umami-preprocessing 0.2.5__tar.gz → 0.2.6__tar.gz

umami_preprocessing-0.2.6/LICENSE

@@ -0,0 +1,201 @@
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{umami_preprocessing-0.2.5 → umami_preprocessing-0.2.6}/PKG-INFO

@@ -1,14 +1,15 @@
 Metadata-Version: 2.4
 Name: umami-preprocessing
-Version: 0.2.5
+Version: 0.2.6
 Summary: Preprocessing for jet tagging
 License: MIT
 Project-URL: Homepage, https://github.com/umami-hep/umami-preprocessing
 Requires-Python: <3.12,>=3.8
 Description-Content-Type: text/markdown
-Requires-Dist: atlas-ftag-tools==0.2.14
+License-File: LICENSE
+Requires-Dist: atlas-ftag-tools==0.2.15
 Requires-Dist: dotmap==1.3.30
-Requires-Dist: puma-hep==0.4.9
+Requires-Dist: puma-hep==0.4.10
 Requires-Dist: pyyaml-include==1.3
 Requires-Dist: PyYAML>=6.0.1
 Requires-Dist: rich==12.6.0
@@ -20,6 +21,7 @@ Requires-Dist: pytest-cov>=4.0.0; extra == "dev"
 Requires-Dist: pytest-mock==3.11.1; extra == "dev"
 Requires-Dist: pytest>=7.2.2; extra == "dev"
 Requires-Dist: ruff==0.6.2; extra == "dev"
+Dynamic: license-file
 
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
 [![codecov](https://codecov.io/gh/umami-hep/umami-preprocessing/graph/badge.svg?token=K8MJI20UZO)](https://codecov.io/gh/umami-hep/umami-preprocessing)

{umami_preprocessing-0.2.5 → umami_preprocessing-0.2.6}/pyproject.toml

@@ -7,9 +7,9 @@ readme = "README.md"
 requires-python = "<3.12,>=3.8"
 
 dependencies = [
-  "atlas-ftag-tools==0.2.14",
+  "atlas-ftag-tools==0.2.15",
   "dotmap==1.3.30",
-  "puma-hep==0.4.9",
+  "puma-hep==0.4.10",
   "pyyaml-include==1.3",
   "PyYAML>=6.0.1",
   "rich==12.6.0",
@@ -31,9 +31,10 @@ dev = [
 
 [project.scripts]
 preprocess = "upp.main:main"
+check_input_samples = "upp.utils.check_input_samples:main"
 
 [tool.setuptools]
-packages = ["upp", "upp.classes", "upp.stages"]
+packages = ["upp", "upp.classes", "upp.stages", "upp.utils"]
 include-package-data = true
 
 [tool.setuptools.dynamic]
@@ -45,7 +46,7 @@ build-backend = "setuptools.build_meta"
 
 [tool.ruff]
 lint.select = ["I", "E", "W", "F", "B", "UP", "ARG", "SIM", "TID", "RUF", "D2", "D3", "D4"]
-lint.ignore = ["D211", "D213", "RUF005"]
+lint.ignore = ["RUF005"]
 line-length = 100
 
 [tool.ruff.lint.isort]

{umami_preprocessing-0.2.5 → umami_preprocessing-0.2.6}/umami_preprocessing.egg-info/PKG-INFO

@@ -1,14 +1,15 @@
 Metadata-Version: 2.4
 Name: umami-preprocessing
-Version: 0.2.5
+Version: 0.2.6
 Summary: Preprocessing for jet tagging
 License: MIT
 Project-URL: Homepage, https://github.com/umami-hep/umami-preprocessing
 Requires-Python: <3.12,>=3.8
 Description-Content-Type: text/markdown
-Requires-Dist: atlas-ftag-tools==0.2.14
+License-File: LICENSE
+Requires-Dist: atlas-ftag-tools==0.2.15
 Requires-Dist: dotmap==1.3.30
-Requires-Dist: puma-hep==0.4.9
+Requires-Dist: puma-hep==0.4.10
 Requires-Dist: pyyaml-include==1.3
 Requires-Dist: PyYAML>=6.0.1
 Requires-Dist: rich==12.6.0
@@ -20,6 +21,7 @@ Requires-Dist: pytest-cov>=4.0.0; extra == "dev"
 Requires-Dist: pytest-mock==3.11.1; extra == "dev"
 Requires-Dist: pytest>=7.2.2; extra == "dev"
 Requires-Dist: ruff==0.6.2; extra == "dev"
+Dynamic: license-file
 
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
 [![codecov](https://codecov.io/gh/umami-hep/umami-preprocessing/graph/badge.svg?token=K8MJI20UZO)](https://codecov.io/gh/umami-hep/umami-preprocessing)

{umami_preprocessing-0.2.5 → umami_preprocessing-0.2.6}/umami_preprocessing.egg-info/SOURCES.txt

@@ -1,3 +1,5 @@
+LICENSE
+MANIFEST.in
 README.md
 pyproject.toml
 umami_preprocessing.egg-info/PKG-INFO
@@ -7,9 +9,7 @@ umami_preprocessing.egg-info/entry_points.txt
 umami_preprocessing.egg-info/requires.txt
 umami_preprocessing.egg-info/top_level.txt
 upp/__init__.py
-upp/logger.py
 upp/main.py
-upp/utils.py
 upp/classes/__init__.py
 upp/classes/components.py
 upp/classes/preprocessing_config.py
@@ -22,4 +22,8 @@ upp/stages/interpolation.py
 upp/stages/merging.py
 upp/stages/normalisation.py
 upp/stages/plot.py
-upp/stages/resampling.py
+upp/stages/resampling.py
+upp/utils/__init__.py
+upp/utils/check_input_samples.py
+upp/utils/logger.py
+upp/utils/tools.py

umami_preprocessing-0.2.6/umami_preprocessing.egg-info/dependency_links.txt

@@ -0,0 +1 @@
+

umami_preprocessing-0.2.6/umami_preprocessing.egg-info/entry_points.txt

@@ -0,0 +1,3 @@
+[console_scripts]
+check_input_samples = upp.utils.check_input_samples:main
+preprocess = upp.main:main

{umami_preprocessing-0.2.5 → umami_preprocessing-0.2.6}/umami_preprocessing.egg-info/requires.txt

@@ -1,6 +1,6 @@
-atlas-ftag-tools==0.2.14
+atlas-ftag-tools==0.2.15
 dotmap==1.3.30
-puma-hep==0.4.9
+puma-hep==0.4.10
 pyyaml-include==1.3
 PyYAML>=6.0.1
 rich==12.6.0

umami_preprocessing-0.2.6/upp/__init__.py

@@ -0,0 +1,15 @@
+"""UPP: Umami PreProcessing."""
+
+from __future__ import annotations
+
+__version__ = "v0.2.6"
+
+from . import classes, stages, utils
+from .main import run_pp
+
+__all__ = [
+    "classes",
+    "run_pp",
+    "stages",
+    "utils",
+]

umami_preprocessing-0.2.6/upp/classes/__init__.py

@@ -0,0 +1,18 @@
+"""Classes from Umami-Preprocessing."""
+
+from __future__ import annotations
+
+from upp.classes.components import Component, Components
+from upp.classes.preprocessing_config import PreprocessingConfig
+from upp.classes.region import Region
+from upp.classes.resampling_config import ResamplingConfig
+from upp.classes.variable_config import VariableConfig
+
+__all__ = [
+    "Component",
+    "Components",
+    "PreprocessingConfig",
+    "Region",
+    "ResamplingConfig",
+    "VariableConfig",
+]

{umami_preprocessing-0.2.5 → umami_preprocessing-0.2.6}/upp/classes/components.py

@@ -25,7 +25,7 @@ class Component:
     It stores the needed information about the component and
     allow for certain features in terms of resampling.
 
-    Parameters
+    Attributes
     ----------
     region : Region
         Region instance of the region for which this instance is setup
@@ -78,8 +78,10 @@ class Component:
             Batch size that is used for loading from file
         jets_name : str, optional
             Name of the group in which the jets are stored, by default "jets"
-        fname : Path | str | list[Path  |  str], optional
+        fname : Path | str | list[Path | str] | None, optional
             Filename of the file(s) from which the jets are loaded, by default None
+        **kwargs
+            Additional kwargs passed to the H5Reader
         """
         if fname is None:
             fname = self.sample.path
@@ -292,13 +294,6 @@ class Components:
     """Components class to store and manage multiple Component instances."""
 
     def __init__(self, components: Components | list):
-        """Init Components instance.
-
-        Parameters
-        ----------
-        components : Components
-            List of all Component instances that are to be managed.
-        """
         self.components = components
 
     @classmethod
@@ -423,7 +418,7 @@ class Components:
 
         Returns
         -------
-        list[str]
+        list[Label]
             List of flavours
         """
         return list(dict.fromkeys(c.flavour for c in self))
@@ -434,8 +429,8 @@ class Components:
 
         Returns
         -------
-        list
-            List with all the cuts
+        Cuts
+            Cuts object with all cuts
         """
         return sum((c.cuts for c in self), Cuts.from_list([]))
 

{umami_preprocessing-0.2.5 → umami_preprocessing-0.2.6}/upp/classes/preprocessing_config.py

@@ -6,11 +6,11 @@ import logging as log
 from copy import copy
 from dataclasses import dataclass
 from pathlib import Path
-from typing import Literal
+from typing import Any, Literal
 
 import yaml
 from dotmap import DotMap
-from ftag import Cuts
+from ftag import Cuts, Extended_Flavours, Flavours
 from ftag.git_check import get_git_hash
 from ftag.labels import LabelContainer
 from ftag.track_selector import TrackSelector
@@ -21,7 +21,7 @@ from upp import __version__
 from upp.classes.components import Components
 from upp.classes.resampling_config import ResamplingConfig
 from upp.classes.variable_config import VariableConfig
-from upp.utils import path_append
+from upp.utils.tools import path_append
 
 # support inclusion of yaml files in the config dir
 YamlIncludeConstructor.add_to_loader_class(
@@ -51,7 +51,7 @@ class PreprocessingConfig:
         ntuple_dir: h5-inputs # resolved path: /my/stuff/h5-inputs/
     ```
 
-    Parameters
+    Attributes
     ----------
     config_path : Path
         Path to the config yaml file that is used. Does not need to be set in config.
@@ -82,20 +82,20 @@ class PreprocessingConfig:
     num_jets_estimate : int, optional
         Any of the further three arguments that are not specified will default to this value
         Is equal to 1_000_000 by default.
-    num_jets_estimate_available : int, optional
+    num_jets_estimate_available : int | None, optional
         A sabsample taken from the whole sample to estimate the number of jets after the cuts.
         Please keep this number high in order to not get poisson error of more then 5%.
         If time allows you can use -1 to get a precise number of jets and not just an estimate
         although it will be slow for large datasets. Is equal to num_jets_estimate by default.
-    num_jets_estimate_hist : int, optional
+    num_jets_estimate_hist : int | None, optional
         Number of jets of each flavour that are used to construct histograms for probability
         density function estimation. Larger numbers give a better quality estmate of the pdfs.
         Is equal to num_jets_estimate by default.
-    num_jets_estimate_norm : int, optional
+    num_jets_estimate_norm : int | None, optional
         Number of jets of each flavour that are used to estimate shifting and scaling during
         normalisation step. Larger numbers give a better quality estmates.
         Is equal to num_jets_estimate by default.
-    num_jets_estimate_plotting : int, optional
+    num_jets_estimate_plotting : int | None, optional
         Number of jets of each flavour used for plotting the initial and the final resampling
         variable distributions. Larger numbers give a better estimate of the full distributions.
         Is equal to num_jets_estimate by default.
@@ -103,6 +103,19 @@ class PreprocessingConfig:
         Merge the test samples of the different processes into one file. By default False.
     jets_name : str, optional
         Name of the jets dataset in the input file. By default "jets".
+    flavour_config : Path | None, optional
+        Flavour config yaml file which is to be used. By default None
+    flavour_category : str, optional
+        Flavour categories that are to be used. By default, the "standard" (non-extended)
+        labels are loaded. The extended labels can be used by setting this value to "extended".
+        By default "standard". To use this option, flavour_config must be None.
+    num_jets_per_output_file : int | None, optional
+        Number of jets per final output file. If the number of total jets is larger
+        than this number, the final h5 output files are splitted in multiple smaller
+        files with this number of jets per file. By default None which produces one
+        huge output file.
+    skip_config_copy : bool, optional
+        Decide, if the config copying is skipped or not. By default False
     """
 
     config_path: Path
@@ -122,7 +135,9 @@ class PreprocessingConfig:
     merge_test_samples: bool = False
     jets_name: str = "jets"
     flavour_config: Path | None = None
+    flavour_category: str = "standard"
     num_jets_per_output_file: int | None = None
+    skip_config_copy: bool = False
 
     def __post_init__(self):
         # postprocess paths
@@ -143,7 +158,25 @@ class PreprocessingConfig:
             raise FileNotFoundError(f"Path {self.ntuple_dir} does not exist")
         self.components_dir = self.components_dir / self.split
         self.out_fname = self.out_dir / path_append(self.out_fname, self.split)
-        self.flavour_cont = LabelContainer.from_yaml(self.flavour_config)
+
+        # Define the content of the flavour label container
+        if self.flavour_config:
+            self.flavour_cont = LabelContainer.from_yaml(
+                yaml_path=self.flavour_config,
+            )
+
+        elif self.flavour_category == "standard":
+            self.flavour_cont = Flavours
+
+        elif self.flavour_category == "extended":
+            self.flavour_cont = Extended_Flavours
+
+        else:
+            raise ValueError(
+                f"flavour_category {self.flavour_category} is not supported in the default "
+                "flavours! If you want to use your own flavour config yaml file, please "
+                "provide flavour_config!"
+            )
 
         # configure classes
         sampl_cfg = copy(self.config["resampling"])
@@ -177,15 +210,22 @@ class PreprocessingConfig:
         self.config["upp_hash"] = self.git_hash
 
         # copy config
-        self.copy_config()
+        if not self.skip_config_copy:
+            self.copy_config()
 
     @classmethod
-    def from_file(cls, config_path: Path, split: Split):
+    def from_file(cls, config_path: Path, split: Split, skip_config_copy: bool = False):
         if not config_path.exists():
             raise FileNotFoundError(f"{config_path} does not exist - check your --config arg")
         with open(config_path) as file:
             config = yaml.safe_load(file)
-            return cls(config_path, split, config, **config["global"])
+            return cls(
+                config_path=config_path,
+                split=split,
+                config=config,
+                skip_config_copy=skip_config_copy,
+                **config["global"],
+            )
 
     def get_path(self, path: Path):
         return path if path.is_absolute() else (self.base_dir / path).absolute()
@@ -204,24 +244,19 @@ class PreprocessingConfig:
                 cuts_list.append([resampling_var, "<", cfg["bins"][-1][1]])
         return Cuts.from_list(cuts_list)
 
-    def copy_config(self, suffix=None, out_dir=None):
-        """
-        Copy the configuration file to a new location with an optional suffix and output directory.
+    def copy_config(self, suffix: str | None = None, out_dir: str | Path | None = None) -> None:
+        """Copy the configuration file to a new location with an optional suffix and out directory.
 
         Parameters
         ----------
-        suffix : str or None, optional
+        suffix : str | None, optional
             A suffix to append to the configuration file name. If None, the current
             `self.split` value will be used as the suffix (default is None).
 
-        out_dir : str or None, optional
+        out_dir : str | Path | None, optional
             The output directory where the copied configuration file will be saved.
             If None, the current `self.out_dir` value will be used as the output directory
             (default is None).
-
-        Returns
-        -------
-        None
         """
         if suffix is None:
             suffix = self.split
@@ -233,11 +268,7 @@ class PreprocessingConfig:
         with open(copy_config_path, "w") as file:
             yaml.dump(self.config, file, sort_keys=False)
 
-    # following aliases and functins are needed to mimic the umami config structure and behaviour
-    # so that --scaling --write and traing steps from umami are compatible with this config
-    copy_to_out_dir = copy_config
-
-    def get_umami_general(self):
+    def get_umami_general(self) -> DotMap:
         """
         Return the arguments to be fed into GeneralSettings class in umami.
 
@@ -260,13 +291,12 @@ class PreprocessingConfig:
             _dynamic=False,
         )
 
-    def mimic_umami_config(self, general):
-        """
-        Make the config mimic the umami config structure and behaviour.
+    def mimic_umami_config(self, general: Any) -> PreprocessingConfig:
+        """Make the config mimic the umami config structure and behaviour.
 
         Parameters
         ----------
-        general : umami.preprocessing_tools.configuration.GeneralSettings
+        general : Any
             first initialised in umami.preprocessing_tools.configuration.Configuration
             class in umami using get_umami_general() for arguments
             then feed it into mimic_umami_config() to get the rest of the config
@@ -274,7 +304,8 @@ class PreprocessingConfig:
 
         Returns
         -------
-        self : upp.classes.preprocessing_config.PreprocessingConfig
+        PreprocessingConfig
+            Mimicing PreprocessingConfig instance
         """
         self.general = general
         self.sampling = DotMap(self.config["umami"]["sampling"], _dynamic=False)
@@ -289,9 +320,8 @@ class PreprocessingConfig:
             self.general.convert_to_tfrecord = self.config["umami"]["convert_to_tfrecord"]
         return self
 
-    def get_file_name(self, option, **_):
-        """
-        Mimics the 'get_file_name()' function in PreprocessingConfig class in umami.
+    def get_file_name(self, option: str) -> Path | str:
+        """Mimics the 'get_file_name()' function in PreprocessingConfig class in umami.
 
         Parameters
         ----------
@@ -302,18 +332,15 @@ class PreprocessingConfig:
             original output file name with '_resampled_scaled_shuffled' appended.
             This option is used to create a new file name.
 
-        use_val : bool, optional
-            Currently not in use (default is False).
-
         Returns
         -------
-        str
+        Path | str
             The resulting file name based on the specified 'option'.
 
         Raises
         ------
         ValueError
-            If 'option' is not one of the recognized options.
+            If the option value is not supported
         """
         if option == "resampled":
             return self.out_fname
@@ -325,3 +352,8 @@ class PreprocessingConfig:
                 + "_resampled_scaled_shuffled"
                 + self.out_fname.suffix
             )
+        else:
+            raise ValueError(
+                f"Option value {option} is not supported! "
+                "Only resampled and resampled_scaled_shuffled are."
+            )