Merge 8c4a23d into 06cd707

doc/api.rst

@@ -6,31 +6,84 @@ The primary method of using RSMTool is via the command-line scripts :ref:`rsmtoo
 
 .. note::
 
-     RSMTool v5.7 and older provided the API functions ``metrics_helper``, ``convert_ipynb_to_html``, and ``remove_outliers``. These functions have now been turned into static methods for different classes. If you are using these functions in your code and want to migrate to the new API, you should replace the follwing statements in your code:
+    RSMTool v5.7 and older provided the API functions ``metrics_helper``, ``convert_ipynb_to_html``, and ``remove_outliers``. These functions have now been turned into static methods for different classes. 
+
+    In addition, with RSMTool v8.0 onwards, the functions ``agreement``, ``difference_of_standardized_means``, ``get_thumbnail_as_html``,  ``parse_json_with_comments``, ``partial_correlations``,  ``quadratic_weighted_kappa``, ``show_thumbnail``,  ``standardized_mean_difference`` that``utils.py`` have been moved to new locations.
+
+    If you are using the above functions in your code and want to migrate to the new API, you should replace the follwing statements in your code:
 
     .. code-block:: python
 
-        from rsmtool.analysis import metrics_helper
-        metrics_helper(...)
+     from rsmtool.analysis import metrics_helper
+     metrics_helper(...)
+
+     from rsmtool.report import convert_ipynb_to_html
+     convert_ipynb_to_html(...)
+        
+     from rsmtool.preprocess import remove_outliers
+     remove_outliers(...)
 
-        from rsmtool.report import convert_ipynb_to_html
-        convert_ipynb_to_html(...)
+     from rsmtool.utils import agreement
+     agreement(...)
+        
+     from rsmtool.utils import difference_of_standardized_means
+     difference_of_standardized_means(...)
+        
+     from rsmtool.utils import partial_correlations
+     partial_correlations(...)
         
-        from rsmtool.preprocess import remove_outliers
-        remove_outliers(...)
+     from rsmtool.utils import quadratic_weighted_kappa
+     quadratic_weighted_kappa(...)
+        
+     from rsmtool.utils import standardized_mean_difference
+     standardized_mean_difference(...)
+        
+     from rsmtool.utils import parse_json_with_comments
+     parse_json_with_comments(...)
+
+     from rsmtool.utils import get_thumbnail_as_html
+     get_thumbnail_as_html(...)
+
+     from rsmtool.utils import show_thumbnail
+     show_thumbnail(...)
 
     with the following, respectively:
 
     .. code-block:: python
 
-        from rsmtool.analyzer import Analyzer
-        Analyzer.metrics_helper(...)
+     from rsmtool.analyzer import Analyzer
+     Analyzer.metrics_helper(...)
+
+     from rsmtool.reporter import Reporter
+     Reporter.convert_ipynb_to_html(...)
+    
+     from rsmtool.preprocessor import FeaturePreprocessor
+     FeaturePreprocessor.remove_outliers(...)
+
+     from rsmtool.utils.metrics import agreement
+     agreement(...)
+    
+     from rsmtool.utils.metrics import difference_of_standardized_means
+     difference_of_standardized_means(...)
+    
+     from rsmtool.utils.metrics import partial_correlations
+     partial_correlations(...)
+    
+     from rsmtool.utils.metrics import quadratic_weighted_kappa
+     quadratic_weighted_kappa(...)
+    
+     from rsmtool.utils.metrics import standardized_mean_difference
+     standardized_mean_difference(...)
+    
+     from rsmtool.utils.files import parse_json_with_comments
+     parse_json_with_comments(...)
+
+     from rsmtool.utils.notebook import get_thumbnail_as_html
+     get_thumbnail_as_html(...)
+
+     from rsmtool.utils.notebook import show_thumbnail
+     show_thumbnail(...)
 
-        from rsmtool.reporter import Reporter
-        Reporter.convert_ipynb_to_html(...)
-        
-        from rsmtool.preprocessor import FeaturePreprocessor
-        FeaturePreprocessor.remove_outliers(...)
 
 :mod:`rsmtool` Package
 ======================
@@ -125,18 +178,18 @@ From :py:mod:`~rsmtool.utils` Module
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 .. _agreement_api:
-.. autofunction:: rsmtool.utils.agreement
-.. autofunction:: rsmtool.utils.partial_correlations
-.. autofunction:: rsmtool.utils.get_thumbnail_as_html
-.. autofunction:: rsmtool.utils.show_thumbnail
-.. autofunction:: rsmtool.utils.compute_expected_scores_from_model
-.. autofunction:: rsmtool.utils.parse_json_with_comments
+.. autofunction:: rsmtool.utils.metrics.agreement
+.. _dsm_api:
+.. autofunction:: rsmtool.utils.metrics.difference_of_standardized_means
+.. autofunction:: rsmtool.utils.metrics.partial_correlations
 .. _qwk_api:
-.. autofunction:: rsmtool.utils.quadratic_weighted_kappa
+.. autofunction:: rsmtool.utils.metrics.quadratic_weighted_kappa
 .. _smd_api:
-.. autofunction:: rsmtool.utils.standardized_mean_difference
-.. _dsm_api:
-.. autofunction:: rsmtool.utils.difference_of_standardized_means
+.. autofunction:: rsmtool.utils.metrics.standardized_mean_difference
+.. autofunction:: rsmtool.utils.metrics.compute_expected_scores_from_model
+.. autofunction:: rsmtool.utils.notebook.get_thumbnail_as_html
+.. autofunction:: rsmtool.utils.notebook.show_thumbnail
+.. autofunction:: rsmtool.utils.files.parse_json_with_comments
 
 From :py:mod:`~rsmtool.writer` Module
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

rsmtool/__init__.py

@@ -30,38 +30,37 @@
 
 from .analyzer import Analyzer
 
-from .convert_feature_json import convert_feature_json_file
+from .convert_feature_json import convert_feature_json_file  # noqa
 
-from .comparer import Comparer
+from .comparer import Comparer  # noqa
 
-from .container import DataContainer
+from .container import DataContainer  # noqa
 
-from .modeler import Modeler
+from .modeler import Modeler  # noqa
 
-from .preprocessor import FeaturePreprocessor
+from .preprocessor import FeaturePreprocessor  # noqa
 
-from .reader import DataReader
+from .reader import DataReader  # noqa
 
-from .reporter import Reporter
+from .reporter import Reporter  # noqa
 
-from .writer import DataWriter
+from .writer import DataWriter  # noqa
 
-from .utils import (agreement,
-                    compute_expected_scores_from_model,
-                    get_thumbnail_as_html,
-                    partial_correlations,
-                    show_thumbnail)
+from .rsmcompare import run_comparison  # noqa
 
-from .rsmcompare import run_comparison
+from .rsmeval import run_evaluation  # noqa
 
-from .rsmeval import run_evaluation
+from .rsmtool import run_experiment  # noqa
 
-from .rsmtool import run_experiment
+from .rsmpredict import compute_and_save_predictions  # noqa
 
-from .rsmpredict import compute_and_save_predictions
+from .rsmsummarize import run_summary  # noqa
 
-from .rsmsummarize import run_summary
+from .utils.metrics import (agreement,  # noqa
+                            compute_expected_scores_from_model,
+                            partial_correlations)
 
+from .utils.notebook import get_thumbnail_as_html, show_thumbnail  # noqa
 
 # Make sure that DeprecationWarnings are always shown
 # within this package unless we are in test mode in

rsmtool/analyzer.py

@@ -20,13 +20,13 @@
 from sklearn.metrics import mean_squared_error
 from sklearn.metrics import r2_score
 
-from rsmtool.container import DataContainer
-from rsmtool.prmse_utils import compute_prmse
-from rsmtool.utils import (agreement,
-                           difference_of_standardized_means,
-                           partial_correlations,
-                           quadratic_weighted_kappa,
-                           standardized_mean_difference)
+from .container import DataContainer
+from .prmse_utils import compute_prmse
+from .utils.metrics import (agreement,
+                            difference_of_standardized_means,
+                            partial_correlations,
+                            quadratic_weighted_kappa,
+                            standardized_mean_difference)
 
 
 class Analyzer:

rsmtool/comparer.py

@@ -17,8 +17,8 @@
 from scipy.stats import pearsonr
 from os.path import exists, join
 
-from rsmtool.reader import DataReader
-from rsmtool.utils import get_output_directory_extension
+from .reader import DataReader
+from .utils.files import get_output_directory_extension
 
 
 _df_eval_columns_existing_raw = ["N", "h_mean", "h_sd",

rsmtool/configuration_parser.py

@@ -24,20 +24,21 @@
 from pathlib import Path
 from ruamel import yaml
 
-from rsmtool import HAS_RSMEXTRA
-from rsmtool.utils import parse_json_with_comments
-from rsmtool.utils import (DEFAULTS,
-                           CHECK_FIELDS,
-                           LIST_FIELDS,
-                           BOOLEAN_FIELDS,
-                           MODEL_NAME_MAPPING,
-                           FIELD_NAME_MAPPING,
-                           ID_FIELDS,
-                           is_skll_model)
-
 from skll import Learner
 from skll.metrics import SCORERS
 
+from . import HAS_RSMEXTRA
+from .utils.constants import (DEFAULTS,
+                              CHECK_FIELDS,
+                              LIST_FIELDS,
+                              BOOLEAN_FIELDS,
+                              MODEL_NAME_MAPPING,
+                              FIELD_NAME_MAPPING,
+                              ID_FIELDS)
+
+from .utils.files import is_skll_model, parse_json_with_comments
+
+
 if HAS_RSMEXTRA:
     from rsmextra.settings import (default_feature_subset_file, # noqa
                                    default_feature_sign)

rsmtool/modeler.py

@@ -24,12 +24,12 @@
 from sklearn.linear_model import LassoCV
 from skll import FeatureSet, Learner
 
-from rsmtool.analyzer import Analyzer
-from rsmtool.utils import compute_expected_scores_from_model, is_skll_model
-from rsmtool.preprocessor import FeaturePreprocessor
-
-from rsmtool.container import DataContainer
-from rsmtool.writer import DataWriter
+from .analyzer import Analyzer
+from .container import DataContainer
+from .utils.files import is_skll_model
+from .utils.metrics import compute_expected_scores_from_model
+from .preprocessor import FeaturePreprocessor
+from .writer import DataWriter
 
 with warnings.catch_warnings():
     warnings.filterwarnings('ignore', category=FutureWarning)

rsmtool/notebooks/comparison/header.ipynb

@@ -53,12 +53,12 @@
     "from rsmtool.reader import DataReader\n",
     "from rsmtool.writer import DataWriter\n",
     "\n",
-    "from rsmtool.utils import (float_format_func,\n",
-    "                           int_or_float_format_func,\n",
-    "                           parse_json_with_comments,\n",
-    "                           bold_highlighter,\n",
-    "                           color_highlighter,\n",
-    "                           show_thumbnail)\n",
+    "from rsmtool.utils.files import parse_json_with_comments\n",
+    "from rsmtool.utils.notebook import (float_format_func,\n",
+    "                                    int_or_float_format_func,\n",
+    "                                    bold_highlighter,\n",
+    "                                    color_highlighter,\n",
+    "                                    show_thumbnail)\n",
     "\n",
     "from rsmtool.version import VERSION as rsmtool_version"
    ]

rsmtool/notebooks/header.ipynb

@@ -48,13 +48,13 @@
     "from IPython.display import display, HTML, Image, Javascript, Markdown, SVG\n",
     "from rsmtool.reader import DataReader\n",
     "from rsmtool.writer import DataWriter\n",
-    "from rsmtool.utils import (float_format_func,\n",
-    "                           int_or_float_format_func,\n",
-    "                           compute_subgroup_plot_params,\n",
-    "                           parse_json_with_comments,\n",
-    "                           bold_highlighter,\n",
-    "                           color_highlighter,\n",
-    "                           show_thumbnail)\n",
+    "from rsmtool.utils.files import parse_json_with_comments\n",
+    "from rsmtool.utils.notebook import (float_format_func,\n",
+    "                                    int_or_float_format_func,\n",
+    "                                    compute_subgroup_plot_params,\n",
+    "                                    bold_highlighter,\n",
+    "                                    color_highlighter,\n",
+    "                                    show_thumbnail)\n",
     "\n",
     "from rsmtool.fairness_utils import (get_fairness_analyses,\n",
     "                                    write_fairness_results)\n",

rsmtool/notebooks/intermediate_file_paths.ipynb

@@ -20,7 +20,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from rsmtool.utils import show_files"
+    "from rsmtool.utils.notebook import show_files"
    ]
   },
   {

rsmtool/notebooks/summary/header.ipynb

@@ -49,13 +49,13 @@
     "from IPython import sys_info\n",
     "from IPython.display import display, HTML, Image, Javascript, Markdown, SVG\n",
     "\n",
-    "from rsmtool.utils import (float_format_func,\n",
-    "                           get_output_directory_extension,\n",
-    "                           int_or_float_format_func,\n",
-    "                           parse_json_with_comments,\n",
-    "                           bold_highlighter,\n",
-    "                           color_highlighter,\n",
-    "                           show_thumbnail)\n",
+    "from rsmtool.utils.files import (get_output_directory_extension,\n",
+    "                                 parse_json_with_comments)\n",
+    "from rsmtool.utils.notebook import (float_format_func,\n",
+    "                                    int_or_float_format_func,\n",
+    "                                    bold_highlighter,\n",
+    "                                    color_highlighter,\n",
+    "                                    show_thumbnail)\n",
     "\n",
     "from rsmtool.reader import DataReader\n",
     "from rsmtool.writer import DataWriter\n",

rsmtool/notebooks/summary/intermediate_file_paths.ipynb

@@ -22,7 +22,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from rsmtool.utils import show_files"
+    "from rsmtool.utils.notebook import show_files"
    ]
   },
   {

rsmtool/preprocessor.py

@@ -19,12 +19,12 @@
 
 from numpy.random import RandomState
 
-from rsmtool.reader import DataReader
-from rsmtool.container import DataContainer
-from rsmtool.reporter import Reporter
-from rsmtool.transformer import FeatureTransformer
-from rsmtool.utils import convert_to_float
-from rsmtool.utils import is_built_in_model, is_skll_model
+from .container import DataContainer
+from .reader import DataReader
+from .reporter import Reporter
+from .transformer import FeatureTransformer
+from .utils.conversion import convert_to_float
+from .utils.files import is_built_in_model, is_skll_model
 
 
 class FeatureSubsetProcessor:

rsmtool/reader.py

@@ -19,7 +19,7 @@
 
 import pandas as pd
 
-from rsmtool.container import DataContainer
+from .container import DataContainer
 
 
 def read_jsonlines(filename, converters=None):

rsmtool/reporter.py

@@ -22,11 +22,11 @@
 from traitlets.config import Config
 from nbconvert.exporters import HTMLExporter
 
-from rsmtool import HAS_RSMEXTRA
-from rsmtool.reader import DataReader
+from . import HAS_RSMEXTRA
+from .reader import DataReader
 
 if HAS_RSMEXTRA:
-    from rsmextra.settings import (special_section_list_rsmtool,
+    from rsmextra.settings import (special_section_list_rsmtool, # noqa
                                    special_section_list_rsmeval,
                                    special_section_list_rsmcompare,
                                    special_section_list_rsmsummarize,