deepflame-ai · xiao312 · Mar 31, 2026 · Mar 31, 2026
diff --git a/AGENTS.md b/AGENTS.md
@@ -25,9 +25,11 @@ This repository contains DFODE-kit, a Python toolkit for sampling combustion sta
 
 ## Structure
 - `dfode_kit/cli/`: CLI entrypoints and subcommands
-- `dfode_kit/data_operations/`: dataset I/O, labeling, augmentation, integration utilities
-- `dfode_kit/dfode_core/`: models, training, preprocessing
-- `dfode_kit/df_interface/`: DeepFlame/OpenFOAM-facing helpers
+- `dfode_kit/cases/`: case init, presets, sampling, and DeepFlame/OpenFOAM-facing helpers
+- `dfode_kit/data/`: data contracts, HDF5 I/O, and integration helpers
+- `dfode_kit/data_operations/`: labeling and augmentation workflows
+- `dfode_kit/models/`: model architectures and registries
+- `dfode_kit/training/`: training configuration, loops, and preprocessing
 - `docs/agents/`: deeper agent-facing docs and workflow conventions
 - `tests/`: lightweight harness tests; keep them fast
 

diff --git a/README.md b/README.md
@@ -133,15 +133,12 @@ If you are working on the repository itself, see:
 
 ## Repository layout
 
-- `dfode_kit/cli/` — canonical CLI entrypoints and subcommands
-- `dfode_kit/cli_tools/` — legacy compatibility shims for older CLI import paths
-- `dfode_kit/cases/` — canonical case init/preset/sampling boundaries for DeepFlame/OpenFOAM workflows
-- `dfode_kit/df_interface/` — legacy compatibility shims for case-facing helpers during the cases migration
-- `dfode_kit/data/` — emerging canonical package for data contracts and HDF5 I/O helpers
-- `dfode_kit/data_operations/` — legacy and transitional dataset I/O, augmentation, labeling, and integration helpers
-- `dfode_kit/models/` — canonical model package
-- `dfode_kit/training/` — canonical training package
-- `dfode_kit/dfode_core/` — legacy compatibility surface for model/training code during migration
+- `dfode_kit/cli/` — CLI entrypoints and subcommands
+- `dfode_kit/cases/` — case init, presets, sampling, and DeepFlame/OpenFOAM-facing helpers
+- `dfode_kit/data/` — data contracts, HDF5 I/O, and integration helpers
+- `dfode_kit/data_operations/` — augmentation and labeling workflows
+- `dfode_kit/models/` — model architectures and registries
+- `dfode_kit/training/` — training configuration, registries, training loops, and preprocessing
 - `canonical_cases/` — canonical flame case templates
 - `tutorials/` — tutorial notebooks and workflow examples
 - `docs/` — published project documentation

diff --git a/canonical_cases/oneD_freely_propagating_flame/dfode_kit_init.ipynb b/canonical_cases/oneD_freely_propagating_flame/dfode_kit_init.ipynb
@@ -20,7 +20,7 @@
     "import numpy as np\n",
     "import matplotlib.pyplot as plt\n",
     "\n",
-    "from dfode_kit.df_interface import (\n",
+    "from dfode_kit.cases import (\n",
     "    OneDFreelyPropagatingFlameConfig,\n",
     "    setup_one_d_flame_case,\n",
     "    df_to_h5,\n",
@@ -32,7 +32,7 @@
     "    label_npy,\n",
     "    integrate_h5,\n",
     ")\n",
-    "from dfode_kit.dfode_core.model.mlp import MLP\n",
+    "from dfode_kit.models.mlp import MLP\n",
     "from dfode_kit.utils import BCT\n",
     "\n",
     "DFODE_ROOT = os.environ['DFODE_ROOT']"

diff --git a/dfode_kit/cli_tools/__init__.py b/dfode_kit/cli_tools/__init__.py
diff --git a/dfode_kit/cli_tools/command_loader.py b/dfode_kit/cli_tools/command_loader.py
diff --git a/dfode_kit/cli_tools/commands/__init__.py b/dfode_kit/cli_tools/commands/__init__.py
diff --git a/dfode_kit/cli_tools/commands/augment.py b/dfode_kit/cli_tools/commands/augment.py
diff --git a/dfode_kit/cli_tools/commands/config.py b/dfode_kit/cli_tools/commands/config.py
diff --git a/dfode_kit/cli_tools/commands/h52npy.py b/dfode_kit/cli_tools/commands/h52npy.py
diff --git a/dfode_kit/cli_tools/commands/init.py b/dfode_kit/cli_tools/commands/init.py
diff --git a/dfode_kit/cli_tools/commands/init_helpers.py b/dfode_kit/cli_tools/commands/init_helpers.py
diff --git a/dfode_kit/cli_tools/commands/label.py b/dfode_kit/cli_tools/commands/label.py
diff --git a/dfode_kit/cli_tools/commands/run_case.py b/dfode_kit/cli_tools/commands/run_case.py
diff --git a/dfode_kit/cli_tools/commands/run_case_helpers.py b/dfode_kit/cli_tools/commands/run_case_helpers.py
diff --git a/dfode_kit/cli_tools/commands/sample.py b/dfode_kit/cli_tools/commands/sample.py
diff --git a/dfode_kit/cli_tools/commands/train.py b/dfode_kit/cli_tools/commands/train.py
diff --git a/dfode_kit/cli_tools/main.py b/dfode_kit/cli_tools/main.py
diff --git a/dfode_kit/df_interface/__init__.py b/dfode_kit/df_interface/__init__.py
diff --git a/dfode_kit/df_interface/case_init.py b/dfode_kit/df_interface/case_init.py
diff --git a/dfode_kit/df_interface/flame_configurations.py b/dfode_kit/df_interface/flame_configurations.py
diff --git a/dfode_kit/df_interface/oneDflame_setup.py b/dfode_kit/df_interface/oneDflame_setup.py
diff --git a/dfode_kit/df_interface/sample_case.py b/dfode_kit/df_interface/sample_case.py
diff --git a/dfode_kit/dfode_core/__init__.py b/dfode_kit/dfode_core/__init__.py
diff --git a/dfode_kit/dfode_core/model/__init__.py b/dfode_kit/dfode_core/model/__init__.py
diff --git a/dfode_kit/dfode_core/model/mlp.py b/dfode_kit/dfode_core/model/mlp.py
diff --git a/dfode_kit/dfode_core/model/registry.py b/dfode_kit/dfode_core/model/registry.py
diff --git a/dfode_kit/dfode_core/train/__init__.py b/dfode_kit/dfode_core/train/__init__.py
diff --git a/dfode_kit/dfode_core/train/config.py b/dfode_kit/dfode_core/train/config.py
diff --git a/dfode_kit/dfode_core/train/formation.py b/dfode_kit/dfode_core/train/formation.py
diff --git a/dfode_kit/dfode_core/train/registry.py b/dfode_kit/dfode_core/train/registry.py
diff --git a/dfode_kit/dfode_core/train/supervised_physics.py b/dfode_kit/dfode_core/train/supervised_physics.py
diff --git a/dfode_kit/dfode_core/train/train.py b/dfode_kit/dfode_core/train/train.py
diff --git a/dfode_kit/runtime_config.py b/dfode_kit/runtime_config.py
diff --git a/dfode_kit/training/__init__.py b/dfode_kit/training/__init__.py
@@ -14,6 +14,7 @@
     "get_trainer_factory",
     "register_trainer",
     "registered_trainers",
+    "DataPreprocessor",
     "train",
 ]
 
@@ -28,6 +29,7 @@
     "get_trainer_factory": ("dfode_kit.training.registry", "get_trainer_factory"),
     "register_trainer": ("dfode_kit.training.registry", "register_trainer"),
     "registered_trainers": ("dfode_kit.training.registry", "registered_trainers"),
+    "DataPreprocessor": ("dfode_kit.training.preprocess", "DataPreprocessor"),
     "train": ("dfode_kit.training.train", "train"),
 }
 

diff --git a/dfode_kit/dfode_core/preprocess.py → dfode_kit/training/preprocess.py b/dfode_kit/dfode_core/preprocess.py → dfode_kit/training/preprocess.py
diff --git a/docs/agents/train-config-plan.md b/docs/agents/train-config-plan.md
@@ -1,7 +1,7 @@
 # Training/config refactor plan
 
 ## Scope
-Keep changes tightly limited to the model/training package boundary (`dfode_kit/models`, `dfode_kit/training`, plus compatibility shims under `dfode_kit/dfode_core/{model,train}`) and the train CLI surface needed to select registered components. Do not redesign data loading, labeling, or DeepFlame integration in this slice.
+Keep changes tightly limited to the canonical model/training package boundary (`dfode_kit/models`, `dfode_kit/training`) and the train CLI surface needed to select registered components. Do not redesign data loading, labeling, or DeepFlame integration in this slice.
 
 ## Current audit
 - `dfode_kit/training/train.py` hard-codes:

diff --git a/docs/architecture.md b/docs/architecture.md
@@ -3,10 +3,11 @@
 ## Current repository structure
 
 - `dfode_kit/cli/`: CLI entrypoints and subcommands
-- `dfode_kit/data_operations/`: dataset I/O, contracts, labeling, augmentation, integration utilities
-- `dfode_kit/dfode_core/`: models, training, registries, preprocessing
-- `dfode_kit/cases/`: explicit case init, preset, sampling, and DeepFlame-facing helpers
-- `dfode_kit/df_interface/`: compatibility layer for the legacy case-facing import paths
+- `dfode_kit/cases/`: explicit case init, presets, sampling, and DeepFlame-facing helpers
+- `dfode_kit/data/`: contracts, HDF5 I/O, and integration utilities
+- `dfode_kit/data_operations/`: augmentation and labeling workflows
+- `dfode_kit/models/`: model architectures and registries
+- `dfode_kit/training/`: training configuration, training loops, registries, and preprocessing
 - `docs/agents/`: agent-facing operational and planning docs
 - `tests/`: lightweight repository and harness tests
 

diff --git a/docs/init.md b/docs/init.md
@@ -39,8 +39,6 @@ This preset preserves the current hardcoded empirical logic from:
 - `dfode_kit/cases/presets.py`
 - method: `OneDFreelyPropagatingFlameConfig.update_config()`
 
-Legacy `dfode_kit/df_interface/*` imports remain as compatibility shims during the package-topology migration.
-
 ## Stable intent
 
 The command is a **preset instantiator**, not a claim of universal best practice.

diff --git a/docs/run-case.md b/docs/run-case.md
@@ -7,7 +7,7 @@ DFODE-kit provides two CLI entrypoints for running DeepFlame/OpenFOAM cases repr
 
 This document is the shared reference for both humans and AI agents.
 
-Implementation note: runtime config helpers now live under `dfode_kit.runtime.config`, and reusable run planning/execution helpers live under `dfode_kit.runtime.run_case`. The legacy import paths remain as compatibility shims during migration.
+Implementation note: runtime config helpers live under `dfode_kit.runtime.config`, and reusable run planning/execution helpers live under `dfode_kit.runtime.run_case`.
 
 ## Why a persistent runtime config exists
 

diff --git a/tests/test_cases_shims.py b/tests/test_cases_shims.py
@@ -1,7 +1,6 @@
 from dfode_kit.cases import init as cases_init
-from dfode_kit.df_interface import case_init as legacy_case_init
 
 
-def test_df_interface_case_init_reexports_cases_symbols():
-    assert legacy_case_init.resolve_oxidizer is cases_init.resolve_oxidizer
-    assert legacy_case_init.DEFAULT_ONE_D_FLAME_PRESET == cases_init.DEFAULT_ONE_D_FLAME_PRESET
+def test_cases_init_exports_expected_symbols():
+    assert callable(cases_init.resolve_oxidizer)
+    assert cases_init.DEFAULT_ONE_D_FLAME_PRESET == "premixed-defaults-v1"
diff --git a/tests/test_cli_main.py b/tests/test_cli_main.py
@@ -140,9 +140,8 @@ def test_main_returns_two_for_missing_handler(monkeypatch, capsys):
     assert "Unknown command: dummy" in captured.err
 
 
-def test_cli_tools_command_loader_shim_re_exports_cli_symbols():
-    shim = import_module("dfode_kit.cli_tools.command_loader")
+def test_cli_command_loader_module_is_importable():
     direct = import_module("dfode_kit.cli.command_loader")
 
-    assert shim.load_command_specs is direct.load_command_specs
-    assert shim.load_command is direct.load_command
+    assert callable(direct.load_command_specs)
+    assert callable(direct.load_command)