fix: fix version comparison, improve autosync behavior

.github/workflows/ci.yml

@@ -124,7 +124,7 @@ jobs:
         working-directory: modflow-devtools/autotest
         env:
           REPOS_PATH: ${{ github.workspace }}
-          MODFLOW_DEVTOOLS_NO_AUTO_SYNC: 1
+          MODFLOW_DEVTOOLS_AUTO_SYNC: 0
           TEST_DFN_PATH: ${{ github.workspace }}/modflow6/doc/mf6io/mf6ivar/dfn
         # use --dist loadfile to so tests requiring pytest-virtualenv run on the same worker
         run: uv run pytest -v -n auto --dist loadfile --durations 0 --ignore test_download.py --ignore test_models.py --ignore test_dfns_registry.py

docs/md/dev/dfns.md

@@ -476,7 +476,7 @@ status = get_sync_status()
 - **At install time**: Best-effort sync to default refs during package installation (fail silently on network errors)
 - **On first use**: If registry cache is empty for requested ref, attempt to sync before raising errors
 - **Lazy loading**: Don't sync until DFN access is actually requested
-- **Configurable**: Users can disable auto-sync via environment variable: `MODFLOW_DEVTOOLS_NO_AUTO_SYNC=1`
+- **Configurable (Experimental)**: Auto-sync is opt-in via environment variable: `MODFLOW_DEVTOOLS_AUTO_SYNC=1` (set to "1", "true", or "yes")
 
 ### Source repository integration
 
@@ -1295,7 +1295,7 @@ dfn.name  # attribute access
 5. Implement `sync_dfns()` function
 6. Add registry metadata caching with hash verification
 7. Implement version-controlled registry discovery
-8. Add auto-sync on first use (with opt-out via `MODFLOW_DEVTOOLS_NO_AUTO_SYNC`)
+8. Add auto-sync on first use (opt-in via `MODFLOW_DEVTOOLS_AUTO_SYNC` while experimental)
 9. **Implement `DfnSpec` dataclass** with `Mapping` protocol for single canonical hierarchical representation with flat dict access
 
 **CLI and module API** (depends on Registry infrastructure):

docs/md/dev/programs.md

@@ -509,7 +509,7 @@ status = get_sync_status()
 
 - **At install time**: Best-effort sync during package installation (fail silently on network errors)
 - **On first use**: If registry cache is empty, attempt to sync before raising errors
-- **Configurable**: Users can disable auto-sync via environment variable: `MODFLOW_DEVTOOLS_NO_AUTO_SYNC=1`
+- **Configurable (Experimental)**: Auto-sync is opt-in via environment variable: `MODFLOW_DEVTOOLS_AUTO_SYNC=1` (set to "1", "true", or "yes")
 
 #### Force semantics
 

docs/md/models.md

@@ -156,7 +156,7 @@ python -m modflow_devtools.models cp mf6/example/ex-gwf-twri01 /path/to/workspac
 ```
 
 The copy command:
-- Automatically attempts to sync registries before copying (unless `MODFLOW_DEVTOOLS_NO_AUTO_SYNC=1`)
+- Automatically attempts to sync registries before copying (if `MODFLOW_DEVTOOLS_AUTO_SYNC=1`)
 - Creates the workspace directory if it doesn't exist
 - Copies all input files for the specified model
 - Preserves subdirectory structure within the workspace
@@ -316,16 +316,16 @@ mf models clear --force
 
 ## Automatic Synchronization
 
-By default, `modflow-devtools` attempts to sync registries:
-- On first import (best-effort, fails silently on network errors)
-- When accessing models (unless `MODFLOW_DEVTOOLS_NO_AUTO_SYNC=1`)
-
-To disable auto-sync:
+Auto-sync is **opt-in** (experimental). To enable:
 
 ```bash
-export MODFLOW_DEVTOOLS_NO_AUTO_SYNC=1
+export MODFLOW_DEVTOOLS_AUTO_SYNC=1  # or "true" or "yes"
 ```
 
+When enabled, `modflow-devtools` attempts to sync registries:
+- On first access (best-effort, fails silently on network errors)
+- When accessing models via the API or CLI
+
 Then manually sync when needed:
 
 ```bash

docs/md/programs.md

@@ -347,17 +347,17 @@ mf programs install mf6 --force
 
 ## Automatic Synchronization
 
-By default, `modflow-devtools` attempts to sync registries:
-- On first import (best-effort, fails silently on network errors)
-- Before installation (unless `MODFLOW_DEVTOOLS_NO_AUTO_SYNC=1`)
-- Before listing available programs
-
-To disable auto-sync:
+Auto-sync is **opt-in** (experimental). To enable:
 
 ```bash
-export MODFLOW_DEVTOOLS_NO_AUTO_SYNC=1
+export MODFLOW_DEVTOOLS_AUTO_SYNC=1  # or "true" or "yes"
 ```
 
+When enabled, `modflow-devtools` attempts to sync registries:
+- On first access (best-effort, fails silently on network errors)
+- Before installation
+- Before listing available programs
+
 Then manually sync when needed:
 
 ```bash

modflow_devtools/cli.py

@@ -2,6 +2,11 @@
 Root CLI for modflow-devtools.
 
 Usage:
+    mf sync
+    mf dfns sync
+    mf dfns info
+    mf dfns list
+    mf dfns clean
     mf models sync
     mf models info
     mf models list
@@ -17,6 +22,56 @@
 
 import argparse
 import sys
+import warnings
+
+
+def _sync_all():
+    """Sync all registries (dfns, models, programs)."""
+    print("Syncing all registries...")
+    print()
+
+    # Sync DFNs
+    print("=== DFNs ===")
+    try:
+        from modflow_devtools.dfns.registry import sync_dfns
+
+        registries = sync_dfns()
+        for registry in registries:
+            meta = registry.registry_meta
+            print(f"  {registry.ref}: {len(meta.files)} files")
+        print(f"Synced {len(registries)} DFN registry(ies)")
+    except Exception as e:
+        print(f"Error syncing DFNs: {e}")
+    print()
+
+    # Sync Models
+    print("=== Models ===")
+    try:
+        from modflow_devtools.models import ModelSourceConfig
+
+        config = ModelSourceConfig.load()
+        config.sync()
+        print("Models synced successfully")
+    except Exception as e:
+        print(f"Error syncing models: {e}")
+    print()
+
+    # Sync Programs
+    print("=== Programs ===")
+    try:
+        # Suppress experimental warning
+        with warnings.catch_warnings():
+            warnings.filterwarnings("ignore", message=".*modflow_devtools.programs.*experimental.*")
+            from modflow_devtools.programs import ProgramSourceConfig
+
+        config = ProgramSourceConfig.load()
+        config.sync()
+        print("Programs synced successfully")
+    except Exception as e:
+        print(f"Error syncing programs: {e}")
+    print()
+
+    print("All registries synced!")
 
 
 def main():
@@ -27,6 +82,12 @@ def main():
     )
     subparsers = parser.add_subparsers(dest="subcommand", help="Available commands")
 
+    # Sync subcommand (syncs all APIs)
+    subparsers.add_parser("sync", help="Sync all registries (dfns, models, programs)")
+
+    # DFNs subcommand
+    subparsers.add_parser("dfns", help="Manage MODFLOW 6 definition files")
+
     # Models subcommand
     subparsers.add_parser("models", help="Manage MODFLOW model registries")
 
@@ -41,7 +102,14 @@ def main():
         sys.exit(1)
 
     # Dispatch to the appropriate module CLI with remaining args
-    if args.subcommand == "models":
+    if args.subcommand == "sync":
+        _sync_all()
+    elif args.subcommand == "dfns":
+        from modflow_devtools.dfns.__main__ import main as dfns_main
+
+        sys.argv = ["mf dfns", *remaining]
+        sys.exit(dfns_main())
+    elif args.subcommand == "models":
         from modflow_devtools.models.__main__ import main as models_main
 
         # Replace sys.argv to make it look like we called the submodule directly

modflow_devtools/dfns/__init__.py

@@ -575,11 +575,12 @@ def map(
     schema_version: str | Version = "2",
 ) -> Dfn:
     """Map a MODFLOW 6 specification to another schema version."""
-    if dfn.schema_version == schema_version:
+    version = Version(str(schema_version))
+    if version == dfn.schema_version:
         return dfn
-    elif Version(str(schema_version)) == Version("1"):
+    elif version == Version("1"):
         raise NotImplementedError("Mapping to schema version 1 is not implemented yet.")
-    elif Version(str(schema_version)) == Version("2"):
+    elif version == Version("2"):
         return MapV1To2().map(dfn)
     raise ValueError(f"Unsupported schema version: {schema_version}. Expected 1 or 2.")
 

modflow_devtools/dfns/__main__.py

@@ -2,10 +2,10 @@
 Command-line interface for the DFNs API.
 
 Usage:
-    python -m modflow_devtools.dfns sync [--ref REF] [--force]
-    python -m modflow_devtools.dfns info
-    python -m modflow_devtools.dfns list [--ref REF]
-    python -m modflow_devtools.dfns clean [--all]
+    mf dfns sync [--ref REF] [--force]
+    mf dfns info
+    mf dfns list [--ref REF]
+    mf dfns clean [--all]
 """
 
 from __future__ import annotations
@@ -138,7 +138,7 @@ def cmd_list(args: argparse.Namespace) -> int:
 
     except DfnRegistryNotFoundError as e:
         print(f"Error: {e}", file=sys.stderr)
-        print("Try running 'python -m modflow_devtools.dfn sync' first.", file=sys.stderr)
+        print("Try running 'mf dfns sync' first.", file=sys.stderr)
         return 1
     except Exception as e:
         print(f"Error: {e}", file=sys.stderr)
@@ -198,7 +198,7 @@ def _format_size(size_bytes: int) -> str:
 def main(argv: list[str] | None = None) -> int:
     """Main entry point for the CLI."""
     parser = argparse.ArgumentParser(
-        prog="python -m modflow_devtools.dfn",
+        prog="mf dfns",
         description="MODFLOW 6 definition file tools",
     )
     parser.add_argument(

modflow_devtools/dfns/registry.py

@@ -734,7 +734,7 @@ def get_sync_status(source: str = "modflow6") -> dict[str, bool]:
 def get_registry(
     source: str = "modflow6",
     ref: str = "develop",
-    auto_sync: bool = True,
+    auto_sync: bool = False,
     path: str | PathLike | None = None,
 ) -> DfnRegistry:
     """
@@ -747,8 +747,9 @@ def get_registry(
     ref : str, optional
         Git ref (branch, tag, or commit hash). Default is "develop".
     auto_sync : bool, optional
-        If True and registry is not cached, automatically sync. Default is True.
-        Can be disabled via MODFLOW_DEVTOOLS_NO_AUTO_SYNC environment variable.
+        If True and registry is not cached, automatically sync. Default is False
+        (opt-in while experimental). Can be enabled via MODFLOW_DEVTOOLS_AUTO_SYNC
+        environment variable (set to "1", "true", or "yes").
         Ignored when path is provided.
     path : str or PathLike, optional
         Path to a local directory containing DFN files. If provided, returns
@@ -775,9 +776,9 @@ def get_registry(
     if path is not None:
         return LocalDfnRegistry(path=Path(path), source=source, ref=ref)
 
-    # Check for auto-sync opt-out
-    if os.environ.get("MODFLOW_DEVTOOLS_NO_AUTO_SYNC", "").lower() in ("1", "true", "yes"):
-        auto_sync = False
+    # Check for auto-sync opt-in (experimental - off by default)
+    if os.environ.get("MODFLOW_DEVTOOLS_AUTO_SYNC", "").lower() in ("1", "true", "yes"):
+        auto_sync = True
 
     registry = RemoteDfnRegistry(source=source, ref=ref)
 

modflow_devtools/models/__init__.py

@@ -1062,15 +1062,15 @@ def _load(self):
         Load registry data from cache.
 
         Raises an error if no cached registries are found.
-        Run 'python -m modflow_devtools.models sync' to populate the cache.
+        Run 'mf models sync' to populate the cache.
         """
         # Try to load from cache
         loaded_from_cache = self._try_load_from_cache()
 
         if not loaded_from_cache:
             raise RuntimeError(
                 "No model registries found in cache. "
-                "Run 'python -m modflow_devtools.models sync' to download registries, "
+                "Run 'mf models sync' to download registries, "
                 "or use ModelSourceConfig.load().sync() programmatically."
             )
 
@@ -1322,13 +1322,19 @@ def get_default_registry():
     This allows the module to import successfully even if the cache
     is empty, with a clear error message on first use.
 
+    Auto-sync can be enabled via MODFLOW_DEVTOOLS_AUTO_SYNC environment variable
+    (currently opt-in while experimental). Set to "1", "true", or "yes" to enable.
+
     Returns
     -------
     PoochRegistry
         The default model registry
     """
     global _default_registry_cache
     if _default_registry_cache is None:
+        # Opt-in auto-sync (experimental - off by default)
+        if os.environ.get("MODFLOW_DEVTOOLS_AUTO_SYNC", "").lower() in ("1", "true", "yes"):
+            _try_best_effort_sync()
         _default_registry_cache = PoochRegistry(base_url=_DEFAULT_BASE_URL, env=_DEFAULT_ENV)
     return _default_registry_cache
 

modflow_devtools/models/__main__.py

@@ -108,7 +108,7 @@ def cmd_sync(args):
 def cmd_info(args):
     """Info command handler."""
     # Attempt auto-sync before showing info (unless disabled)
-    if not os.environ.get("MODFLOW_DEVTOOLS_NO_AUTO_SYNC"):
+    if os.environ.get("MODFLOW_DEVTOOLS_AUTO_SYNC", "").lower() in ("1", "true", "yes"):
         _try_best_effort_sync()
 
     config = ModelSourceConfig.load()
@@ -176,7 +176,7 @@ def cmd_info(args):
 def cmd_list(args):
     """List command handler."""
     # Attempt auto-sync before listing (unless disabled)
-    if not os.environ.get("MODFLOW_DEVTOOLS_NO_AUTO_SYNC"):
+    if os.environ.get("MODFLOW_DEVTOOLS_AUTO_SYNC", "").lower() in ("1", "true", "yes"):
         _try_best_effort_sync()
 
     cached = _DEFAULT_CACHE.list()
@@ -285,7 +285,7 @@ def cmd_clear(args):
 def cmd_copy(args):
     """Copy command handler."""
     # Attempt auto-sync before copying (unless disabled)
-    if not os.environ.get("MODFLOW_DEVTOOLS_NO_AUTO_SYNC"):
+    if os.environ.get("MODFLOW_DEVTOOLS_AUTO_SYNC", "").lower() in ("1", "true", "yes"):
         _try_best_effort_sync()
 
     from . import copy_to

modflow_devtools/programs/__main__.py

@@ -139,13 +139,15 @@ def cmd_info(args):
 def cmd_list(args):
     """List command handler."""
     # Attempt auto-sync before listing (unless disabled)
-    if not os.environ.get("MODFLOW_DEVTOOLS_NO_AUTO_SYNC"):
+    if os.environ.get("MODFLOW_DEVTOOLS_AUTO_SYNC", "").lower() in ("1", "true", "yes"):
         _try_best_effort_sync()
 
     cached = _DEFAULT_CACHE.list()
 
     if not cached:
-        print("No cached program registries. Run 'sync' first.")
+        print(
+            "No program registries found in cache. Run 'mf programs sync' to download registries."
+        )
         return
 
     # Apply filters
@@ -193,7 +195,7 @@ def cmd_list(args):
 def cmd_install(args):
     """Install command handler."""
     # Attempt auto-sync before installation (unless disabled)
-    if not os.environ.get("MODFLOW_DEVTOOLS_NO_AUTO_SYNC"):
+    if os.environ.get("MODFLOW_DEVTOOLS_AUTO_SYNC", "").lower() in ("1", "true", "yes"):
         _try_best_effort_sync()
 
     # Parse program@version syntax if provided