fixes

Author: wpbonelli

.github/workflows/ci.yml

@@ -102,6 +102,9 @@ jobs:
           cache-dependency-glob: "**/pyproject.toml"
           python-version: ${{ matrix.python }}
 
+      - name: Setup Fortran
+        uses: fortran-lang/setup-fortran@v1
+
       - name: Install project
         working-directory: modflow-devtools
         run: uv sync --all-extras

autotest/test_dfns_registry.py

@@ -11,6 +11,7 @@
 from unittest.mock import patch
 
 import pytest
+from flaky import flaky
 from packaging.version import Version
 
 from modflow_devtools.dfns.fetch import fetch_dfns
@@ -634,6 +635,7 @@ def test_construct_raw_url_with_repo_override(self):
         assert TEST_DFN_REPO in url
         assert TEST_DFN_REF in url
 
+    @flaky(max_runs=3, min_passes=1)
     def test_fetch_registry(self):
         """Test fetching registry from the test repository."""
         from modflow_devtools.dfns.registry import RemoteDfnRegistry
@@ -652,6 +654,7 @@ def test_fetch_registry(self):
         # (e.g., generated from develop branch but accessed on registry branch)
         assert meta.ref is not None
 
+    @flaky(max_runs=3, min_passes=1)
     def test_sync_files(self):
         """Test syncing DFN files from the test repository."""
         from modflow_devtools.dfns.registry import RemoteDfnRegistry
@@ -669,6 +672,7 @@ def test_sync_files(self):
         path = registry.get_dfn_path("gwf-chd")
         assert path.exists()
 
+    @flaky(max_runs=3, min_passes=1)
     def test_get_dfn(self):
         """Test getting a DFN from the test repository."""
         from modflow_devtools.dfns import Dfn
@@ -688,6 +692,7 @@ def test_get_dfn(self):
         assert isinstance(dfn, Dfn)
         assert dfn.name == "gwf-chd"
 
+    @flaky(max_runs=3, min_passes=1)
     def test_get_spec(self):
         """Test getting the full spec from the test repository."""
         from modflow_devtools.dfns import DfnSpec
@@ -708,6 +713,7 @@ def test_get_spec(self):
         assert "gwf-chd" in spec
         assert "sim-nam" in spec
 
+    @flaky(max_runs=3, min_passes=1)
     def test_list_components(self):
         """Test listing available components from the test repository."""
         from modflow_devtools.dfns.registry import RemoteDfnRegistry

autotest/test_models.py

@@ -10,6 +10,7 @@
 from pathlib import Path
 
 import pytest
+from flaky import flaky
 
 from modflow_devtools.models import (
     _DEFAULT_CACHE,
@@ -231,6 +232,7 @@ def test_get_registry_cache_dir(self):
 class TestDiscovery:
     """Test registry discovery."""
 
+    @flaky(max_runs=3, min_passes=1)
     def test_discover_registry(self):
         """Test discovering registry for test repo."""
         # Use test repo/ref from environment
@@ -248,6 +250,7 @@ def test_discover_registry(self):
         assert discovered.mode == "version_controlled"
         assert isinstance(discovered.registry, ModelRegistry)
 
+    @flaky(max_runs=3, min_passes=1)
     def test_discover_registry_nonexistent_ref(self):
         """Test that discovery fails gracefully for nonexistent ref."""
         source = ModelSourceRepo(
@@ -264,6 +267,7 @@ def test_discover_registry_nonexistent_ref(self):
 class TestSync:
     """Test registry synchronization."""
 
+    @flaky(max_runs=3, min_passes=1)
     def test_sync_single_source_single_ref(self):
         """Test syncing a single source/ref."""
         _DEFAULT_CACHE.clear(source=TEST_MODELS_SOURCE_NAME, ref=TEST_MODELS_REF)
@@ -280,6 +284,7 @@ def test_sync_single_source_single_ref(self):
         assert len(result.failed) == 0
         assert (TEST_MODELS_SOURCE_NAME, TEST_MODELS_REF) in result.synced
 
+    @flaky(max_runs=3, min_passes=1)
     def test_sync_creates_cache(self):
         """Test that sync creates cached registry."""
         _DEFAULT_CACHE.clear(source=TEST_MODELS_SOURCE_NAME, ref=TEST_MODELS_REF)
@@ -293,6 +298,7 @@ def test_sync_creates_cache(self):
         source.sync(ref=TEST_MODELS_REF)
         assert _DEFAULT_CACHE.has(TEST_MODELS_SOURCE_NAME, TEST_MODELS_REF)
 
+    @flaky(max_runs=3, min_passes=1)
     def test_sync_skip_cached(self):
         """Test that sync skips already-cached registries."""
         _DEFAULT_CACHE.clear(source=TEST_MODELS_SOURCE_NAME, ref=TEST_MODELS_REF)
@@ -312,6 +318,7 @@ def test_sync_skip_cached(self):
         assert len(result2.synced) == 0
         assert len(result2.skipped) == 1
 
+    @flaky(max_runs=3, min_passes=1)
     def test_sync_force(self):
         """Test that force flag re-syncs cached registries."""
         _DEFAULT_CACHE.clear(source=TEST_MODELS_SOURCE_NAME, ref=TEST_MODELS_REF)
@@ -331,6 +338,7 @@ def test_sync_force(self):
         assert len(result.synced) == 1
         assert len(result.skipped) == 0
 
+    @flaky(max_runs=3, min_passes=1)
     def test_sync_via_source_method(self):
         """Test syncing via ModelSourceRepo.sync() method."""
         _DEFAULT_CACHE.clear(source=TEST_MODELS_SOURCE_NAME, ref=TEST_MODELS_REF)
@@ -348,6 +356,7 @@ def test_sync_via_source_method(self):
         assert len(result.synced) == 1
         assert (TEST_MODELS_SOURCE_NAME, TEST_MODELS_REF) in result.synced
 
+    @flaky(max_runs=3, min_passes=1)
     def test_source_is_synced_method(self):
         """Test ModelSourceRepo.is_synced() method."""
         _DEFAULT_CACHE.clear(source=TEST_MODELS_SOURCE_NAME, ref=TEST_MODELS_REF)
@@ -362,6 +371,7 @@ def test_source_is_synced_method(self):
         source.sync(ref=TEST_MODELS_REF)
         assert source.is_synced(TEST_MODELS_REF)
 
+    @flaky(max_runs=3, min_passes=1)
     def test_source_list_synced_refs_method(self):
         """Test ModelSourceRepo.list_synced_refs() method."""
         _DEFAULT_CACHE.clear(source=TEST_MODELS_SOURCE_NAME, ref=TEST_MODELS_REF)
@@ -509,6 +519,7 @@ def test_cli_clear(self, capsys):
 class TestIntegration:
     """Integration tests for full workflows."""
 
+    @flaky(max_runs=3, min_passes=1)
     def test_full_workflow(self):
         """Test complete workflow: discover -> cache -> load."""
         _DEFAULT_CACHE.clear(source=TEST_MODELS_SOURCE_NAME, ref=TEST_MODELS_REF)
@@ -531,6 +542,7 @@ def test_full_workflow(self):
         assert loaded is not None
         assert len(loaded.models) == len(discovered.registry.models)
 
+    @flaky(max_runs=3, min_passes=1)
     def test_sync_and_list_models(self):
         """Test syncing and listing available models."""
         _DEFAULT_CACHE.clear(source=TEST_MODELS_SOURCE_NAME, ref=TEST_MODELS_REF)

autotest/test_programs.py

@@ -2,6 +2,7 @@
 from pathlib import Path
 
 import pytest
+from flaky import flaky
 
 from modflow_devtools.programs import (
     _DEFAULT_CACHE,
@@ -493,6 +494,7 @@ def test_nonexistent_platform_uses_fallback(self):
 class TestForceSemantics:
     """Test force flag semantics for sync and install."""
 
+    @flaky(max_runs=3, min_passes=1)
     def test_sync_force_flag(self):
         """Test that sync --force re-downloads even if cached."""
         # Clear cache first