Unify showdiff reports

docs/conf.py

@@ -41,8 +41,15 @@
     "sphinx.ext.todo",
     "sphinx.ext.intersphinx",
     "sphinx_click.ext",
+    "sphinx_autodoc_typehints",
 ]
 
+# Add intersphinx mappings for libraries.
+intersphinx_mapping = {
+    "python": ("https://docs.python.org/3", None),
+    "pandas": ("https://pandas.pydata.org/docs", None),
+}
+
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ["_templates"]
 
@@ -185,7 +192,13 @@
     ),
 ]
 
-nitpick_ignore = [("py:class", "ModelRecord"), ("py:class", "pandas.DataFrame")]
+nitpick_ignore = [
+    ("py:class", "perun.utils.structs.common_structs.ModelRecord"),
+    ("py:class", "perun.utils.common.common_kit.Aggregations"),
+    ("py:class", "TempTextIO"),
+    ("py:class", "polars.lazyframe.frame.LazyFrame"),
+    ("py:class", "pandas.core.frame.DataFrame"), # Needed only for Python 3.10
+]
 
 
 def doctree_read_handler(_, doctree):

docs/config.rst

@@ -207,7 +207,7 @@ List of Supported Options
     multi-key sort semantics by providing a list of the following attributes specified by the
     class attribute ``ProfileInfo.valid_attributes``:
 
-.. currentmodule:: perun.profile.helpers
+.. currentmodule:: perun.profiles.native.helpers
 .. autoattribute:: ProfileInfo.valid_attributes
 
 .. confkey:: format.sort_profiles_order

docs/profile.rst

@@ -355,9 +355,9 @@ to the look-up table should greatly reduce the size of profiles.
 Profile API
 -----------
 
-.. automodule:: perun.profile.helpers
+.. automodule:: perun.profiles.native.helpers
 
-.. automodule:: perun.profile.factory
+.. automodule:: perun.profiles.native.factory
 
 .. autoclass:: Profile
    :members: all_resources, all_snapshots, all_models, all_filtered_models
@@ -367,20 +367,46 @@ Profile API
 Profile Conversions API
 -----------------------
 
-.. automodule:: perun.profile.convert
+.. automodule:: perun.profiles.conversions.elk_native
+
+.. autofunction:: import_elk_from_json
+
+.. automodule:: perun.profiles.conversions.folded_polars
+
+.. autofunction:: folded_profiles_to_polars_lf
+
+.. automodule:: perun.profiles.conversions.native_folded
+
+.. autofunction:: native_to_folded
+
+.. automodule:: perun.profiles.conversions.native_pandas
 
 .. autofunction:: resources_to_pandas_dataframe
 
-.. autofunction:: to_flame_graph_format
+.. autofunction:: models_to_pandas_dataframe
+
+.. automodule:: perun.profiles.conversions.native_polars
+
+.. autofunction:: native_to_polars_lf
+
+.. automodule:: perun.profiles.conversions.perf_native
+
+.. autofunction:: import_perf_from_record
+
+.. autofunction:: import_perf_from_script
 
-.. autofunction:: plot_data_from_coefficients_of
+.. autofunction:: import_perf_from_stack
+
+.. automodule:: perun.profiles.conversions.polars_folded
+
+.. autofunction:: store_polars_as_folded_profile
 
 .. _profile-query-api:
 
 Profile Query API
 -----------------
 
-.. automodule:: perun.profile.query
+.. automodule:: perun.profiles.native.query
 
 .. autofunction:: all_items_of
 
@@ -391,3 +417,18 @@ Profile Query API
 .. autofunction:: all_key_values_of
 
 .. autofunction:: unique_model_values_of
+
+Helper Structures
+-----------------
+
+.. automodule:: perun.profiles.structs
+
+.. autoclass:: PostprocessParameters
+
+.. autoclass:: ProfileFeatures
+
+.. automodule:: perun.profiles.polars.structs
+
+.. autoclass:: FunctionMaps
+
+.. autoclass:: PolarsTraceProfile

perun/check/detection_kit.py

@@ -19,7 +19,7 @@
 # Perun Imports
 from perun.check.methods import linear_regression, polynomial_regression, fast_check
 from perun.postprocess.regression_analysis import regression_models
-from perun.profile import query
+from perun.profiles.native import query
 from perun.utils.common import common_kit
 from perun.utils.structs.common_structs import (
     PerformanceChange,
@@ -29,7 +29,7 @@
 )
 
 if TYPE_CHECKING:
-    from perun.profile.factory import Profile
+    from perun.profiles.native import Profile
 
 
 SAMPLES: int = 1000

perun/check/factory.py

@@ -14,8 +14,6 @@
 # Third-Party Imports
 
 # Perun Imports
-from perun.logic import config, pcs, runner, store
-from perun.select.abstract_base_selection import AbstractBaseSelection
 from perun.check.methods import (
     average_amount_threshold,
     best_model_order_equality,
@@ -26,22 +24,24 @@
     local_statistics,
     polynomial_regression,
 )
+from perun.logic import config, pcs, runner, store
+from perun.profiles.native import helpers as profile_helpers
+from perun.selection.abstract_base_selection import AbstractBaseSelection
+import perun.selection.factory as select
 from perun.utils import decorators, log
+from perun.utils.common import common_kit
+from perun.utils.exceptions import UnsupportedModuleException
 from perun.utils.structs.common_structs import (
     DetectionChangeResult,
     DegradationInfo,
     PerformanceChange,
     MinorVersion,
     ModelRecord,
 )
-from perun.utils.common import common_kit
-from perun.utils.exceptions import UnsupportedModuleException
-import perun.profile.helpers as profiles
-import perun.select.factory as select
 
 if TYPE_CHECKING:
-    from perun.profile.factory import Profile
-    from perun.profile.helpers import ProfileInfo
+    from perun.profiles.native import Profile
+    from perun.profiles.native.helpers import ProfileInfo
 
 # Minimal confidence rate from both models to perform the detection
 _MIN_CONFIDENCE_RATE = 0.15
@@ -71,7 +71,7 @@ def profiles_to_queue(
     :param minor_version: minor version for which we are retrieving the profile queue
     :returns: dictionary mapping configurations of profiles to the actual profiles
     """
-    minor_version_profiles = profiles.load_list_for_minor_version(minor_version)
+    minor_version_profiles = profile_helpers.load_list_for_minor_version(minor_version)
     return {profile.config_tuple: profile for profile in minor_version_profiles}
 
 
@@ -133,7 +133,7 @@ def degradation_in_minor(
     for target_config, target_profile_info in profile_queue.items():
         # Iterate through the profiles and check degradation between those of same configuration
         target_prof = store.load_profile_from_file(target_profile_info.realpath, False, True)
-        cmdstr = profiles.config_tuple_to_cmdstr(target_config)
+        cmdstr = profile_helpers.config_tuple_to_cmdstr(target_config)
 
         for baseline_info, baseline_profile_info in selection.get_profiles(
             minor_version_info, target_prof
@@ -262,8 +262,8 @@ def degradation_between_files(
     """
     log.major_info("Checking two compatible profiles")
     # First check if the configurations are compatible
-    baseline_config = profiles.to_config_tuple(baseline_file)
-    target_config = profiles.to_config_tuple(target_file)
+    baseline_config = profile_helpers.to_config_tuple(baseline_file)
+    target_config = profile_helpers.to_config_tuple(target_file)
     target_minor_version = target_file.get("origin", minor_version)
     if not force:
         if baseline_config != target_config:
@@ -276,7 +276,7 @@ def degradation_between_files(
     for deg in degradation_between_profiles(baseline_file, target_file, models_strategy):
         if deg.result != PerformanceChange.NoChange:
             detected_changes.append(
-                (deg, profiles.config_tuple_to_cmdstr(baseline_config), target_minor_version)
+                (deg, profile_helpers.config_tuple_to_cmdstr(baseline_config), target_minor_version)
             )
 
     # Store the detected changes for given minor version

perun/check/methods/abstract_base_checker.py

@@ -15,7 +15,7 @@
 
 # Perun Imports
 if TYPE_CHECKING:
-    from perun.profile.factory import Profile
+    from perun.profiles.native import Profile
     from perun.utils.structs.common_structs import DegradationInfo
 
 

perun/check/methods/average_amount_threshold.py

@@ -44,12 +44,13 @@
 
 # Perun Imports
 from perun.check.methods.abstract_base_checker import AbstractBaseChecker
-from perun.profile import convert
+from perun.profiles.conversions import native_pandas
 from perun.utils.common import common_kit
 from perun.utils.structs.common_structs import DegradationInfo, PerformanceChange
 
 if TYPE_CHECKING:
-    from perun.profile.factory import Profile
+    from perun.profiles.native import Profile
+
 
 DEGRADATION_THRESHOLD = 2.0
 OPTIMIZATION_THRESHOLD = 0.5
@@ -61,7 +62,7 @@ def get_averages(profile: Profile) -> dict[str, float]:
     :param profile: dictionary representation of profile
     :returns: dictionary with averages for all uids
     """
-    data_frame = convert.resources_to_pandas_dataframe(profile)
+    data_frame = native_pandas.resources_to_pandas_dataframe(profile)
     # Short fix for non-measured (static) profiles
     if "amount" not in data_frame:
         data_frame["amount"] = 0

perun/check/methods/best_model_order_equality.py

@@ -53,7 +53,7 @@
 from perun.utils.structs.common_structs import DegradationInfo, PerformanceChange
 
 if TYPE_CHECKING:
-    from perun.profile.factory import Profile
+    from perun.profiles.native import Profile
 
 
 CONFIDENCE_THRESHOLD = 0.9

perun/check/methods/exclusive_time_outliers.py

@@ -67,7 +67,7 @@
 from __future__ import annotations
 
 # Standard Imports
-from typing import Optional, Iterable, Any, TYPE_CHECKING
+from typing import Any, Iterable, Optional, TYPE_CHECKING
 
 # Third-Party Imports
 import difflib
@@ -78,11 +78,12 @@
 # Perun Imports
 from perun.check.methods.abstract_base_checker import AbstractBaseChecker
 from perun.logic import config
-from perun.profile import convert
+from perun.profiles.conversions import native_pandas
 from perun.utils.structs.common_structs import DegradationInfo, PerformanceChange
 
 if TYPE_CHECKING:
-    from perun.profile.factory import Profile
+    from perun.profiles.native import Profile
+
 
 OldLocMap = dict[str, str]
 NewLocMap = dict[str, str]
@@ -366,7 +367,7 @@ def _prepare_profile(self, profile: Profile) -> pd.DataFrame:
         # Obtain "Uid (function name), exclusive time, location" DataFrame
         # and sum the exclusive times of individual functions
         df = (
-            convert.resources_to_pandas_dataframe(profile)[columns]
+            native_pandas.resources_to_pandas_dataframe(profile)[columns]
             .groupby(["uid", "location"])
             .sum()
             .reset_index()

perun/check/methods/fast_check.py

@@ -20,7 +20,7 @@
 from perun.utils.structs.common_structs import DegradationInfo, ClassificationMethod
 
 if TYPE_CHECKING:
-    from perun.profile.factory import Profile
+    from perun.profiles.native import Profile
 
 
 class FastCheck(AbstractBaseChecker):

perun/check/methods/integral_comparison.py

@@ -20,7 +20,7 @@
 from perun.utils.structs.common_structs import DegradationInfo, ModelRecord, DetectionChangeResult
 
 if TYPE_CHECKING:
-    from perun.profile.factory import Profile
+    from perun.profiles.native import Profile
 
 
 # acceptable value of relative error between compared profiles to detect NO_CHANGE state

perun/check/methods/linear_regression.py

@@ -24,7 +24,7 @@
     import numpy
     import numpy.typing as npt
 
-    from perun.profile.factory import Profile
+    from perun.profiles.native import Profile
 
 
 class LinearRegression(AbstractBaseChecker):

perun/check/methods/local_statistics.py

@@ -15,7 +15,7 @@
 # Perun Imports
 from perun import check as check
 from perun.check.methods.abstract_base_checker import AbstractBaseChecker
-from perun.profile.factory import Profile
+from perun.profiles.native import Profile
 from perun.utils.common import common_kit
 from perun.utils.structs.common_structs import DegradationInfo, ModelRecord, DetectionChangeResult
 

perun/check/methods/polynomial_regression.py

@@ -20,7 +20,7 @@
 if TYPE_CHECKING:
     import numpy.typing as npt
 
-    from perun.profile.factory import Profile
+    from perun.profiles.native import Profile
 
 THRESHOLD = 100000000
 

perun/check/nonparam_kit.py

@@ -15,7 +15,7 @@
 import perun.postprocess.regressogram.methods as rg_methods
 
 if TYPE_CHECKING:
-    from perun.profile.factory import Profile
+    from perun.profiles.native import Profile
 
 
 def classify_change(

perun/cli.py

@@ -79,7 +79,7 @@
 import perun.deltadebugging.factory as delta
 
 if TYPE_CHECKING:
-    from perun.profile.factory import Profile
+    from perun.profiles.native import Profile
 
 
 DEV_MODE = False

perun/cli_groups/check_cli.py

@@ -16,7 +16,7 @@
 from perun.utils.structs import check_structs
 
 if TYPE_CHECKING:
-    from perun.profile.factory import Profile
+    from perun.profiles.native import Profile
 
 
 @click.group("check")

perun/cli_groups/collect_cli.py

@@ -7,7 +7,7 @@
 # Perun Imports
 from perun.utils.structs import collect_structs
 from perun.utils.common import cli_kit
-from perun import profile
+from perun.profiles.native import helpers as profile_helpers
 from perun.logic import commands, config as perun_config
 
 
@@ -208,7 +208,7 @@ def collect(ctx: click.Context, **kwargs: Any) -> None:
     ``perun run job --help``.
     """
     commands.try_init()
-    kwargs["profile_path"] = profile.ProfilePath(
+    kwargs["profile_path"] = profile_helpers.ProfilePath(
         kwargs.get("profile_name"), kwargs.get("profile_dir")
     )
     ctx.obj = kwargs