Replace meta_tags.csv with hparams.yaml (#1271)

* Add support for hierarchical dict

* Support nested Namespace

* Add docstring

* Migrate hparam flattening to each logger

* Modify URLs in CHANGELOG

* typo

* Simplify the conditional branch about Namespace

Co-Authored-By: Jirka Borovec <Borda@users.noreply.github.com>

* Update CHANGELOG.md

Co-Authored-By: Jirka Borovec <Borda@users.noreply.github.com>

* added examples section to docstring

* renamed _dict -> input_dict

* mata_tags.csv -> hparams.yaml

* code style fixes

* add pyyaml

* remove unused import

* create the member NAME_HPARAMS_FILE

* improve tests

* Update tensorboard.py

* pass the local test w/o relavents of Horovod

* formatting

* update dependencies

* fix dependencies

* Apply suggestions from code review

* add savings

* warn

* docstrings

* tests

* Apply suggestions from code review

* saving

* Apply suggestions from code review

* use default

* remove logging

* typo fixes

* update docs

* update CHANGELOG

* clean imports

* add blank lines

* Update pytorch_lightning/core/lightning.py

Co-authored-by: Adrian Wälchli <aedu.waelchli@gmail.com>

* Update pytorch_lightning/core/lightning.py

Co-authored-by: Adrian Wälchli <aedu.waelchli@gmail.com>

* back to namespace

* add docs

* test fix

* update dependencies

* add space

Co-authored-by: Jirka Borovec <Borda@users.noreply.github.com>
Co-authored-by: Adrian Wälchli <aedu.waelchli@gmail.com>

CHANGELOG.md

@@ -26,6 +26,8 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/).
 
 ### Changed
 
+- Replace mata_tags.csv with hparams.yaml ([#1271](https://github.com/PyTorchLightning/pytorch-lightning/pull/1271))
+
 - Reduction when `batch_size < num_gpus` ([#1609](https://github.com/PyTorchLightning/pytorch-lightning/pull/1609))
 
 - Updated LightningTemplateModel to look more like Colab example ([#1577](https://github.com/PyTorchLightning/pytorch-lightning/pull/1577))
@@ -36,6 +38,8 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/).
 
 ### Deprecated
 
+- Deprecated `tags_csv` in favor of `hparams_file` ([#1271](https://github.com/PyTorchLightning/pytorch-lightning/pull/1271))
+
 ### Removed
 
 ### Fixed

docs/source/test_set.rst

@@ -21,10 +21,9 @@ To run the test set on a pre-trained model, use this method.
 
 .. code-block:: python
 
-    model = MyLightningModule.load_from_metrics(
-        weights_path='/path/to/pytorch_checkpoint.ckpt',
-        tags_csv='/path/to/test_tube/experiment/version/meta_tags.csv',
-        on_gpu=True,
+    model = MyLightningModule.load_from_checkpoint(
+        checkpoint_path='/path/to/pytorch_checkpoint.ckpt',
+        hparams_file='/path/to/test_tube/experiment/version/hparams.yaml',
         map_location=None
     )
 

environment.yml

@@ -13,6 +13,7 @@ dependencies:
     - pytorch>=1.1
     - tensorboard>=1.14
     - future>=0.17.1
+    - pyyaml>=3.13
 
     # For dev and testing
     - tox

pytorch_lightning/core/lightning.py

@@ -1,6 +1,7 @@
 import collections
 import inspect
 import os
+import warnings
 from abc import ABC, abstractmethod
 from argparse import Namespace
 from typing import Any, Callable, Dict, List, Optional, Tuple, Union, Sequence
@@ -16,7 +17,7 @@
 from pytorch_lightning.core.grads import GradInformation
 from pytorch_lightning.core.hooks import ModelHooks
 from pytorch_lightning.core.memory import ModelSummary
-from pytorch_lightning.core.saving import ModelIO, load_hparams_from_tags_csv, update_hparams
+from pytorch_lightning.core.saving import ModelIO, load_hparams_from_tags_csv, load_hparams_from_yaml, update_hparams
 from pytorch_lightning.core.properties import DeviceDtypeModuleMixin
 from pytorch_lightning.overrides.data_parallel import LightningDistributedDataParallel
 from pytorch_lightning.utilities.exceptions import MisconfigurationException
@@ -1438,49 +1439,88 @@ def load_from_checkpoint(
             cls,
             checkpoint_path: str,
             map_location: Optional[Union[Dict[str, str], str, torch.device, int, Callable]] = None,
-            tags_csv: Optional[str] = None,
+            hparams_file: Optional[str] = None,
+            tags_csv: Optional[str] = None,  # backward compatible, todo: remove in v0.9.0
             hparam_overrides: Optional[Dict] = None,
             *args, **kwargs
     ) -> 'LightningModule':
         r"""
         Primary way of loading a model from a checkpoint. When Lightning saves a checkpoint
         it stores the hyperparameters in the checkpoint if you initialized your :class:`LightningModule`
-        with an argument called ``hparams`` which is a :class:`~argparse.Namespace`
-        (output of :meth:`~argparse.ArgumentParser.parse_args` when parsing command line arguments).
+        with an argument called ``hparams`` which is an object of :class:`~dict` or
+        :class:`~argparse.Namespace` (output of :meth:`~argparse.ArgumentParser.parse_args`
+        when parsing command line arguments).
+        If you want `hparams` to have a hierarchical structure, you have to define it as :class:`~dict`.
         Any other arguments specified through \*args and \*\*kwargs will be passed to the model.
 
         Example:
             .. code-block:: python
 
+                # define hparams as Namespace
                 from argparse import Namespace
                 hparams = Namespace(**{'learning_rate': 0.1})
 
                 model = MyModel(hparams)
 
                 class MyModel(LightningModule):
-                    def __init__(self, hparams):
+                    def __init__(self, hparams: Namespace):
                         self.learning_rate = hparams.learning_rate
 
+                # ----------
+
+                # define hparams as dict
+                hparams = {
+                    drop_prob: 0.2,
+                    dataloader: {
+                        batch_size: 32
+                    }
+                }
+
+                model = MyModel(hparams)
+
+                class MyModel(LightningModule):
+                    def __init__(self, hparams: dict):
+                        self.learning_rate = hparams['learning_rate']
+
         Args:
             checkpoint_path: Path to checkpoint.
             model_args: Any keyword args needed to init the model.
             map_location:
                 If your checkpoint saved a GPU model and you now load on CPUs
                 or a different number of GPUs, use this to map to the new setup.
                 The behaviour is the same as in :func:`torch.load`.
-            tags_csv: Optional path to a .csv file with two columns (key, value)
+            hparams_file: Optional path to a .yaml file with hierarchical structure
                 as in this example::
 
-                    key,value
-                    drop_prob,0.2
-                    batch_size,32
+                    drop_prob: 0.2
+                    dataloader:
+                        batch_size: 32
 
                 You most likely won't need this since Lightning will always save the hyperparameters
                 to the checkpoint.
                 However, if your checkpoint weights don't have the hyperparameters saved,
-                use this method to pass in a .csv file with the hparams you'd like to use.
-                These will be converted into a :class:`~argparse.Namespace` and passed into your
+                use this method to pass in a .yaml file with the hparams you'd like to use.
+                These will be converted into a :class:`~dict` and passed into your
                 :class:`LightningModule` for use.
+
+                If your model's `hparams` argument is :class:`~argparse.Namespace`
+                and .yaml file has hierarchical structure, you need to refactor your model to treat
+                `hparams` as :class:`~dict`.
+
+                .csv files are acceptable here till v0.9.0, see tags_csv argument for detailed usage.
+            tags_csv:
+                .. warning:: .. deprecated:: 0.7.6
+
+                    `tags_csv` argument is deprecated in v0.7.6. Will be removed v0.9.0.
+
+                Optional path to a .csv file with two columns (key, value)
+                as in this example::
+
+                    key,value
+                    drop_prob,0.2
+                    batch_size,32
+
+                Use this method to pass in a .csv file with the hparams you'd like to use.
             hparam_overrides: A dictionary with keys to override in the hparams
 
         Return:
@@ -1502,7 +1542,7 @@ def __init__(self, hparams):
                 # or load weights and hyperparameters from separate files.
                 MyLightningModule.load_from_checkpoint(
                     'path/to/checkpoint.ckpt',
-                    tags_csv='/path/to/hparams_file.csv'
+                    hparams_file='/path/to/hparams_file.yaml'
                 )
 
                 # override some of the params with new values
@@ -1531,9 +1571,22 @@ def __init__(self, hparams):
 
         # add the hparams from csv file to checkpoint
         if tags_csv is not None:
-            hparams = load_hparams_from_tags_csv(tags_csv)
-            hparams.__setattr__('on_gpu', False)
-            checkpoint['hparams'] = vars(hparams)
+            hparams_file = tags_csv
+            rank_zero_warn('`tags_csv` argument is deprecated in v0.7.6. Will be removed v0.9.0', DeprecationWarning)
+
+        if hparams_file is not None:
+            extension = hparams_file.split('.')[-1]
+            if extension.lower() in ('csv'):
+                hparams = load_hparams_from_tags_csv(hparams_file)
+            elif extension.lower() in ('yml', 'yaml'):
+                hparams = load_hparams_from_yaml(hparams_file)
+            else:
+                raise ValueError('.csv, .yml or .yaml is required for `hparams_file`')
+
+            hparams['on_gpu'] = False
+
+            # overwrite hparams by the given file
+            checkpoint['hparams'] = hparams
 
         # override the hparam keys that were passed in
         if hparam_overrides is not None:
@@ -1549,15 +1602,18 @@ def _load_model_state(cls, checkpoint: Dict[str, Any], *args, **kwargs) -> 'Ligh
 
         if cls_takes_hparams:
             if ckpt_hparams is not None:
-                is_namespace = checkpoint.get('hparams_type', 'namespace') == 'namespace'
-                hparams = Namespace(**ckpt_hparams) if is_namespace else ckpt_hparams
+                hparams_type = checkpoint.get('hparams_type', 'Namespace')
+                if hparams_type.lower() == 'dict':
+                    hparams = ckpt_hparams
+                elif hparams_type.lower() == 'namespace':
+                    hparams = Namespace(**ckpt_hparams)
             else:
                 rank_zero_warn(
                     f"Checkpoint does not contain hyperparameters but {cls.__name__}'s __init__"
                     " contains argument 'hparams'. Will pass in an empty Namespace instead."
                     " Did you forget to store your model hyperparameters in self.hparams?"
                 )
-                hparams = Namespace()
+                hparams = {}
         else:  # The user's LightningModule does not define a hparams argument
             if ckpt_hparams is None:
                 hparams = None
@@ -1568,7 +1624,7 @@ def _load_model_state(cls, checkpoint: Dict[str, Any], *args, **kwargs) -> 'Ligh
                 )
 
         # load the state_dict on the model automatically
-        if hparams:
+        if cls_takes_hparams:
             kwargs.update(hparams=hparams)
         model = cls(*args, **kwargs)
         model.load_state_dict(checkpoint['state_dict'])

pytorch_lightning/core/saving.py

@@ -1,9 +1,12 @@
+import ast
 import csv
 import os
+import yaml
 from argparse import Namespace
 from typing import Union, Dict, Any
 
 from pytorch_lightning import _logger as log
+from pytorch_lightning.utilities import rank_zero_warn
 
 
 class ModelIO(object):
@@ -79,30 +82,78 @@ def update_hparams(hparams: dict, updates: dict) -> None:
             hparams.update({k: v})
 
 
-def load_hparams_from_tags_csv(tags_csv: str) -> Namespace:
+def load_hparams_from_tags_csv(tags_csv: str) -> Dict[str, Any]:
+    """Load hparams from a file.
+
+    >>> hparams = Namespace(batch_size=32, learning_rate=0.001, data_root='./any/path/here')
+    >>> path_csv = './testing-hparams.csv'
+    >>> save_hparams_to_tags_csv(path_csv, hparams)
+    >>> hparams_new = load_hparams_from_tags_csv(path_csv)
+    >>> vars(hparams) == hparams_new
+    True
+    >>> os.remove(path_csv)
+    """
     if not os.path.isfile(tags_csv):
-        log.warning(f'Missing Tags: {tags_csv}.')
-        return Namespace()
+        rank_zero_warn(f'Missing Tags: {tags_csv}.', RuntimeWarning)
+        return {}
 
-    with open(tags_csv) as f:
-        csv_reader = csv.reader(f, delimiter=',')
+    with open(tags_csv) as fp:
+        csv_reader = csv.reader(fp, delimiter=',')
         tags = {row[0]: convert(row[1]) for row in list(csv_reader)[1:]}
-    ns = Namespace(**tags)
-    return ns
+
+    return tags
+
+
+def save_hparams_to_tags_csv(tags_csv: str, hparams: Union[dict, Namespace]) -> None:
+    if not os.path.isdir(os.path.dirname(tags_csv)):
+        raise RuntimeError(f'Missing folder: {os.path.dirname(tags_csv)}.')
+
+    if isinstance(hparams, Namespace):
+        hparams = vars(hparams)
+
+    with open(tags_csv, 'w') as fp:
+        fieldnames = ['key', 'value']
+        writer = csv.DictWriter(fp, fieldnames=fieldnames)
+        writer.writerow({'key': 'key', 'value': 'value'})
+        for k, v in hparams.items():
+            writer.writerow({'key': k, 'value': v})
+
+
+def load_hparams_from_yaml(config_yaml: str) -> Dict[str, Any]:
+    """Load hparams from a file.
+
+    >>> hparams = Namespace(batch_size=32, learning_rate=0.001, data_root='./any/path/here')
+    >>> path_yaml = './testing-hparams.yaml'
+    >>> save_hparams_to_yaml(path_yaml, hparams)
+    >>> hparams_new = load_hparams_from_yaml(path_yaml)
+    >>> vars(hparams) == hparams_new
+    True
+    >>> os.remove(path_yaml)
+    """
+    if not os.path.isfile(config_yaml):
+        rank_zero_warn(f'Missing Tags: {config_yaml}.', RuntimeWarning)
+        return {}
+
+    with open(config_yaml) as fp:
+        tags = yaml.load(fp, Loader=yaml.SafeLoader)
+
+    return tags
+
+
+def save_hparams_to_yaml(config_yaml, hparams: Union[dict, Namespace]) -> None:
+    if not os.path.isdir(os.path.dirname(config_yaml)):
+        raise RuntimeError(f'Missing folder: {os.path.dirname(config_yaml)}.')
+
+    if isinstance(hparams, Namespace):
+        hparams = vars(hparams)
+
+    with open(config_yaml, 'w', newline='') as fp:
+        yaml.dump(hparams, fp)
 
 
 def convert(val: str) -> Union[int, float, bool, str]:
-    constructors = [int, float, str]
-
-    if isinstance(val, str):
-        if val.lower() == 'true':
-            return True
-        if val.lower() == 'false':
-            return False
-
-    for c in constructors:
-        try:
-            return c(val)
-        except ValueError:
-            pass
-    return val
+    try:
+        return ast.literal_eval(val)
+    except (ValueError, SyntaxError) as e:
+        log.debug(e)
+        return val