Add files using upload-large-folder tool

client_secrets.json

@@ -0,0 +1 @@
+{"installed":{"client_id":"880310693118-2v0cddkb4occnc45bmji0v9pmv8nrebv.apps.googleusercontent.com","project_id":"rare-deployment-367809","auth_uri":"https://accounts.google.com/o/oauth2/auth","token_uri":"https://oauth2.googleapis.com/token","auth_provider_x509_cert_url":"https://www.googleapis.com/oauth2/v1/certs","client_secret":"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","redirect_uris":["http://localhost"]}}

gemini-gen3.py

@@ -0,0 +1,41 @@
+import os
+from dotenv import load_dotenv
+import google.generativeai as genai
+import json
+
+data = None
+with open('problmes.json', 'rt') as f:
+    data = json.load(f)
+
+problems = [d['problem'].replace('\n\n', '\n') for d in data]
+
+print(len(problems))
+print(len(problems)//50)
+
+# .envファイルの読み込み
+load_dotenv()
+
+# API-KEYの設定
+GOOGLE_API_KEY=os.getenv('GOOGLE_API_KEY')
+genai.configure(api_key=GOOGLE_API_KEY)
+gemini_pro = genai.GenerativeModel("gemini-1.5-flash")
+
+
+for i in range(len(problems)//50):
+    start = i*50
+    end = (i+1)*50
+    text_problems = '\n\n'.join(problems[start:end])
+    prompt = "以下のテキストを行ごとに日本語に翻訳して，1行ずつ空けて出力してください．ただし，LATEX文字列には変更を加えずそのまま出力してください．\n\n" + text_problems
+
+    print('prompt:\n'+ prompt + '\n\n')
+    print("total_tokens: ", gemini_pro.count_tokens(prompt))
+    response = gemini_pro.generate_content(prompt)
+    print(response.text)
+    print('----- meta data -----')
+    print(response.usage_metadata)
+    print('---------------------')
+
+    output_dir = 'gens'
+    file_name = f'gens{start}-{end}.txt'
+    with open(os.path.join(output_dir, file_name), 'wt') as f:
+        f.write(response.text)

tuning-competition-baseline/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+.static_storage/
+.media/
+local_settings.py
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+
+# weights and biases
+wandb/
+outputs/
+
+# config
+configs/base.yaml
+
+# local debugging
+pretrained_model
+tokenizer
+result
+log
+
+# data
+datasets
+
+# dependncies
+apex/
+flash-attention/
+
+# tmp dir
+tmp/

tuning-competition-baseline/.pre-commit-config.yaml

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+default_language_version:
+  python: python3.11
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+      - id: check-yaml
+      - id: check-toml
+      - id: check-added-large-files
+  - repo: https://github.com/psf/black-pre-commit-mirror
+    rev: 23.9.0
+    hooks:
+      - id: black
+  - repo: https://github.com/PyCQA/flake8
+    rev: 6.1.0
+    hooks:
+      - id: flake8
+        additional_dependencies: [Flake8-pyproject]
+  - repo: https://github.com/PyCQA/isort
+    rev: 5.12.0
+    hooks:
+      - id: isort
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.5.1
+    hooks:
+      - id: mypy
+        additional_dependencies:
+          - hydra-core==1.3.2
+          - torch==2.2.2
+          - torchmetrics==1.1.0
+          - tokenizers==0.13.3
+          - wandb==0.16.6
+          - typer==0.9.0
+          - types-PyYAML==6.0.12.11
+          - git+https://github.com/nobu-g/[email protected]
+  - repo: https://github.com/asottile/pyupgrade
+    rev: v3.10.1
+    hooks:
+      - id: pyupgrade
+        args:
+          - --py38-plus

tuning-competition-baseline/.venv/bin/Activate.ps1

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+<#
+.Synopsis
+Activate a Python virtual environment for the current PowerShell session.
+
+.Description
+Pushes the python executable for a virtual environment to the front of the
+$Env:PATH environment variable and sets the prompt to signify that you are
+in a Python virtual environment. Makes use of the command line switches as
+well as the `pyvenv.cfg` file values present in the virtual environment.
+
+.Parameter VenvDir
+Path to the directory that contains the virtual environment to activate. The
+default value for this is the parent of the directory that the Activate.ps1
+script is located within.
+
+.Parameter Prompt
+The prompt prefix to display when this virtual environment is activated. By
+default, this prompt is the name of the virtual environment folder (VenvDir)
+surrounded by parentheses and followed by a single space (ie. '(.venv) ').
+
+.Example
+Activate.ps1
+Activates the Python virtual environment that contains the Activate.ps1 script.
+
+.Example
+Activate.ps1 -Verbose
+Activates the Python virtual environment that contains the Activate.ps1 script,
+and shows extra information about the activation as it executes.
+
+.Example
+Activate.ps1 -VenvDir C:\Users\MyUser\Common\.venv
+Activates the Python virtual environment located in the specified location.
+
+.Example
+Activate.ps1 -Prompt "MyPython"
+Activates the Python virtual environment that contains the Activate.ps1 script,
+and prefixes the current prompt with the specified string (surrounded in
+parentheses) while the virtual environment is active.
+
+.Notes
+On Windows, it may be required to enable this Activate.ps1 script by setting the
+execution policy for the user. You can do this by issuing the following PowerShell
+command:
+
+PS C:\> Set-ExecutionPolicy -ExecutionPolicy RemoteSigned -Scope CurrentUser
+
+For more information on Execution Policies: 
+https://go.microsoft.com/fwlink/?LinkID=135170
+
+#>
+Param(
+    [Parameter(Mandatory = $false)]
+    [String]
+    $VenvDir,
+    [Parameter(Mandatory = $false)]
+    [String]
+    $Prompt
+)
+
+<# Function declarations --------------------------------------------------- #>
+
+<#
+.Synopsis
+Remove all shell session elements added by the Activate script, including the
+addition of the virtual environment's Python executable from the beginning of
+the PATH variable.
+
+.Parameter NonDestructive
+If present, do not remove this function from the global namespace for the
+session.
+
+#>
+function global:deactivate ([switch]$NonDestructive) {
+    # Revert to original values
+
+    # The prior prompt:
+    if (Test-Path -Path Function:_OLD_VIRTUAL_PROMPT) {
+        Copy-Item -Path Function:_OLD_VIRTUAL_PROMPT -Destination Function:prompt
+        Remove-Item -Path Function:_OLD_VIRTUAL_PROMPT
+    }
+
+    # The prior PYTHONHOME:
+    if (Test-Path -Path Env:_OLD_VIRTUAL_PYTHONHOME) {
+        Copy-Item -Path Env:_OLD_VIRTUAL_PYTHONHOME -Destination Env:PYTHONHOME
+        Remove-Item -Path Env:_OLD_VIRTUAL_PYTHONHOME
+    }
+
+    # The prior PATH:
+    if (Test-Path -Path Env:_OLD_VIRTUAL_PATH) {
+        Copy-Item -Path Env:_OLD_VIRTUAL_PATH -Destination Env:PATH
+        Remove-Item -Path Env:_OLD_VIRTUAL_PATH
+    }
+
+    # Just remove the VIRTUAL_ENV altogether:
+    if (Test-Path -Path Env:VIRTUAL_ENV) {
+        Remove-Item -Path env:VIRTUAL_ENV
+    }
+
+    # Just remove VIRTUAL_ENV_PROMPT altogether.
+    if (Test-Path -Path Env:VIRTUAL_ENV_PROMPT) {
+        Remove-Item -Path env:VIRTUAL_ENV_PROMPT
+    }
+
+    # Just remove the _PYTHON_VENV_PROMPT_PREFIX altogether:
+    if (Get-Variable -Name "_PYTHON_VENV_PROMPT_PREFIX" -ErrorAction SilentlyContinue) {
+        Remove-Variable -Name _PYTHON_VENV_PROMPT_PREFIX -Scope Global -Force
+    }
+
+    # Leave deactivate function in the global namespace if requested:
+    if (-not $NonDestructive) {
+        Remove-Item -Path function:deactivate
+    }
+}
+
+<#
+.Description
+Get-PyVenvConfig parses the values from the pyvenv.cfg file located in the
+given folder, and returns them in a map.
+
+For each line in the pyvenv.cfg file, if that line can be parsed into exactly
+two strings separated by `=` (with any amount of whitespace surrounding the =)
+then it is considered a `key = value` line. The left hand string is the key,
+the right hand is the value.
+
+If the value starts with a `'` or a `"` then the first and last character is
+stripped from the value before being captured.
+
+.Parameter ConfigDir
+Path to the directory that contains the `pyvenv.cfg` file.
+#>
+function Get-PyVenvConfig(
+    [String]
+    $ConfigDir
+) {
+    Write-Verbose "Given ConfigDir=$ConfigDir, obtain values in pyvenv.cfg"
+
+    # Ensure the file exists, and issue a warning if it doesn't (but still allow the function to continue).
+    $pyvenvConfigPath = Join-Path -Resolve -Path $ConfigDir -ChildPath 'pyvenv.cfg' -ErrorAction Continue
+
+    # An empty map will be returned if no config file is found.
+    $pyvenvConfig = @{ }
+
+    if ($pyvenvConfigPath) {
+
+        Write-Verbose "File exists, parse `key = value` lines"
+        $pyvenvConfigContent = Get-Content -Path $pyvenvConfigPath
+
+        $pyvenvConfigContent | ForEach-Object {
+            $keyval = $PSItem -split "\s*=\s*", 2
+            if ($keyval[0] -and $keyval[1]) {
+                $val = $keyval[1]
+
+                # Remove extraneous quotations around a string value.
+                if ("'""".Contains($val.Substring(0, 1))) {
+                    $val = $val.Substring(1, $val.Length - 2)
+                }
+
+                $pyvenvConfig[$keyval[0]] = $val
+                Write-Verbose "Adding Key: '$($keyval[0])'='$val'"
+            }
+        }
+    }
+    return $pyvenvConfig
+}
+
+
+<# Begin Activate script --------------------------------------------------- #>
+
+# Determine the containing directory of this script
+$VenvExecPath = Split-Path -Parent $MyInvocation.MyCommand.Definition
+$VenvExecDir = Get-Item -Path $VenvExecPath
+
+Write-Verbose "Activation script is located in path: '$VenvExecPath'"
+Write-Verbose "VenvExecDir Fullname: '$($VenvExecDir.FullName)"
+Write-Verbose "VenvExecDir Name: '$($VenvExecDir.Name)"
+
+# Set values required in priority: CmdLine, ConfigFile, Default
+# First, get the location of the virtual environment, it might not be
+# VenvExecDir if specified on the command line.
+if ($VenvDir) {
+    Write-Verbose "VenvDir given as parameter, using '$VenvDir' to determine values"
+}
+else {
+    Write-Verbose "VenvDir not given as a parameter, using parent directory name as VenvDir."
+    $VenvDir = $VenvExecDir.Parent.FullName.TrimEnd("\\/")
+    Write-Verbose "VenvDir=$VenvDir"
+}
+
+# Next, read the `pyvenv.cfg` file to determine any required value such
+# as `prompt`.
+$pyvenvCfg = Get-PyVenvConfig -ConfigDir $VenvDir
+
+# Next, set the prompt from the command line, or the config file, or
+# just use the name of the virtual environment folder.
+if ($Prompt) {
+    Write-Verbose "Prompt specified as argument, using '$Prompt'"
+}
+else {
+    Write-Verbose "Prompt not specified as argument to script, checking pyvenv.cfg value"
+    if ($pyvenvCfg -and $pyvenvCfg['prompt']) {
+        Write-Verbose "  Setting based on value in pyvenv.cfg='$($pyvenvCfg['prompt'])'"
+        $Prompt = $pyvenvCfg['prompt'];
+    }
+    else {
+        Write-Verbose "  Setting prompt based on parent's directory's name. (Is the directory name passed to venv module when creating the virtual environment)"
+        Write-Verbose "  Got leaf-name of $VenvDir='$(Split-Path -Path $venvDir -Leaf)'"
+        $Prompt = Split-Path -Path $venvDir -Leaf
+    }
+}
+
+Write-Verbose "Prompt = '$Prompt'"
+Write-Verbose "VenvDir='$VenvDir'"
+
+# Deactivate any currently active virtual environment, but leave the
+# deactivate function in place.
+deactivate -nondestructive
+
+# Now set the environment variable VIRTUAL_ENV, used by many tools to determine
+# that there is an activated venv.
+$env:VIRTUAL_ENV = $VenvDir
+
+if (-not $Env:VIRTUAL_ENV_DISABLE_PROMPT) {
+
+    Write-Verbose "Setting prompt to '$Prompt'"
+
+    # Set the prompt to include the env name
+    # Make sure _OLD_VIRTUAL_PROMPT is global
+    function global:_OLD_VIRTUAL_PROMPT { "" }
+    Copy-Item -Path function:prompt -Destination function:_OLD_VIRTUAL_PROMPT
+    New-Variable -Name _PYTHON_VENV_PROMPT_PREFIX -Description "Python virtual environment prompt prefix" -Scope Global -Option ReadOnly -Visibility Public -Value $Prompt
+
+    function global:prompt {
+        Write-Host -NoNewline -ForegroundColor Green "($_PYTHON_VENV_PROMPT_PREFIX) "
+        _OLD_VIRTUAL_PROMPT
+    }
+    $env:VIRTUAL_ENV_PROMPT = $Prompt
+}
+
+# Clear PYTHONHOME
+if (Test-Path -Path Env:PYTHONHOME) {
+    Copy-Item -Path Env:PYTHONHOME -Destination Env:_OLD_VIRTUAL_PYTHONHOME
+    Remove-Item -Path Env:PYTHONHOME
+}
+
+# Add the venv to the PATH
+Copy-Item -Path Env:PATH -Destination Env:_OLD_VIRTUAL_PATH
+$Env:PATH = "$VenvExecDir$([System.IO.Path]::PathSeparator)$Env:PATH"

tuning-competition-baseline/.venv/bin/activate

@@ -0,0 +1,63 @@
+# This file must be used with "source bin/activate" *from bash*
+# you cannot run it directly
+
+deactivate () {
+    # reset old environment variables
+    if [ -n "${_OLD_VIRTUAL_PATH:-}" ] ; then
+        PATH="${_OLD_VIRTUAL_PATH:-}"
+        export PATH
+        unset _OLD_VIRTUAL_PATH
+    fi
+    if [ -n "${_OLD_VIRTUAL_PYTHONHOME:-}" ] ; then
+        PYTHONHOME="${_OLD_VIRTUAL_PYTHONHOME:-}"
+        export PYTHONHOME
+        unset _OLD_VIRTUAL_PYTHONHOME
+    fi
+
+    # Call hash to forget past commands. Without forgetting
+    # past commands the $PATH changes we made may not be respected
+    hash -r 2> /dev/null
+
+    if [ -n "${_OLD_VIRTUAL_PS1:-}" ] ; then
+        PS1="${_OLD_VIRTUAL_PS1:-}"
+        export PS1
+        unset _OLD_VIRTUAL_PS1
+    fi
+
+    unset VIRTUAL_ENV
+    unset VIRTUAL_ENV_PROMPT
+    if [ ! "${1:-}" = "nondestructive" ] ; then
+    # Self destruct!
+        unset -f deactivate
+    fi
+}
+
+# unset irrelevant variables
+deactivate nondestructive
+
+VIRTUAL_ENV="/home/koiwa/work/tuning-competition-baseline/.venv"
+export VIRTUAL_ENV
+
+_OLD_VIRTUAL_PATH="$PATH"
+PATH="$VIRTUAL_ENV/bin:$PATH"
+export PATH
+
+# unset PYTHONHOME if set
+# this will fail if PYTHONHOME is set to the empty string (which is bad anyway)
+# could use `if (set -u; : $PYTHONHOME) ;` in bash
+if [ -n "${PYTHONHOME:-}" ] ; then
+    _OLD_VIRTUAL_PYTHONHOME="${PYTHONHOME:-}"
+    unset PYTHONHOME
+fi
+
+if [ -z "${VIRTUAL_ENV_DISABLE_PROMPT:-}" ] ; then
+    _OLD_VIRTUAL_PS1="${PS1:-}"
+    PS1="(.venv) ${PS1:-}"
+    export PS1
+    VIRTUAL_ENV_PROMPT="(.venv) "
+    export VIRTUAL_ENV_PROMPT
+fi
+
+# Call hash to forget past commands. Without forgetting
+# past commands the $PATH changes we made may not be respected
+hash -r 2> /dev/null

tuning-competition-baseline/.venv/bin/activate.csh

@@ -0,0 +1,26 @@
+# This file must be used with "source bin/activate.csh" *from csh*.
+# You cannot run it directly.
+# Created by Davide Di Blasi <[email protected]>.
+# Ported to Python 3.3 venv by Andrew Svetlov <[email protected]>
+
+alias deactivate 'test $?_OLD_VIRTUAL_PATH != 0 && setenv PATH "$_OLD_VIRTUAL_PATH" && unset _OLD_VIRTUAL_PATH; rehash; test $?_OLD_VIRTUAL_PROMPT != 0 && set prompt="$_OLD_VIRTUAL_PROMPT" && unset _OLD_VIRTUAL_PROMPT; unsetenv VIRTUAL_ENV; unsetenv VIRTUAL_ENV_PROMPT; test "\!:*" != "nondestructive" && unalias deactivate'
+
+# Unset irrelevant variables.
+deactivate nondestructive
+
+setenv VIRTUAL_ENV "/home/koiwa/work/tuning-competition-baseline/.venv"
+
+set _OLD_VIRTUAL_PATH="$PATH"
+setenv PATH "$VIRTUAL_ENV/bin:$PATH"
+
+
+set _OLD_VIRTUAL_PROMPT="$prompt"
+
+if (! "$?VIRTUAL_ENV_DISABLE_PROMPT") then
+    set prompt = "(.venv) $prompt"
+    setenv VIRTUAL_ENV_PROMPT "(.venv) "
+endif
+
+alias pydoc python -m pydoc
+
+rehash

tuning-competition-baseline/.venv/bin/activate.fish

@@ -0,0 +1,69 @@
+# This file must be used with "source <venv>/bin/activate.fish" *from fish*
+# (https://fishshell.com/); you cannot run it directly.
+
+function deactivate  -d "Exit virtual environment and return to normal shell environment"
+    # reset old environment variables
+    if test -n "$_OLD_VIRTUAL_PATH"
+        set -gx PATH $_OLD_VIRTUAL_PATH
+        set -e _OLD_VIRTUAL_PATH
+    end
+    if test -n "$_OLD_VIRTUAL_PYTHONHOME"
+        set -gx PYTHONHOME $_OLD_VIRTUAL_PYTHONHOME
+        set -e _OLD_VIRTUAL_PYTHONHOME
+    end
+
+    if test -n "$_OLD_FISH_PROMPT_OVERRIDE"
+        set -e _OLD_FISH_PROMPT_OVERRIDE
+        # prevents error when using nested fish instances (Issue #93858)
+        if functions -q _old_fish_prompt
+            functions -e fish_prompt
+            functions -c _old_fish_prompt fish_prompt
+            functions -e _old_fish_prompt
+        end
+    end
+
+    set -e VIRTUAL_ENV
+    set -e VIRTUAL_ENV_PROMPT
+    if test "$argv[1]" != "nondestructive"
+        # Self-destruct!
+        functions -e deactivate
+    end
+end
+
+# Unset irrelevant variables.
+deactivate nondestructive
+
+set -gx VIRTUAL_ENV "/home/koiwa/work/tuning-competition-baseline/.venv"
+
+set -gx _OLD_VIRTUAL_PATH $PATH
+set -gx PATH "$VIRTUAL_ENV/bin" $PATH
+
+# Unset PYTHONHOME if set.
+if set -q PYTHONHOME
+    set -gx _OLD_VIRTUAL_PYTHONHOME $PYTHONHOME
+    set -e PYTHONHOME
+end
+
+if test -z "$VIRTUAL_ENV_DISABLE_PROMPT"
+    # fish uses a function instead of an env var to generate the prompt.
+
+    # Save the current fish_prompt function as the function _old_fish_prompt.
+    functions -c fish_prompt _old_fish_prompt
+
+    # With the original prompt function renamed, we can override with our own.
+    function fish_prompt
+        # Save the return status of the last command.
+        set -l old_status $status
+
+        # Output the venv prompt; color taken from the blue of the Python logo.
+        printf "%s%s%s" (set_color 4B8BBE) "(.venv) " (set_color normal)
+
+        # Restore the return status of the previous command.
+        echo "exit $old_status" | .
+        # Output the original/"old" prompt.
+        _old_fish_prompt
+    end
+
+    set -gx _OLD_FISH_PROMPT_OVERRIDE "$VIRTUAL_ENV"
+    set -gx VIRTUAL_ENV_PROMPT "(.venv) "
+end

tuning-competition-baseline/.venv/bin/convert-caffe2-to-onnx

@@ -0,0 +1,8 @@
+#!/home/koiwa/work/tuning-competition-baseline/.venv/bin/python3.11
+# -*- coding: utf-8 -*-
+import re
+import sys
+from caffe2.python.onnx.bin.conversion import caffe2_to_onnx
+if __name__ == '__main__':
+    sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0])
+    sys.exit(caffe2_to_onnx())

tuning-competition-baseline/.venv/bin/convert-onnx-to-caffe2

@@ -0,0 +1,8 @@
+#!/home/koiwa/work/tuning-competition-baseline/.venv/bin/python3.11
+# -*- coding: utf-8 -*-
+import re
+import sys
+from caffe2.python.onnx.bin.conversion import onnx_to_caffe2
+if __name__ == '__main__':
+    sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0])
+    sys.exit(onnx_to_caffe2())

tuning-competition-baseline/.venv/bin/cygdb

@@ -0,0 +1,8 @@
+#!/home/koiwa/work/tuning-competition-baseline/.venv/bin/python3.11
+# -*- coding: utf-8 -*-
+import re
+import sys
+from Cython.Debugger.Cygdb import main
+if __name__ == '__main__':
+    sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0])
+    sys.exit(main())

tuning-competition-baseline/.venv/bin/cython

@@ -0,0 +1,8 @@
+#!/home/koiwa/work/tuning-competition-baseline/.venv/bin/python3.11
+# -*- coding: utf-8 -*-
+import re
+import sys
+from Cython.Compiler.Main import setuptools_main
+if __name__ == '__main__':
+    sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0])
+    sys.exit(setuptools_main())

tuning-competition-baseline/.venv/bin/cythonize

@@ -0,0 +1,8 @@
+#!/home/koiwa/work/tuning-competition-baseline/.venv/bin/python3.11
+# -*- coding: utf-8 -*-
+import re
+import sys
+from Cython.Build.Cythonize import main
+if __name__ == '__main__':
+    sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0])
+    sys.exit(main())

tuning-competition-baseline/.venv/bin/pip

@@ -0,0 +1,8 @@
+#!/home/koiwa/work/tuning-competition-baseline/.venv/bin/python3.11
+# -*- coding: utf-8 -*-
+import re
+import sys
+from pip._internal.cli.main import main
+if __name__ == '__main__':
+    sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0])
+    sys.exit(main())

tuning-competition-baseline/.venv/bin/pip3.11

@@ -0,0 +1,8 @@
+#!/home/koiwa/work/tuning-competition-baseline/.venv/bin/python3.11
+# -*- coding: utf-8 -*-
+import re
+import sys
+from pip._internal.cli.main import main
+if __name__ == '__main__':
+    sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0])
+    sys.exit(main())

tuning-competition-baseline/.venv/bin/pybind11-config

@@ -0,0 +1,8 @@
+#!/home/koiwa/work/tuning-competition-baseline/.venv/bin/python3.11
+# -*- coding: utf-8 -*-
+import re
+import sys
+from pybind11.__main__ import main
+if __name__ == '__main__':
+    sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0])
+    sys.exit(main())

tuning-competition-baseline/.venv/bin/torchrun

@@ -0,0 +1,8 @@
+#!/home/koiwa/work/tuning-competition-baseline/.venv/bin/python3.11
+# -*- coding: utf-8 -*-
+import re
+import sys
+from torch.distributed.run import main
+if __name__ == '__main__':
+    sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0])
+    sys.exit(main())

tuning-competition-baseline/.venv/bin/wheel

@@ -0,0 +1,8 @@
+#!/home/koiwa/work/tuning-competition-baseline/.venv/bin/python3.11
+# -*- coding: utf-8 -*-
+import re
+import sys
+from wheel.cli import main
+if __name__ == '__main__':
+    sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0])
+    sys.exit(main())

tuning-competition-baseline/.venv/lib/python3.11/site-packages/Jinja2-3.1.3.dist-info/INSTALLER

@@ -0,0 +1 @@
+pip

tuning-competition-baseline/.venv/lib/python3.11/site-packages/Jinja2-3.1.3.dist-info/LICENSE.rst

@@ -0,0 +1,28 @@
+Copyright 2007 Pallets
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are
+met:
+
+1.  Redistributions of source code must retain the above copyright
+    notice, this list of conditions and the following disclaimer.
+
+2.  Redistributions in binary form must reproduce the above copyright
+    notice, this list of conditions and the following disclaimer in the
+    documentation and/or other materials provided with the distribution.
+
+3.  Neither the name of the copyright holder nor the names of its
+    contributors may be used to endorse or promote products derived from
+    this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED
+TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

tuning-competition-baseline/.venv/lib/python3.11/site-packages/Jinja2-3.1.3.dist-info/RECORD

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+Jinja2-3.1.3.dist-info/METADATA,sha256=0cLNbRCI91jytc7Bzv3XAQfZzFDF2gxkJuH46eF5vew,3301
+Jinja2-3.1.3.dist-info/RECORD,,
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+Jinja2-3.1.3.dist-info/entry_points.txt,sha256=zRd62fbqIyfUpsRtU7EVIFyiu1tPwfgO7EvPErnxgTE,59
+Jinja2-3.1.3.dist-info/top_level.txt,sha256=PkeVWtLb3-CqjWi1fO29OCbj55EhX_chhKrCdrVe_zs,7
+jinja2/__init__.py,sha256=NTBwMwsECrdHmxeXF7seusHLzrh6Ldn1A9qhS5cDuf0,1927
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+jinja2/tests.py,sha256=Am5Z6Lmfr2XaH_npIfJJ8MdXtWsbLjMULZJulTAj30E,5905
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tuning-competition-baseline/.venv/lib/python3.11/site-packages/Jinja2-3.1.3.dist-info/entry_points.txt

@@ -0,0 +1,2 @@
+[babel.extractors]
+jinja2 = jinja2.ext:babel_extract[i18n]

tuning-competition-baseline/.venv/lib/python3.11/site-packages/cython.py

@@ -0,0 +1,24 @@
+#!/usr/bin/env python
+
+#
+#   Cython -- Main Program, generic
+#
+
+if __name__ == '__main__':
+
+    import os
+    import sys
+
+    # Make sure we import the right Cython
+    cythonpath, _ = os.path.split(os.path.realpath(__file__))
+    sys.path.insert(0, cythonpath)
+
+    from Cython.Compiler.Main import main
+    main(command_line = 1)
+
+else:
+    # Void cython.* directives.
+    from Cython.Shadow import *
+    ## and bring in the __version__
+    from Cython import __version__
+    from Cython import load_ipython_extension

tuning-competition-baseline/.venv/lib/python3.11/site-packages/isympy.py

@@ -0,0 +1,342 @@
+"""
+Python shell for SymPy.
+
+This is just a normal Python shell (IPython shell if you have the
+IPython package installed), that executes the following commands for
+the user:
+
+    >>> from __future__ import division
+    >>> from sympy import *
+    >>> x, y, z, t = symbols('x y z t')
+    >>> k, m, n = symbols('k m n', integer=True)
+    >>> f, g, h = symbols('f g h', cls=Function)
+    >>> init_printing()
+
+So starting 'isympy' is equivalent to starting Python (or IPython) and
+executing the above commands by hand.  It is intended for easy and quick
+experimentation with SymPy.  isympy is a good way to use SymPy as an
+interactive calculator. If you have IPython and Matplotlib installed, then
+interactive plotting is enabled by default.
+
+COMMAND LINE OPTIONS
+--------------------
+
+-c CONSOLE, --console=CONSOLE
+
+     Use the specified shell (Python or IPython) shell as the console
+     backend instead of the default one (IPython if present, Python
+     otherwise), e.g.:
+
+        $isympy -c python
+
+    CONSOLE must be one of 'ipython' or 'python'
+
+-p PRETTY, --pretty PRETTY
+
+    Setup pretty-printing in SymPy. When pretty-printing is enabled,
+    expressions can be printed with Unicode or ASCII. The default is
+    to use pretty-printing (with Unicode if the terminal supports it).
+    When this option is 'no', expressions will not be pretty-printed
+    and ASCII will be used:
+
+        $isympy -p no
+
+    PRETTY must be one of 'unicode', 'ascii', or 'no'
+
+-t TYPES, --types=TYPES
+
+    Setup the ground types for the polys.  By default, gmpy ground types
+    are used if gmpy2 or gmpy is installed, otherwise it falls back to python
+    ground types, which are a little bit slower.  You can manually
+    choose python ground types even if gmpy is installed (e.g., for
+    testing purposes):
+
+        $isympy -t python
+
+    TYPES must be one of 'gmpy', 'gmpy1' or 'python'
+
+    Note that the ground type gmpy1 is primarily intended for testing; it
+    forces the use of gmpy version 1 even if gmpy2 is available.
+
+    This is the same as setting the environment variable
+    SYMPY_GROUND_TYPES to the given ground type (e.g.,
+    SYMPY_GROUND_TYPES='gmpy')
+
+    The ground types can be determined interactively from the variable
+    sympy.polys.domains.GROUND_TYPES.
+
+-o ORDER, --order ORDER
+
+    Setup the ordering of terms for printing.  The default is lex, which
+    orders terms lexicographically (e.g., x**2 + x + 1). You can choose
+    other orderings, such as rev-lex, which will use reverse
+    lexicographic ordering (e.g., 1 + x + x**2):
+
+        $isympy -o rev-lex
+
+    ORDER must be one of 'lex', 'rev-lex', 'grlex', 'rev-grlex',
+    'grevlex', 'rev-grevlex', 'old', or 'none'.
+
+    Note that for very large expressions, ORDER='none' may speed up
+    printing considerably but the terms will have no canonical order.
+
+-q, --quiet
+
+    Print only Python's and SymPy's versions to stdout at startup.
+
+-d, --doctest
+
+    Use the same format that should be used for doctests.  This is
+    equivalent to -c python -p no.
+
+-C, --no-cache
+
+    Disable the caching mechanism.  Disabling the cache may slow certain
+    operations down considerably.  This is useful for testing the cache,
+    or for benchmarking, as the cache can result in deceptive timings.
+
+    This is equivalent to setting the environment variable
+    SYMPY_USE_CACHE to 'no'.
+
+-a, --auto-symbols (requires at least IPython 0.11)
+
+    Automatically create missing symbols.  Normally, typing a name of a
+    Symbol that has not been instantiated first would raise NameError,
+    but with this option enabled, any undefined name will be
+    automatically created as a Symbol.
+
+    Note that this is intended only for interactive, calculator style
+    usage. In a script that uses SymPy, Symbols should be instantiated
+    at the top, so that it's clear what they are.
+
+    This will not override any names that are already defined, which
+    includes the single character letters represented by the mnemonic
+    QCOSINE (see the "Gotchas and Pitfalls" document in the
+    documentation). You can delete existing names by executing "del
+    name".  If a name is defined, typing "'name' in dir()" will return True.
+
+    The Symbols that are created using this have default assumptions.
+    If you want to place assumptions on symbols, you should create them
+    using symbols() or var().
+
+    Finally, this only works in the top level namespace. So, for
+    example, if you define a function in isympy with an undefined
+    Symbol, it will not work.
+
+    See also the -i and -I options.
+
+-i, --int-to-Integer (requires at least IPython 0.11)
+
+    Automatically wrap int literals with Integer.  This makes it so that
+    things like 1/2 will come out as Rational(1, 2), rather than 0.5.  This
+    works by preprocessing the source and wrapping all int literals with
+    Integer.  Note that this will not change the behavior of int literals
+    assigned to variables, and it also won't change the behavior of functions
+    that return int literals.
+
+    If you want an int, you can wrap the literal in int(), e.g. int(3)/int(2)
+    gives 1.5 (with division imported from __future__).
+
+-I, --interactive (requires at least IPython 0.11)
+
+    This is equivalent to --auto-symbols --int-to-Integer.  Future options
+    designed for ease of interactive use may be added to this.
+
+-D, --debug
+
+    Enable debugging output.  This is the same as setting the
+    environment variable SYMPY_DEBUG to 'True'.  The debug status is set
+    in the variable SYMPY_DEBUG within isympy.
+
+-- IPython options
+
+    Additionally you can pass command line options directly to the IPython
+    interpreter (the standard Python shell is not supported).  However you
+    need to add the '--' separator between two types of options, e.g the
+    startup banner option and the colors option. You need to enter the
+    options as required by the version of IPython that you are using, too:
+
+    in IPython 0.11,
+
+        $isympy -q -- --colors=NoColor
+
+    or older versions of IPython,
+
+        $isympy -q -- -colors NoColor
+
+See also isympy --help.
+"""
+
+import os
+import sys
+
+# DO NOT IMPORT SYMPY HERE! Or the setting of the sympy environment variables
+# by the command line will break.
+
+def main() -> None:
+    from argparse import ArgumentParser, RawDescriptionHelpFormatter
+
+    VERSION = None
+    if '--version' in sys.argv:
+        # We cannot import sympy before this is run, because flags like -C and
+        # -t set environment variables that must be set before SymPy is
+        # imported. The only thing we need to import it for is to get the
+        # version, which only matters with the --version flag.
+        import sympy
+        VERSION = sympy.__version__
+
+    usage = 'isympy [options] -- [ipython options]'
+    parser = ArgumentParser(
+        usage=usage,
+        description=__doc__,
+        formatter_class=RawDescriptionHelpFormatter,
+    )
+
+    parser.add_argument('--version', action='version', version=VERSION)
+
+    parser.add_argument(
+        '-c', '--console',
+        dest='console',
+        action='store',
+        default=None,
+        choices=['ipython', 'python'],
+        metavar='CONSOLE',
+        help='select type of interactive session: ipython | python; defaults '
+        'to ipython if IPython is installed, otherwise python')
+
+    parser.add_argument(
+        '-p', '--pretty',
+        dest='pretty',
+        action='store',
+        default=None,
+        metavar='PRETTY',
+        choices=['unicode', 'ascii', 'no'],
+        help='setup pretty printing: unicode | ascii | no; defaults to '
+        'unicode printing if the terminal supports it, otherwise ascii')
+
+    parser.add_argument(
+        '-t', '--types',
+        dest='types',
+        action='store',
+        default=None,
+        metavar='TYPES',
+        choices=['gmpy', 'gmpy1', 'python'],
+        help='setup ground types: gmpy | gmpy1 | python; defaults to gmpy if gmpy2 '
+        'or gmpy is installed, otherwise python')
+
+    parser.add_argument(
+        '-o', '--order',
+        dest='order',
+        action='store',
+        default=None,
+        metavar='ORDER',
+        choices=['lex', 'grlex', 'grevlex', 'rev-lex', 'rev-grlex', 'rev-grevlex', 'old', 'none'],
+        help='setup ordering of terms: [rev-]lex | [rev-]grlex | [rev-]grevlex | old | none; defaults to lex')
+
+    parser.add_argument(
+        '-q', '--quiet',
+        dest='quiet',
+        action='store_true',
+        default=False,
+        help='print only version information at startup')
+
+    parser.add_argument(
+        '-d', '--doctest',
+        dest='doctest',
+        action='store_true',
+        default=False,
+        help='use the doctest format for output (you can just copy and paste it)')
+
+    parser.add_argument(
+        '-C', '--no-cache',
+        dest='cache',
+        action='store_false',
+        default=True,
+        help='disable caching mechanism')
+
+    parser.add_argument(
+        '-a', '--auto-symbols',
+        dest='auto_symbols',
+        action='store_true',
+        default=False,
+        help='automatically construct missing symbols')
+
+    parser.add_argument(
+        '-i', '--int-to-Integer',
+        dest='auto_int_to_Integer',
+        action='store_true',
+        default=False,
+        help="automatically wrap int literals with Integer")
+
+    parser.add_argument(
+        '-I', '--interactive',
+        dest='interactive',
+        action='store_true',
+        default=False,
+        help="equivalent to -a -i")
+
+    parser.add_argument(
+        '-D', '--debug',
+        dest='debug',
+        action='store_true',
+        default=False,
+        help='enable debugging output')
+
+    (options, ipy_args) = parser.parse_known_args()
+    if '--' in ipy_args:
+        ipy_args.remove('--')
+
+    if not options.cache:
+        os.environ['SYMPY_USE_CACHE'] = 'no'
+
+    if options.types:
+        os.environ['SYMPY_GROUND_TYPES'] = options.types
+
+    if options.debug:
+        os.environ['SYMPY_DEBUG'] = str(options.debug)
+
+    if options.doctest:
+        options.pretty = 'no'
+        options.console = 'python'
+
+    session = options.console
+
+    if session is not None:
+        ipython = session == 'ipython'
+    else:
+        try:
+            import IPython
+            ipython = True
+        except ImportError:
+            if not options.quiet:
+                from sympy.interactive.session import no_ipython
+                print(no_ipython)
+            ipython = False
+
+    args = {
+        'pretty_print': True,
+        'use_unicode':  None,
+        'use_latex':    None,
+        'order':        None,
+        'argv':         ipy_args,
+    }
+
+    if options.pretty == 'unicode':
+        args['use_unicode'] = True
+    elif options.pretty == 'ascii':
+        args['use_unicode'] = False
+    elif options.pretty == 'no':
+        args['pretty_print'] = False
+
+    if options.order is not None:
+        args['order'] = options.order
+
+    args['quiet'] = options.quiet
+    args['auto_symbols'] = options.auto_symbols or options.interactive
+    args['auto_int_to_Integer'] = options.auto_int_to_Integer or options.interactive
+
+    from sympy.interactive import init_session
+    init_session(ipython, **args)
+
+if __name__ == "__main__":
+    main()

tuning-competition-baseline/.venv/lib/python3.11/site-packages/networkx/lazy_imports.py

@@ -0,0 +1,190 @@
+import importlib
+import importlib.util
+import inspect
+import os
+import sys
+import types
+
+__all__ = ["attach", "_lazy_import"]
+
+
+def attach(module_name, submodules=None, submod_attrs=None):
+    """Attach lazily loaded submodules, and functions or other attributes.
+
+    Typically, modules import submodules and attributes as follows::
+
+      import mysubmodule
+      import anothersubmodule
+
+      from .foo import someattr
+
+    The idea of  this function is to replace the `__init__.py`
+    module's `__getattr__`, `__dir__`, and `__all__` attributes such that
+    all imports work exactly the way they normally would, except that the
+    actual import is delayed until the resulting module object is first used.
+
+    The typical way to call this function, replacing the above imports, is::
+
+      __getattr__, __lazy_dir__, __all__ = lazy.attach(
+          __name__,
+          ['mysubmodule', 'anothersubmodule'],
+          {'foo': 'someattr'}
+      )
+
+    This functionality requires Python 3.7 or higher.
+
+    Parameters
+    ----------
+    module_name : str
+        Typically use __name__.
+    submodules : set
+        List of submodules to lazily import.
+    submod_attrs : dict
+        Dictionary of submodule -> list of attributes / functions.
+        These attributes are imported as they are used.
+
+    Returns
+    -------
+    __getattr__, __dir__, __all__
+
+    """
+    if submod_attrs is None:
+        submod_attrs = {}
+
+    if submodules is None:
+        submodules = set()
+    else:
+        submodules = set(submodules)
+
+    attr_to_modules = {
+        attr: mod for mod, attrs in submod_attrs.items() for attr in attrs
+    }
+
+    __all__ = list(submodules | attr_to_modules.keys())
+
+    def __getattr__(name):
+        if name in submodules:
+            return importlib.import_module(f"{module_name}.{name}")
+        elif name in attr_to_modules:
+            submod = importlib.import_module(f"{module_name}.{attr_to_modules[name]}")
+            return getattr(submod, name)
+        else:
+            raise AttributeError(f"No {module_name} attribute {name}")
+
+    def __dir__():
+        return __all__
+
+    if os.environ.get("EAGER_IMPORT", ""):
+        for attr in set(attr_to_modules.keys()) | submodules:
+            __getattr__(attr)
+
+    return __getattr__, __dir__, list(__all__)
+
+
+class DelayedImportErrorModule(types.ModuleType):
+    def __init__(self, frame_data, *args, **kwargs):
+        self.__frame_data = frame_data
+        super().__init__(*args, **kwargs)
+
+    def __getattr__(self, x):
+        if x in ("__class__", "__file__", "__frame_data"):
+            super().__getattr__(x)
+        else:
+            fd = self.__frame_data
+            raise ModuleNotFoundError(
+                f"No module named '{fd['spec']}'\n\n"
+                "This error is lazily reported, having originally occurred in\n"
+                f'  File {fd["filename"]}, line {fd["lineno"]}, in {fd["function"]}\n\n'
+                f'----> {"".join(fd["code_context"] or "").strip()}'
+            )
+
+
+def _lazy_import(fullname):
+    """Return a lazily imported proxy for a module or library.
+
+    Warning
+    -------
+    Importing using this function can currently cause trouble
+    when the user tries to import from a subpackage of a module before
+    the package is fully imported. In particular, this idiom may not work:
+
+      np = lazy_import("numpy")
+      from numpy.lib import recfunctions
+
+    This is due to a difference in the way Python's LazyLoader handles
+    subpackage imports compared to the normal import process. Hopefully
+    we will get Python's LazyLoader to fix this, or find a workaround.
+    In the meantime, this is a potential problem.
+
+    The workaround is to import numpy before importing from the subpackage.
+
+    Notes
+    -----
+    We often see the following pattern::
+
+      def myfunc():
+          import scipy as sp
+          sp.argmin(...)
+          ....
+
+    This is to prevent a library, in this case `scipy`, from being
+    imported at function definition time, since that can be slow.
+
+    This function provides a proxy module that, upon access, imports
+    the actual module.  So the idiom equivalent to the above example is::
+
+      sp = lazy.load("scipy")
+
+      def myfunc():
+          sp.argmin(...)
+          ....
+
+    The initial import time is fast because the actual import is delayed
+    until the first attribute is requested. The overall import time may
+    decrease as well for users that don't make use of large portions
+    of the library.
+
+    Parameters
+    ----------
+    fullname : str
+        The full name of the package or subpackage to import.  For example::
+
+          sp = lazy.load('scipy')  # import scipy as sp
+          spla = lazy.load('scipy.linalg')  # import scipy.linalg as spla
+
+    Returns
+    -------
+    pm : importlib.util._LazyModule
+        Proxy module. Can be used like any regularly imported module.
+        Actual loading of the module occurs upon first attribute request.
+
+    """
+    try:
+        return sys.modules[fullname]
+    except:
+        pass
+
+    # Not previously loaded -- look it up
+    spec = importlib.util.find_spec(fullname)
+
+    if spec is None:
+        try:
+            parent = inspect.stack()[1]
+            frame_data = {
+                "spec": fullname,
+                "filename": parent.filename,
+                "lineno": parent.lineno,
+                "function": parent.function,
+                "code_context": parent.code_context,
+            }
+            return DelayedImportErrorModule(frame_data, "DelayedImportErrorModule")
+        finally:
+            del parent
+
+    module = importlib.util.module_from_spec(spec)
+    sys.modules[fullname] = module
+
+    loader = importlib.util.LazyLoader(spec.loader)
+    loader.exec_module(module)
+
+    return module

tuning-competition-baseline/.venv/lib/python3.11/site-packages/networkx/linalg/graphmatrix.py

@@ -0,0 +1,166 @@
+"""
+Adjacency matrix and incidence matrix of graphs.
+"""
+import networkx as nx
+
+__all__ = ["incidence_matrix", "adjacency_matrix"]
+
+
+@nx._dispatch(edge_attrs="weight")
+def incidence_matrix(
+    G, nodelist=None, edgelist=None, oriented=False, weight=None, *, dtype=None
+):
+    """Returns incidence matrix of G.
+
+    The incidence matrix assigns each row to a node and each column to an edge.
+    For a standard incidence matrix a 1 appears wherever a row's node is
+    incident on the column's edge.  For an oriented incidence matrix each
+    edge is assigned an orientation (arbitrarily for undirected and aligning to
+    direction for directed).  A -1 appears for the source (tail) of an edge and
+    1 for the destination (head) of the edge.  The elements are zero otherwise.
+
+    Parameters
+    ----------
+    G : graph
+       A NetworkX graph
+
+    nodelist : list, optional   (default= all nodes in G)
+       The rows are ordered according to the nodes in nodelist.
+       If nodelist is None, then the ordering is produced by G.nodes().
+
+    edgelist : list, optional (default= all edges in G)
+       The columns are ordered according to the edges in edgelist.
+       If edgelist is None, then the ordering is produced by G.edges().
+
+    oriented: bool, optional (default=False)
+       If True, matrix elements are +1 or -1 for the head or tail node
+       respectively of each edge.  If False, +1 occurs at both nodes.
+
+    weight : string or None, optional (default=None)
+       The edge data key used to provide each value in the matrix.
+       If None, then each edge has weight 1.  Edge weights, if used,
+       should be positive so that the orientation can provide the sign.
+
+    dtype : a NumPy dtype or None (default=None)
+        The dtype of the output sparse array. This type should be a compatible
+        type of the weight argument, eg. if weight would return a float this
+        argument should also be a float.
+        If None, then the default for SciPy is used.
+
+    Returns
+    -------
+    A : SciPy sparse array
+      The incidence matrix of G.
+
+    Notes
+    -----
+    For MultiGraph/MultiDiGraph, the edges in edgelist should be
+    (u,v,key) 3-tuples.
+
+    "Networks are the best discrete model for so many problems in
+    applied mathematics" [1]_.
+
+    References
+    ----------
+    .. [1] Gil Strang, Network applications: A = incidence matrix,
+       http://videolectures.net/mit18085f07_strang_lec03/
+    """
+    import scipy as sp
+
+    if nodelist is None:
+        nodelist = list(G)
+    if edgelist is None:
+        if G.is_multigraph():
+            edgelist = list(G.edges(keys=True))
+        else:
+            edgelist = list(G.edges())
+    A = sp.sparse.lil_array((len(nodelist), len(edgelist)), dtype=dtype)
+    node_index = {node: i for i, node in enumerate(nodelist)}
+    for ei, e in enumerate(edgelist):
+        (u, v) = e[:2]
+        if u == v:
+            continue  # self loops give zero column
+        try:
+            ui = node_index[u]
+            vi = node_index[v]
+        except KeyError as err:
+            raise nx.NetworkXError(
+                f"node {u} or {v} in edgelist but not in nodelist"
+            ) from err
+        if weight is None:
+            wt = 1
+        else:
+            if G.is_multigraph():
+                ekey = e[2]
+                wt = G[u][v][ekey].get(weight, 1)
+            else:
+                wt = G[u][v].get(weight, 1)
+        if oriented:
+            A[ui, ei] = -wt
+            A[vi, ei] = wt
+        else:
+            A[ui, ei] = wt
+            A[vi, ei] = wt
+    return A.asformat("csc")
+
+
+@nx._dispatch(edge_attrs="weight")
+def adjacency_matrix(G, nodelist=None, dtype=None, weight="weight"):
+    """Returns adjacency matrix of G.
+
+    Parameters
+    ----------
+    G : graph
+       A NetworkX graph
+
+    nodelist : list, optional
+       The rows and columns are ordered according to the nodes in nodelist.
+       If nodelist is None, then the ordering is produced by G.nodes().
+
+    dtype : NumPy data-type, optional
+        The desired data-type for the array.
+        If None, then the NumPy default is used.
+
+    weight : string or None, optional (default='weight')
+       The edge data key used to provide each value in the matrix.
+       If None, then each edge has weight 1.
+
+    Returns
+    -------
+    A : SciPy sparse array
+      Adjacency matrix representation of G.
+
+    Notes
+    -----
+    For directed graphs, entry i,j corresponds to an edge from i to j.
+
+    If you want a pure Python adjacency matrix representation try
+    networkx.convert.to_dict_of_dicts which will return a
+    dictionary-of-dictionaries format that can be addressed as a
+    sparse matrix.
+
+    For MultiGraph/MultiDiGraph with parallel edges the weights are summed.
+    See `to_numpy_array` for other options.
+
+    The convention used for self-loop edges in graphs is to assign the
+    diagonal matrix entry value to the edge weight attribute
+    (or the number 1 if the edge has no weight attribute).  If the
+    alternate convention of doubling the edge weight is desired the
+    resulting SciPy sparse array can be modified as follows:
+
+    >>> G = nx.Graph([(1, 1)])
+    >>> A = nx.adjacency_matrix(G)
+    >>> print(A.todense())
+    [[1]]
+    >>> A.setdiag(A.diagonal() * 2)
+    >>> print(A.todense())
+    [[2]]
+
+    See Also
+    --------
+    to_numpy_array
+    to_scipy_sparse_array
+    to_dict_of_dicts
+    adjacency_spectrum
+    """
+    return nx.to_scipy_sparse_array(G, nodelist=nodelist, dtype=dtype, weight=weight)

tuning-competition-baseline/.venv/lib/python3.11/site-packages/networkx/linalg/modularitymatrix.py

@@ -0,0 +1,166 @@
+"""Modularity matrix of graphs.
+"""
+import networkx as nx
+from networkx.utils import not_implemented_for
+
+__all__ = ["modularity_matrix", "directed_modularity_matrix"]
+
+
+@not_implemented_for("directed")
+@not_implemented_for("multigraph")
+@nx._dispatch(edge_attrs="weight")
+def modularity_matrix(G, nodelist=None, weight=None):
+    r"""Returns the modularity matrix of G.
+
+    The modularity matrix is the matrix B = A - <A>, where A is the adjacency
+    matrix and <A> is the average adjacency matrix, assuming that the graph
+    is described by the configuration model.
+
+    More specifically, the element B_ij of B is defined as
+
+    .. math::
+        A_{ij} - {k_i k_j \over 2 m}
+
+    where k_i is the degree of node i, and where m is the number of edges
+    in the graph. When weight is set to a name of an attribute edge, Aij, k_i,
+    k_j and m are computed using its value.
+
+    Parameters
+    ----------
+    G : Graph
+       A NetworkX graph
+
+    nodelist : list, optional
+       The rows and columns are ordered according to the nodes in nodelist.
+       If nodelist is None, then the ordering is produced by G.nodes().
+
+    weight : string or None, optional (default=None)
+       The edge attribute that holds the numerical value used for
+       the edge weight.  If None then all edge weights are 1.
+
+    Returns
+    -------
+    B : Numpy array
+      The modularity matrix of G.
+
+    Examples
+    --------
+    >>> k = [3, 2, 2, 1, 0]
+    >>> G = nx.havel_hakimi_graph(k)
+    >>> B = nx.modularity_matrix(G)
+
+
+    See Also
+    --------
+    to_numpy_array
+    modularity_spectrum
+    adjacency_matrix
+    directed_modularity_matrix
+
+    References
+    ----------
+    .. [1] M. E. J. Newman, "Modularity and community structure in networks",
+           Proc. Natl. Acad. Sci. USA, vol. 103, pp. 8577-8582, 2006.
+    """
+    import numpy as np
+
+    if nodelist is None:
+        nodelist = list(G)
+    A = nx.to_scipy_sparse_array(G, nodelist=nodelist, weight=weight, format="csr")
+    k = A.sum(axis=1)
+    m = k.sum() * 0.5
+    # Expected adjacency matrix
+    X = np.outer(k, k) / (2 * m)
+
+    return A - X
+
+
+@not_implemented_for("undirected")
+@not_implemented_for("multigraph")
+@nx._dispatch(edge_attrs="weight")
+def directed_modularity_matrix(G, nodelist=None, weight=None):
+    """Returns the directed modularity matrix of G.
+
+    The modularity matrix is the matrix B = A - <A>, where A is the adjacency
+    matrix and <A> is the expected adjacency matrix, assuming that the graph
+    is described by the configuration model.
+
+    More specifically, the element B_ij of B is defined as
+
+    .. math::
+        B_{ij} = A_{ij} - k_i^{out} k_j^{in} / m
+
+    where :math:`k_i^{in}` is the in degree of node i, and :math:`k_j^{out}` is the out degree
+    of node j, with m the number of edges in the graph. When weight is set
+    to a name of an attribute edge, Aij, k_i, k_j and m are computed using
+    its value.
+
+    Parameters
+    ----------
+    G : DiGraph
+       A NetworkX DiGraph
+
+    nodelist : list, optional
+       The rows and columns are ordered according to the nodes in nodelist.
+       If nodelist is None, then the ordering is produced by G.nodes().
+
+    weight : string or None, optional (default=None)
+       The edge attribute that holds the numerical value used for
+       the edge weight.  If None then all edge weights are 1.
+
+    Returns
+    -------
+    B : Numpy array
+      The modularity matrix of G.
+
+    Examples
+    --------
+    >>> G = nx.DiGraph()
+    >>> G.add_edges_from(
+    ...     (
+    ...         (1, 2),
+    ...         (1, 3),
+    ...         (3, 1),
+    ...         (3, 2),
+    ...         (3, 5),
+    ...         (4, 5),
+    ...         (4, 6),
+    ...         (5, 4),
+    ...         (5, 6),
+    ...         (6, 4),
+    ...     )
+    ... )
+    >>> B = nx.directed_modularity_matrix(G)
+
+
+    Notes
+    -----
+    NetworkX defines the element A_ij of the adjacency matrix as 1 if there
+    is a link going from node i to node j. Leicht and Newman use the opposite
+    definition. This explains the different expression for B_ij.
+
+    See Also
+    --------
+    to_numpy_array
+    modularity_spectrum
+    adjacency_matrix
+    modularity_matrix
+
+    References
+    ----------
+    .. [1] E. A. Leicht, M. E. J. Newman,
+        "Community structure in directed networks",
+        Phys. Rev Lett., vol. 100, no. 11, p. 118703, 2008.
+    """
+    import numpy as np
+
+    if nodelist is None:
+        nodelist = list(G)
+    A = nx.to_scipy_sparse_array(G, nodelist=nodelist, weight=weight, format="csr")
+    k_in = A.sum(axis=0)
+    k_out = A.sum(axis=1)
+    m = k_in.sum()
+    # Expected adjacency matrix
+    X = np.outer(k_out, k_in) / m
+
+    return A - X

tuning-competition-baseline/.venv/lib/python3.11/site-packages/networkx/linalg/tests/test_algebraic_connectivity.py

@@ -0,0 +1,402 @@
+from math import sqrt
+
+import pytest
+
+np = pytest.importorskip("numpy")
+
+
+import networkx as nx
+
+methods = ("tracemin_pcg", "tracemin_lu", "lanczos", "lobpcg")
+
+
+def test_algebraic_connectivity_tracemin_chol():
+    """Test that "tracemin_chol" raises an exception."""
+    pytest.importorskip("scipy")
+    G = nx.barbell_graph(5, 4)
+    with pytest.raises(nx.NetworkXError):
+        nx.algebraic_connectivity(G, method="tracemin_chol")
+
+
+def test_fiedler_vector_tracemin_chol():
+    """Test that "tracemin_chol" raises an exception."""
+    pytest.importorskip("scipy")
+    G = nx.barbell_graph(5, 4)
+    with pytest.raises(nx.NetworkXError):
+        nx.fiedler_vector(G, method="tracemin_chol")
+
+
+def test_spectral_ordering_tracemin_chol():
+    """Test that "tracemin_chol" raises an exception."""
+    pytest.importorskip("scipy")
+    G = nx.barbell_graph(5, 4)
+    with pytest.raises(nx.NetworkXError):
+        nx.spectral_ordering(G, method="tracemin_chol")
+
+
+def test_fiedler_vector_tracemin_unknown():
+    """Test that "tracemin_unknown" raises an exception."""
+    pytest.importorskip("scipy")
+    G = nx.barbell_graph(5, 4)
+    L = nx.laplacian_matrix(G)
+    X = np.asarray(np.random.normal(size=(1, L.shape[0]))).T
+    with pytest.raises(nx.NetworkXError, match="Unknown linear system solver"):
+        nx.linalg.algebraicconnectivity._tracemin_fiedler(
+            L, X, normalized=False, tol=1e-8, method="tracemin_unknown"
+        )
+
+
+def test_spectral_bisection():
+    pytest.importorskip("scipy")
+    G = nx.barbell_graph(3, 0)
+    C = nx.spectral_bisection(G)
+    assert C == ({0, 1, 2}, {3, 4, 5})
+
+    mapping = dict(enumerate("badfec"))
+    G = nx.relabel_nodes(G, mapping)
+    C = nx.spectral_bisection(G)
+    assert C == (
+        {mapping[0], mapping[1], mapping[2]},
+        {mapping[3], mapping[4], mapping[5]},
+    )
+
+
+def check_eigenvector(A, l, x):
+    nx = np.linalg.norm(x)
+    # Check zeroness.
+    assert nx != pytest.approx(0, abs=1e-07)
+    y = A @ x
+    ny = np.linalg.norm(y)
+    # Check collinearity.
+    assert x @ y == pytest.approx(nx * ny, abs=1e-7)
+    # Check eigenvalue.
+    assert ny == pytest.approx(l * nx, abs=1e-7)
+
+
+class TestAlgebraicConnectivity:
+    @pytest.mark.parametrize("method", methods)
+    def test_directed(self, method):
+        G = nx.DiGraph()
+        pytest.raises(
+            nx.NetworkXNotImplemented, nx.algebraic_connectivity, G, method=method
+        )
+        pytest.raises(nx.NetworkXNotImplemented, nx.fiedler_vector, G, method=method)
+
+    @pytest.mark.parametrize("method", methods)
+    def test_null_and_singleton(self, method):
+        G = nx.Graph()
+        pytest.raises(nx.NetworkXError, nx.algebraic_connectivity, G, method=method)
+        pytest.raises(nx.NetworkXError, nx.fiedler_vector, G, method=method)
+        G.add_edge(0, 0)
+        pytest.raises(nx.NetworkXError, nx.algebraic_connectivity, G, method=method)
+        pytest.raises(nx.NetworkXError, nx.fiedler_vector, G, method=method)
+
+    @pytest.mark.parametrize("method", methods)
+    def test_disconnected(self, method):
+        G = nx.Graph()
+        G.add_nodes_from(range(2))
+        assert nx.algebraic_connectivity(G) == 0
+        pytest.raises(nx.NetworkXError, nx.fiedler_vector, G, method=method)
+        G.add_edge(0, 1, weight=0)
+        assert nx.algebraic_connectivity(G) == 0
+        pytest.raises(nx.NetworkXError, nx.fiedler_vector, G, method=method)
+
+    def test_unrecognized_method(self):
+        pytest.importorskip("scipy")
+        G = nx.path_graph(4)
+        pytest.raises(nx.NetworkXError, nx.algebraic_connectivity, G, method="unknown")
+        pytest.raises(nx.NetworkXError, nx.fiedler_vector, G, method="unknown")
+
+    @pytest.mark.parametrize("method", methods)
+    def test_two_nodes(self, method):
+        pytest.importorskip("scipy")
+        G = nx.Graph()
+        G.add_edge(0, 1, weight=1)
+        A = nx.laplacian_matrix(G)
+        assert nx.algebraic_connectivity(G, tol=1e-12, method=method) == pytest.approx(
+            2, abs=1e-7
+        )
+        x = nx.fiedler_vector(G, tol=1e-12, method=method)
+        check_eigenvector(A, 2, x)
+
+    @pytest.mark.parametrize("method", methods)
+    def test_two_nodes_multigraph(self, method):
+        pytest.importorskip("scipy")
+        G = nx.MultiGraph()
+        G.add_edge(0, 0, spam=1e8)
+        G.add_edge(0, 1, spam=1)
+        G.add_edge(0, 1, spam=-2)
+        A = -3 * nx.laplacian_matrix(G, weight="spam")
+        assert nx.algebraic_connectivity(
+            G, weight="spam", tol=1e-12, method=method
+        ) == pytest.approx(6, abs=1e-7)
+        x = nx.fiedler_vector(G, weight="spam", tol=1e-12, method=method)
+        check_eigenvector(A, 6, x)
+
+    def test_abbreviation_of_method(self):
+        pytest.importorskip("scipy")
+        G = nx.path_graph(8)
+        A = nx.laplacian_matrix(G)
+        sigma = 2 - sqrt(2 + sqrt(2))
+        ac = nx.algebraic_connectivity(G, tol=1e-12, method="tracemin")
+        assert ac == pytest.approx(sigma, abs=1e-7)
+        x = nx.fiedler_vector(G, tol=1e-12, method="tracemin")
+        check_eigenvector(A, sigma, x)
+
+    @pytest.mark.parametrize("method", methods)
+    def test_path(self, method):
+        pytest.importorskip("scipy")
+        G = nx.path_graph(8)
+        A = nx.laplacian_matrix(G)
+        sigma = 2 - sqrt(2 + sqrt(2))
+        ac = nx.algebraic_connectivity(G, tol=1e-12, method=method)
+        assert ac == pytest.approx(sigma, abs=1e-7)
+        x = nx.fiedler_vector(G, tol=1e-12, method=method)
+        check_eigenvector(A, sigma, x)
+
+    @pytest.mark.parametrize("method", methods)
+    def test_problematic_graph_issue_2381(self, method):
+        pytest.importorskip("scipy")
+        G = nx.path_graph(4)
+        G.add_edges_from([(4, 2), (5, 1)])
+        A = nx.laplacian_matrix(G)
+        sigma = 0.438447187191
+        ac = nx.algebraic_connectivity(G, tol=1e-12, method=method)
+        assert ac == pytest.approx(sigma, abs=1e-7)
+        x = nx.fiedler_vector(G, tol=1e-12, method=method)
+        check_eigenvector(A, sigma, x)
+
+    @pytest.mark.parametrize("method", methods)
+    def test_cycle(self, method):
+        pytest.importorskip("scipy")
+        G = nx.cycle_graph(8)
+        A = nx.laplacian_matrix(G)
+        sigma = 2 - sqrt(2)
+        ac = nx.algebraic_connectivity(G, tol=1e-12, method=method)
+        assert ac == pytest.approx(sigma, abs=1e-7)
+        x = nx.fiedler_vector(G, tol=1e-12, method=method)
+        check_eigenvector(A, sigma, x)
+
+    @pytest.mark.parametrize("method", methods)
+    def test_seed_argument(self, method):
+        pytest.importorskip("scipy")
+        G = nx.cycle_graph(8)
+        A = nx.laplacian_matrix(G)
+        sigma = 2 - sqrt(2)
+        ac = nx.algebraic_connectivity(G, tol=1e-12, method=method, seed=1)
+        assert ac == pytest.approx(sigma, abs=1e-7)
+        x = nx.fiedler_vector(G, tol=1e-12, method=method, seed=1)
+        check_eigenvector(A, sigma, x)
+
+    @pytest.mark.parametrize(
+        ("normalized", "sigma", "laplacian_fn"),
+        (
+            (False, 0.2434017461399311, nx.laplacian_matrix),
+            (True, 0.08113391537997749, nx.normalized_laplacian_matrix),
+        ),
+    )
+    @pytest.mark.parametrize("method", methods)
+    def test_buckminsterfullerene(self, normalized, sigma, laplacian_fn, method):
+        pytest.importorskip("scipy")
+        G = nx.Graph(
+            [
+                (1, 10),
+                (1, 41),
+                (1, 59),
+                (2, 12),
+                (2, 42),
+                (2, 60),
+                (3, 6),
+                (3, 43),
+                (3, 57),
+                (4, 8),
+                (4, 44),
+                (4, 58),
+                (5, 13),
+                (5, 56),
+                (5, 57),
+                (6, 10),
+                (6, 31),
+                (7, 14),
+                (7, 56),
+                (7, 58),
+                (8, 12),
+                (8, 32),
+                (9, 23),
+                (9, 53),
+                (9, 59),
+                (10, 15),
+                (11, 24),
+                (11, 53),
+                (11, 60),
+                (12, 16),
+                (13, 14),
+                (13, 25),
+                (14, 26),
+                (15, 27),
+                (15, 49),
+                (16, 28),
+                (16, 50),
+                (17, 18),
+                (17, 19),
+                (17, 54),
+                (18, 20),
+                (18, 55),
+                (19, 23),
+                (19, 41),
+                (20, 24),
+                (20, 42),
+                (21, 31),
+                (21, 33),
+                (21, 57),
+                (22, 32),
+                (22, 34),
+                (22, 58),
+                (23, 24),
+                (25, 35),
+                (25, 43),
+                (26, 36),
+                (26, 44),
+                (27, 51),
+                (27, 59),
+                (28, 52),
+                (28, 60),
+                (29, 33),
+                (29, 34),
+                (29, 56),
+                (30, 51),
+                (30, 52),
+                (30, 53),
+                (31, 47),
+                (32, 48),
+                (33, 45),
+                (34, 46),
+                (35, 36),
+                (35, 37),
+                (36, 38),
+                (37, 39),
+                (37, 49),
+                (38, 40),
+                (38, 50),
+                (39, 40),
+                (39, 51),
+                (40, 52),
+                (41, 47),
+                (42, 48),
+                (43, 49),
+                (44, 50),
+                (45, 46),
+                (45, 54),
+                (46, 55),
+                (47, 54),
+                (48, 55),
+            ]
+        )
+        A = laplacian_fn(G)
+        try:
+            assert nx.algebraic_connectivity(
+                G, normalized=normalized, tol=1e-12, method=method
+            ) == pytest.approx(sigma, abs=1e-7)
+            x = nx.fiedler_vector(G, normalized=normalized, tol=1e-12, method=method)
+            check_eigenvector(A, sigma, x)
+        except nx.NetworkXError as err:
+            if err.args not in (
+                ("Cholesky solver unavailable.",),
+                ("LU solver unavailable.",),
+            ):
+                raise
+
+
+class TestSpectralOrdering:
+    _graphs = (nx.Graph, nx.DiGraph, nx.MultiGraph, nx.MultiDiGraph)
+
+    @pytest.mark.parametrize("graph", _graphs)
+    def test_nullgraph(self, graph):
+        G = graph()
+        pytest.raises(nx.NetworkXError, nx.spectral_ordering, G)
+
+    @pytest.mark.parametrize("graph", _graphs)
+    def test_singleton(self, graph):
+        G = graph()
+        G.add_node("x")
+        assert nx.spectral_ordering(G) == ["x"]
+        G.add_edge("x", "x", weight=33)
+        G.add_edge("x", "x", weight=33)
+        assert nx.spectral_ordering(G) == ["x"]
+
+    def test_unrecognized_method(self):
+        G = nx.path_graph(4)
+        pytest.raises(nx.NetworkXError, nx.spectral_ordering, G, method="unknown")
+
+    @pytest.mark.parametrize("method", methods)
+    def test_three_nodes(self, method):
+        pytest.importorskip("scipy")
+        G = nx.Graph()
+        G.add_weighted_edges_from([(1, 2, 1), (1, 3, 2), (2, 3, 1)], weight="spam")
+        order = nx.spectral_ordering(G, weight="spam", method=method)
+        assert set(order) == set(G)
+        assert {1, 3} in (set(order[:-1]), set(order[1:]))
+
+    @pytest.mark.parametrize("method", methods)
+    def test_three_nodes_multigraph(self, method):
+        pytest.importorskip("scipy")
+        G = nx.MultiDiGraph()
+        G.add_weighted_edges_from([(1, 2, 1), (1, 3, 2), (2, 3, 1), (2, 3, 2)])
+        order = nx.spectral_ordering(G, method=method)
+        assert set(order) == set(G)
+        assert {2, 3} in (set(order[:-1]), set(order[1:]))
+
+    @pytest.mark.parametrize("method", methods)
+    def test_path(self, method):
+        pytest.importorskip("scipy")
+        path = list(range(10))
+        np.random.shuffle(path)
+        G = nx.Graph()
+        nx.add_path(G, path)
+        order = nx.spectral_ordering(G, method=method)
+        assert order in [path, list(reversed(path))]
+
+    @pytest.mark.parametrize("method", methods)
+    def test_seed_argument(self, method):
+        pytest.importorskip("scipy")
+        path = list(range(10))
+        np.random.shuffle(path)
+        G = nx.Graph()
+        nx.add_path(G, path)
+        order = nx.spectral_ordering(G, method=method, seed=1)
+        assert order in [path, list(reversed(path))]
+
+    @pytest.mark.parametrize("method", methods)
+    def test_disconnected(self, method):
+        pytest.importorskip("scipy")
+        G = nx.Graph()
+        nx.add_path(G, range(0, 10, 2))
+        nx.add_path(G, range(1, 10, 2))
+        order = nx.spectral_ordering(G, method=method)
+        assert set(order) == set(G)
+        seqs = [
+            list(range(0, 10, 2)),
+            list(range(8, -1, -2)),
+            list(range(1, 10, 2)),
+            list(range(9, -1, -2)),
+        ]
+        assert order[:5] in seqs
+        assert order[5:] in seqs
+
+    @pytest.mark.parametrize(
+        ("normalized", "expected_order"),
+        (
+            (False, [[1, 2, 0, 3, 4, 5, 6, 9, 7, 8], [8, 7, 9, 6, 5, 4, 3, 0, 2, 1]]),
+            (True, [[1, 2, 3, 0, 4, 5, 9, 6, 7, 8], [8, 7, 6, 9, 5, 4, 0, 3, 2, 1]]),
+        ),
+    )
+    @pytest.mark.parametrize("method", methods)
+    def test_cycle(self, normalized, expected_order, method):
+        pytest.importorskip("scipy")
+        path = list(range(10))
+        G = nx.Graph()
+        nx.add_path(G, path, weight=5)
+        G.add_edge(path[-1], path[0], weight=1)
+        A = nx.laplacian_matrix(G).todense()
+        order = nx.spectral_ordering(G, normalized=normalized, method=method)
+        assert order in expected_order

tuning-competition-baseline/.venv/lib/python3.11/site-packages/networkx/linalg/tests/test_bethehessian.py

@@ -0,0 +1,41 @@
+import pytest
+
+np = pytest.importorskip("numpy")
+pytest.importorskip("scipy")
+
+import networkx as nx
+from networkx.generators.degree_seq import havel_hakimi_graph
+
+
+class TestBetheHessian:
+    @classmethod
+    def setup_class(cls):
+        deg = [3, 2, 2, 1, 0]
+        cls.G = havel_hakimi_graph(deg)
+        cls.P = nx.path_graph(3)
+
+    def test_bethe_hessian(self):
+        "Bethe Hessian matrix"
+        # fmt: off
+        H = np.array([[4, -2, 0],
+                      [-2, 5, -2],
+                      [0, -2, 4]])
+        # fmt: on
+        permutation = [2, 0, 1]
+        # Bethe Hessian gives expected form
+        np.testing.assert_equal(nx.bethe_hessian_matrix(self.P, r=2).todense(), H)
+        # nodelist is correctly implemented
+        np.testing.assert_equal(
+            nx.bethe_hessian_matrix(self.P, r=2, nodelist=permutation).todense(),
+            H[np.ix_(permutation, permutation)],
+        )
+        # Equal to Laplacian matrix when r=1
+        np.testing.assert_equal(
+            nx.bethe_hessian_matrix(self.G, r=1).todense(),
+            nx.laplacian_matrix(self.G).todense(),
+        )
+        # Correct default for the regularizer r
+        np.testing.assert_equal(
+            nx.bethe_hessian_matrix(self.G).todense(),
+            nx.bethe_hessian_matrix(self.G, r=1.25).todense(),
+        )

tuning-competition-baseline/.venv/lib/python3.11/site-packages/networkx/linalg/tests/test_laplacian.py

@@ -0,0 +1,242 @@
+import pytest
+
+np = pytest.importorskip("numpy")
+pytest.importorskip("scipy")
+
+import networkx as nx
+from networkx.generators.degree_seq import havel_hakimi_graph
+from networkx.generators.expanders import margulis_gabber_galil_graph
+
+
+class TestLaplacian:
+    @classmethod
+    def setup_class(cls):
+        deg = [3, 2, 2, 1, 0]
+        cls.G = havel_hakimi_graph(deg)
+        cls.WG = nx.Graph(
+            (u, v, {"weight": 0.5, "other": 0.3}) for (u, v) in cls.G.edges()
+        )
+        cls.WG.add_node(4)
+        cls.MG = nx.MultiGraph(cls.G)
+
+        # Graph with clsloops
+        cls.Gsl = cls.G.copy()
+        for node in cls.Gsl.nodes():
+            cls.Gsl.add_edge(node, node)
+
+    def test_laplacian(self):
+        "Graph Laplacian"
+        # fmt: off
+        NL = np.array([[ 3, -1, -1, -1,  0],
+                       [-1,  2, -1,  0,  0],
+                       [-1, -1,  2,  0,  0],
+                       [-1,  0,  0,  1,  0],
+                       [ 0,  0,  0,  0,  0]])
+        # fmt: on
+        WL = 0.5 * NL
+        OL = 0.3 * NL
+        np.testing.assert_equal(nx.laplacian_matrix(self.G).todense(), NL)
+        np.testing.assert_equal(nx.laplacian_matrix(self.MG).todense(), NL)
+        np.testing.assert_equal(
+            nx.laplacian_matrix(self.G, nodelist=[0, 1]).todense(),
+            np.array([[1, -1], [-1, 1]]),
+        )
+        np.testing.assert_equal(nx.laplacian_matrix(self.WG).todense(), WL)
+        np.testing.assert_equal(nx.laplacian_matrix(self.WG, weight=None).todense(), NL)
+        np.testing.assert_equal(
+            nx.laplacian_matrix(self.WG, weight="other").todense(), OL
+        )
+
+    def test_normalized_laplacian(self):
+        "Generalized Graph Laplacian"
+        # fmt: off
+        G = np.array([[ 1.   , -0.408, -0.408, -0.577,  0.],
+                      [-0.408,  1.   , -0.5  ,  0.   ,  0.],
+                      [-0.408, -0.5  ,  1.   ,  0.   ,  0.],
+                      [-0.577,  0.   ,  0.   ,  1.   ,  0.],
+                      [ 0.   ,  0.   ,  0.   ,  0.   ,  0.]])
+        GL = np.array([[ 1.   , -0.408, -0.408, -0.577,  0.   ],
+                       [-0.408,  1.   , -0.5  ,  0.   ,  0.   ],
+                       [-0.408, -0.5  ,  1.   ,  0.   ,  0.   ],
+                       [-0.577,  0.   ,  0.   ,  1.   ,  0.   ],
+                       [ 0.   ,  0.   ,  0.   ,  0.   ,  0.   ]])
+        Lsl = np.array([[ 0.75  , -0.2887, -0.2887, -0.3536,  0.    ],
+                        [-0.2887,  0.6667, -0.3333,  0.    ,  0.    ],
+                        [-0.2887, -0.3333,  0.6667,  0.    ,  0.    ],
+                        [-0.3536,  0.    ,  0.    ,  0.5   ,  0.    ],
+                        [ 0.    ,  0.    ,  0.    ,  0.    ,  0.    ]])
+        # fmt: on
+
+        np.testing.assert_almost_equal(
+            nx.normalized_laplacian_matrix(self.G, nodelist=range(5)).todense(),
+            G,
+            decimal=3,
+        )
+        np.testing.assert_almost_equal(
+            nx.normalized_laplacian_matrix(self.G).todense(), GL, decimal=3
+        )
+        np.testing.assert_almost_equal(
+            nx.normalized_laplacian_matrix(self.MG).todense(), GL, decimal=3
+        )
+        np.testing.assert_almost_equal(
+            nx.normalized_laplacian_matrix(self.WG).todense(), GL, decimal=3
+        )
+        np.testing.assert_almost_equal(
+            nx.normalized_laplacian_matrix(self.WG, weight="other").todense(),
+            GL,
+            decimal=3,
+        )
+        np.testing.assert_almost_equal(
+            nx.normalized_laplacian_matrix(self.Gsl).todense(), Lsl, decimal=3
+        )
+
+
+def test_directed_laplacian():
+    "Directed Laplacian"
+    # Graph used as an example in Sec. 4.1 of Langville and Meyer,
+    # "Google's PageRank and Beyond". The graph contains dangling nodes, so
+    # the pagerank random walk is selected by directed_laplacian
+    G = nx.DiGraph()
+    G.add_edges_from(
+        (
+            (1, 2),
+            (1, 3),
+            (3, 1),
+            (3, 2),
+            (3, 5),
+            (4, 5),
+            (4, 6),
+            (5, 4),
+            (5, 6),
+            (6, 4),
+        )
+    )
+    # fmt: off
+    GL = np.array([[ 0.9833, -0.2941, -0.3882, -0.0291, -0.0231, -0.0261],
+                   [-0.2941,  0.8333, -0.2339, -0.0536, -0.0589, -0.0554],
+                   [-0.3882, -0.2339,  0.9833, -0.0278, -0.0896, -0.0251],
+                   [-0.0291, -0.0536, -0.0278,  0.9833, -0.4878, -0.6675],
+                   [-0.0231, -0.0589, -0.0896, -0.4878,  0.9833, -0.2078],
+                   [-0.0261, -0.0554, -0.0251, -0.6675, -0.2078,  0.9833]])
+    # fmt: on
+    L = nx.directed_laplacian_matrix(G, alpha=0.9, nodelist=sorted(G))
+    np.testing.assert_almost_equal(L, GL, decimal=3)
+
+    # Make the graph strongly connected, so we can use a random and lazy walk
+    G.add_edges_from(((2, 5), (6, 1)))
+    # fmt: off
+    GL = np.array([[ 1.    , -0.3062, -0.4714,  0.    ,  0.    , -0.3227],
+                   [-0.3062,  1.    , -0.1443,  0.    , -0.3162,  0.    ],
+                   [-0.4714, -0.1443,  1.    ,  0.    , -0.0913,  0.    ],
+                   [ 0.    ,  0.    ,  0.    ,  1.    , -0.5   , -0.5   ],
+                   [ 0.    , -0.3162, -0.0913, -0.5   ,  1.    , -0.25  ],
+                   [-0.3227,  0.    ,  0.    , -0.5   , -0.25  ,  1.    ]])
+    # fmt: on
+    L = nx.directed_laplacian_matrix(
+        G, alpha=0.9, nodelist=sorted(G), walk_type="random"
+    )
+    np.testing.assert_almost_equal(L, GL, decimal=3)
+
+    # fmt: off
+    GL = np.array([[ 0.5   , -0.1531, -0.2357,  0.    ,  0.    , -0.1614],
+                   [-0.1531,  0.5   , -0.0722,  0.    , -0.1581,  0.    ],
+                   [-0.2357, -0.0722,  0.5   ,  0.    , -0.0456,  0.    ],
+                   [ 0.    ,  0.    ,  0.    ,  0.5   , -0.25  , -0.25  ],
+                   [ 0.    , -0.1581, -0.0456, -0.25  ,  0.5   , -0.125 ],
+                   [-0.1614,  0.    ,  0.    , -0.25  , -0.125 ,  0.5   ]])  
+    # fmt: on
+    L = nx.directed_laplacian_matrix(G, alpha=0.9, nodelist=sorted(G), walk_type="lazy")
+    np.testing.assert_almost_equal(L, GL, decimal=3)
+
+    # Make a strongly connected periodic graph
+    G = nx.DiGraph()
+    G.add_edges_from(((1, 2), (2, 4), (4, 1), (1, 3), (3, 4)))
+    # fmt: off
+    GL = np.array([[ 0.5  , -0.176, -0.176, -0.25 ],
+                   [-0.176,  0.5  ,  0.   , -0.176],
+                   [-0.176,  0.   ,  0.5  , -0.176],
+                   [-0.25 , -0.176, -0.176,  0.5  ]])
+    # fmt: on
+    L = nx.directed_laplacian_matrix(G, alpha=0.9, nodelist=sorted(G))
+    np.testing.assert_almost_equal(L, GL, decimal=3)
+
+
+def test_directed_combinatorial_laplacian():
+    "Directed combinatorial Laplacian"
+    # Graph used as an example in Sec. 4.1 of Langville and Meyer,
+    # "Google's PageRank and Beyond". The graph contains dangling nodes, so
+    # the pagerank random walk is selected by directed_laplacian
+    G = nx.DiGraph()
+    G.add_edges_from(
+        (
+            (1, 2),
+            (1, 3),
+            (3, 1),
+            (3, 2),
+            (3, 5),
+            (4, 5),
+            (4, 6),
+            (5, 4),
+            (5, 6),
+            (6, 4),
+        )
+    )
+    # fmt: off
+    GL = np.array([[ 0.0366, -0.0132, -0.0153, -0.0034, -0.0020, -0.0027],
+                   [-0.0132,  0.0450, -0.0111, -0.0076, -0.0062, -0.0069],
+                   [-0.0153, -0.0111,  0.0408, -0.0035, -0.0083, -0.0027],
+                   [-0.0034, -0.0076, -0.0035,  0.3688, -0.1356, -0.2187],
+                   [-0.0020, -0.0062, -0.0083, -0.1356,  0.2026, -0.0505],
+                   [-0.0027, -0.0069, -0.0027, -0.2187, -0.0505,  0.2815]])
+    # fmt: on
+
+    L = nx.directed_combinatorial_laplacian_matrix(G, alpha=0.9, nodelist=sorted(G))
+    np.testing.assert_almost_equal(L, GL, decimal=3)
+
+    # Make the graph strongly connected, so we can use a random and lazy walk
+    G.add_edges_from(((2, 5), (6, 1)))
+
+    # fmt: off
+    GL = np.array([[ 0.1395, -0.0349, -0.0465,  0.    ,  0.    , -0.0581],
+                   [-0.0349,  0.093 , -0.0116,  0.    , -0.0465,  0.    ],
+                   [-0.0465, -0.0116,  0.0698,  0.    , -0.0116,  0.    ],
+                   [ 0.    ,  0.    ,  0.    ,  0.2326, -0.1163, -0.1163],
+                   [ 0.    , -0.0465, -0.0116, -0.1163,  0.2326, -0.0581],
+                   [-0.0581,  0.    ,  0.    , -0.1163, -0.0581,  0.2326]])
+    # fmt: on
+
+    L = nx.directed_combinatorial_laplacian_matrix(
+        G, alpha=0.9, nodelist=sorted(G), walk_type="random"
+    )
+    np.testing.assert_almost_equal(L, GL, decimal=3)
+
+    # fmt: off
+    GL = np.array([[ 0.0698, -0.0174, -0.0233,  0.    ,  0.    , -0.0291],
+                   [-0.0174,  0.0465, -0.0058,  0.    , -0.0233,  0.    ],
+                   [-0.0233, -0.0058,  0.0349,  0.    , -0.0058,  0.    ],
+                   [ 0.    ,  0.    ,  0.    ,  0.1163, -0.0581, -0.0581],
+                   [ 0.    , -0.0233, -0.0058, -0.0581,  0.1163, -0.0291],
+                   [-0.0291,  0.    ,  0.    , -0.0581, -0.0291,  0.1163]])
+    # fmt: on
+
+    L = nx.directed_combinatorial_laplacian_matrix(
+        G, alpha=0.9, nodelist=sorted(G), walk_type="lazy"
+    )
+    np.testing.assert_almost_equal(L, GL, decimal=3)
+
+    E = nx.DiGraph(margulis_gabber_galil_graph(2))
+    L = nx.directed_combinatorial_laplacian_matrix(E)
+    # fmt: off
+    expected = np.array(
+        [[ 0.16666667, -0.08333333, -0.08333333,  0.        ],
+         [-0.08333333,  0.16666667,  0.        , -0.08333333],
+         [-0.08333333,  0.        ,  0.16666667, -0.08333333],
+         [ 0.        , -0.08333333, -0.08333333,  0.16666667]]
+    )
+    # fmt: on
+    np.testing.assert_almost_equal(L, expected, decimal=6)
+
+    with pytest.raises(nx.NetworkXError):
+        nx.directed_combinatorial_laplacian_matrix(G, walk_type="pagerank", alpha=100)
+    with pytest.raises(nx.NetworkXError):
+        nx.directed_combinatorial_laplacian_matrix(G, walk_type="silly")

tuning-competition-baseline/.venv/lib/python3.11/site-packages/networkx/readwrite/gml.py

@@ -0,0 +1,878 @@
+"""
+Read graphs in GML format.
+
+"GML, the Graph Modelling Language, is our proposal for a portable
+file format for graphs. GML's key features are portability, simple
+syntax, extensibility and flexibility. A GML file consists of a
+hierarchical key-value lists. Graphs can be annotated with arbitrary
+data structures. The idea for a common file format was born at the
+GD'95; this proposal is the outcome of many discussions. GML is the
+standard file format in the Graphlet graph editor system. It has been
+overtaken and adapted by several other systems for drawing graphs."
+
+GML files are stored using a 7-bit ASCII encoding with any extended
+ASCII characters (iso8859-1) appearing as HTML character entities.
+You will need to give some thought into how the exported data should
+interact with different languages and even different Python versions.
+Re-importing from gml is also a concern.
+
+Without specifying a `stringizer`/`destringizer`, the code is capable of
+writing `int`/`float`/`str`/`dict`/`list` data as required by the GML 
+specification.  For writing other data types, and for reading data other
+than `str` you need to explicitly supply a `stringizer`/`destringizer`.
+
+For additional documentation on the GML file format, please see the
+`GML website <https://web.archive.org/web/20190207140002/http://www.fim.uni-passau.de/index.php?id=17297&L=1>`_.
+
+Several example graphs in GML format may be found on Mark Newman's
+`Network data page <http://www-personal.umich.edu/~mejn/netdata/>`_.
+"""
+import html.entities as htmlentitydefs
+import re
+import warnings
+from ast import literal_eval
+from collections import defaultdict
+from enum import Enum
+from io import StringIO
+from typing import Any, NamedTuple
+
+import networkx as nx
+from networkx.exception import NetworkXError
+from networkx.utils import open_file
+
+__all__ = ["read_gml", "parse_gml", "generate_gml", "write_gml"]
+
+
+def escape(text):
+    """Use XML character references to escape characters.
+
+    Use XML character references for unprintable or non-ASCII
+    characters, double quotes and ampersands in a string
+    """
+
+    def fixup(m):
+        ch = m.group(0)
+        return "&#" + str(ord(ch)) + ";"
+
+    text = re.sub('[^ -~]|[&"]', fixup, text)
+    return text if isinstance(text, str) else str(text)
+
+
+def unescape(text):
+    """Replace XML character references with the referenced characters"""
+
+    def fixup(m):
+        text = m.group(0)
+        if text[1] == "#":
+            # Character reference
+            if text[2] == "x":
+                code = int(text[3:-1], 16)
+            else:
+                code = int(text[2:-1])
+        else:
+            # Named entity
+            try:
+                code = htmlentitydefs.name2codepoint[text[1:-1]]
+            except KeyError:
+                return text  # leave unchanged
+        try:
+            return chr(code)
+        except (ValueError, OverflowError):
+            return text  # leave unchanged
+
+    return re.sub("&(?:[0-9A-Za-z]+|#(?:[0-9]+|x[0-9A-Fa-f]+));", fixup, text)
+
+
+def literal_destringizer(rep):
+    """Convert a Python literal to the value it represents.
+
+    Parameters
+    ----------
+    rep : string
+        A Python literal.
+
+    Returns
+    -------
+    value : object
+        The value of the Python literal.
+
+    Raises
+    ------
+    ValueError
+        If `rep` is not a Python literal.
+    """
+    if isinstance(rep, str):
+        orig_rep = rep
+        try:
+            return literal_eval(rep)
+        except SyntaxError as err:
+            raise ValueError(f"{orig_rep!r} is not a valid Python literal") from err
+    else:
+        raise ValueError(f"{rep!r} is not a string")
+
+
+@open_file(0, mode="rb")
+@nx._dispatch(graphs=None)
+def read_gml(path, label="label", destringizer=None):
+    """Read graph in GML format from `path`.
+
+    Parameters
+    ----------
+    path : filename or filehandle
+        The filename or filehandle to read from.
+
+    label : string, optional
+        If not None, the parsed nodes will be renamed according to node
+        attributes indicated by `label`. Default value: 'label'.
+
+    destringizer : callable, optional
+        A `destringizer` that recovers values stored as strings in GML. If it
+        cannot convert a string to a value, a `ValueError` is raised. Default
+        value : None.
+
+    Returns
+    -------
+    G : NetworkX graph
+        The parsed graph.
+
+    Raises
+    ------
+    NetworkXError
+        If the input cannot be parsed.
+
+    See Also
+    --------
+    write_gml, parse_gml
+    literal_destringizer
+
+    Notes
+    -----
+    GML files are stored using a 7-bit ASCII encoding with any extended
+    ASCII characters (iso8859-1) appearing as HTML character entities.
+    Without specifying a `stringizer`/`destringizer`, the code is capable of
+    writing `int`/`float`/`str`/`dict`/`list` data as required by the GML
+    specification.  For writing other data types, and for reading data other
+    than `str` you need to explicitly supply a `stringizer`/`destringizer`.
+
+    For additional documentation on the GML file format, please see the
+    `GML url <https://web.archive.org/web/20190207140002/http://www.fim.uni-passau.de/index.php?id=17297&L=1>`_.
+
+    See the module docstring :mod:`networkx.readwrite.gml` for more details.
+
+    Examples
+    --------
+    >>> G = nx.path_graph(4)
+    >>> nx.write_gml(G, "test.gml")
+
+    GML values are interpreted as strings by default:
+
+    >>> H = nx.read_gml("test.gml")
+    >>> H.nodes
+    NodeView(('0', '1', '2', '3'))
+
+    When a `destringizer` is provided, GML values are converted to the provided type.
+    For example, integer nodes can be recovered as shown below:
+
+    >>> J = nx.read_gml("test.gml", destringizer=int)
+    >>> J.nodes
+    NodeView((0, 1, 2, 3))
+
+    """
+
+    def filter_lines(lines):
+        for line in lines:
+            try:
+                line = line.decode("ascii")
+            except UnicodeDecodeError as err:
+                raise NetworkXError("input is not ASCII-encoded") from err
+            if not isinstance(line, str):
+                lines = str(lines)
+            if line and line[-1] == "\n":
+                line = line[:-1]
+            yield line
+
+    G = parse_gml_lines(filter_lines(path), label, destringizer)
+    return G
+
+
+@nx._dispatch(graphs=None)
+def parse_gml(lines, label="label", destringizer=None):
+    """Parse GML graph from a string or iterable.
+
+    Parameters
+    ----------
+    lines : string or iterable of strings
+       Data in GML format.
+
+    label : string, optional
+        If not None, the parsed nodes will be renamed according to node
+        attributes indicated by `label`. Default value: 'label'.
+
+    destringizer : callable, optional
+        A `destringizer` that recovers values stored as strings in GML. If it
+        cannot convert a string to a value, a `ValueError` is raised. Default
+        value : None.
+
+    Returns
+    -------
+    G : NetworkX graph
+        The parsed graph.
+
+    Raises
+    ------
+    NetworkXError
+        If the input cannot be parsed.
+
+    See Also
+    --------
+    write_gml, read_gml
+
+    Notes
+    -----
+    This stores nested GML attributes as dictionaries in the NetworkX graph,
+    node, and edge attribute structures.
+
+    GML files are stored using a 7-bit ASCII encoding with any extended
+    ASCII characters (iso8859-1) appearing as HTML character entities.
+    Without specifying a `stringizer`/`destringizer`, the code is capable of
+    writing `int`/`float`/`str`/`dict`/`list` data as required by the GML
+    specification.  For writing other data types, and for reading data other
+    than `str` you need to explicitly supply a `stringizer`/`destringizer`.
+
+    For additional documentation on the GML file format, please see the
+    `GML url <https://web.archive.org/web/20190207140002/http://www.fim.uni-passau.de/index.php?id=17297&L=1>`_.
+
+    See the module docstring :mod:`networkx.readwrite.gml` for more details.
+    """
+
+    def decode_line(line):
+        if isinstance(line, bytes):
+            try:
+                line.decode("ascii")
+            except UnicodeDecodeError as err:
+                raise NetworkXError("input is not ASCII-encoded") from err
+        if not isinstance(line, str):
+            line = str(line)
+        return line
+
+    def filter_lines(lines):
+        if isinstance(lines, str):
+            lines = decode_line(lines)
+            lines = lines.splitlines()
+            yield from lines
+        else:
+            for line in lines:
+                line = decode_line(line)
+                if line and line[-1] == "\n":
+                    line = line[:-1]
+                if line.find("\n") != -1:
+                    raise NetworkXError("input line contains newline")
+                yield line
+
+    G = parse_gml_lines(filter_lines(lines), label, destringizer)
+    return G
+
+
+class Pattern(Enum):
+    """encodes the index of each token-matching pattern in `tokenize`."""
+
+    KEYS = 0
+    REALS = 1
+    INTS = 2
+    STRINGS = 3
+    DICT_START = 4
+    DICT_END = 5
+    COMMENT_WHITESPACE = 6
+
+
+class Token(NamedTuple):
+    category: Pattern
+    value: Any
+    line: int
+    position: int
+
+
+LIST_START_VALUE = "_networkx_list_start"
+
+
+def parse_gml_lines(lines, label, destringizer):
+    """Parse GML `lines` into a graph."""
+
+    def tokenize():
+        patterns = [
+            r"[A-Za-z][0-9A-Za-z_]*\b",  # keys
+            # reals
+            r"[+-]?(?:[0-9]*\.[0-9]+|[0-9]+\.[0-9]*|INF)(?:[Ee][+-]?[0-9]+)?",
+            r"[+-]?[0-9]+",  # ints
+            r'".*?"',  # strings
+            r"\[",  # dict start
+            r"\]",  # dict end
+            r"#.*$|\s+",  # comments and whitespaces
+        ]
+        tokens = re.compile("|".join(f"({pattern})" for pattern in patterns))
+        lineno = 0
+        multilines = []  # entries spread across multiple lines
+        for line in lines:
+            pos = 0
+
+            # deal with entries spread across multiple lines
+            #
+            # should we actually have to deal with escaped "s then do it here
+            if multilines:
+                multilines.append(line.strip())
+                if line[-1] == '"':  # closing multiline entry
+                    # multiline entries will be joined by space. cannot
+                    # reintroduce newlines as this will break the tokenizer
+                    line = " ".join(multilines)
+                    multilines = []
+                else:  # continued multiline entry
+                    lineno += 1
+                    continue
+            else:
+                if line.count('"') == 1:  # opening multiline entry
+                    if line.strip()[0] != '"' and line.strip()[-1] != '"':
+                        # since we expect something like key "value", the " should not be found at ends
+                        # otherwise tokenizer will pick up the formatting mistake.
+                        multilines = [line.rstrip()]
+                        lineno += 1
+                        continue
+
+            length = len(line)
+
+            while pos < length:
+                match = tokens.match(line, pos)
+                if match is None:
+                    m = f"cannot tokenize {line[pos:]} at ({lineno + 1}, {pos + 1})"
+                    raise NetworkXError(m)
+                for i in range(len(patterns)):
+                    group = match.group(i + 1)
+                    if group is not None:
+                        if i == 0:  # keys
+                            value = group.rstrip()
+                        elif i == 1:  # reals
+                            value = float(group)
+                        elif i == 2:  # ints
+                            value = int(group)
+                        else:
+                            value = group
+                        if i != 6:  # comments and whitespaces
+                            yield Token(Pattern(i), value, lineno + 1, pos + 1)
+                        pos += len(group)
+                        break
+            lineno += 1
+        yield Token(None, None, lineno + 1, 1)  # EOF
+
+    def unexpected(curr_token, expected):
+        category, value, lineno, pos = curr_token
+        value = repr(value) if value is not None else "EOF"
+        raise NetworkXError(f"expected {expected}, found {value} at ({lineno}, {pos})")
+
+    def consume(curr_token, category, expected):
+        if curr_token.category == category:
+            return next(tokens)
+        unexpected(curr_token, expected)
+
+    def parse_kv(curr_token):
+        dct = defaultdict(list)
+        while curr_token.category == Pattern.KEYS:
+            key = curr_token.value
+            curr_token = next(tokens)
+            category = curr_token.category
+            if category == Pattern.REALS or category == Pattern.INTS:
+                value = curr_token.value
+                curr_token = next(tokens)
+            elif category == Pattern.STRINGS:
+                value = unescape(curr_token.value[1:-1])
+                if destringizer:
+                    try:
+                        value = destringizer(value)
+                    except ValueError:
+                        pass
+                # Special handling for empty lists and tuples
+                if value == "()":
+                    value = ()
+                if value == "[]":
+                    value = []
+                curr_token = next(tokens)
+            elif category == Pattern.DICT_START:
+                curr_token, value = parse_dict(curr_token)
+            else:
+                # Allow for string convertible id and label values
+                if key in ("id", "label", "source", "target"):
+                    try:
+                        # String convert the token value
+                        value = unescape(str(curr_token.value))
+                        if destringizer:
+                            try:
+                                value = destringizer(value)
+                            except ValueError:
+                                pass
+                        curr_token = next(tokens)
+                    except Exception:
+                        msg = (
+                            "an int, float, string, '[' or string"
+                            + " convertible ASCII value for node id or label"
+                        )
+                        unexpected(curr_token, msg)
+                # Special handling for nan and infinity.  Since the gml language
+                # defines unquoted strings as keys, the numeric and string branches
+                # are skipped and we end up in this special branch, so we need to
+                # convert the current token value to a float for NAN and plain INF.
+                # +/-INF are handled in the pattern for 'reals' in tokenize().  This
+                # allows labels and values to be nan or infinity, but not keys.
+                elif curr_token.value in {"NAN", "INF"}:
+                    value = float(curr_token.value)
+                    curr_token = next(tokens)
+                else:  # Otherwise error out
+                    unexpected(curr_token, "an int, float, string or '['")
+            dct[key].append(value)
+
+        def clean_dict_value(value):
+            if not isinstance(value, list):
+                return value
+            if len(value) == 1:
+                return value[0]
+            if value[0] == LIST_START_VALUE:
+                return value[1:]
+            return value
+
+        dct = {key: clean_dict_value(value) for key, value in dct.items()}
+        return curr_token, dct
+
+    def parse_dict(curr_token):
+        # dict start
+        curr_token = consume(curr_token, Pattern.DICT_START, "'['")
+        # dict contents
+        curr_token, dct = parse_kv(curr_token)
+        # dict end
+        curr_token = consume(curr_token, Pattern.DICT_END, "']'")
+        return curr_token, dct
+
+    def parse_graph():
+        curr_token, dct = parse_kv(next(tokens))
+        if curr_token.category is not None:  # EOF
+            unexpected(curr_token, "EOF")
+        if "graph" not in dct:
+            raise NetworkXError("input contains no graph")
+        graph = dct["graph"]
+        if isinstance(graph, list):
+            raise NetworkXError("input contains more than one graph")
+        return graph
+
+    tokens = tokenize()
+    graph = parse_graph()
+
+    directed = graph.pop("directed", False)
+    multigraph = graph.pop("multigraph", False)
+    if not multigraph:
+        G = nx.DiGraph() if directed else nx.Graph()
+    else:
+        G = nx.MultiDiGraph() if directed else nx.MultiGraph()
+    graph_attr = {k: v for k, v in graph.items() if k not in ("node", "edge")}
+    G.graph.update(graph_attr)
+
+    def pop_attr(dct, category, attr, i):
+        try:
+            return dct.pop(attr)
+        except KeyError as err:
+            raise NetworkXError(f"{category} #{i} has no {attr!r} attribute") from err
+
+    nodes = graph.get("node", [])
+    mapping = {}
+    node_labels = set()
+    for i, node in enumerate(nodes if isinstance(nodes, list) else [nodes]):
+        id = pop_attr(node, "node", "id", i)
+        if id in G:
+            raise NetworkXError(f"node id {id!r} is duplicated")
+        if label is not None and label != "id":
+            node_label = pop_attr(node, "node", label, i)
+            if node_label in node_labels:
+                raise NetworkXError(f"node label {node_label!r} is duplicated")
+            node_labels.add(node_label)
+            mapping[id] = node_label
+        G.add_node(id, **node)
+
+    edges = graph.get("edge", [])
+    for i, edge in enumerate(edges if isinstance(edges, list) else [edges]):
+        source = pop_attr(edge, "edge", "source", i)
+        target = pop_attr(edge, "edge", "target", i)
+        if source not in G:
+            raise NetworkXError(f"edge #{i} has undefined source {source!r}")
+        if target not in G:
+            raise NetworkXError(f"edge #{i} has undefined target {target!r}")
+        if not multigraph:
+            if not G.has_edge(source, target):
+                G.add_edge(source, target, **edge)
+            else:
+                arrow = "->" if directed else "--"
+                msg = f"edge #{i} ({source!r}{arrow}{target!r}) is duplicated"
+                raise nx.NetworkXError(msg)
+        else:
+            key = edge.pop("key", None)
+            if key is not None and G.has_edge(source, target, key):
+                arrow = "->" if directed else "--"
+                msg = f"edge #{i} ({source!r}{arrow}{target!r}, {key!r})"
+                msg2 = 'Hint: If multigraph add "multigraph 1" to file header.'
+                raise nx.NetworkXError(msg + " is duplicated\n" + msg2)
+            G.add_edge(source, target, key, **edge)
+
+    if label is not None and label != "id":
+        G = nx.relabel_nodes(G, mapping)
+    return G
+
+
+def literal_stringizer(value):
+    """Convert a `value` to a Python literal in GML representation.
+
+    Parameters
+    ----------
+    value : object
+        The `value` to be converted to GML representation.
+
+    Returns
+    -------
+    rep : string
+        A double-quoted Python literal representing value. Unprintable
+        characters are replaced by XML character references.
+
+    Raises
+    ------
+    ValueError
+        If `value` cannot be converted to GML.
+
+    Notes
+    -----
+    The original value can be recovered using the
+    :func:`networkx.readwrite.gml.literal_destringizer` function.
+    """
+
+    def stringize(value):
+        if isinstance(value, (int, bool)) or value is None:
+            if value is True:  # GML uses 1/0 for boolean values.
+                buf.write(str(1))
+            elif value is False:
+                buf.write(str(0))
+            else:
+                buf.write(str(value))
+        elif isinstance(value, str):
+            text = repr(value)
+            if text[0] != "u":
+                try:
+                    value.encode("latin1")
+                except UnicodeEncodeError:
+                    text = "u" + text
+            buf.write(text)
+        elif isinstance(value, (float, complex, str, bytes)):
+            buf.write(repr(value))
+        elif isinstance(value, list):
+            buf.write("[")
+            first = True
+            for item in value:
+                if not first:
+                    buf.write(",")
+                else:
+                    first = False
+                stringize(item)
+            buf.write("]")
+        elif isinstance(value, tuple):
+            if len(value) > 1:
+                buf.write("(")
+                first = True
+                for item in value:
+                    if not first:
+                        buf.write(",")
+                    else:
+                        first = False
+                    stringize(item)
+                buf.write(")")
+            elif value:
+                buf.write("(")
+                stringize(value[0])
+                buf.write(",)")
+            else:
+                buf.write("()")
+        elif isinstance(value, dict):
+            buf.write("{")
+            first = True
+            for key, value in value.items():
+                if not first:
+                    buf.write(",")
+                else:
+                    first = False
+                stringize(key)
+                buf.write(":")
+                stringize(value)
+            buf.write("}")
+        elif isinstance(value, set):
+            buf.write("{")
+            first = True
+            for item in value:
+                if not first:
+                    buf.write(",")
+                else:
+                    first = False
+                stringize(item)
+            buf.write("}")
+        else:
+            msg = f"{value!r} cannot be converted into a Python literal"
+            raise ValueError(msg)
+
+    buf = StringIO()
+    stringize(value)
+    return buf.getvalue()
+
+
+def generate_gml(G, stringizer=None):
+    r"""Generate a single entry of the graph `G` in GML format.
+
+    Parameters
+    ----------
+    G : NetworkX graph
+        The graph to be converted to GML.
+
+    stringizer : callable, optional
+        A `stringizer` which converts non-int/non-float/non-dict values into
+        strings. If it cannot convert a value into a string, it should raise a
+        `ValueError` to indicate that. Default value: None.
+
+    Returns
+    -------
+    lines: generator of strings
+        Lines of GML data. Newlines are not appended.
+
+    Raises
+    ------
+    NetworkXError
+        If `stringizer` cannot convert a value into a string, or the value to
+        convert is not a string while `stringizer` is None.
+
+    See Also
+    --------
+    literal_stringizer
+
+    Notes
+    -----
+    Graph attributes named 'directed', 'multigraph', 'node' or
+    'edge', node attributes named 'id' or 'label', edge attributes
+    named 'source' or 'target' (or 'key' if `G` is a multigraph)
+    are ignored because these attribute names are used to encode the graph
+    structure.
+
+    GML files are stored using a 7-bit ASCII encoding with any extended
+    ASCII characters (iso8859-1) appearing as HTML character entities.
+    Without specifying a `stringizer`/`destringizer`, the code is capable of
+    writing `int`/`float`/`str`/`dict`/`list` data as required by the GML
+    specification.  For writing other data types, and for reading data other
+    than `str` you need to explicitly supply a `stringizer`/`destringizer`.
+
+    For additional documentation on the GML file format, please see the
+    `GML url <https://web.archive.org/web/20190207140002/http://www.fim.uni-passau.de/index.php?id=17297&L=1>`_.
+
+    See the module docstring :mod:`networkx.readwrite.gml` for more details.
+
+    Examples
+    --------
+    >>> G = nx.Graph()
+    >>> G.add_node("1")
+    >>> print("\n".join(nx.generate_gml(G)))
+    graph [
+      node [
+        id 0
+        label "1"
+      ]
+    ]
+    >>> G = nx.MultiGraph([("a", "b"), ("a", "b")])
+    >>> print("\n".join(nx.generate_gml(G)))
+    graph [
+      multigraph 1
+      node [
+        id 0
+        label "a"
+      ]
+      node [
+        id 1
+        label "b"
+      ]
+      edge [
+        source 0
+        target 1
+        key 0
+      ]
+      edge [
+        source 0
+        target 1
+        key 1
+      ]
+    ]
+    """
+    valid_keys = re.compile("^[A-Za-z][0-9A-Za-z_]*$")
+
+    def stringize(key, value, ignored_keys, indent, in_list=False):
+        if not isinstance(key, str):
+            raise NetworkXError(f"{key!r} is not a string")
+        if not valid_keys.match(key):
+            raise NetworkXError(f"{key!r} is not a valid key")
+        if not isinstance(key, str):
+            key = str(key)
+        if key not in ignored_keys:
+            if isinstance(value, (int, bool)):
+                if key == "label":
+                    yield indent + key + ' "' + str(value) + '"'
+                elif value is True:
+                    # python bool is an instance of int
+                    yield indent + key + " 1"
+                elif value is False:
+                    yield indent + key + " 0"
+                # GML only supports signed 32-bit integers
+                elif value < -(2**31) or value >= 2**31:
+                    yield indent + key + ' "' + str(value) + '"'
+                else:
+                    yield indent + key + " " + str(value)
+            elif isinstance(value, float):
+                text = repr(value).upper()
+                # GML matches INF to keys, so prepend + to INF. Use repr(float(*))
+                # instead of string literal to future proof against changes to repr.
+                if text == repr(float("inf")).upper():
+                    text = "+" + text
+                else:
+                    # GML requires that a real literal contain a decimal point, but
+                    # repr may not output a decimal point when the mantissa is
+                    # integral and hence needs fixing.
+                    epos = text.rfind("E")
+                    if epos != -1 and text.find(".", 0, epos) == -1:
+                        text = text[:epos] + "." + text[epos:]
+                if key == "label":
+                    yield indent + key + ' "' + text + '"'
+                else:
+                    yield indent + key + " " + text
+            elif isinstance(value, dict):
+                yield indent + key + " ["
+                next_indent = indent + "  "
+                for key, value in value.items():
+                    yield from stringize(key, value, (), next_indent)
+                yield indent + "]"
+            elif isinstance(value, tuple) and key == "label":
+                yield indent + key + f" \"({','.join(repr(v) for v in value)})\""
+            elif isinstance(value, (list, tuple)) and key != "label" and not in_list:
+                if len(value) == 0:
+                    yield indent + key + " " + f'"{value!r}"'
+                if len(value) == 1:
+                    yield indent + key + " " + f'"{LIST_START_VALUE}"'
+                for val in value:
+                    yield from stringize(key, val, (), indent, True)
+            else:
+                if stringizer:
+                    try:
+                        value = stringizer(value)
+                    except ValueError as err:
+                        raise NetworkXError(
+                            f"{value!r} cannot be converted into a string"
+                        ) from err
+                if not isinstance(value, str):
+                    raise NetworkXError(f"{value!r} is not a string")
+                yield indent + key + ' "' + escape(value) + '"'
+
+    multigraph = G.is_multigraph()
+    yield "graph ["
+
+    # Output graph attributes
+    if G.is_directed():
+        yield "  directed 1"
+    if multigraph:
+        yield "  multigraph 1"
+    ignored_keys = {"directed", "multigraph", "node", "edge"}
+    for attr, value in G.graph.items():
+        yield from stringize(attr, value, ignored_keys, "  ")
+
+    # Output node data
+    node_id = dict(zip(G, range(len(G))))
+    ignored_keys = {"id", "label"}
+    for node, attrs in G.nodes.items():
+        yield "  node ["
+        yield "    id " + str(node_id[node])
+        yield from stringize("label", node, (), "    ")
+        for attr, value in attrs.items():
+            yield from stringize(attr, value, ignored_keys, "    ")
+        yield "  ]"
+
+    # Output edge data
+    ignored_keys = {"source", "target"}
+    kwargs = {"data": True}
+    if multigraph:
+        ignored_keys.add("key")
+        kwargs["keys"] = True
+    for e in G.edges(**kwargs):
+        yield "  edge ["
+        yield "    source " + str(node_id[e[0]])
+        yield "    target " + str(node_id[e[1]])
+        if multigraph:
+            yield from stringize("key", e[2], (), "    ")
+        for attr, value in e[-1].items():
+            yield from stringize(attr, value, ignored_keys, "    ")
+        yield "  ]"
+    yield "]"
+
+
+@open_file(1, mode="wb")
+def write_gml(G, path, stringizer=None):
+    """Write a graph `G` in GML format to the file or file handle `path`.
+
+    Parameters
+    ----------
+    G : NetworkX graph
+        The graph to be converted to GML.
+
+    path : filename or filehandle
+        The filename or filehandle to write. Files whose names end with .gz or
+        .bz2 will be compressed.
+
+    stringizer : callable, optional
+        A `stringizer` which converts non-int/non-float/non-dict values into
+        strings. If it cannot convert a value into a string, it should raise a
+        `ValueError` to indicate that. Default value: None.
+
+    Raises
+    ------
+    NetworkXError
+        If `stringizer` cannot convert a value into a string, or the value to
+        convert is not a string while `stringizer` is None.
+
+    See Also
+    --------
+    read_gml, generate_gml
+    literal_stringizer
+
+    Notes
+    -----
+    Graph attributes named 'directed', 'multigraph', 'node' or
+    'edge', node attributes named 'id' or 'label', edge attributes
+    named 'source' or 'target' (or 'key' if `G` is a multigraph)
+    are ignored because these attribute names are used to encode the graph
+    structure.
+
+    GML files are stored using a 7-bit ASCII encoding with any extended
+    ASCII characters (iso8859-1) appearing as HTML character entities.
+    Without specifying a `stringizer`/`destringizer`, the code is capable of
+    writing `int`/`float`/`str`/`dict`/`list` data as required by the GML
+    specification.  For writing other data types, and for reading data other
+    than `str` you need to explicitly supply a `stringizer`/`destringizer`.
+
+    Note that while we allow non-standard GML to be read from a file, we make
+    sure to write GML format. In particular, underscores are not allowed in
+    attribute names.
+    For additional documentation on the GML file format, please see the
+    `GML url <https://web.archive.org/web/20190207140002/http://www.fim.uni-passau.de/index.php?id=17297&L=1>`_.
+
+    See the module docstring :mod:`networkx.readwrite.gml` for more details.
+
+    Examples
+    --------
+    >>> G = nx.path_graph(4)
+    >>> nx.write_gml(G, "test.gml")
+
+    Filenames ending in .gz or .bz2 will be compressed.
+
+    >>> nx.write_gml(G, "test.gml.gz")
+    """
+    for line in generate_gml(G, stringizer):
+        path.write((line + "\n").encode("ascii"))

tuning-competition-baseline/.venv/lib/python3.11/site-packages/networkx/readwrite/graphml.py

@@ -0,0 +1,1051 @@
+"""
+*******
+GraphML
+*******
+Read and write graphs in GraphML format.
+
+.. warning::
+
+    This parser uses the standard xml library present in Python, which is
+    insecure - see :external+python:mod:`xml` for additional information.
+    Only parse GraphML files you trust.
+
+This implementation does not support mixed graphs (directed and unidirected
+edges together), hyperedges, nested graphs, or ports.
+
+"GraphML is a comprehensive and easy-to-use file format for graphs. It
+consists of a language core to describe the structural properties of a
+graph and a flexible extension mechanism to add application-specific
+data. Its main features include support of
+
+    * directed, undirected, and mixed graphs,
+    * hypergraphs,
+    * hierarchical graphs,
+    * graphical representations,
+    * references to external data,
+    * application-specific attribute data, and
+    * light-weight parsers.
+
+Unlike many other file formats for graphs, GraphML does not use a
+custom syntax. Instead, it is based on XML and hence ideally suited as
+a common denominator for all kinds of services generating, archiving,
+or processing graphs."
+
+http://graphml.graphdrawing.org/
+
+Format
+------
+GraphML is an XML format.  See
+http://graphml.graphdrawing.org/specification.html for the specification and
+http://graphml.graphdrawing.org/primer/graphml-primer.html
+for examples.
+"""
+import warnings
+from collections import defaultdict
+
+import networkx as nx
+from networkx.utils import open_file
+
+__all__ = [
+    "write_graphml",
+    "read_graphml",
+    "generate_graphml",
+    "write_graphml_xml",
+    "write_graphml_lxml",
+    "parse_graphml",
+    "GraphMLWriter",
+    "GraphMLReader",
+]
+
+
+@open_file(1, mode="wb")
+def write_graphml_xml(
+    G,
+    path,
+    encoding="utf-8",
+    prettyprint=True,
+    infer_numeric_types=False,
+    named_key_ids=False,
+    edge_id_from_attribute=None,
+):
+    """Write G in GraphML XML format to path
+
+    Parameters
+    ----------
+    G : graph
+       A networkx graph
+    path : file or string
+       File or filename to write.
+       Filenames ending in .gz or .bz2 will be compressed.
+    encoding : string (optional)
+       Encoding for text data.
+    prettyprint : bool (optional)
+       If True use line breaks and indenting in output XML.
+    infer_numeric_types : boolean
+       Determine if numeric types should be generalized.
+       For example, if edges have both int and float 'weight' attributes,
+       we infer in GraphML that both are floats.
+    named_key_ids : bool (optional)
+       If True use attr.name as value for key elements' id attribute.
+    edge_id_from_attribute : dict key (optional)
+        If provided, the graphml edge id is set by looking up the corresponding
+        edge data attribute keyed by this parameter. If `None` or the key does not exist in edge data,
+        the edge id is set by the edge key if `G` is a MultiGraph, else the edge id is left unset.
+
+    Examples
+    --------
+    >>> G = nx.path_graph(4)
+    >>> nx.write_graphml(G, "test.graphml")
+
+    Notes
+    -----
+    This implementation does not support mixed graphs (directed
+    and unidirected edges together) hyperedges, nested graphs, or ports.
+    """
+    writer = GraphMLWriter(
+        encoding=encoding,
+        prettyprint=prettyprint,
+        infer_numeric_types=infer_numeric_types,
+        named_key_ids=named_key_ids,
+        edge_id_from_attribute=edge_id_from_attribute,
+    )
+    writer.add_graph_element(G)
+    writer.dump(path)
+
+
+@open_file(1, mode="wb")
+def write_graphml_lxml(
+    G,
+    path,
+    encoding="utf-8",
+    prettyprint=True,
+    infer_numeric_types=False,
+    named_key_ids=False,
+    edge_id_from_attribute=None,
+):
+    """Write G in GraphML XML format to path
+
+    This function uses the LXML framework and should be faster than
+    the version using the xml library.
+
+    Parameters
+    ----------
+    G : graph
+       A networkx graph
+    path : file or string
+       File or filename to write.
+       Filenames ending in .gz or .bz2 will be compressed.
+    encoding : string (optional)
+       Encoding for text data.
+    prettyprint : bool (optional)
+       If True use line breaks and indenting in output XML.
+    infer_numeric_types : boolean
+       Determine if numeric types should be generalized.
+       For example, if edges have both int and float 'weight' attributes,
+       we infer in GraphML that both are floats.
+    named_key_ids : bool (optional)
+       If True use attr.name as value for key elements' id attribute.
+    edge_id_from_attribute : dict key (optional)
+        If provided, the graphml edge id is set by looking up the corresponding
+        edge data attribute keyed by this parameter. If `None` or the key does not exist in edge data,
+        the edge id is set by the edge key if `G` is a MultiGraph, else the edge id is left unset.
+
+    Examples
+    --------
+    >>> G = nx.path_graph(4)
+    >>> nx.write_graphml_lxml(G, "fourpath.graphml")
+
+    Notes
+    -----
+    This implementation does not support mixed graphs (directed
+    and unidirected edges together) hyperedges, nested graphs, or ports.
+    """
+    try:
+        import lxml.etree as lxmletree
+    except ImportError:
+        return write_graphml_xml(
+            G,
+            path,
+            encoding,
+            prettyprint,
+            infer_numeric_types,
+            named_key_ids,
+            edge_id_from_attribute,
+        )
+
+    writer = GraphMLWriterLxml(
+        path,
+        graph=G,
+        encoding=encoding,
+        prettyprint=prettyprint,
+        infer_numeric_types=infer_numeric_types,
+        named_key_ids=named_key_ids,
+        edge_id_from_attribute=edge_id_from_attribute,
+    )
+    writer.dump()
+
+
+def generate_graphml(
+    G,
+    encoding="utf-8",
+    prettyprint=True,
+    named_key_ids=False,
+    edge_id_from_attribute=None,
+):
+    """Generate GraphML lines for G
+
+    Parameters
+    ----------
+    G : graph
+       A networkx graph
+    encoding : string (optional)
+       Encoding for text data.
+    prettyprint : bool (optional)
+       If True use line breaks and indenting in output XML.
+    named_key_ids : bool (optional)
+       If True use attr.name as value for key elements' id attribute.
+    edge_id_from_attribute : dict key (optional)
+        If provided, the graphml edge id is set by looking up the corresponding
+        edge data attribute keyed by this parameter. If `None` or the key does not exist in edge data,
+        the edge id is set by the edge key if `G` is a MultiGraph, else the edge id is left unset.
+
+    Examples
+    --------
+    >>> G = nx.path_graph(4)
+    >>> linefeed = chr(10)  # linefeed = \n
+    >>> s = linefeed.join(nx.generate_graphml(G))
+    >>> for line in nx.generate_graphml(G):  # doctest: +SKIP
+    ...     print(line)
+
+    Notes
+    -----
+    This implementation does not support mixed graphs (directed and unidirected
+    edges together) hyperedges, nested graphs, or ports.
+    """
+    writer = GraphMLWriter(
+        encoding=encoding,
+        prettyprint=prettyprint,
+        named_key_ids=named_key_ids,
+        edge_id_from_attribute=edge_id_from_attribute,
+    )
+    writer.add_graph_element(G)
+    yield from str(writer).splitlines()
+
+
+@open_file(0, mode="rb")
+@nx._dispatch(graphs=None)
+def read_graphml(path, node_type=str, edge_key_type=int, force_multigraph=False):
+    """Read graph in GraphML format from path.
+
+    Parameters
+    ----------
+    path : file or string
+       File or filename to write.
+       Filenames ending in .gz or .bz2 will be compressed.
+
+    node_type: Python type (default: str)
+       Convert node ids to this type
+
+    edge_key_type: Python type (default: int)
+       Convert graphml edge ids to this type. Multigraphs use id as edge key.
+       Non-multigraphs add to edge attribute dict with name "id".
+
+    force_multigraph : bool (default: False)
+       If True, return a multigraph with edge keys. If False (the default)
+       return a multigraph when multiedges are in the graph.
+
+    Returns
+    -------
+    graph: NetworkX graph
+        If parallel edges are present or `force_multigraph=True` then
+        a MultiGraph or MultiDiGraph is returned. Otherwise a Graph/DiGraph.
+        The returned graph is directed if the file indicates it should be.
+
+    Notes
+    -----
+    Default node and edge attributes are not propagated to each node and edge.
+    They can be obtained from `G.graph` and applied to node and edge attributes
+    if desired using something like this:
+
+    >>> default_color = G.graph["node_default"]["color"]  # doctest: +SKIP
+    >>> for node, data in G.nodes(data=True):  # doctest: +SKIP
+    ...     if "color" not in data:
+    ...         data["color"] = default_color
+    >>> default_color = G.graph["edge_default"]["color"]  # doctest: +SKIP
+    >>> for u, v, data in G.edges(data=True):  # doctest: +SKIP
+    ...     if "color" not in data:
+    ...         data["color"] = default_color
+
+    This implementation does not support mixed graphs (directed and unidirected
+    edges together), hypergraphs, nested graphs, or ports.
+
+    For multigraphs the GraphML edge "id" will be used as the edge
+    key.  If not specified then they "key" attribute will be used.  If
+    there is no "key" attribute a default NetworkX multigraph edge key
+    will be provided.
+
+    Files with the yEd "yfiles" extension can be read. The type of the node's
+    shape is preserved in the `shape_type` node attribute.
+
+    yEd compressed files ("file.graphmlz" extension) can be read by renaming
+    the file to "file.graphml.gz".
+
+    """
+    reader = GraphMLReader(node_type, edge_key_type, force_multigraph)
+    # need to check for multiple graphs
+    glist = list(reader(path=path))
+    if len(glist) == 0:
+        # If no graph comes back, try looking for an incomplete header
+        header = b'<graphml xmlns="http://graphml.graphdrawing.org/xmlns">'
+        path.seek(0)
+        old_bytes = path.read()
+        new_bytes = old_bytes.replace(b"<graphml>", header)
+        glist = list(reader(string=new_bytes))
+        if len(glist) == 0:
+            raise nx.NetworkXError("file not successfully read as graphml")
+    return glist[0]
+
+
+@nx._dispatch(graphs=None)
+def parse_graphml(
+    graphml_string, node_type=str, edge_key_type=int, force_multigraph=False
+):
+    """Read graph in GraphML format from string.
+
+    Parameters
+    ----------
+    graphml_string : string
+       String containing graphml information
+       (e.g., contents of a graphml file).
+
+    node_type: Python type (default: str)
+       Convert node ids to this type
+
+    edge_key_type: Python type (default: int)
+       Convert graphml edge ids to this type. Multigraphs use id as edge key.
+       Non-multigraphs add to edge attribute dict with name "id".
+
+    force_multigraph : bool (default: False)
+       If True, return a multigraph with edge keys. If False (the default)
+       return a multigraph when multiedges are in the graph.
+
+
+    Returns
+    -------
+    graph: NetworkX graph
+        If no parallel edges are found a Graph or DiGraph is returned.
+        Otherwise a MultiGraph or MultiDiGraph is returned.
+
+    Examples
+    --------
+    >>> G = nx.path_graph(4)
+    >>> linefeed = chr(10)  # linefeed = \n
+    >>> s = linefeed.join(nx.generate_graphml(G))
+    >>> H = nx.parse_graphml(s)
+
+    Notes
+    -----
+    Default node and edge attributes are not propagated to each node and edge.
+    They can be obtained from `G.graph` and applied to node and edge attributes
+    if desired using something like this:
+
+    >>> default_color = G.graph["node_default"]["color"]  # doctest: +SKIP
+    >>> for node, data in G.nodes(data=True):  # doctest: +SKIP
+    ...     if "color" not in data:
+    ...         data["color"] = default_color
+    >>> default_color = G.graph["edge_default"]["color"]  # doctest: +SKIP
+    >>> for u, v, data in G.edges(data=True):  # doctest: +SKIP
+    ...     if "color" not in data:
+    ...         data["color"] = default_color
+
+    This implementation does not support mixed graphs (directed and unidirected
+    edges together), hypergraphs, nested graphs, or ports.
+
+    For multigraphs the GraphML edge "id" will be used as the edge
+    key.  If not specified then they "key" attribute will be used.  If
+    there is no "key" attribute a default NetworkX multigraph edge key
+    will be provided.
+
+    """
+    reader = GraphMLReader(node_type, edge_key_type, force_multigraph)
+    # need to check for multiple graphs
+    glist = list(reader(string=graphml_string))
+    if len(glist) == 0:
+        # If no graph comes back, try looking for an incomplete header
+        header = '<graphml xmlns="http://graphml.graphdrawing.org/xmlns">'
+        new_string = graphml_string.replace("<graphml>", header)
+        glist = list(reader(string=new_string))
+        if len(glist) == 0:
+            raise nx.NetworkXError("file not successfully read as graphml")
+    return glist[0]
+
+
+class GraphML:
+    NS_GRAPHML = "http://graphml.graphdrawing.org/xmlns"
+    NS_XSI = "http://www.w3.org/2001/XMLSchema-instance"
+    # xmlns:y="http://www.yworks.com/xml/graphml"
+    NS_Y = "http://www.yworks.com/xml/graphml"
+    SCHEMALOCATION = " ".join(
+        [
+            "http://graphml.graphdrawing.org/xmlns",
+            "http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd",
+        ]
+    )
+
+    def construct_types(self):
+        types = [
+            (int, "integer"),  # for Gephi GraphML bug
+            (str, "yfiles"),
+            (str, "string"),
+            (int, "int"),
+            (int, "long"),
+            (float, "float"),
+            (float, "double"),
+            (bool, "boolean"),
+        ]
+
+        # These additions to types allow writing numpy types
+        try:
+            import numpy as np
+        except:
+            pass
+        else:
+            # prepend so that python types are created upon read (last entry wins)
+            types = [
+                (np.float64, "float"),
+                (np.float32, "float"),
+                (np.float16, "float"),
+                (np.int_, "int"),
+                (np.int8, "int"),
+                (np.int16, "int"),
+                (np.int32, "int"),
+                (np.int64, "int"),
+                (np.uint8, "int"),
+                (np.uint16, "int"),
+                (np.uint32, "int"),
+                (np.uint64, "int"),
+                (np.int_, "int"),
+                (np.intc, "int"),
+                (np.intp, "int"),
+            ] + types
+
+        self.xml_type = dict(types)
+        self.python_type = dict(reversed(a) for a in types)
+
+    # This page says that data types in GraphML follow Java(TM).
+    #  http://graphml.graphdrawing.org/primer/graphml-primer.html#AttributesDefinition
+    # true and false are the only boolean literals:
+    #  http://en.wikibooks.org/wiki/Java_Programming/Literals#Boolean_Literals
+    convert_bool = {
+        # We use data.lower() in actual use.
+        "true": True,
+        "false": False,
+        # Include integer strings for convenience.
+        "0": False,
+        0: False,
+        "1": True,
+        1: True,
+    }
+
+    def get_xml_type(self, key):
+        """Wrapper around the xml_type dict that raises a more informative
+        exception message when a user attempts to use data of a type not
+        supported by GraphML."""
+        try:
+            return self.xml_type[key]
+        except KeyError as err:
+            raise TypeError(
+                f"GraphML does not support type {type(key)} as data values."
+            ) from err
+
+
+class GraphMLWriter(GraphML):
+    def __init__(
+        self,
+        graph=None,
+        encoding="utf-8",
+        prettyprint=True,
+        infer_numeric_types=False,
+        named_key_ids=False,
+        edge_id_from_attribute=None,
+    ):
+        self.construct_types()
+        from xml.etree.ElementTree import Element
+
+        self.myElement = Element
+
+        self.infer_numeric_types = infer_numeric_types
+        self.prettyprint = prettyprint
+        self.named_key_ids = named_key_ids
+        self.edge_id_from_attribute = edge_id_from_attribute
+        self.encoding = encoding
+        self.xml = self.myElement(
+            "graphml",
+            {
+                "xmlns": self.NS_GRAPHML,
+                "xmlns:xsi": self.NS_XSI,
+                "xsi:schemaLocation": self.SCHEMALOCATION,
+            },
+        )
+        self.keys = {}
+        self.attributes = defaultdict(list)
+        self.attribute_types = defaultdict(set)
+
+        if graph is not None:
+            self.add_graph_element(graph)
+
+    def __str__(self):
+        from xml.etree.ElementTree import tostring
+
+        if self.prettyprint:
+            self.indent(self.xml)
+        s = tostring(self.xml).decode(self.encoding)
+        return s
+
+    def attr_type(self, name, scope, value):
+        """Infer the attribute type of data named name. Currently this only
+        supports inference of numeric types.
+
+        If self.infer_numeric_types is false, type is used. Otherwise, pick the
+        most general of types found across all values with name and scope. This
+        means edges with data named 'weight' are treated separately from nodes
+        with data named 'weight'.
+        """
+        if self.infer_numeric_types:
+            types = self.attribute_types[(name, scope)]
+
+            if len(types) > 1:
+                types = {self.get_xml_type(t) for t in types}
+                if "string" in types:
+                    return str
+                elif "float" in types or "double" in types:
+                    return float
+                else:
+                    return int
+            else:
+                return list(types)[0]
+        else:
+            return type(value)
+
+    def get_key(self, name, attr_type, scope, default):
+        keys_key = (name, attr_type, scope)
+        try:
+            return self.keys[keys_key]
+        except KeyError:
+            if self.named_key_ids:
+                new_id = name
+            else:
+                new_id = f"d{len(list(self.keys))}"
+
+            self.keys[keys_key] = new_id
+            key_kwargs = {
+                "id": new_id,
+                "for": scope,
+                "attr.name": name,
+                "attr.type": attr_type,
+            }
+            key_element = self.myElement("key", **key_kwargs)
+            # add subelement for data default value if present
+            if default is not None:
+                default_element = self.myElement("default")
+                default_element.text = str(default)
+                key_element.append(default_element)
+            self.xml.insert(0, key_element)
+        return new_id
+
+    def add_data(self, name, element_type, value, scope="all", default=None):
+        """
+        Make a data element for an edge or a node. Keep a log of the
+        type in the keys table.
+        """
+        if element_type not in self.xml_type:
+            raise nx.NetworkXError(
+                f"GraphML writer does not support {element_type} as data values."
+            )
+        keyid = self.get_key(name, self.get_xml_type(element_type), scope, default)
+        data_element = self.myElement("data", key=keyid)
+        data_element.text = str(value)
+        return data_element
+
+    def add_attributes(self, scope, xml_obj, data, default):
+        """Appends attribute data to edges or nodes, and stores type information
+        to be added later. See add_graph_element.
+        """
+        for k, v in data.items():
+            self.attribute_types[(str(k), scope)].add(type(v))
+            self.attributes[xml_obj].append([k, v, scope, default.get(k)])
+
+    def add_nodes(self, G, graph_element):
+        default = G.graph.get("node_default", {})
+        for node, data in G.nodes(data=True):
+            node_element = self.myElement("node", id=str(node))
+            self.add_attributes("node", node_element, data, default)
+            graph_element.append(node_element)
+
+    def add_edges(self, G, graph_element):
+        if G.is_multigraph():
+            for u, v, key, data in G.edges(data=True, keys=True):
+                edge_element = self.myElement(
+                    "edge",
+                    source=str(u),
+                    target=str(v),
+                    id=str(data.get(self.edge_id_from_attribute))
+                    if self.edge_id_from_attribute
+                    and self.edge_id_from_attribute in data
+                    else str(key),
+                )
+                default = G.graph.get("edge_default", {})
+                self.add_attributes("edge", edge_element, data, default)
+                graph_element.append(edge_element)
+        else:
+            for u, v, data in G.edges(data=True):
+                if self.edge_id_from_attribute and self.edge_id_from_attribute in data:
+                    # select attribute to be edge id
+                    edge_element = self.myElement(
+                        "edge",
+                        source=str(u),
+                        target=str(v),
+                        id=str(data.get(self.edge_id_from_attribute)),
+                    )
+                else:
+                    # default: no edge id
+                    edge_element = self.myElement("edge", source=str(u), target=str(v))
+                default = G.graph.get("edge_default", {})
+                self.add_attributes("edge", edge_element, data, default)
+                graph_element.append(edge_element)
+
+    def add_graph_element(self, G):
+        """
+        Serialize graph G in GraphML to the stream.
+        """
+        if G.is_directed():
+            default_edge_type = "directed"
+        else:
+            default_edge_type = "undirected"
+
+        graphid = G.graph.pop("id", None)
+        if graphid is None:
+            graph_element = self.myElement("graph", edgedefault=default_edge_type)
+        else:
+            graph_element = self.myElement(
+                "graph", edgedefault=default_edge_type, id=graphid
+            )
+        default = {}
+        data = {
+            k: v
+            for (k, v) in G.graph.items()
+            if k not in ["node_default", "edge_default"]
+        }
+        self.add_attributes("graph", graph_element, data, default)
+        self.add_nodes(G, graph_element)
+        self.add_edges(G, graph_element)
+
+        # self.attributes contains a mapping from XML Objects to a list of
+        # data that needs to be added to them.
+        # We postpone processing in order to do type inference/generalization.
+        # See self.attr_type
+        for xml_obj, data in self.attributes.items():
+            for k, v, scope, default in data:
+                xml_obj.append(
+                    self.add_data(
+                        str(k), self.attr_type(k, scope, v), str(v), scope, default
+                    )
+                )
+        self.xml.append(graph_element)
+
+    def add_graphs(self, graph_list):
+        """Add many graphs to this GraphML document."""
+        for G in graph_list:
+            self.add_graph_element(G)
+
+    def dump(self, stream):
+        from xml.etree.ElementTree import ElementTree
+
+        if self.prettyprint:
+            self.indent(self.xml)
+        document = ElementTree(self.xml)
+        document.write(stream, encoding=self.encoding, xml_declaration=True)
+
+    def indent(self, elem, level=0):
+        # in-place prettyprint formatter
+        i = "\n" + level * "  "
+        if len(elem):
+            if not elem.text or not elem.text.strip():
+                elem.text = i + "  "
+            if not elem.tail or not elem.tail.strip():
+                elem.tail = i
+            for elem in elem:
+                self.indent(elem, level + 1)
+            if not elem.tail or not elem.tail.strip():
+                elem.tail = i
+        else:
+            if level and (not elem.tail or not elem.tail.strip()):
+                elem.tail = i
+
+
+class IncrementalElement:
+    """Wrapper for _IncrementalWriter providing an Element like interface.
+
+    This wrapper does not intend to be a complete implementation but rather to
+    deal with those calls used in GraphMLWriter.
+    """
+
+    def __init__(self, xml, prettyprint):
+        self.xml = xml
+        self.prettyprint = prettyprint
+
+    def append(self, element):
+        self.xml.write(element, pretty_print=self.prettyprint)
+
+
+class GraphMLWriterLxml(GraphMLWriter):
+    def __init__(
+        self,
+        path,
+        graph=None,
+        encoding="utf-8",
+        prettyprint=True,
+        infer_numeric_types=False,
+        named_key_ids=False,
+        edge_id_from_attribute=None,
+    ):
+        self.construct_types()
+        import lxml.etree as lxmletree
+
+        self.myElement = lxmletree.Element
+
+        self._encoding = encoding
+        self._prettyprint = prettyprint
+        self.named_key_ids = named_key_ids
+        self.edge_id_from_attribute = edge_id_from_attribute
+        self.infer_numeric_types = infer_numeric_types
+
+        self._xml_base = lxmletree.xmlfile(path, encoding=encoding)
+        self._xml = self._xml_base.__enter__()
+        self._xml.write_declaration()
+
+        # We need to have a xml variable that support insertion. This call is
+        # used for adding the keys to the document.
+        # We will store those keys in a plain list, and then after the graph
+        # element is closed we will add them to the main graphml element.
+        self.xml = []
+        self._keys = self.xml
+        self._graphml = self._xml.element(
+            "graphml",
+            {
+                "xmlns": self.NS_GRAPHML,
+                "xmlns:xsi": self.NS_XSI,
+                "xsi:schemaLocation": self.SCHEMALOCATION,
+            },
+        )
+        self._graphml.__enter__()
+        self.keys = {}
+        self.attribute_types = defaultdict(set)
+
+        if graph is not None:
+            self.add_graph_element(graph)
+
+    def add_graph_element(self, G):
+        """
+        Serialize graph G in GraphML to the stream.
+        """
+        if G.is_directed():
+            default_edge_type = "directed"
+        else:
+            default_edge_type = "undirected"
+
+        graphid = G.graph.pop("id", None)
+        if graphid is None:
+            graph_element = self._xml.element("graph", edgedefault=default_edge_type)
+        else:
+            graph_element = self._xml.element(
+                "graph", edgedefault=default_edge_type, id=graphid
+            )
+
+        # gather attributes types for the whole graph
+        # to find the most general numeric format needed.
+        # Then pass through attributes to create key_id for each.
+        graphdata = {
+            k: v
+            for k, v in G.graph.items()
+            if k not in ("node_default", "edge_default")
+        }
+        node_default = G.graph.get("node_default", {})
+        edge_default = G.graph.get("edge_default", {})
+        # Graph attributes
+        for k, v in graphdata.items():
+            self.attribute_types[(str(k), "graph")].add(type(v))
+        for k, v in graphdata.items():
+            element_type = self.get_xml_type(self.attr_type(k, "graph", v))
+            self.get_key(str(k), element_type, "graph", None)
+        # Nodes and data
+        for node, d in G.nodes(data=True):
+            for k, v in d.items():
+                self.attribute_types[(str(k), "node")].add(type(v))
+        for node, d in G.nodes(data=True):
+            for k, v in d.items():
+                T = self.get_xml_type(self.attr_type(k, "node", v))
+                self.get_key(str(k), T, "node", node_default.get(k))
+        # Edges and data
+        if G.is_multigraph():
+            for u, v, ekey, d in G.edges(keys=True, data=True):
+                for k, v in d.items():
+                    self.attribute_types[(str(k), "edge")].add(type(v))
+            for u, v, ekey, d in G.edges(keys=True, data=True):
+                for k, v in d.items():
+                    T = self.get_xml_type(self.attr_type(k, "edge", v))
+                    self.get_key(str(k), T, "edge", edge_default.get(k))
+        else:
+            for u, v, d in G.edges(data=True):
+                for k, v in d.items():
+                    self.attribute_types[(str(k), "edge")].add(type(v))
+            for u, v, d in G.edges(data=True):
+                for k, v in d.items():
+                    T = self.get_xml_type(self.attr_type(k, "edge", v))
+                    self.get_key(str(k), T, "edge", edge_default.get(k))
+
+        # Now add attribute keys to the xml file
+        for key in self.xml:
+            self._xml.write(key, pretty_print=self._prettyprint)
+
+        # The incremental_writer writes each node/edge as it is created
+        incremental_writer = IncrementalElement(self._xml, self._prettyprint)
+        with graph_element:
+            self.add_attributes("graph", incremental_writer, graphdata, {})
+            self.add_nodes(G, incremental_writer)  # adds attributes too
+            self.add_edges(G, incremental_writer)  # adds attributes too
+
+    def add_attributes(self, scope, xml_obj, data, default):
+        """Appends attribute data."""
+        for k, v in data.items():
+            data_element = self.add_data(
+                str(k), self.attr_type(str(k), scope, v), str(v), scope, default.get(k)
+            )
+            xml_obj.append(data_element)
+
+    def __str__(self):
+        return object.__str__(self)
+
+    def dump(self):
+        self._graphml.__exit__(None, None, None)
+        self._xml_base.__exit__(None, None, None)
+
+
+# default is lxml is present.
+write_graphml = write_graphml_lxml
+
+
+class GraphMLReader(GraphML):
+    """Read a GraphML document.  Produces NetworkX graph objects."""
+
+    def __init__(self, node_type=str, edge_key_type=int, force_multigraph=False):
+        self.construct_types()
+        self.node_type = node_type
+        self.edge_key_type = edge_key_type
+        self.multigraph = force_multigraph  # If False, test for multiedges
+        self.edge_ids = {}  # dict mapping (u,v) tuples to edge id attributes
+
+    def __call__(self, path=None, string=None):
+        from xml.etree.ElementTree import ElementTree, fromstring
+
+        if path is not None:
+            self.xml = ElementTree(file=path)
+        elif string is not None:
+            self.xml = fromstring(string)
+        else:
+            raise ValueError("Must specify either 'path' or 'string' as kwarg")
+        (keys, defaults) = self.find_graphml_keys(self.xml)
+        for g in self.xml.findall(f"{{{self.NS_GRAPHML}}}graph"):
+            yield self.make_graph(g, keys, defaults)
+
+    def make_graph(self, graph_xml, graphml_keys, defaults, G=None):
+        # set default graph type
+        edgedefault = graph_xml.get("edgedefault", None)
+        if G is None:
+            if edgedefault == "directed":
+                G = nx.MultiDiGraph()
+            else:
+                G = nx.MultiGraph()
+        # set defaults for graph attributes
+        G.graph["node_default"] = {}
+        G.graph["edge_default"] = {}
+        for key_id, value in defaults.items():
+            key_for = graphml_keys[key_id]["for"]
+            name = graphml_keys[key_id]["name"]
+            python_type = graphml_keys[key_id]["type"]
+            if key_for == "node":
+                G.graph["node_default"].update({name: python_type(value)})
+            if key_for == "edge":
+                G.graph["edge_default"].update({name: python_type(value)})
+        # hyperedges are not supported
+        hyperedge = graph_xml.find(f"{{{self.NS_GRAPHML}}}hyperedge")
+        if hyperedge is not None:
+            raise nx.NetworkXError("GraphML reader doesn't support hyperedges")
+        # add nodes
+        for node_xml in graph_xml.findall(f"{{{self.NS_GRAPHML}}}node"):
+            self.add_node(G, node_xml, graphml_keys, defaults)
+        # add edges
+        for edge_xml in graph_xml.findall(f"{{{self.NS_GRAPHML}}}edge"):
+            self.add_edge(G, edge_xml, graphml_keys)
+        # add graph data
+        data = self.decode_data_elements(graphml_keys, graph_xml)
+        G.graph.update(data)
+
+        # switch to Graph or DiGraph if no parallel edges were found
+        if self.multigraph:
+            return G
+
+        G = nx.DiGraph(G) if G.is_directed() else nx.Graph(G)
+        # add explicit edge "id" from file as attribute in NX graph.
+        nx.set_edge_attributes(G, values=self.edge_ids, name="id")
+        return G
+
+    def add_node(self, G, node_xml, graphml_keys, defaults):
+        """Add a node to the graph."""
+        # warn on finding unsupported ports tag
+        ports = node_xml.find(f"{{{self.NS_GRAPHML}}}port")
+        if ports is not None:
+            warnings.warn("GraphML port tag not supported.")
+        # find the node by id and cast it to the appropriate type
+        node_id = self.node_type(node_xml.get("id"))
+        # get data/attributes for node
+        data = self.decode_data_elements(graphml_keys, node_xml)
+        G.add_node(node_id, **data)
+        # get child nodes
+        if node_xml.attrib.get("yfiles.foldertype") == "group":
+            graph_xml = node_xml.find(f"{{{self.NS_GRAPHML}}}graph")
+            self.make_graph(graph_xml, graphml_keys, defaults, G)
+
+    def add_edge(self, G, edge_element, graphml_keys):
+        """Add an edge to the graph."""
+        # warn on finding unsupported ports tag
+        ports = edge_element.find(f"{{{self.NS_GRAPHML}}}port")
+        if ports is not None:
+            warnings.warn("GraphML port tag not supported.")
+
+        # raise error if we find mixed directed and undirected edges
+        directed = edge_element.get("directed")
+        if G.is_directed() and directed == "false":
+            msg = "directed=false edge found in directed graph."
+            raise nx.NetworkXError(msg)
+        if (not G.is_directed()) and directed == "true":
+            msg = "directed=true edge found in undirected graph."
+            raise nx.NetworkXError(msg)
+
+        source = self.node_type(edge_element.get("source"))
+        target = self.node_type(edge_element.get("target"))
+        data = self.decode_data_elements(graphml_keys, edge_element)
+        # GraphML stores edge ids as an attribute
+        # NetworkX uses them as keys in multigraphs too if no key
+        # attribute is specified
+        edge_id = edge_element.get("id")
+        if edge_id:
+            # self.edge_ids is used by `make_graph` method for non-multigraphs
+            self.edge_ids[source, target] = edge_id
+            try:
+                edge_id = self.edge_key_type(edge_id)
+            except ValueError:  # Could not convert.
+                pass
+        else:
+            edge_id = data.get("key")
+
+        if G.has_edge(source, target):
+            # mark this as a multigraph
+            self.multigraph = True
+
+        # Use add_edges_from to avoid error with add_edge when `'key' in data`
+        # Note there is only one edge here...
+        G.add_edges_from([(source, target, edge_id, data)])
+
+    def decode_data_elements(self, graphml_keys, obj_xml):
+        """Use the key information to decode the data XML if present."""
+        data = {}
+        for data_element in obj_xml.findall(f"{{{self.NS_GRAPHML}}}data"):
+            key = data_element.get("key")
+            try:
+                data_name = graphml_keys[key]["name"]
+                data_type = graphml_keys[key]["type"]
+            except KeyError as err:
+                raise nx.NetworkXError(f"Bad GraphML data: no key {key}") from err
+            text = data_element.text
+            # assume anything with subelements is a yfiles extension
+            if text is not None and len(list(data_element)) == 0:
+                if data_type == bool:
+                    # Ignore cases.
+                    # http://docs.oracle.com/javase/6/docs/api/java/lang/
+                    # Boolean.html#parseBoolean%28java.lang.String%29
+                    data[data_name] = self.convert_bool[text.lower()]
+                else:
+                    data[data_name] = data_type(text)
+            elif len(list(data_element)) > 0:
+                # Assume yfiles as subelements, try to extract node_label
+                node_label = None
+                # set GenericNode's configuration as shape type
+                gn = data_element.find(f"{{{self.NS_Y}}}GenericNode")
+                if gn:
+                    data["shape_type"] = gn.get("configuration")
+                for node_type in ["GenericNode", "ShapeNode", "SVGNode", "ImageNode"]:
+                    pref = f"{{{self.NS_Y}}}{node_type}/{{{self.NS_Y}}}"
+                    geometry = data_element.find(f"{pref}Geometry")
+                    if geometry is not None:
+                        data["x"] = geometry.get("x")
+                        data["y"] = geometry.get("y")
+                    if node_label is None:
+                        node_label = data_element.find(f"{pref}NodeLabel")
+                    shape = data_element.find(f"{pref}Shape")
+                    if shape is not None:
+                        data["shape_type"] = shape.get("type")
+                if node_label is not None:
+                    data["label"] = node_label.text
+
+                # check all the different types of edges available in yEd.
+                for edge_type in [
+                    "PolyLineEdge",
+                    "SplineEdge",
+                    "QuadCurveEdge",
+                    "BezierEdge",
+                    "ArcEdge",
+                ]:
+                    pref = f"{{{self.NS_Y}}}{edge_type}/{{{self.NS_Y}}}"
+                    edge_label = data_element.find(f"{pref}EdgeLabel")
+                    if edge_label is not None:
+                        break
+
+                if edge_label is not None:
+                    data["label"] = edge_label.text
+        return data
+
+    def find_graphml_keys(self, graph_element):
+        """Extracts all the keys and key defaults from the xml."""
+        graphml_keys = {}
+        graphml_key_defaults = {}
+        for k in graph_element.findall(f"{{{self.NS_GRAPHML}}}key"):
+            attr_id = k.get("id")
+            attr_type = k.get("attr.type")
+            attr_name = k.get("attr.name")
+            yfiles_type = k.get("yfiles.type")
+            if yfiles_type is not None:
+                attr_name = yfiles_type
+                attr_type = "yfiles"
+            if attr_type is None:
+                attr_type = "string"
+                warnings.warn(f"No key type for id {attr_id}. Using string")
+            if attr_name is None:
+                raise nx.NetworkXError(f"Unknown key for id {attr_id}.")
+            graphml_keys[attr_id] = {
+                "name": attr_name,
+                "type": self.python_type[attr_type],
+                "for": k.get("for"),
+            }
+            # check for "default" sub-element of key element
+            default = k.find(f"{{{self.NS_GRAPHML}}}default")
+            if default is not None:
+                # Handle default values identically to data element values
+                python_type = graphml_keys[attr_id]["type"]
+                if python_type == bool:
+                    graphml_key_defaults[attr_id] = self.convert_bool[
+                        default.text.lower()
+                    ]
+                else:
+                    graphml_key_defaults[attr_id] = python_type(default.text)
+        return graphml_keys, graphml_key_defaults

tuning-competition-baseline/.venv/lib/python3.11/site-packages/networkx/readwrite/json_graph/__init__.py

@@ -0,0 +1,18 @@
+"""
+*********
+JSON data
+*********
+Generate and parse JSON serializable data for NetworkX graphs.
+
+These formats are suitable for use with the d3.js examples https://d3js.org/
+
+The three formats that you can generate with NetworkX are:
+
+ - node-link like in the d3.js example https://bl.ocks.org/mbostock/4062045
+ - tree like in the d3.js example https://bl.ocks.org/mbostock/4063550
+ - adjacency like in the d3.js example https://bost.ocks.org/mike/miserables/
+"""
+from networkx.readwrite.json_graph.node_link import *
+from networkx.readwrite.json_graph.adjacency import *
+from networkx.readwrite.json_graph.tree import *
+from networkx.readwrite.json_graph.cytoscape import *