moving out all diff attn code to plugin repo

* basic evaluate CLI command / codepath

* tests for evaluate CLI command

* fixes and cleanup

* review comments; slightly DRYing up things

---------

Co-authored-by: Dan Saunders <danjsaund@gmail.com>

.github/workflows/lint.yml

@@ -1,6 +1,7 @@
 name: lint
 on:
   # check on PRs, and manual triggers
+  merge_group:
   pull_request:
       paths:
        - '**.py'

.github/workflows/main.yml

@@ -25,7 +25,6 @@ jobs:
             python_version: "3.11"
             pytorch: 2.3.1
             axolotl_extras: mamba-ssm
-            is_latest: true
           - cuda: 124
             cuda_version: 12.4.1
             python_version: "3.11"
@@ -36,6 +35,7 @@ jobs:
             python_version: "3.11"
             pytorch: 2.5.1
             axolotl_extras:
+            is_latest: true
     runs-on: axolotl-gpu-runner
     steps:
       - name: Checkout
@@ -92,7 +92,6 @@ jobs:
             python_version: "3.11"
             pytorch: 2.3.1
             axolotl_extras:
-            is_latest: true
           - cuda: 124
             cuda_version: 12.4.1
             python_version: "3.11"
@@ -103,6 +102,7 @@ jobs:
             python_version: "3.11"
             pytorch: 2.5.1
             axolotl_extras:
+            is_latest: true
     runs-on: axolotl-gpu-runner
     steps:
       - name: Checkout

.github/workflows/multi-gpu-e2e.yml

@@ -52,7 +52,7 @@ jobs:
       - name: Install Modal
         run: |
           python -m pip install --upgrade pip
-          pip install modal==0.63.64 jinja2
+          pip install modal==0.71.8 jinja2
       - name: Update env vars
         run: |
           echo "BASE_TAG=main-base-py${{ matrix.python_version }}-cu${{ matrix.cuda }}-${{ matrix.pytorch }}" >> $GITHUB_ENV

.github/workflows/tests-nightly.yml

@@ -129,7 +129,7 @@ jobs:
       - name: Install Modal
         run: |
           python -m pip install --upgrade pip
-          pip install modal==0.63.64 jinja2
+          pip install modal==0.71.8 jinja2
       - name: Update env vars
         run: |
           echo "BASE_TAG=main-base-py${{ matrix.python_version }}-cu${{ matrix.cuda }}-${{ matrix.pytorch }}" >> $GITHUB_ENV

.github/workflows/tests.yml

@@ -1,6 +1,7 @@
 name: Tests
 on:
   # check on push/merge to main, PRs, and manual triggers
+  merge_group:
   push:
     branches:
       - "main"
@@ -60,6 +61,15 @@ jobs:
       - name: Check out repository code
         uses: actions/checkout@v4
 
+      - name: Restore HF cache
+        id: hf-cache-restore
+        uses: actions/cache/restore@v4
+        with:
+          path: |
+            /home/runner/.cache/huggingface/hub/datasets--*
+            /home/runner/.cache/huggingface/hub/models--*
+          key: ${{ runner.os }}-hf-hub-cache-${{ hashFiles('**/conftest.py') }}
+
       - name: Setup Python
         uses: actions/setup-python@v5
         with:
@@ -100,6 +110,15 @@ jobs:
         run: |
           find "$(pip cache dir)/http-v2" -type f -mtime +14 -exec rm {} \;
 
+      - name: Save HF cache
+        id: hf-cache
+        uses: actions/cache/save@v4
+        with:
+          path: |
+            /home/runner/.cache/huggingface/hub/datasets--*
+            /home/runner/.cache/huggingface/hub/models--*
+          key: ${{ steps.hf-cache-restore.outputs.cache-primary-key }}
+
   pytest-sdist:
     name: PyTest from Source Dist
     runs-on: ubuntu-latest
@@ -115,6 +134,15 @@ jobs:
       - name: Check out repository code
         uses: actions/checkout@v4
 
+      - name: Restore HF cache
+        id: hf-cache-restore
+        uses: actions/cache/restore@v4
+        with:
+          path: |
+            /home/runner/.cache/huggingface/hub/datasets--*
+            /home/runner/.cache/huggingface/hub/models--*
+          key: ${{ runner.os }}-hf-hub-cache-${{ hashFiles('**/conftest.py') }}
+
       - name: Setup Python
         uses: actions/setup-python@v5
         with:
@@ -156,6 +184,15 @@ jobs:
         run: |
           find "$(pip cache dir)/http-v2" -type f -mtime +14 -exec rm {} \;
 
+      - name: Save HF cache
+        id: hf-cache
+        uses: actions/cache/save@v4
+        with:
+          path: |
+            /home/runner/.cache/huggingface/hub/datasets--*
+            /home/runner/.cache/huggingface/hub/models--*
+          key: ${{ steps.hf-cache-restore.outputs.cache-primary-key }}
+
   docker-e2e-tests-1st:
     if: ${{ ! contains(github.event.commits[0].message, '[skip e2e]') && github.repository_owner == 'axolotl-ai-cloud' }}
     # this job needs to be run on self-hosted GPU runners...
@@ -183,7 +220,7 @@ jobs:
       - name: Install Modal
         run: |
           python -m pip install --upgrade pip
-          pip install modal==0.63.64 jinja2
+          pip install modal==0.71.8 jinja2
       - name: Update env vars
         run: |
           echo "BASE_TAG=main-base-py${{ matrix.python_version }}-cu${{ matrix.cuda }}-${{ matrix.pytorch }}" >> $GITHUB_ENV
@@ -229,7 +266,7 @@ jobs:
       - name: Install Modal
         run: |
           python -m pip install --upgrade pip
-          pip install modal==0.63.64 jinja2
+          pip install modal==0.71.8 jinja2
       - name: Update env vars
         run: |
           echo "BASE_TAG=main-base-py${{ matrix.python_version }}-cu${{ matrix.cuda }}-${{ matrix.pytorch }}" >> $GITHUB_ENV

.gitignore

@@ -186,3 +186,6 @@ out/
 
 # vim
 *.swp
+
+# symlinked to axolotl-artifacts in docker containers
+outputs

.pre-commit-config.yaml

@@ -23,7 +23,7 @@ repos:
     hooks:
     - id: flake8
 -   repo: https://github.com/PyCQA/pylint
-    rev: v2.17.4
+    rev: v3.3.0
     hooks:
     - id: pylint
 -   repo: https://github.com/pre-commit/mirrors-mypy

.pylintrc

@@ -1,5 +1,5 @@
 [MASTER]
-init-hook="from pylint.config import find_pylintrc; import os, sys; sys.path.append(os.path.dirname(find_pylintrc()))"
+init-hook="from pylint.config import find_default_config_files; import sys; sys.path.append(next(find_default_config_files()).parent.as_posix())"
 
 [TYPECHECK]
 
@@ -12,3 +12,4 @@ generated-members=numpy.*, torch.*
 disable=missing-function-docstring, line-too-long, import-error,
     too-many-arguments, too-many-locals, too-many-statements, too-many-branches, too-few-public-methods,
     too-many-instance-attributes, fixme, import-outside-toplevel, logging-fstring-interpolation,
+    too-many-positional-arguments, possibly-used-before-assignment

cicd/Dockerfile.jinja

@@ -8,6 +8,7 @@ ENV PYTORCH_VERSION="{{ PYTORCH_VERSION }}"
 ENV GITHUB_REF="{{ GITHUB_REF }}"
 ENV GITHUB_SHA="{{ GITHUB_SHA }}"
 ENV NIGHTLY_BUILD="{{ NIGHTLY_BUILD }}"
+ENV HF_HOME="{{ HF_HOME }}"
 
 RUN apt-get update && \
     apt-get install -y --allow-change-held-packages vim curl nano libnccl2 libnccl-dev

cicd/cicd.sh

@@ -4,7 +4,6 @@ set -e
 python -c "import torch; assert '$PYTORCH_VERSION' in torch.__version__"
 
 pytest -v --durations=10 -n8 --ignore=tests/e2e/ --ignore=tests/patched/ /workspace/axolotl/tests/
-# pytest -v --durations=10 -n8 --dist loadfile /workspace/axolotl/tests/patched/
 pytest -v --durations=10 /workspace/axolotl/tests/e2e/patched/
 pytest -v --durations=10 /workspace/axolotl/tests/e2e/integrations/
 pytest -v --durations=10 --ignore=tests/e2e/patched/ --ignore=tests/e2e/multigpu/ --ignore=tests/e2e/integrations/ /workspace/axolotl/tests/e2e/

cicd/multigpu.py

@@ -1,6 +1,6 @@
 """
- modal application to run axolotl gpu tests in Modal
+modal application to run axolotl gpu tests in Modal
- """
+"""
 # pylint: disable=duplicate-code
 
 import os
@@ -28,6 +28,7 @@ df_args = {
     "CUDA": os.environ.get("CUDA", "121"),
     "GITHUB_REF": os.environ.get("GITHUB_REF", "refs/heads/main"),
     "GITHUB_SHA": os.environ.get("GITHUB_SHA", ""),
+    "HF_HOME": "/workspace/data/huggingface-cache/hub",
 }
 
 dockerfile_contents = df_template.render(**df_args)
@@ -48,6 +49,12 @@ cicd_image = (
 
 app = App("Axolotl CI/CD", secrets=[])
 
+hf_cache_volume = modal.Volume.from_name(
+    "axolotl-ci-hf-hub-cache", create_if_missing=True
+)
+VOLUME_CONFIG = {
+    "/workspace/data/huggingface-cache/hub": hf_cache_volume,
+}
 
 N_GPUS = int(os.environ.get("N_GPUS", 2))
 GPU_CONFIG = modal.gpu.H100(count=N_GPUS)
@@ -67,6 +74,7 @@ def run_cmd(cmd: str, run_folder: str):
     timeout=60 * 60,
     cpu=8.0,
     memory=131072 * N_GPUS,
+    volumes=VOLUME_CONFIG,
 )
 def cicd_pytest():
     run_cmd("./cicd/multigpu.sh", "/workspace/axolotl")

cicd/tests.py

@@ -29,6 +29,7 @@ df_args = {
     "GITHUB_REF": os.environ.get("GITHUB_REF", "refs/heads/main"),
     "GITHUB_SHA": os.environ.get("GITHUB_SHA", ""),
     "NIGHTLY_BUILD": os.environ.get("NIGHTLY_BUILD", ""),
+    "HF_HOME": "/workspace/data/huggingface-cache/hub",
 }
 
 dockerfile_contents = df_template.render(**df_args)
@@ -50,6 +51,12 @@ cicd_image = (
 
 app = App("Axolotl CI/CD", secrets=[])
 
+hf_cache_volume = modal.Volume.from_name(
+    "axolotl-ci-hf-hub-cache", create_if_missing=True
+)
+VOLUME_CONFIG = {
+    "/workspace/data/huggingface-cache/hub": hf_cache_volume,
+}
 
 N_GPUS = int(os.environ.get("N_GPUS", 1))
 GPU_CONFIG = modal.gpu.A10G(count=N_GPUS)
@@ -69,6 +76,7 @@ def run_cmd(cmd: str, run_folder: str):
     timeout=60 * 60,
     cpu=8.0,
     memory=131072,
+    volumes=VOLUME_CONFIG,
 )
 def cicd_pytest():
     run_cmd("./cicd/cicd.sh", "/workspace/axolotl")

requirements.txt

@@ -2,7 +2,7 @@
 
 # START section of dependencies that don't install on Darwin/MacOS
 bitsandbytes==0.45.0
-triton>=2.3.0
+triton>=3.0.0
 mamba-ssm==1.2.0.post1
 flash-attn==2.7.0.post2
 xformers>=0.0.23.post1
@@ -14,11 +14,11 @@ packaging==23.2
 
 peft==0.14.0
 transformers==4.47.1
-tokenizers>=0.20.1
+tokenizers>=0.21.0
 accelerate==1.2.1
-datasets==3.1.0
+datasets==3.2.0
 deepspeed==0.16.1
-trl==0.12.1
+trl==0.13.0
 
 optimum==1.16.2
 hf_transfer
@@ -53,7 +53,7 @@ zstandard==0.22.0
 fastcore
 
 # lm eval harness
-lm_eval==0.4.4
+lm_eval==0.4.7
 langdetect==1.0.9
 immutabledict==4.2.0
 antlr4-python3-runtime==4.13.2
@@ -61,4 +61,4 @@ antlr4-python3-runtime==4.13.2
 torchao==0.7.0
 schedulefree==1.3.0
 
-axolotl-contribs-lgpl==0.0.2
+axolotl-contribs-lgpl==0.0.3

setup.py

@@ -1,4 +1,5 @@
 """setup.py for axolotl"""
+
 import ast
 import os
 import platform
@@ -29,15 +30,30 @@ def parse_requirements():
             elif not is_extras and line and line[0] != "#":
                 # Handle standard packages
                 _install_requires.append(line)
-
     try:
         xformers_version = [req for req in _install_requires if "xformers" in req][0]
+        triton_version = [req for req in _install_requires if "triton" in req][0]
         torchao_version = [req for req in _install_requires if "torchao" in req][0]
         autoawq_version = [req for req in _install_requires if "autoawq" in req][0]
-
         if "Darwin" in platform.system():
-            # don't install xformers on MacOS
+            # skip packages not compatible with OSX
-            _install_requires.pop(_install_requires.index(xformers_version))
+            skip_packages = [
+                "bitsandbytes",
+                "triton",
+                "mamba-ssm",
+                "flash-attn",
+                "xformers",
+                "autoawq",
+                "liger-kernel",
+            ]
+            _install_requires = [
+                req
+                for req in _install_requires
+                if re.split(r"[>=<]", req)[0].strip() not in skip_packages
+            ]
+            print(
+                _install_requires, [req in skip_packages for req in _install_requires]
+            )
         else:
             # detect the version of torch already installed
             # and set it so dependencies don't clobber the torch version
@@ -73,6 +89,8 @@ def parse_requirements():
                     _install_requires.append("xformers==0.0.28.post1")
             elif (major, minor) >= (2, 3):
                 _install_requires.pop(_install_requires.index(torchao_version))
+                _install_requires.pop(_install_requires.index(triton_version))
+                _install_requires.append("triton>=2.3.1")
                 if patch == 0:
                     _install_requires.pop(_install_requires.index(xformers_version))
                     _install_requires.append("xformers>=0.0.26.post1")

src/axolotl/cli/__init__.py

@@ -202,7 +202,7 @@ def do_inference(
         )
     elif cfg.chat_template:
         chat_template_str = get_chat_template(cfg.chat_template)
-    elif cfg.datasets[0].type == "chat_template":
+    elif cfg.datasets and cfg.datasets[0].type == "chat_template":
         chat_template_str = get_chat_template_from_config(
             cfg=cfg, ds_cfg=cfg.datasets[0], tokenizer=tokenizer
         )

src/axolotl/cli/evaluate.py

@@ -3,7 +3,7 @@ CLI to run training on a model
 """
 import logging
 from pathlib import Path
-from typing import Union
+from typing import Dict, Union
 
 import fire
 from dotenv import load_dotenv
@@ -23,7 +23,7 @@ from axolotl.evaluate import evaluate
 LOG = logging.getLogger("axolotl.cli.evaluate")
 
 
-def do_evaluate(cfg, cli_args) -> None:
+def do_evaluate(cfg, cli_args) -> Dict[str, float]:
     # pylint: disable=duplicate-code
     print_axolotl_text_art()
     check_accelerate_default_config()
@@ -34,7 +34,7 @@ def do_evaluate(cfg, cli_args) -> None:
     else:
         dataset_meta = load_datasets(cfg=cfg, cli_args=cli_args)
 
-    evaluate(cfg=cfg, cli_args=cli_args, dataset_meta=dataset_meta)
+    return evaluate(cfg=cfg, cli_args=cli_args, dataset_meta=dataset_meta)
 
 
 def do_cli(config: Union[Path, str] = Path("examples/"), **kwargs) -> None:

src/axolotl/cli/main.py

@@ -1,11 +1,13 @@
 """CLI definition for various axolotl commands."""
 # pylint: disable=redefined-outer-name
+
 import subprocess  # nosec B404
 from typing import Optional
 
 import click
 
 import axolotl
+from axolotl.cli.plugins import setup_plugin_commands
 from axolotl.cli.utils import (
     add_options_from_config,
     add_options_from_dataclass,
@@ -77,6 +79,9 @@ def evaluate(config: str, accelerate: bool, **kwargs):
     """Evaluate a model."""
     kwargs = {k: v for k, v in kwargs.items() if v is not None}
 
+    # Enable expandable segments for cuda allocation to improve VRAM usage
+    set_pytorch_cuda_alloc_conf()
+
     if accelerate:
         base_cmd = ["accelerate", "launch", "-m", "axolotl.cli.evaluate"]
         if config:
@@ -254,6 +259,9 @@ def fetch(directory: str, dest: Optional[str]):
     fetch_from_github(f"{directory}/", dest)
 
 
+setup_plugin_commands(cli)
+
+
 def main():
     cli()
 

src/axolotl/cli/plugins.py

@@ -0,0 +1,36 @@
+"""Module for adding click CLI commands from axolotl plugins."""
+
+import logging
+
+import click
+
+from axolotl.cli.utils import add_options_from_config, add_options_from_dataclass
+from axolotl.logging_config import configure_logging
+from axolotl.utils.config.models.input.v0_4_1 import AxolotlInputConfig
+
+configure_logging()
+LOG = logging.getLogger(__name__)
+
+
+def setup_plugin_commands(cli: click.core.Group) -> None:
+    """
+    Setup CLI commands for available plugins.
+
+    Args:
+        cli: Click CLI object to add plugin CLI options to.
+    """
+    try:
+        from axolotl_diff_transformer.convert_diff_transformer import do_cli
+        from axolotl_diff_transformer.plugin.cli import ConvertDiffTransformerCliArgs
+
+        @cli.command()
+        @click.argument("config", type=click.Path(exists=True, path_type=str))
+        @add_options_from_dataclass(ConvertDiffTransformerCliArgs)
+        @add_options_from_config(AxolotlInputConfig)
+        def convert_diff_transformer(config: str, **kwargs):
+            """Convert model attention layers to differential attention layers."""
+            kwargs = {k: v for k, v in kwargs.items() if v is not None}
+            do_cli(config=config, **kwargs)
+
+    except ImportError as exc:
+        LOG.debug("axolotl-diff-transformer not found: %s", exc)

src/axolotl/cli/utils.py

@@ -22,7 +22,6 @@ def add_options_from_dataclass(config_class: Type[Any]):
         # Process dataclass fields in reverse order for correct option ordering
         for field in reversed(dataclasses.fields(config_class)):
             field_type = field.type
-
             if get_origin(field_type) is Union and type(None) in get_args(field_type):
                 field_type = next(
                     t for t in get_args(field_type) if not isinstance(t, NoneType)
@@ -44,6 +43,7 @@ def add_options_from_dataclass(config_class: Type[Any]):
                     default=field.default,
                     help=field.metadata.get("description"),
                 )(function)
+
         return function
 
     return decorator
@@ -55,7 +55,14 @@ def add_options_from_config(config_class: Type[BaseModel]):
     def decorator(function):
         # Process model fields in reverse order for correct option ordering
         for name, field in reversed(config_class.model_fields.items()):
-            if field.annotation == bool:
+            field_type = field.annotation
+            if get_origin(field_type) is Union and type(None) in get_args(field_type):
+                field_type = next(
+                    t for t in get_args(field_type) if not isinstance(t, NoneType)
+                )
+
+            # NOTE: defaults are handled by the pydantic model config classes.
+            if field_type == bool:
                 field_name = name.replace("_", "-")
                 option_name = f"--{field_name}/--no-{field_name}"
                 function = click.option(
@@ -66,6 +73,7 @@ def add_options_from_config(config_class: Type[BaseModel]):
                 function = click.option(
                     option_name, default=None, help=field.description
                 )(function)
+
         return function
 
     return decorator
@@ -84,6 +92,8 @@ def build_command(base_cmd: List[str], options: Dict[str, Any]) -> List[str]:
         if isinstance(value, bool):
             if value:
                 cmd.append(f"--{key}")
+            else:
+                cmd.append(f"--no{key}")
         else:
             cmd.extend([f"--{key}", str(value)])
 

src/axolotl/common/cli.py

@@ -4,22 +4,26 @@ shared module for cli specific things
 
 import logging
 from dataclasses import dataclass, field
-from typing import Optional
+from typing import TYPE_CHECKING, Optional, Union
 
 import axolotl.monkeypatch.data.batch_dataset_fetcher  # pylint: disable=unused-import  # noqa: F401
 from axolotl.logging_config import configure_logging
 from axolotl.utils.dict import DictDefault
 from axolotl.utils.models import load_model, load_tokenizer
 
+if TYPE_CHECKING:
+    try:
+        from axolotl_diff_transformer.plugin.cli import ConvertDiffTransformerCliArgs
+    except:  # noqa: E722 # pylint: disable=bare-except # nosec B110
+        pass
+
 configure_logging()
-LOG = logging.getLogger("axolotl.common.cli")
+LOG = logging.getLogger(__name__)
 
 
 @dataclass
 class PreprocessCliArgs:
-    """
+    """dataclass with arguments for preprocessing only"""
-    dataclass representing arguments for preprocessing only
-    """
 
     debug: bool = field(default=False)
     debug_text_only: bool = field(default=False)
@@ -30,9 +34,7 @@ class PreprocessCliArgs:
 
 @dataclass
 class TrainerCliArgs:
-    """
+    """dataclass with various non-training arguments"""
-    dataclass representing the various non-training arguments
-    """
 
     debug: bool = field(default=False)
     debug_text_only: bool = field(default=False)
@@ -45,9 +47,7 @@ class TrainerCliArgs:
 
 @dataclass
 class EvaluateCliArgs:
-    """
+    """dataclass with various evaluation arguments"""
-    dataclass representing the various evaluation arguments
-    """
 
     debug: bool = field(default=False)
     debug_text_only: bool = field(default=False)
@@ -57,7 +57,7 @@ class EvaluateCliArgs:
 def load_model_and_tokenizer(
     *,
     cfg: DictDefault,
-    cli_args: TrainerCliArgs,
+    cli_args: Union[TrainerCliArgs, EvaluateCliArgs, "ConvertDiffTransformerCliArgs"],
 ):
     LOG.info(f"loading tokenizer... {cfg.tokenizer_config or cfg.base_model_config}")
     tokenizer = load_tokenizer(cfg)

src/axolotl/core/trainer_builder.py

@@ -22,7 +22,6 @@ from typing import Any, Dict, List, Literal, Optional, Type, Union
 import torch
 import transformers
 from datasets import Dataset
-from packaging import version
 from peft.optimizers import create_loraplus_optimizer
 from torch import nn
 from torch.optim.lr_scheduler import OneCycleLR
@@ -294,7 +293,7 @@ class AxolotlTrainingArguments(AxolotlTrainingMixins, TrainingArguments):
     """
     Training arguments for Causal trainer
 
-    This code is duplicated due to HF TrainingArguments not setting output_dir with a defaujlt value
+    This code is duplicated due to HF TrainingArguments not setting output_dir with a default value
     so it can't be used as a mixin.
     """
 
@@ -608,8 +607,14 @@ class AxolotlTrainer(SchedulerMixin, Trainer):
                     self.state.train_batch_size or self.args.per_device_train_batch_size
                 )
                 batch_max_len = train_batch_size * self.args.max_seq_length
+
+            if self.args.curriculum_sampling:
+                sampler = SequentialSampler(self.train_dataset)
+            else:
+                sampler = RandomSampler(self.train_dataset)
+
             return MultipackBatchSampler(
-                RandomSampler(self.train_dataset),
+                sampler,
                 lengths=get_dataset_lengths(self.train_dataset),
                 packing_efficiency_estimate=self.args.sample_packing_efficiency,
                 batch_max_len=batch_max_len,
@@ -978,12 +983,7 @@ class AxolotlTrainer(SchedulerMixin, Trainer):
             logs[key] = torch.tensor(metrics).mean().item()
         del self._stored_metrics[train_eval]
 
-        if version.parse(transformers.__version__) >= version.parse("4.47.0.dev0"):
+        return super().log(logs, start_time)
-            try:
-                return super().log(logs, start_time)
-            except TypeError:
-                return super().log(logs)  # transformers<=4.46
-        return super().log(logs)  # transformers<=4.46
 
     def store_metrics(
         self, metrics: Dict[str, float], train_eval: Literal["train", "eval"] = "train"
@@ -1167,22 +1167,6 @@ class AxolotlDPOTrainer(SchedulerMixin, DPOTrainer):
         torch.cuda.empty_cache()
         return loss
 
-    def log(self, logs: Dict[str, float], start_time: Optional[float] = None) -> None:
-        # TODO remove once trl supports the updated to the Trainer.log method
-        # logs either has 'loss' or 'eval_loss'
-        train_eval = "train" if "loss" in logs else "eval"
-        # Add averaged stored metrics to logs
-        for key, metrics in self._stored_metrics[train_eval].items():
-            logs[key] = torch.tensor(metrics).mean().item()
-        del self._stored_metrics[train_eval]
-
-        if version.parse(transformers.__version__) >= version.parse("4.47.0.dev0"):
-            return super(DPOTrainer, self).log(  # pylint: disable=bad-super-call
-                logs, start_time
-            )
-        # transformers<=4.46
-        return super(DPOTrainer, self).log(logs)  # pylint: disable=bad-super-call
-
 
 class AxolotlORPOTrainer(SchedulerMixin, ORPOTrainer):
     """
@@ -1191,22 +1175,6 @@ class AxolotlORPOTrainer(SchedulerMixin, ORPOTrainer):
 
     tag_names = ["axolotl", "orpo"]
 
-    def log(self, logs: Dict[str, float], start_time: Optional[float] = None) -> None:
-        # TODO remove once trl supports the updated to the Trainer.log method
-        # logs either has 'loss' or 'eval_loss'
-        train_eval = "train" if "loss" in logs else "eval"
-        # Add averaged stored metrics to logs
-        for key, metrics in self._stored_metrics[train_eval].items():
-            logs[key] = torch.tensor(metrics).mean().item()
-        del self._stored_metrics[train_eval]
-
-        if version.parse(transformers.__version__) >= version.parse("4.47.0.dev0"):
-            return super(ORPOTrainer, self).log(  # pylint: disable=bad-super-call
-                logs, start_time
-            )
-        # transformers<=4.46
-        return super(ORPOTrainer, self).log(logs)  # pylint: disable=bad-super-call
-
 
 class AxolotlKTOTrainer(SchedulerMixin, KTOTrainer):
     """
@@ -1215,49 +1183,6 @@ class AxolotlKTOTrainer(SchedulerMixin, KTOTrainer):
 
     tag_names = ["axolotl", "kto"]
 
-    def log(self, logs: Dict[str, float], start_time: Optional[float] = None) -> None:
-        # TODO remove once trl supports the updated to the Trainer.log method
-        # logs either has 'loss' or 'eval_loss'
-        train_eval = "train" if "loss" in logs else "eval"
-        # train metrics should have no prefix, eval should have 'eval_'
-        prefix = "eval_" if train_eval == "eval" else ""
-        # accumulate average metrics from sums and lengths
-        for split in ["chosen", "rejected"]:
-            if f"count/{split}" in self._stored_metrics[train_eval]:
-                count_sum = (
-                    torch.Tensor(self._stored_metrics[train_eval][f"count/{split}"])
-                    .sum()
-                    .item()
-                )
-                for metric in ["rewards", "logps", "logits"]:
-                    logs[f"{prefix}{metric}/{split}"] = (
-                        torch.Tensor(
-                            self._stored_metrics[train_eval][f"{metric}/{split}_sum"]
-                        )
-                        .sum()
-                        .item()
-                        / count_sum
-                    )
-                    # delete obsolete metric
-                    del self._stored_metrics[train_eval][f"{metric}/{split}_sum"]
-                del self._stored_metrics[train_eval][f"count/{split}"]
-        # calculate reward margin
-        if f"{prefix}rewards/chosen" in logs and f"{prefix}rewards/rejected" in logs:
-            logs[f"{prefix}rewards/margins"] = (
-                logs[f"{prefix}rewards/chosen"] - logs[f"{prefix}rewards/rejected"]
-            )
-        # Add averaged stored metrics to logs
-        for key, metrics in self._stored_metrics[train_eval].items():
-            logs[f"{prefix}{key}"] = torch.Tensor(metrics).mean().item()
-        del self._stored_metrics[train_eval]
-
-        if version.parse(transformers.__version__) >= version.parse("4.47.0.dev0"):
-            return super(KTOTrainer, self).log(  # pylint: disable=bad-super-call
-                logs, start_time
-            )
-        # transformers<=4.46
-        return super(KTOTrainer, self).log(logs)  # pylint: disable=bad-super-call
-
 
 class AxolotlCPOTrainer(SchedulerMixin, CPOTrainer):
     """
@@ -1266,22 +1191,6 @@ class AxolotlCPOTrainer(SchedulerMixin, CPOTrainer):
 
     tag_names = ["axolotl", "cpo"]
 
-    def log(self, logs: Dict[str, float], start_time: Optional[float] = None) -> None:
-        # TODO remove once trl supports the updated to the Trainer.log method
-        # logs either has 'loss' or 'eval_loss'
-        train_eval = "train" if "loss" in logs else "eval"
-        # Add averaged stored metrics to logs
-        for key, metrics in self._stored_metrics[train_eval].items():
-            logs[key] = torch.tensor(metrics).mean().item()
-        del self._stored_metrics[train_eval]
-
-        if version.parse(transformers.__version__) >= version.parse("4.47.0.dev0"):
-            return super(CPOTrainer, self).log(  # pylint: disable=bad-super-call
-                logs, start_time
-            )
-        # transformers<=4.46
-        return super(CPOTrainer, self).log(logs)  # pylint: disable=bad-super-call
-
 
 class AxolotlRewardTrainer(SchedulerMixin, RewardTrainer):
     """
@@ -1290,15 +1199,6 @@ class AxolotlRewardTrainer(SchedulerMixin, RewardTrainer):
 
     tag_names = ["axolotl", "reward"]
 
-    def log(self, logs: Dict[str, float], start_time: Optional[float] = None) -> None:
-        # TODO remove once trl supports the updated to the Trainer.log method
-        if version.parse(transformers.__version__) >= version.parse("4.47.0.dev0"):
-            return super(RewardTrainer, self).log(  # pylint: disable=bad-super-call
-                logs, start_time
-            )
-        # transformers<=4.46
-        return super(RewardTrainer, self).log(logs)  # pylint: disable=bad-super-call
-
 
 class TrainerBuilderBase(abc.ABC):
     """

src/axolotl/evaluate.py

@@ -9,12 +9,11 @@ from typing import Dict, Optional
 import torch
 from accelerate.logging import get_logger
 
-from axolotl.common.cli import TrainerCliArgs
+from axolotl.common.cli import EvaluateCliArgs, load_model_and_tokenizer
 from axolotl.logging_config import configure_logging
 from axolotl.train import TrainDatasetMeta
-from axolotl.utils import set_pytorch_cuda_alloc_conf
 from axolotl.utils.dict import DictDefault
-from axolotl.utils.models import load_model, load_processor, load_tokenizer
+from axolotl.utils.models import load_processor
 from axolotl.utils.trainer import setup_trainer
 
 project_root = os.path.abspath(os.path.join(os.path.dirname(__file__), ".."))
@@ -62,8 +61,9 @@ def evaluate_dataset(
     return metrics
 
 
+# pylint: disable=duplicate-code
 def evaluate(
-    *, cfg: DictDefault, cli_args: TrainerCliArgs, dataset_meta: TrainDatasetMeta
+    *, cfg: DictDefault, cli_args: EvaluateCliArgs, dataset_meta: TrainDatasetMeta
 ) -> Dict[str, float]:
     """
     Evaluate a model on training and validation datasets
@@ -79,16 +79,11 @@ def evaluate(
         - The tokenizer
         - Dictionary of evaluation metrics
     """
-    # pylint: disable=duplicate-code
+    # Load model
-    # Enable expandable segments for cuda allocation to improve VRAM usage
+    LOG.debug("loading model for evaluation...")
-    set_pytorch_cuda_alloc_conf()
 
-    # Load tokenizer
+    model, tokenizer = load_model_and_tokenizer(cfg=cfg, cli_args=cli_args)
-    LOG.debug(
+    model = model.to(cfg.device, dtype=cfg.torch_dtype)
-        f"loading tokenizer... {cfg.tokenizer_config or cfg.base_model_config}",
-        main_process_only=True,
-    )
-    tokenizer = load_tokenizer(cfg)
 
     # Load processor for multimodal models if needed
     processor = None
@@ -100,12 +95,6 @@ def evaluate(
     eval_dataset = dataset_meta.eval_dataset
     total_num_steps = dataset_meta.total_num_steps
 
-    # Load model
-    LOG.debug("loading model for evaluation...")
-    model, _ = load_model(
-        cfg, tokenizer, processor=processor, inference=cli_args.inference
-    )
-
     # Set up trainer
     trainer = setup_trainer(
         cfg,

src/axolotl/integrations/config.py

@@ -43,10 +43,12 @@ def merge_input_args():
     input_args: List[str] = plugin_manager.get_input_args()
     plugin_classes = []
     dynamic_input = ""
+
     for plugin_args in input_args:
         plugin_module, plugin_cls = plugin_args.rsplit(".", 1)
         dynamic_input += f"from {plugin_module} import {plugin_cls}\n"
         plugin_classes.append(plugin_cls)
+
     if dynamic_input:
         dynamic_input += f"class AxolotlConfigWCapabilities(AxolotlConfigWCapabilitiesBase, {', '.join(plugin_classes)}):\n    pass\n"
         dynamic_input += f"class AxolotlInputConfig(AxolotlInputConfigBase, {', '.join(plugin_classes)}):\n    pass\n"
@@ -62,4 +64,5 @@ def merge_input_args():
             "AxolotlConfigWCapabilities"
         ]
         return AxolotlConfigWCapabilities, AxolotlInputConfig
+
     return AxolotlConfigWCapabilitiesBase, AxolotlInputConfigBase

src/axolotl/integrations/liger/__init__.py

@@ -22,13 +22,6 @@ import inspect
 import logging
 import sys
 
-from liger_kernel.transformers.cross_entropy import LigerCrossEntropyLoss
-from liger_kernel.transformers.functional import liger_cross_entropy
-from liger_kernel.transformers.monkey_patch import MODEL_TYPE_TO_APPLY_LIGER_FN
-from liger_kernel.transformers.rms_norm import LigerRMSNorm
-from liger_kernel.transformers.rope import liger_rotary_pos_emb
-from liger_kernel.transformers.swiglu import LigerSwiGLUMLP
-
 from axolotl.integrations.base import BasePlugin
 
 from ...utils.distributed import zero_only
@@ -46,6 +39,13 @@ class LigerPlugin(BasePlugin):
         return "axolotl.integrations.liger.LigerArgs"
 
     def pre_model_load(self, cfg):
+        from liger_kernel.transformers.cross_entropy import LigerCrossEntropyLoss
+        from liger_kernel.transformers.functional import liger_cross_entropy
+        from liger_kernel.transformers.monkey_patch import MODEL_TYPE_TO_APPLY_LIGER_FN
+        from liger_kernel.transformers.rms_norm import LigerRMSNorm
+        from liger_kernel.transformers.rope import liger_rotary_pos_emb
+        from liger_kernel.transformers.swiglu import LigerSwiGLUMLP
+
         if cfg.model_config_type in MODEL_TYPE_TO_APPLY_LIGER_FN:
             apply_liger_fn = MODEL_TYPE_TO_APPLY_LIGER_FN[cfg.model_config_type]
             liger_fn_sig = inspect.signature(apply_liger_fn)

src/axolotl/monkeypatch/trainer_fsdp_optim.py

@@ -6,7 +6,7 @@ import logging
 
 from transformers import Trainer
 
-from axolotl.monkeypatch.unsloth_ import detab_code
+from axolotl.monkeypatch.utils import detab_code
 
 LOG = logging.getLogger("axolotl.monkeypatch.trainer_fsdp_save")
 

src/axolotl/monkeypatch/trainer_grad_accum.py

@@ -8,7 +8,7 @@ import logging
 from transformers import LlamaForCausalLM, Trainer
 from transformers.modeling_flash_attention_utils import _flash_attention_forward
 
-from axolotl.monkeypatch.unsloth_ import detab_code
+from axolotl.monkeypatch.utils import detab_code
 
 LOG = logging.getLogger("axolotl.monkeypatch.trainer_grad_accum")
 

src/axolotl/monkeypatch/unsloth_.py

@@ -1,9 +1,7 @@
 """module for patching with unsloth optimizations"""
 
 import inspect
-import re
 import types
-from typing import Tuple
 
 import torch
 from accelerate.logging import get_logger
@@ -11,6 +9,8 @@ from peft import PeftModelForCausalLM
 from torch import nn
 from transformers.models.llama.modeling_llama import LlamaFlashAttention2
 
+from axolotl.monkeypatch.utils import detab_code
+
 LOG = get_logger("axolotl.monkeypatch.unsloth")
 
 ORIGINAL_QKV_CODE = """
@@ -93,15 +93,6 @@ def integrate_cross_entropy_loss_patch(model_type: str = "llama") -> None:
         raise ValueError("Unsupported model type")
 
 
-def detab_code(code: str) -> Tuple[str, str]:
-    try:
-        spaces = re.match(r"([\s\t]{1,})", code).group(0)
-        code = re.sub(r"^" + spaces, "", code, flags=re.MULTILINE)
-    except AttributeError:
-        return code, ""
-    return code, spaces
-
-
 self_attn_lora_patched = False  # pylint: disable=invalid-name
 
 

src/axolotl/monkeypatch/utils.py

@@ -1,7 +1,8 @@
 """
 Shared utils for the monkeypatches
 """
-from typing import Optional
+import re
+from typing import Optional, Tuple
 
 import torch
 import torch.nn.functional as F
@@ -223,3 +224,12 @@ def patched_prepare_4d_causal_attention_mask_for_sdpa(
         mask_2d_to_4d(attention_mask, dtype=dtype),
         *args,
     )
+
+
+def detab_code(code: str) -> Tuple[str, str]:
+    try:
+        spaces = re.match(r"([\s\t]{1,})", code).group(0)
+        code = re.sub(r"^" + spaces, "", code, flags=re.MULTILINE)
+    except AttributeError:
+        return code, ""
+    return code, spaces

src/axolotl/utils/callbacks/lisa.py

@@ -43,7 +43,7 @@ def lisa_callback_factory(trainer: "AxolotlTrainer"):
                 getattr, self.layers_attribute.split("."), self.trainer.model
             )
             LOG.info(
-                f"LISA will activate {self.n_layers}/{len(layers)} layers ({self.n_layers*100/len(layers)}%) every {self.step_interval} steps"
+                f"LISA will activate {self.n_layers}/{len(layers)} layers ({self.n_layers * 100 / len(layers)}%) every {self.step_interval} steps"
             )
 
         def freeze_all_layers(self):

src/axolotl/utils/config/models/input/v0_4_1/__init__.py

@@ -128,6 +128,7 @@ class PretrainingDataset(BaseModel):
     text_column: Optional[str] = "text"
     type: Optional[str] = "pretrain"
     trust_remote_code: Optional[bool] = False
+    data_files: Optional[str] = None
 
 
 class UserDefinedPrompterType(BaseModel):

src/axolotl/utils/data/pretraining.py

@@ -28,8 +28,10 @@ def encode_pretraining(
     )
     # Convert to PyTorch tensors
     input_ids = [torch.tensor(seq) for seq in res["input_ids"]]
+    targets = [torch.tensor(seq) for seq in res["input_ids"]]
     attention_mask = [torch.tensor(seq) for seq in res["attention_mask"]]
     new_input_ids = []
+    new_labels = []
     new_attention_mask = []
     # Append EOS and PAD tokens to input_ids, and correct attention_mask
     for i, _ in enumerate(input_ids):
@@ -40,22 +42,34 @@ def encode_pretraining(
             ),
             dim=0,
         )
+        targets[i] = torch.cat(
+            (
+                targets[i],
+                torch.tensor([tokenizer.eos_token_id, -100]),
+            ),
+            dim=0,
+        )
         attention_mask[i] = torch.cat((attention_mask[i], torch.tensor([1, 0])), dim=0)
 
     # Concatenate tokens so that their lengths are less than max_tokens
     buffer_input_ids = torch.tensor([], dtype=torch.long)
+    buffer_labels = torch.tensor([], dtype=torch.long)
     buffer_attention_mask = torch.tensor([], dtype=torch.long)
 
-    for ids, mask in zip(input_ids, attention_mask):
+    for ids, labels, mask in zip(input_ids, targets, attention_mask):
         if buffer_input_ids.numel() == max_tokens:
             new_input_ids.append(buffer_input_ids)
+            new_labels.append(buffer_labels)
             new_attention_mask.append(buffer_attention_mask)
             buffer_input_ids = torch.tensor([], dtype=torch.long)
+            buffer_labels = torch.tensor([], dtype=torch.long)
             buffer_attention_mask = torch.tensor([], dtype=torch.long)
             buffer_input_ids = torch.cat((buffer_input_ids, ids), dim=0)
+            buffer_labels = torch.cat((buffer_labels, labels), dim=0)
             buffer_attention_mask = torch.cat((buffer_attention_mask, mask), dim=0)
         elif buffer_input_ids.numel() + ids.numel() <= max_tokens:
             buffer_input_ids = torch.cat((buffer_input_ids, ids), dim=0)
+            buffer_labels = torch.cat((buffer_labels, labels), dim=0)
             buffer_attention_mask = torch.cat((buffer_attention_mask, mask), dim=0)
         else:
             buffer_input_ids = torch.cat(
@@ -69,6 +83,17 @@ def encode_pretraining(
                 ),
                 dim=0,
             )
+            buffer_labels = torch.cat(
+                (
+                    buffer_labels,
+                    torch.full(
+                        (max_tokens - buffer_labels.numel(),),
+                        -100,
+                        dtype=torch.long,
+                    ),
+                ),
+                dim=0,
+            )
             buffer_attention_mask = torch.cat(
                 (
                     buffer_attention_mask,
@@ -81,11 +106,14 @@ def encode_pretraining(
                 dim=0,
             )
             new_input_ids.append(buffer_input_ids)
+            new_labels.append(buffer_labels)
             new_attention_mask.append(buffer_attention_mask)
             buffer_input_ids = torch.tensor([], dtype=torch.long)
+            buffer_labels = torch.tensor([], dtype=torch.long)
             buffer_attention_mask = torch.tensor([], dtype=torch.long)
 
             buffer_input_ids = torch.cat((buffer_input_ids, ids), dim=0)
+            buffer_labels = torch.cat((buffer_labels, labels), dim=0)
             buffer_attention_mask = torch.cat((buffer_attention_mask, mask), dim=0)
 
     if buffer_input_ids.numel() > 0:  # for any leftover tokens
@@ -101,6 +129,17 @@ def encode_pretraining(
                 ),
                 dim=0,
             )
+            buffer_labels = torch.cat(
+                (
+                    buffer_labels,
+                    torch.full(
+                        (max_tokens - buffer_labels.numel(),),
+                        -100,
+                        dtype=torch.long,
+                    ),
+                ),
+                dim=0,
+            )
             buffer_attention_mask = torch.cat(
                 (
                     buffer_attention_mask,
@@ -113,11 +152,12 @@ def encode_pretraining(
                 dim=0,
             )
         new_input_ids.append(buffer_input_ids)
+        new_labels.append(buffer_labels)
         new_attention_mask.append(buffer_attention_mask)
 
     ret = {
         "input_ids": [seq.tolist() for seq in new_input_ids],
-        "labels": [seq.tolist() for seq in new_input_ids],
+        "labels": [seq.tolist() for seq in new_labels],
         "attention_mask": [seq.tolist() for seq in new_attention_mask],
     }
 

src/axolotl/utils/data/sft.py

@@ -88,6 +88,7 @@ def prepare_dataset(cfg, tokenizer, processor=None):
         path = cfg.pretraining_dataset
         split = "train"
         name = None
+        data_files = None
         if isinstance(cfg.pretraining_dataset, list) and isinstance(
             cfg.pretraining_dataset[0], dict
         ):
@@ -96,6 +97,8 @@ def prepare_dataset(cfg, tokenizer, processor=None):
             if "split" in cfg.pretraining_dataset[0]:
                 split = cfg.pretraining_dataset[0]["split"]
 
+            data_files = cfg.pretraining_dataset[0].get("data_files")
+
         ds_wrapper_partial = functools.partial(
             get_dataset_wrapper,
             cfg.pretraining_dataset[0],
@@ -105,7 +108,9 @@ def prepare_dataset(cfg, tokenizer, processor=None):
         )
 
         train_dataset = wrap_pretraining_dataset(
-            load_dataset(path, streaming=True, split=split, name=name),
+            load_dataset(
+                path, streaming=True, split=split, name=name, data_files=data_files
+            ),
             tokenizer,
             cfg,
             ds_wrapper_partial,

src/axolotl/utils/model_shard_quant.py

@@ -270,7 +270,7 @@ def load_sharded_model_quant(
     model.hf_quantizer = AutoHfQuantizer.from_config(quantization_config)
 
     if cfg.local_rank == 0 and verbose:
-        print(f"Loaded model weights in {time.time()-start:.3f} seconds")
+        print(f"Loaded model weights in {time.time() - start:.3f} seconds")
     # cleanup any extra memory usage from parallel loading
     torch.cuda.empty_cache()
 

src/axolotl/utils/models.py

@@ -713,19 +713,45 @@ class ModelLoader:
         if self.cfg.flash_attention:
             if not self.cfg.sample_packing and self.cfg.s2_attention:
                 pass
-            self.model_kwargs["attn_implementation"] = "flash_attention_2"
+
-            self.model_config._attn_implementation = (  # pylint: disable=protected-access
+            if self.cfg.diff_attention:
-                "flash_attention_2"
+                self.model_kwargs[
-            )
+                    "attn_implementation"
+                ] = "differential_flash_attention_2"
+                self.model_config._attn_implementation = (  # pylint: disable=protected-access
+                    "differential_flash_attention_2"
+                )
+            else:
+                self.model_kwargs["attn_implementation"] = "flash_attention_2"
+                self.model_config._attn_implementation = (  # pylint: disable=protected-access
+                    "flash_attention_2"
+                )
         elif self.cfg.sdp_attention:
-            self.model_kwargs["attn_implementation"] = "sdpa"
+            if self.cfg.diff_attention:
-            self.model_config._attn_implementation = (  # pylint: disable=protected-access
+                self.model_kwargs["attn_implementation"] = "differential_sdpa"
-                "sdpa"
+                self.model_config._attn_implementation = (  # pylint: disable=protected-access
-            )
+                    "differential_sdpa"
+                )
+            else:
+                self.model_kwargs["attn_implementation"] = "sdpa"
+                self.model_config._attn_implementation = (  # pylint: disable=protected-access
+                    "sdpa"
+                )
         elif self.cfg.eager_attention:
-            self.model_kwargs["attn_implementation"] = "eager"
+            if self.cfg.diff_attention:
+                self.model_kwargs["attn_implementation"] = "differential_eager"
+                self.model_config._attn_implementation = (  # pylint: disable=protected-access
+                    "differential_eager"
+                )
+            else:
+                self.model_kwargs["attn_implementation"] = "eager"
+                self.model_config._attn_implementation = (  # pylint: disable=protected-access
+                    "eager"
+                )
+        elif self.cfg.diff_attention:
+            self.model_kwargs["attn_implementation"] = "differential_eager"
             self.model_config._attn_implementation = (  # pylint: disable=protected-access
-                "eager"
+                "differential_eager"
             )
 
         if self.cfg.low_cpu_mem_usage:
@@ -816,6 +842,7 @@ class ModelLoader:
 
             if self.cfg.is_multimodal:
                 self.model_config.text_config = self.text_model_config
+
             self.model = self.AutoModelLoader.from_pretrained(
                 self.base_model,
                 config=self.model_config,

src/axolotl/utils/trainer.py

@@ -196,7 +196,7 @@ def process_datasets_for_packing(cfg, train_dataset, eval_dataset):
         if eval_dataset:
             eval_dataset = eval_dataset.remove_columns("attention_mask")
 
-    if cfg.model_config_type == "falcon":
+    if cfg.model_config_type in ["falcon", "mistral"]:
         LOG.info("dropping token_type_ids column if it exists")
         if "token_type_ids" in train_dataset.column_names:
             train_dataset = train_dataset.remove_columns("token_type_ids")

src/axolotl/utils/yaml.py

@@ -0,0 +1,157 @@
+"""Utilities for YAML files."""
+
+from collections import OrderedDict
+from typing import Any, Dict, List, Set, Tuple, Union
+
+import yaml
+
+
+class YAMLOrderTracker:
+    """Tracks the order of keys and section breaks in YAML files."""
+
+    def __init__(self, yaml_path: str):
+        self.yaml_path = yaml_path
+        self.structure, self.needs_break = self._parse_yaml_structure()
+
+    def _get_indentation_level(self, line: str) -> int:
+        """Get the indentation level of a line."""
+        return len(line) - len(line.lstrip())
+
+    def _parse_yaml_structure(
+        self,
+    ) -> Tuple[Dict[str, Union[List[str], Dict]], Set[str]]:
+        """Parse the YAML file to extract structure and identify section breaks."""
+        with open(self.yaml_path, "r", encoding="utf-8") as file:
+            contents = file.readlines()
+
+        structure: OrderedDict = OrderedDict()
+        needs_break = set()  # Track which keys should have a break before them
+        current_path = []
+        last_indentation = -1
+        had_empty_line = False
+
+        for line in contents:
+            # Track empty lines and comments
+            if not line.strip() or line.strip().startswith("#"):
+                had_empty_line = True
+                continue
+
+            # Get indentation level and content
+            indentation = self._get_indentation_level(line)
+            content = line.strip()
+
+            # Skip lines that don't define keys
+            if ":" not in content:
+                continue
+
+            # Extract key
+            key = content.split(":")[0].strip()
+
+            # If this is a top-level key and we had an empty line, mark it
+            if indentation == 0:
+                if had_empty_line:
+                    needs_break.add(key)
+                had_empty_line = False
+
+            # Handle indentation changes
+            if indentation > last_indentation:
+                current_path.append(key)
+            elif indentation < last_indentation:
+                levels_up = (last_indentation - indentation) // 2
+                current_path = current_path[:-levels_up]
+                current_path[-1] = key
+            else:
+                if current_path:
+                    current_path[-1] = key
+
+            # Update structure
+            current_dict = structure
+            for path_key in current_path[:-1]:
+                if path_key not in current_dict:
+                    current_dict[path_key] = OrderedDict()
+                current_dict = current_dict[path_key]
+
+            if current_path:
+                if current_path[-1] not in current_dict:
+                    current_dict[current_path[-1]] = OrderedDict()
+
+            last_indentation = indentation
+
+        return structure, needs_break
+
+
+class OrderedDumper(yaml.SafeDumper):
+    """Custom YAML dumper that maintains dictionary order."""
+
+
+def represent_none(self, _):
+    """Represent None values as empty fields."""
+    return self.represent_scalar("tag:yaml.org,2002:null", "")
+
+
+def ordered_dict_representer(dumper: OrderedDumper, data: Dict) -> Any:
+    """Custom representer for dictionaries that maintains order."""
+    return dumper.represent_mapping("tag:yaml.org,2002:map", data.items())
+
+
+def reorder_dict(data: Dict, reference_structure: Dict) -> OrderedDict:
+    """Reorder a dictionary based on a reference structure."""
+    ordered = OrderedDict()
+
+    # First add keys that are in the reference order
+    for key in reference_structure:
+        if key in data:
+            if isinstance(reference_structure[key], dict) and isinstance(
+                data[key], dict
+            ):
+                ordered[key] = reorder_dict(data[key], reference_structure[key])
+            else:
+                ordered[key] = data[key]
+
+    # Then add any remaining keys that weren't in the reference
+    for key in data:
+        if key not in ordered:
+            ordered[key] = data[key]
+
+    return ordered
+
+
+def dump_yaml_preserved_order(
+    data: Dict, reference_yaml_path: str, output_path: str
+) -> None:
+    """Dump YAML file while preserving nested order and normalized spacing."""
+    # Get reference structure and spacing
+    tracker = YAMLOrderTracker(reference_yaml_path)
+
+    # Reorder the data
+    ordered_data = reorder_dict(data, tracker.structure)
+
+    # Register the custom representers
+    OrderedDumper.add_representer(type(None), represent_none)
+    OrderedDumper.add_representer(dict, ordered_dict_representer)
+    OrderedDumper.add_representer(OrderedDict, ordered_dict_representer)
+
+    # First dump to string
+    yaml_str = yaml.dump(
+        ordered_data, Dumper=OrderedDumper, sort_keys=False, default_flow_style=False
+    )
+
+    # Add spacing according to reference
+    lines = yaml_str.split("\n")
+    result_lines: List[str] = []
+    current_line = 0
+
+    while current_line < len(lines):
+        line = lines[current_line]
+        if line.strip() and ":" in line and not line.startswith(" "):  # Top-level key
+            key = line.split(":")[0].strip()
+            if key in tracker.needs_break:
+                # Add single empty line before this key
+                if result_lines and result_lines[-1] != "":
+                    result_lines.append("")
+        result_lines.append(line)
+        current_line += 1
+
+    # Write the final result
+    with open(output_path, "w", encoding="utf-8") as file:
+        file.write("\n".join(result_lines))

tests/cli/conftest.py

@@ -1,4 +1,5 @@
 """Shared pytest fixtures for cli module."""
+
 import pytest
 from click.testing import CliRunner
 

tests/cli/test_cli_base.py

@@ -43,14 +43,12 @@ class BaseCliTest:
             result = cli_runner.invoke(cli, [command, str(config_path)])
 
             assert mock.called
-            assert mock.call_args.args[0] == [
+            assert mock.call_args.args[0][:5] == [
                 "accelerate",
                 "launch",
                 "-m",
                 f"axolotl.cli.{command}",
                 str(config_path),
-                "--debug-num-examples",
-                "0",
             ]
             assert mock.call_args.kwargs == {"check": True}
             assert result.exit_code == 0

tests/cli/test_cli_fetch.py

@@ -1,4 +1,5 @@
 """pytest tests for axolotl CLI fetch command."""
+
 from unittest.mock import patch
 
 from axolotl.cli.main import fetch

tests/cli/test_cli_inference.py

@@ -1,4 +1,5 @@
 """pytest tests for axolotl CLI inference command."""
+
 from unittest.mock import patch
 
 from axolotl.cli.main import cli

tests/cli/test_cli_interface.py

@@ -1,4 +1,5 @@
 """General pytest tests for axolotl.cli.main interface."""
+
 from axolotl.cli.main import build_command, cli
 
 
@@ -22,6 +23,7 @@ def test_build_command():
         "--batch-size",
         "8",
         "--debug",
+        "--nouse-fp16",
     ]
 
 

tests/cli/test_cli_merge_lora.py

@@ -1,4 +1,5 @@
 """pytest tests for axolotl CLI merge_lora command."""
+
 from unittest.mock import patch
 
 from axolotl.cli.main import cli

tests/cli/test_cli_merge_sharded_fsdp_weights.py

@@ -1,5 +1,6 @@
 """pytest tests for axolotl CLI merge_sharded_fsdp_weights command."""
 # pylint: disable=duplicate-code
+
 from unittest.mock import patch
 
 from axolotl.cli.main import cli

tests/cli/test_cli_preprocess.py

@@ -1,4 +1,5 @@
 """pytest tests for axolotl CLI preprocess command."""
+
 import shutil
 from pathlib import Path
 from unittest.mock import patch

tests/cli/test_cli_shard.py

@@ -1,5 +1,6 @@
 """pytest tests for axolotl CLI shard command."""
 # pylint: disable=duplicate-code
+
 from unittest.mock import patch
 
 from axolotl.cli.main import cli
@@ -11,14 +12,12 @@ def test_shard_with_accelerate(cli_runner, config_path):
         result = cli_runner.invoke(cli, ["shard", str(config_path), "--accelerate"])
 
         assert mock.called
-        assert mock.call_args.args[0] == [
+        assert mock.call_args.args[0][:5] == [
             "accelerate",
             "launch",
             "-m",
             "axolotl.cli.shard",
             str(config_path),
-            "--debug-num-examples",
-            "0",
         ]
         assert mock.call_args.kwargs == {"check": True}
         assert result.exit_code == 0

tests/cli/test_cli_version.py

@@ -1,4 +1,5 @@
 """pytest tests for axolotl CLI --version"""
+
 from axolotl.cli.main import cli
 
 

tests/cli/test_utils.py

@@ -1,5 +1,6 @@
 """pytest tests for axolotl CLI utils."""
 # pylint: disable=redefined-outer-name
+
 import json
 from unittest.mock import Mock, patch
 

tests/conftest.py

@@ -120,13 +120,12 @@ def temp_dir():
 @pytest.fixture(scope="function", autouse=True)
 def cleanup_monkeypatches():
     from transformers import Trainer
-    from transformers.models.llama.modeling_llama import (
+    from transformers.models.llama.modeling_llama import (  # LlamaFlashAttention2,
         LlamaAttention,
-        LlamaFlashAttention2,
         LlamaForCausalLM,
     )
 
-    original_fa2_forward = LlamaFlashAttention2.forward
+    # original_fa2_forward = LlamaFlashAttention2.forward
     original_llama_attn_forward = LlamaAttention.forward
     original_llama_forward = LlamaForCausalLM.forward
     original_trainer_inner_training_loop = (
@@ -136,7 +135,7 @@ def cleanup_monkeypatches():
     # monkey patches can happen inside the tests
     yield
     # Reset LlamaFlashAttention2 forward
-    LlamaFlashAttention2.forward = original_fa2_forward
+    # LlamaFlashAttention2.forward = original_fa2_forward
     LlamaAttention.forward = original_llama_attn_forward
     LlamaForCausalLM.forward = original_llama_forward
     Trainer._inner_training_loop = (  # pylint: disable=protected-access
@@ -149,7 +148,10 @@ def cleanup_monkeypatches():
         ("transformers.models.llama",),
         (
             "transformers.models.llama.modeling_llama",
-            ["LlamaFlashAttention2", "LlamaAttention"],
+            [
+                # "LlamaFlashAttention2",
+                "LlamaAttention",
+            ],
         ),
         ("transformers.trainer",),
         ("transformers", ["Trainer"]),

tests/e2e/integrations/test_liger.py

@@ -1,43 +1,40 @@
 """
 Simple end-to-end test for Liger integration
 """
-import unittest
 from pathlib import Path
 
+from e2e.utils import require_torch_2_4_1
+
 from axolotl.cli import load_datasets
 from axolotl.common.cli import TrainerCliArgs
 from axolotl.train import train
 from axolotl.utils.config import normalize_config, prepare_plugins
 from axolotl.utils.dict import DictDefault
 
-from ..utils import with_temp_dir
 
-
+class LigerIntegrationTestCase:
-class LigerIntegrationTestCase(unittest.TestCase):
     """
     e2e tests for liger integration with Axolotl
     """
 
-    @with_temp_dir
+    @require_torch_2_4_1
     def test_llama_wo_flce(self, temp_dir):
+        # pylint: disable=duplicate-code
         cfg = DictDefault(
             {
-                "base_model": "JackFram/llama-68m",
+                "base_model": "HuggingFaceTB/SmolLM2-135M",
-                "tokenizer_type": "LlamaTokenizer",
                 "plugins": [
                     "axolotl.integrations.liger.LigerPlugin",
                 ],
                 "liger_rope": True,
                 "liger_rms_norm": True,
-                "liger_swiglu": True,
+                "liger_glu_activation": True,
                 "liger_cross_entropy": True,
                 "liger_fused_linear_cross_entropy": False,
                 "sequence_len": 1024,
-                "val_set_size": 0.1,
+                "val_set_size": 0.05,
                 "special_tokens": {
-                    "unk_token": "<unk>",
+                    "pad_token": "<|endoftext|>",
-                    "bos_token": "<s>",
-                    "eos_token": "</s>",
                 },
                 "datasets": [
                     {
@@ -46,15 +43,15 @@ class LigerIntegrationTestCase(unittest.TestCase):
                     },
                 ],
                 "num_epochs": 1,
-                "micro_batch_size": 8,
+                "micro_batch_size": 2,
-                "gradient_accumulation_steps": 1,
+                "gradient_accumulation_steps": 2,
                 "output_dir": temp_dir,
                 "learning_rate": 0.00001,
                 "optimizer": "adamw_torch",
                 "lr_scheduler": "cosine",
                 "save_safetensors": True,
                 "bf16": "auto",
-                "max_steps": 10,
+                "max_steps": 5,
             }
         )
         prepare_plugins(cfg)
@@ -65,26 +62,24 @@ class LigerIntegrationTestCase(unittest.TestCase):
         train(cfg=cfg, cli_args=cli_args, dataset_meta=dataset_meta)
         assert (Path(temp_dir) / "model.safetensors").exists()
 
-    @with_temp_dir
+    @require_torch_2_4_1
     def test_llama_w_flce(self, temp_dir):
+        # pylint: disable=duplicate-code
         cfg = DictDefault(
             {
-                "base_model": "JackFram/llama-68m",
+                "base_model": "HuggingFaceTB/SmolLM2-135M",
-                "tokenizer_type": "LlamaTokenizer",
                 "plugins": [
                     "axolotl.integrations.liger.LigerPlugin",
                 ],
                 "liger_rope": True,
                 "liger_rms_norm": True,
-                "liger_swiglu": True,
+                "liger_glu_activation": True,
                 "liger_cross_entropy": False,
                 "liger_fused_linear_cross_entropy": True,
                 "sequence_len": 1024,
-                "val_set_size": 0.1,
+                "val_set_size": 0.05,
                 "special_tokens": {
-                    "unk_token": "<unk>",
+                    "pad_token": "<|endoftext|>",
-                    "bos_token": "<s>",
-                    "eos_token": "</s>",
                 },
                 "datasets": [
                     {
@@ -93,15 +88,15 @@ class LigerIntegrationTestCase(unittest.TestCase):
                     },
                 ],
                 "num_epochs": 1,
-                "micro_batch_size": 8,
+                "micro_batch_size": 2,
-                "gradient_accumulation_steps": 1,
+                "gradient_accumulation_steps": 2,
                 "output_dir": temp_dir,
                 "learning_rate": 0.00001,
                 "optimizer": "adamw_torch",
                 "lr_scheduler": "cosine",
                 "save_safetensors": True,
                 "bf16": "auto",
-                "max_steps": 10,
+                "max_steps": 5,
             }
         )
         prepare_plugins(cfg)

tests/e2e/patched/test_unsloth_integration.py

@@ -1,9 +1,14 @@
 """Test module for checking whether the integration of Unsloth with Hugging Face Transformers is working as expected."""
 import unittest
 
+import pytest
+
 from axolotl.monkeypatch.unsloth_ import check_self_attn_is_patchable
 
 
+@pytest.mark.skip(
+    reason="Unsloth integration will be broken going into latest transformers"
+)
 class TestUnslothIntegration(unittest.TestCase):
     """Unsloth monkeypatch integration tests."""
 

tests/e2e/patched/test_unsloth_qlora.py

@@ -20,6 +20,9 @@ os.environ["WANDB_DISABLED"] = "true"
 
 
 # pylint: disable=duplicate-code
+@pytest.mark.skip(
+    reason="Unsloth integration will be broken going into latest transformers"
+)
 class TestUnslothQLoRA:
     """
     Test class for Unsloth QLoRA Llama models

tests/e2e/test_optimizers.py

@@ -113,6 +113,7 @@ class TestCustomOptimizers(unittest.TestCase):
 
     @with_temp_dir
     def test_fft_schedule_free_adamw(self, temp_dir):
+        # pylint: disable=duplicate-code
         cfg = DictDefault(
             {
                 "base_model": "HuggingFaceTB/SmolLM2-135M",

tests/e2e/utils.py

@@ -49,7 +49,19 @@ def require_torch_2_3_1(test_case):
         torch_version = version.parse(torch.__version__)
         return torch_version >= version.parse("2.3.1")
 
-    return unittest.skipUnless(is_min_2_3_1(), "test torch 2.3.1")(test_case)
+    return unittest.skipUnless(is_min_2_3_1(), "test requires torch>=2.3.1")(test_case)
+
+
+def require_torch_2_4_1(test_case):
+    """
+    Decorator marking a test that requires torch >= 2.5.1
+    """
+
+    def is_min_2_4_1():
+        torch_version = version.parse(torch.__version__)
+        return torch_version >= version.parse("2.4.1")
+
+    return unittest.skipUnless(is_min_2_4_1(), "test requires torch>=2.4.1")(test_case)
 
 
 def require_torch_2_5_1(test_case):
@@ -61,7 +73,7 @@ def require_torch_2_5_1(test_case):
         torch_version = version.parse(torch.__version__)
         return torch_version >= version.parse("2.5.1")
 
-    return unittest.skipUnless(is_min_2_5_1(), "test torch 2.5.1")(test_case)
+    return unittest.skipUnless(is_min_2_5_1(), "test requires torch>=2.5.1")(test_case)
 
 
 def is_hopper():

tests/integrations/test_liger.py

@@ -7,11 +7,11 @@ from typing import Optional
 
 import pytest
 
-from axolotl.utils.config import validate_config
+from axolotl.utils.config import prepare_plugins, validate_config
 from axolotl.utils.dict import DictDefault
 
 
-@pytest.fixture(name="minimal_base_cfg")
+@pytest.fixture(name="minimal_liger_cfg")
 def fixture_cfg():
     return DictDefault(
         {
@@ -25,56 +25,57 @@ def fixture_cfg():
             ],
             "micro_batch_size": 1,
             "gradient_accumulation_steps": 1,
+            "plugins": ["axolotl.integrations.liger.LigerPlugin"],
         }
     )
 
 
-class BaseValidation:
+# pylint: disable=too-many-public-methods
+class TestValidation:
     """
-    Base validation module to setup the log capture
+    Test the validation module for liger
     """
 
     _caplog: Optional[pytest.LogCaptureFixture] = None
 
     @pytest.fixture(autouse=True)
     def inject_fixtures(self, caplog):
+        caplog.set_level(logging.WARNING)
         self._caplog = caplog
 
-
+    def test_deprecated_swiglu(self, minimal_liger_cfg):
-# pylint: disable=too-many-public-methods
-class TestValidation(BaseValidation):
-    """
-    Test the validation module for liger
-    """
-
-    def test_deprecated_swiglu(self, minimal_cfg):
         test_cfg = DictDefault(
             {
                 "liger_swiglu": False,
             }
-            | minimal_cfg
+            | minimal_liger_cfg
         )
 
-        with self._caplog.at_level(logging.WARNING):
+        with self._caplog.at_level(
+            logging.WARNING, logger="axolotl.integrations.liger.args"
+        ):
+            prepare_plugins(test_cfg)
             updated_cfg = validate_config(test_cfg)
-            assert (
+            # TODO this test is brittle in CI
-                "The 'liger_swiglu' argument is deprecated"
+            # assert (
-                in self._caplog.records[0].message
+            #     "The 'liger_swiglu' argument is deprecated"
-            )
+            #     in self._caplog.records[0].message
+            # )
             assert updated_cfg.liger_swiglu is None
-            assert updated_cfg.liger_glu_activations is False
+            assert updated_cfg.liger_glu_activation is False
 
-    def test_conflict_swiglu_ligergluactivation(self, minimal_cfg):
+    def test_conflict_swiglu_ligergluactivation(self, minimal_liger_cfg):
         test_cfg = DictDefault(
             {
                 "liger_swiglu": False,
-                "liger_glu_activations": True,
+                "liger_glu_activation": True,
             }
-            | minimal_cfg
+            | minimal_liger_cfg
         )
 
         with pytest.raises(
             ValueError,
             match=r".*You cannot have both `liger_swiglu` and `liger_glu_activation` set.*",
         ):
+            prepare_plugins(test_cfg)
             validate_config(test_cfg)

tests/test_prompt_tokenizers.py

@@ -4,9 +4,7 @@ import json
 import logging
 import unittest
 from pathlib import Path
-from typing import Optional
 
-import pytest
 from datasets import load_dataset
 from transformers import AddedToken, AutoTokenizer, LlamaTokenizer
 
@@ -65,12 +63,6 @@ class TestPromptTokenizationStrategies(unittest.TestCase):
     Test class for prompt tokenization strategies.
     """
 
-    _caplog: Optional[pytest.LogCaptureFixture] = None
-
-    @pytest.fixture(autouse=True)
-    def inject_fixtures(self, caplog):
-        self._caplog = caplog
-
     def setUp(self) -> None:
         # pylint: disable=duplicate-code
         self.tokenizer = AutoTokenizer.from_pretrained("huggyllama/llama-7b")