsma.sacsma import SacSmaState
+            from jsacsma.parameters import SacSmaParameters
+            from jsacsma.sacsma import SacSmaState
             # Unpack flat array → SacSmaState namedtuple
             sac_state = SacSmaState(
                 uztwc=state[0], uzfwc=state[1], lztwc=state[2],

{symfluence-0.7.2 → symfluence-0.7.4}/symfluence/data/preprocessing/__init__.py

@@ -59,7 +59,7 @@ try:
     from .elevation_correction import ElevationCorrectionProcessor
 except ImportError as _e:
     ElevationCorrectionProcessor: Any = None  # type: ignore[no-redef]
-    _logger.warning("Failed to import ElevationCorrectionProcessor: %s", _e)
+    _logger.debug("ElevationCorrectionProcessor not available: %s", _e)
 
 __all__ = [
     'ForcingResampler',

{symfluence-0.7.2 → symfluence-0.7.4}/symfluence/models/__init__.py

@@ -61,9 +61,9 @@ warnings.filterwarnings('ignore', message='.*import failed.*')
 # RuntimeError on daemon threads (e.g. Panel's Tornado IO loop).
 _model_names = [
     'summa', 'fuse', 'ngen', 'mizuroute', 'troute', 'droute',
-    'hype', 'mesh', 'lstm', 'gr', 'gnn', 'rhessys', 'hbv',
-    'sacsma', 'jfuse', 'cfuse', 'ignacio', 'vic', 'clm', 'hechms',
-    'topmodel', 'modflow', 'parflow', 'clmparflow', 'xinanjiang', 'snow17',
+    'hype', 'mesh', 'lstm', 'gr', 'gnn', 'rhessys',
+    'jfuse', 'cfuse', 'ignacio', 'vic', 'clm',
+    'modflow', 'parflow', 'clmparflow',
     'swat', 'mhm', 'crhm', 'wrfhydro', 'prms',
     'pihm', 'wmfire',
     'gsflow', 'watflood', 'wflow',

{symfluence-0.7.2 → symfluence-0.7.4}/symfluence/models/gr/postprocessor.py

@@ -22,10 +22,14 @@ from ..spatial_modes import SpatialMode
 # Broad exception handling is intentional here: rpy2 can raise RuntimeError, RRuntimeError,
 # ImportError, or other exceptions when R is installed but broken (missing core packages,
 # incompatible versions, etc.). We must catch all to provide graceful fallback.
+# rpy2 prints noisy messages to stderr during R initialization — redirect to suppress.
 try:
-    import rpy2.robjects as robjects
-    from rpy2.robjects import pandas2ri
-    from rpy2.robjects.conversion import localconverter
+    import contextlib
+    import io
+    with contextlib.redirect_stderr(io.StringIO()):
+        import rpy2.robjects as robjects
+        from rpy2.robjects import pandas2ri
+        from rpy2.robjects.conversion import localconverter
     HAS_RPY2 = True
 except Exception:  # noqa: BLE001 - Broad exception required for rpy2 import failures
     HAS_RPY2 = False

{symfluence-0.7.2 → symfluence-0.7.4}/symfluence/models/gr/runner.py

@@ -36,11 +36,16 @@ from ..spatial_modes import SpatialMode
 # Broad exception handling is intentional here: rpy2 can raise RuntimeError, RRuntimeError,
 # ImportError, or other exceptions when R is installed but broken (missing core packages,
 # incompatible versions, etc.). We must catch all to provide graceful fallback.
+# rpy2 prints noisy messages to stderr during R initialization (e.g. "Error importing in
+# API mode", "Trying to import in ABI mode") — redirect stderr to suppress them.
 try:
-    import rpy2.robjects as robjects
-    from rpy2.robjects import pandas2ri
-    from rpy2.robjects.conversion import localconverter
-    from rpy2.robjects.packages import importr
+    import contextlib
+    import io
+    with contextlib.redirect_stderr(io.StringIO()):
+        import rpy2.robjects as robjects
+        from rpy2.robjects import pandas2ri
+        from rpy2.robjects.conversion import localconverter
+        from rpy2.robjects.packages import importr
     HAS_RPY2 = True
 except Exception:  # noqa: BLE001 - Broad exception required for rpy2 import failures
     HAS_RPY2 = False

symfluence-0.7.4/symfluence/models/hbv/__init__.py

@@ -0,0 +1,12 @@
+# SPDX-License-Identifier: GPL-3.0-or-later
+# Copyright (C) 2024-2026 SYMFLUENCE Team <dev@symfluence.org>
+
+"""
+Backward-compatibility shim for ``from symfluence.models.hbv import ...``.
+
+The HBV model has been extracted into the standalone ``jhbv`` package.
+This module re-exports from ``jhbv`` so existing code continues to work.
+"""
+
+from jhbv import *  # noqa: F401,F403
+from jhbv import __all__, register  # noqa: F401

symfluence-0.7.4/symfluence/models/hechms/__init__.py

@@ -0,0 +1,12 @@
+# SPDX-License-Identifier: GPL-3.0-or-later
+# Copyright (C) 2024-2026 SYMFLUENCE Team <dev@symfluence.org>
+
+"""
+Backward-compatibility shim for ``from symfluence.models.hechms import ...``.
+
+The HEC-HMS model has been extracted into the standalone ``jhechms`` package.
+This module re-exports from ``jhechms`` so existing code continues to work.
+"""
+
+from jhechms import *  # noqa: F401,F403
+from jhechms import __all__, register  # noqa: F401

{symfluence-0.7.2 → symfluence-0.7.4}/symfluence/models/mesh/build_instructions.py

@@ -181,7 +181,7 @@ make veryclean 2>/dev/null || make clean 2>/dev/null || true
 # If NetCDF-C is in a separate prefix from NetCDF-Fortran, patch the Makefile
 # link line so the linker can find -lnetcdf. The Makefile sets LIBNCL from
 # nf-config --flibs which only has -L for the Fortran prefix.
-if [ -n "${NETCDF_C_LIBDIR}" ]; then
+if [ -n "${NETCDF_C_LIBDIR}" ] && [ -f Makefile ]; then
     echo "Patching Makefile to add NetCDF-C library path..."
     sed -i.bak "s|LIBNCL=\$(shell nf-config --flibs)|LIBNCL=-L${NETCDF_C_LIBDIR} \$(shell nf-config --flibs)|" Makefile
 fi

symfluence-0.7.4/symfluence/models/sacsma/__init__.py

@@ -0,0 +1,12 @@
+# SPDX-License-Identifier: GPL-3.0-or-later
+# Copyright (C) 2024-2026 SYMFLUENCE Team <dev@symfluence.org>
+
+"""
+Backward-compatibility shim for ``from symfluence.models.sacsma import ...``.
+
+The SAC-SMA model has been extracted into the standalone ``jsacsma`` package.
+This module re-exports from ``jsacsma`` so existing code continues to work.
+"""
+
+from jsacsma import *  # noqa: F401,F403
+from jsacsma import __all__, register  # noqa: F401

symfluence-0.7.4/symfluence/models/snow17/__init__.py

@@ -0,0 +1,12 @@
+# SPDX-License-Identifier: GPL-3.0-or-later
+# Copyright (C) 2024-2026 SYMFLUENCE Team <dev@symfluence.org>
+
+"""
+Backward-compatibility shim for ``from symfluence.models.snow17 import ...``.
+
+The Snow-17 model has been extracted into the standalone ``jsnow17`` package.
+This module re-exports from ``jsnow17`` so existing code continues to work.
+"""
+
+from jsnow17 import *  # noqa: F401,F403
+from jsnow17 import __all__, register  # noqa: F401

symfluence-0.7.4/symfluence/models/topmodel/__init__.py

@@ -0,0 +1,12 @@
+# SPDX-License-Identifier: GPL-3.0-or-later
+# Copyright (C) 2024-2026 SYMFLUENCE Team <dev@symfluence.org>
+
+"""
+Backward-compatibility shim for ``from symfluence.models.topmodel import ...``.
+
+The TOPMODEL model has been extracted into the standalone ``jtopmodel`` package.
+This module re-exports from ``jtopmodel`` so existing code continues to work.
+"""
+
+from jtopmodel import *  # noqa: F401,F403
+from jtopmodel import __all__, register  # noqa: F401

symfluence-0.7.4/symfluence/models/xinanjiang/__init__.py

@@ -0,0 +1,12 @@
+# SPDX-License-Identifier: GPL-3.0-or-later
+# Copyright (C) 2024-2026 SYMFLUENCE Team <dev@symfluence.org>
+
+"""
+Backward-compatibility shim for ``from symfluence.models.xinanjiang import ...``.
+
+The Xinanjiang model has been extracted into the standalone ``jxaj`` package.
+This module re-exports from ``jxaj`` so existing code continues to work.
+"""
+
+from jxaj import *  # noqa: F401,F403
+from jxaj import __all__, register  # noqa: F401

{symfluence-0.7.2 → symfluence-0.7.4}/symfluence/optimization/parameter_managers/__init__.py

@@ -62,17 +62,17 @@ from symfluence.models.fuse.calibration.parameter_manager import FUSEParameterMa
 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 symfluence.models.hbv.calibration.parameter_manager import HBVParameterManager
+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 symfluence.models.sacsma.calibration.parameter_manager import SacSmaParameterManager
+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 symfluence.models.xinanjiang.calibration.parameter_manager import XinanjiangParameterManager
+from jxaj.calibration.parameter_manager import XinanjiangParameterManager
 
 __all__ = [
     'FUSEParameterManager',

{symfluence-0.7.2 → symfluence-0.7.4}/symfluence/optimization/workers/__init__.py

@@ -38,7 +38,7 @@ def __getattr__(name):
         'JFUSEWorker': 'symfluence.models.jfuse.calibration.worker',
         'CFUSEWorker': 'symfluence.models.cfuse.calibration.worker',
         'GRWorker': 'symfluence.models.gr.calibration.worker',
-        'HBVWorker': 'symfluence.models.hbv.calibration.worker',
+        'HBVWorker': 'jhbv.calibration.worker',
         'HYPEWorker': 'symfluence.models.hype.calibration.worker',
         'MESHWorker': 'symfluence.models.mesh.calibration.worker',
         'NgenWorker': 'symfluence.models.ngen.calibration.worker',
@@ -46,8 +46,8 @@ def __getattr__(name):
         'SUMMAWorker': 'symfluence.models.summa.calibration.worker',
         'GNNWorker': 'symfluence.models.gnn.calibration.worker',
         'LSTMWorker': 'symfluence.models.lstm.calibration.worker',
-        'SacSmaWorker': 'symfluence.models.sacsma.calibration.worker',
-        'XinanjiangWorker': 'symfluence.models.xinanjiang.calibration.worker',
+        'SacSmaWorker': 'jsacsma.calibration.worker',
+        'XinanjiangWorker': 'jxaj.calibration.worker',
     }
 
     if name in worker_mapping:

{symfluence-0.7.2 → symfluence-0.7.4}/symfluence/resources/system_deps.yml

@@ -100,6 +100,7 @@ dependencies:
       version_flag: "--version"
       version_regex: "(\\d+\\.\\d+(?:\\.\\d+)?)"
       pkg_config: netcdf
+      conda_header: include/netcdf.h
     packages:
       apt: libnetcdf-dev
       dnf: netcdf-devel
@@ -119,6 +120,7 @@ dependencies:
       version_flag: "--version"
       version_regex: "(\\d+\\.\\d+(?:\\.\\d+)?)"
       pkg_config: netcdf-fortran
+      conda_header: include/netcdf.inc
     packages:
       apt: libnetcdff-dev
       dnf: netcdf-fortran-devel
@@ -139,6 +141,7 @@ dependencies:
       version_regex: "HDF5 Version:\\s+(\\d+\\.\\d+\\.\\d+)"
       alternatives: [h5dump]
       pkg_config: hdf5
+      conda_header: include/hdf5.h
     packages:
       apt: libhdf5-dev
       dnf: hdf5-devel
@@ -159,6 +162,7 @@ dependencies:
       version_regex: "(\\d+\\.\\d+(?:\\.\\d+)?)"
       alternatives: [gdalinfo]
       pkg_config: gdal
+      conda_header: include/gdal.h
     packages:
       apt: gdal-bin libgdal-dev
       dnf: gdal gdal-devel
@@ -178,6 +182,7 @@ dependencies:
       version_flag: ""
       version_regex: "Rel\\. (\\d+\\.\\d+\\.\\d+)"
       pkg_config: proj
+      conda_header: include/proj.h
     packages:
       apt: libproj-dev
       dnf: proj-devel
@@ -197,6 +202,7 @@ dependencies:
       version_flag: "--version"
       version_regex: "(\\d+\\.\\d+(?:\\.\\d+)?)"
       pkg_config: geos
+      conda_header: include/geos_c.h
     packages:
       apt: libgeos-dev
       dnf: geos-devel
@@ -216,6 +222,7 @@ dependencies:
       version_flag: "--version"
       version_regex: "(?:Open MPI|HYDRA|mpirun).*?(\\d+\\.\\d+(?:\\.\\d+)?)"
       alternatives: [mpiexec, mpicc]
+      conda_header: include/mpi.h
     packages:
       apt: libopenmpi-dev openmpi-bin
       dnf: openmpi-devel
@@ -235,6 +242,7 @@ dependencies:
       version_flag: ""
       version_regex: ""
       pkg_config: openblas
+      conda_header: include/openblas_config.h
     packages:
       apt: libopenblas-dev liblapack-dev
       dnf: openblas-devel lapack-devel

{symfluence-0.7.2 → symfluence-0.7.4}/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__ = "0.7.2"
+__version__ = "0.7.4"