Read Coco Data format #9

Dinu23 · 2025-09-25T09:15:10Z

No description provided.

Copilot

Pull Request Overview

This PR adds support for reading COCO (Comparing Continuous Optimizers) data format alongside the existing JSON format support. The changes enable the inspector to parse and load COCO .info files and their associated data files.

Adds COCO data format parsing and loading capabilities
Extends file discovery to include .info files in addition to JSON files
Implements dedicated methods for handling COCO-specific data structures and file formats

Reviewed Changes

Copilot reviewed 3 out of 5 changed files in this pull request and generated 8 comments.

File	Description
src/iohinspector/manager.py	Adds COCO file discovery, parsing methods, and loading logic with bug fixes for attribute names
src/iohinspector/data.py	Implements COCO text format parsing, data loading methods, and header processing utilities
pyproject.toml	Updates version and pins moocore dependency to specific version

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Copilot · 2025-09-25T09:17:25Z

src/iohinspector/data.py

@@ -1,3 +1,4 @@
+from email import header


This import appears to be accidentally added and is unused. The email module's header is unrelated to the header processing being done in this file.

Suggested change

from email import header

Copilot · 2025-09-25T09:17:26Z

src/iohinspector/manager.py

                for run in scen.runs:
                    if run.instance not in iids:
-                        iids.append(run.instancem)
+                        iids.append(run.instance)


Fixed typo from 'run.instancem' to 'run.instance' - this was a bug fix.

Copilot · 2025-09-25T09:17:26Z

src/iohinspector/manager.py

+            raise FileNotFoundError(f"{coco_info_file} not found")
+
+        data_set = Dataset.from_coco_info(coco_info_file)
+        if(data_set is not None):


Unnecessary parentheses around the condition. Should be if data_set is not None:

Suggested change

if(data_set is not None):

if data_set is not None:

Copilot · 2025-09-25T09:17:26Z

src/iohinspector/data.py

+        with open(self.data_file) as f:
+            header = process_header(next(f))
+            nextline = next(f).strip().split()
+        if(len(nextline) > len(header)):


Unnecessary parentheses around the condition. Should be if len(nextline) > len(header):

Suggested change

if(len(nextline) > len(header)):

if len(nextline) > len(header):

Copilot · 2025-09-25T09:17:27Z

src/iohinspector/data.py

+        try:
+            with open(coco_info_file) as f:
+                data = f.read()
+                if( len(data.strip()) == 0):


Unnecessary parentheses and extra space around the condition. Should be if len(data.strip()) == 0:

Suggested change

if( len(data.strip()) == 0):

if len(data.strip()) == 0:

Copilot · 2025-09-25T09:17:27Z

src/iohinspector/data.py

+        if(len(algorithms) != 1):
+            raise ValueError("Multiple algorithms found in COCO text, expected one.")
+        if(len(function_ids) != 1):


Unnecessary parentheses around the conditions. Should be if len(algorithms) != 1: and if len(function_ids) != 1:

Suggested change

if(len(algorithms) != 1):

raise ValueError("Multiple algorithms found in COCO text, expected one.")

if(len(function_ids) != 1):

if len(algorithms) != 1:

raise ValueError("Multiple algorithms found in COCO text, expected one.")

if len(function_ids) != 1:

Copilot · 2025-09-25T09:17:27Z

src/iohinspector/data.py

+        if(len(algorithms) != 1):
+            raise ValueError("Multiple algorithms found in COCO text, expected one.")
+        if(len(function_ids) != 1):


Unnecessary parentheses around the conditions. Should be if len(algorithms) != 1: and if len(function_ids) != 1:

Suggested change

if(len(algorithms) != 1):

raise ValueError("Multiple algorithms found in COCO text, expected one.")

if(len(function_ids) != 1):

if len(algorithms) != 1:

raise ValueError("Multiple algorithms found in COCO text, expected one.")

if len(function_ids) != 1:

Copilot · 2025-09-25T09:17:28Z

src/iohinspector/manager.py

+        for data_set in self.data_sets: 
            for scen in data_set.scenarios:
-                df = scen.load(monotonic, data_set.function.maximization, x_values)
+                if(data_set.source =="coco"):


Unnecessary parentheses around the condition and missing space around the equality operator. Should be if data_set.source == \"coco\":

Suggested change

if(data_set.source =="coco"):

if data_set.source == "coco":

Copilot

Pull Request Overview

Copilot reviewed 3 out of 5 changed files in this pull request and generated 5 comments.

_{Tip: Customize your code reviews with copilot-instructions.md. Create the file or learn how to get started.}

Copilot · 2025-09-26T08:33:15Z

src/iohinspector/manager.py

                for run in scen.runs:
                    if run.instance not in iids:
-                        iids.append(run.instancem)
+                        iids.append(run.instance)


Fixed typo: 'instancem' was corrected to 'instance'.

Copilot · 2025-09-26T08:33:15Z

src/iohinspector/manager.py

+                if scen.dimension not in dims:
+                    dims.append(scen.dimension)


Property name 'dim' was changed to 'dimension' but this may cause issues if the Scenario class still uses 'dim' as the property name. Verify that the Scenario class has a 'dimension' property.

Suggested change

if scen.dimension not in dims:

dims.append(scen.dimension)

dim_value = getattr(scen, "dimension", getattr(scen, "dim", None))

if dim_value is not None and dim_value not in dims:

dims.append(dim_value)

Copilot · 2025-09-26T08:33:15Z

src/iohinspector/manager.py

+            raise FileNotFoundError(f"{coco_info_file} not found")
+
+        data_set = Dataset.from_coco_info(coco_info_file)
+        if(data_set is not None):


[nitpick] Unnecessary parentheses around the condition. Python style prefers 'if data_set is not None:' without parentheses.

Suggested change

if(data_set is not None):

if data_set is not None:

Copilot · 2025-09-26T08:33:16Z

src/iohinspector/data.py

+            scenarios=scenarios
+        )
+
+def process_header(line:str):


[nitpick] Missing space after colon in type annotation. Should be 'line: str' according to PEP 8.

Suggested change

def process_header(line:str):

def process_header(line: str):

Copilot · 2025-09-26T08:33:16Z

src/iohinspector/data.py


 @dataclass
 class Dataset:
+    source: str


Adding a new required field 'source' to the Dataset class is a breaking change. Consider making this field optional with a default value to maintain backward compatibility.

Suggested change

source: str

source: str = ""

Copilot

Pull Request Overview

Copilot reviewed 67 out of 461 changed files in this pull request and generated no new comments.

_{Tip: Customize your code reviews with copilot-instructions.md. Create the file or learn how to get started.}

Copilot

Pull Request Overview

Copilot reviewed 67 out of 461 changed files in this pull request and generated no new comments.

_{Tip: Customize your code reviews with copilot-instructions.md. Create the file or learn how to get started.}

Copilot

Pull Request Overview

Copilot reviewed 8 out of 9 changed files in this pull request and generated 2 comments.

_{Tip: Customize your code reviews with copilot-instructions.md. Create the file or learn how to get started.}

Copilot · 2025-09-26T13:37:54Z

tests/test_data.py

        self.assertListEqual(selection.columns, ["function_id", "data_id", "run_id", "evaluations", "raw_y"])

+    def test_process_header_handles_raw_y_and_evaluations(self):
+


[nitpick] Extra whitespace after the colon on line 126. Remove the trailing space for consistent formatting.

Suggested change

Copilot · 2025-09-26T13:37:54Z

src/iohinspector/data.py

+def process_header(line: str):
+


Add a docstring to explain the purpose of this function, its parameters, and return value. The function processes COCO header lines and transforms them into standardized column names.

Suggested change

def process_header(line: str):

def process_header(line: str):

"""

Processes a COCO header line and transforms it into standardized column names.

Parameters

----------

line : str

The header line from a COCO data file.

Returns

-------

list of str

A list of standardized column names extracted and transformed from the header line.

"""

Dinu23 added 8 commits July 28, 2025 12:31

coco

ca32fac

Merge remote-tracking branch 'origin/main' into coco-format

d39cbda

update

1c757c1

moocore update

78b5534

update coco format

3fd85e4

changes

c367359

solve data_id duplicates

4204d6d

update regex for .info file

3bfd097

Dinu23 requested review from Dvermetten and Copilot and removed request for Copilot September 25, 2025 09:15

Copilot AI reviewed Sep 25, 2025

View reviewed changes

minor fix

54706d0

Dinu23 requested a review from Copilot September 26, 2025 08:32

Copilot AI reviewed Sep 26, 2025

View reviewed changes

Dinu23 added 3 commits September 26, 2025 10:48

Merge branch 'main' into coco-format

107384c

tests coco

eea8176

tests coco

9fbdded

Dinu23 requested a review from Copilot September 26, 2025 12:59

Copilot AI reviewed Sep 26, 2025

View reviewed changes

Dinu23 requested a review from Copilot September 26, 2025 13:00

Copilot AI reviewed Sep 26, 2025

View reviewed changes

shorter test

edf7eb7

Dinu23 requested a review from Copilot September 26, 2025 13:37

Copilot AI reviewed Sep 26, 2025

View reviewed changes

Dvermetten approved these changes Sep 26, 2025

View reviewed changes

Dinu23 merged commit e0585a0 into main Sep 26, 2025
3 checks passed

jacobdenobel deleted the coco-format branch December 2, 2025 14:06

	if(len(nextline) > len(header)):
	if len(nextline) > len(header):

-                if scen.dimension not in dims:
-                    dims.append(scen.dimension)
+                dim_value = getattr(scen, "dimension", getattr(scen, "dim", None))
+                if dim_value is not None and dim_value not in dims:
+                    dims.append(dim_value)

		self.assertListEqual(selection.columns, ["function_id", "data_id", "run_id", "evaluations", "raw_y"])

		def test_process_header_handles_raw_y_and_evaluations(self):

-def process_header(line: str):
+def process_header(line: str):
+    """
+    Processes a COCO header line and transforms it into standardized column names.
+    Parameters
+    ----------
+    line : str
+        The header line from a COCO data file.
+    Returns
+    -------
+    list of str
+        A list of standardized column names extracted and transformed from the header line.
+    """

Read Coco Data format #9

Read Coco Data format #9

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Dinu23 commented Sep 25, 2025

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