symfluence 0.7.1__tar.gz → 0.7.3__tar.gz

{symfluence-0.7.1 → symfluence-0.7.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: symfluence
-Version: 0.7.1
+Version: 0.7.3
 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-0.7.3/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-0.7.1 → symfluence-0.7.3}/symfluence/cli/argument_parser.py

@@ -371,8 +371,18 @@ For more help on a specific command:
 
         binary_parser = subparsers.add_parser(
             'binary',
-            help='External tool management',
-            description='Install, validate, and manage external tools'
+            help='External tool management and pass-through execution',
+            formatter_class=argparse.RawDescriptionHelpFormatter,
+            description=(
+                'Install, validate, and manage external tools.\n\n'
+                'Pass-through execution:\n'
+                '  symfluence binary <tool> [args...]   Run a bundled binary directly\n\n'
+                'Examples:\n'
+                '  symfluence binary summa --version     Run SUMMA with --version\n'
+                '  symfluence binary summa -m fm.txt     Run SUMMA with a file-manager\n'
+                '  symfluence binary fuse.exe --help     Show FUSE help\n'
+                '  symfluence binary pitremove ...       Run a TauDEM sub-tool'
+            ),
         )
         binary_subparsers = binary_parser.add_subparsers(
             dest='action',

{symfluence-0.7.1 → symfluence-0.7.3}/symfluence/cli/commands/binary_commands.py

@@ -4,11 +4,15 @@
 """
 Binary/tool management command handlers for SYMFLUENCE CLI.
 
-This module implements handlers for external tool installation and validation.
+This module implements handlers for external tool installation and validation,
+plus a pass-through ``exec_binary()`` for running bundled binaries directly.
 """
 
 import subprocess
+import sys
 from argparse import Namespace
+from pathlib import Path
+from typing import List, Optional
 
 from ..exit_codes import ExitCode
 from .base import BaseCommand, cli_exception_handler
@@ -298,3 +302,102 @@ class BinaryCommands(BaseCommand):
         else:
             BaseCommand._console.error("Failed to retrieve tools information")
             return ExitCode.GENERAL_ERROR
+
+    # ------------------------------------------------------------------
+    # Pass-through: symfluence binary <tool_name> [args...]
+    # ------------------------------------------------------------------
+
+    @staticmethod
+    def exec_binary(tool_name: str, tool_args: List[str]) -> int:
+        """Run a bundled binary directly with full stdio pass-through.
+
+        Resolution order:
+          1. npm-installed binaries  (``$(npm root -g)/symfluence/dist/bin/<tool>``)
+          2. Source installs          (``$SYMFLUENCE_DATA_DIR/<path>/<exe>``)
+          3. Direct name match in npm bin directory (e.g. TauDEM sub-tools)
+
+        Args:
+            tool_name: Name of the binary to run (e.g. ``summa``, ``fuse.exe``).
+            tool_args: Arguments forwarded verbatim to the binary.
+
+        Returns:
+            The native binary's exit code, or 1 on error.
+        """
+        from symfluence.cli.binary_service import BinaryService
+        from symfluence.cli.external_tools_config import get_external_tools_definitions
+
+        binary_path: Optional[Path] = None
+        service = BinaryService()
+
+        # --- 1. npm-installed binaries ---
+        npm_bin_dir = service.detect_npm_binaries()
+        if npm_bin_dir is not None:
+            tools_defs = get_external_tools_definitions()
+            tool_def = tools_defs.get(tool_name)
+            if tool_def is not None:
+                exe_name = tool_def.get("default_exe", tool_name)
+                candidate = npm_bin_dir / exe_name
+                if candidate.is_file():
+                    binary_path = candidate
+
+        # --- 2. Source installs ($SYMFLUENCE_DATA_DIR/<suffix>/<exe>) ---
+        if binary_path is None:
+            tools_defs = get_external_tools_definitions()
+            tool_def = tools_defs.get(tool_name)
+            if tool_def is not None:
+                path_suffix = tool_def.get("default_path_suffix")
+                exe_name = tool_def.get("default_exe")
+                if path_suffix and exe_name:
+                    config = service._load_config()
+                    data_dir = service._get_data_dir(config)
+                    candidate = data_dir / path_suffix / exe_name
+                    if candidate.is_file():
+                        binary_path = candidate
+
+        # --- 3. Direct name match in npm bin/ (TauDEM sub-tools etc.) ---
+        if binary_path is None and npm_bin_dir is not None:
+            candidate = npm_bin_dir / tool_name
+            if candidate.is_file():
+                binary_path = candidate
+
+        if binary_path is None:
+            print(
+                f"Binary '{tool_name}' not found.\n\n"
+                f"Install it with:\n"
+                f"  symfluence binary install {tool_name}\n\n"
+                f"Or install pre-built binaries:\n"
+                f"  npm install -g symfluence",
+                file=sys.stderr,
+            )
+            return ExitCode.BINARY_ERROR
+
+        return BinaryCommands._run_binary(binary_path, tool_args)
+
+    @staticmethod
+    def _run_binary(binary_path: Path, args: List[str]) -> int:
+        """Execute a binary with full stdio pass-through.
+
+        Args:
+            binary_path: Absolute path to the executable.
+            args: Arguments forwarded to the binary.
+
+        Returns:
+            The process exit code.
+        """
+        cmd = [str(binary_path)] + args
+        try:
+            result = subprocess.run(
+                cmd,
+                stdin=sys.stdin,
+                stdout=sys.stdout,
+                stderr=sys.stderr,
+            )
+            return result.returncode
+        except FileNotFoundError:
+            print(f"Binary not found: {binary_path}", file=sys.stderr)
+            return ExitCode.BINARY_ERROR
+        except PermissionError:
+            print(f"Permission denied: {binary_path}", file=sys.stderr)
+            return ExitCode.PERMISSION_ERROR
+        except KeyboardInterrupt:
+            return ExitCode.USER_INTERRUPT

{symfluence-0.7.1 → symfluence-0.7.3}/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-0.7.1 → symfluence-0.7.3}/symfluence/main_cli.py

@@ -37,6 +37,20 @@ def main():
 
     from symfluence.cli.argument_parser import CLIParser
 
+    # --- binary pass-through: symfluence binary <tool> [args...] ---
+    # Intercept before argparse so tool flags (e.g. -m, --help) are not
+    # consumed by symfluence's own parser.
+    _BINARY_ACTIONS = {'install', 'validate', 'doctor', 'install-sysdeps', 'info'}
+    argv = sys.argv[1:]
+    if (
+        len(argv) >= 2
+        and argv[0] == 'binary'
+        and argv[1] not in _BINARY_ACTIONS
+        and not argv[1].startswith('-')
+    ):
+        from symfluence.cli.commands.binary_commands import BinaryCommands
+        return BinaryCommands.exec_binary(argv[1], argv[2:])
+
     try:
         # Create parser and parse arguments
         parser = CLIParser()

{symfluence-0.7.1 → symfluence-0.7.3}/symfluence/models/ngen/build_instructions.py

@@ -55,6 +55,29 @@ set -e
 set -o pipefail  # Make pipelines return exit code of failed command, not just last command
 echo "Building ngen with full BMI support (C, C++, Fortran)..."
 
+# Detect venv Python BEFORE modifying PATH (setup-python Python must be found first)
+if [ -n "$VIRTUAL_ENV" ]; then
+  PYTHON_EXE="$VIRTUAL_ENV/bin/python3"
+elif [ -n "$CONDA_PREFIX" ]; then
+  # On Windows conda, python3 might be at Scripts/python or just python
+  if [ -x "$CONDA_PREFIX/bin/python3" ]; then
+    PYTHON_EXE="$CONDA_PREFIX/bin/python3"
+  elif [ -x "$CONDA_PREFIX/python.exe" ]; then
+    PYTHON_EXE="$CONDA_PREFIX/python.exe"
+  else
+    PYTHON_EXE=$(which python3 || which python)
+  fi
+else
+  PYTHON_EXE=$(which python3 || which python)
+fi
+echo "Using Python: $PYTHON_EXE"
+NUMPY_VERSION=$($PYTHON_EXE -c "import numpy; print(numpy.__version__)" 2>/dev/null || echo "")
+if [ -n "$NUMPY_VERSION" ]; then
+  echo "Using NumPy: $NUMPY_VERSION"
+else
+  echo "WARNING: numpy not available in $PYTHON_EXE"
+fi
+
 # Ensure system tools are preferred (fix for 2i2c environments)
 export PATH="/usr/bin:$PATH"
 
@@ -90,24 +113,6 @@ case "$(uname -s 2>/dev/null)" in
         ;;
 esac
 
-# Detect venv Python - prefer VIRTUAL_ENV, otherwise use which python3
-if [ -n "$VIRTUAL_ENV" ]; then
-  PYTHON_EXE="$VIRTUAL_ENV/bin/python3"
-elif [ -n "$CONDA_PREFIX" ]; then
-  # On Windows conda, python3 might be at Scripts/python or just python
-  if [ -x "$CONDA_PREFIX/bin/python3" ]; then
-    PYTHON_EXE="$CONDA_PREFIX/bin/python3"
-  elif [ -x "$CONDA_PREFIX/python.exe" ]; then
-    PYTHON_EXE="$CONDA_PREFIX/python.exe"
-  else
-    PYTHON_EXE=$(which python3 || which python)
-  fi
-else
-  PYTHON_EXE=$(which python3 || which python)
-fi
-echo "Using Python: $PYTHON_EXE"
-$PYTHON_EXE -c "import numpy as np; print('Using NumPy:', np.__version__)"
-
 # Boost (local)
 if [ ! -d "boost_1_79_0" ]; then
   echo "Fetching Boost 1.79.0..."
@@ -348,9 +353,13 @@ if [ "${NGEN_WITH_BMI_FORTRAN:-ON}" = "ON" ] && [ -n "$FC" ]; then
 fi
 
 # Check NumPy version - ngen doesn't support NumPy 2.x yet
-NUMPY_VERSION=$($PYTHON_EXE -c "import numpy; print(numpy.__version__)" 2>/dev/null || echo "0")
-NUMPY_MAJOR=$(echo "$NUMPY_VERSION" | cut -d. -f1)
-if [ "$NUMPY_MAJOR" -ge 2 ] 2>/dev/null; then
+# NUMPY_VERSION was detected earlier (before PATH modification)
+NUMPY_MAJOR=$(echo "${NUMPY_VERSION:-}" | cut -d. -f1)
+if [ -z "$NUMPY_VERSION" ]; then
+  echo "NumPy not available. Disabling Python and routing support."
+  CMAKE_ARGS="$CMAKE_ARGS -DNGEN_WITH_PYTHON=OFF"
+  CMAKE_ARGS="$CMAKE_ARGS -DNGEN_WITH_ROUTING=OFF"
+elif [ "$NUMPY_MAJOR" -ge 2 ] 2>/dev/null; then
   echo "NumPy $NUMPY_VERSION detected (>=2.0). Disabling Python and routing support (not yet compatible with ngen)."
   CMAKE_ARGS="$CMAKE_ARGS -DNGEN_WITH_PYTHON=OFF"
   CMAKE_ARGS="$CMAKE_ARGS -DNGEN_WITH_ROUTING=OFF"

{symfluence-0.7.1 → symfluence-0.7.3}/symfluence/resources/system_deps.yml

@@ -60,6 +60,7 @@ dependencies:
       command: gfortran
       version_flag: "--version"
       version_regex: "GNU Fortran.*?(\\d+\\.\\d+(?:\\.\\d+)?)"
+      alternatives: ["gfortran-14", "gfortran-13", "gfortran-12"]
     packages:
       apt: gfortran
       dnf: gcc-gfortran
@@ -99,6 +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
@@ -118,6 +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
@@ -138,6 +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
@@ -158,6 +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
@@ -177,6 +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
@@ -196,6 +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
@@ -215,6 +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
@@ -234,6 +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-0.7.1 → symfluence-0.7.3}/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__ = "0.7.1"
+__version__ = "0.7.3"