mirror of
https://github.com/Doctorado-ML/benchmark.git
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Add github ci and badges
refactor setup
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56
.github/workflows/codeql-analysis.yml
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56
.github/workflows/codeql-analysis.yml
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name: "CodeQL"
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on:
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push:
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branches: [ master ]
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pull_request:
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# The branches below must be a subset of the branches above
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branches: [ master ]
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schedule:
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- cron: '16 17 * * 3'
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jobs:
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analyze:
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name: Analyze
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runs-on: ubuntu-latest
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strategy:
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fail-fast: false
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matrix:
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language: [ 'python' ]
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# CodeQL supports [ 'cpp', 'csharp', 'go', 'java', 'javascript', 'python' ]
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# Learn more:
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# https://docs.github.com/en/free-pro-team@latest/github/finding-security-vulnerabilities-and-errors-in-your-code/configuring-code-scanning#changing-the-languages-that-are-analyzed
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steps:
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- name: Checkout repository
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uses: actions/checkout@v2
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# Initializes the CodeQL tools for scanning.
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- name: Initialize CodeQL
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uses: github/codeql-action/init@v1
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with:
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languages: ${{ matrix.language }}
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# If you wish to specify custom queries, you can do so here or in a config file.
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# By default, queries listed here will override any specified in a config file.
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# Prefix the list here with "+" to use these queries and those in the config file.
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# queries: ./path/to/local/query, your-org/your-repo/queries@main
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# Autobuild attempts to build any compiled languages (C/C++, C#, or Java).
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# If this step fails, then you should remove it and run the build manually (see below)
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- name: Autobuild
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uses: github/codeql-action/autobuild@v1
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# ℹ️ Command-line programs to run using the OS shell.
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# 📚 https://git.io/JvXDl
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# ✏️ If the Autobuild fails above, remove it and uncomment the following three lines
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# and modify them (or add more) to build your code if your project
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# uses a compiled language
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#- run: |
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# make bootstrap
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# make release
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- name: Perform CodeQL Analysis
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uses: github/codeql-action/analyze@v1
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41
.github/workflows/main.yml
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41
.github/workflows/main.yml
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name: CI
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on:
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push:
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branches: [master]
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pull_request:
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branches: [master]
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workflow_dispatch:
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jobs:
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build:
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runs-on: ${{ matrix.os }}
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strategy:
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matrix:
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os: [macos-latest, ubuntu-latest, windows-latest]
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python: [3.8]
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steps:
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- uses: actions/checkout@v2
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- name: Set up Python ${{ matrix.python }}
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uses: actions/setup-python@v2
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with:
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python-version: ${{ matrix.python }}
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- name: Install dependencies
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run: |
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pip install -q --upgrade pip
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pip install -q -r requirements.txt
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pip install -q --upgrade codecov coverage black flake8
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- name: Lint
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run: |
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black --check --diff stree
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flake8 --count stree
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- name: Tests
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run: |
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coverage run -m unittest -v stree.tests
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coverage xml
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- name: Upload coverage to Codecov
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uses: codecov/codecov-action@v1
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with:
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token: ${{ secrets.CODECOV_TOKEN }}
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files: ./coverage.xml
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36
README.md
36
README.md
@@ -1,3 +1,7 @@
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[](https://codecov.io/gh/doctorado-ml/benchmark)
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[](https://lgtm.com/projects/g/Doctorado-ML/STree/context:python)
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# benchmark
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Benchmarking models
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@@ -6,53 +10,55 @@ Benchmarking models
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```python
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# 5 Fold 10 seeds with STree with default hyperparameters and report
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python src/main.py -m STree -P iMac27 -r 1
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be_main -m STree -P iMac27 -r 1
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# Setting number of folds, in this case 7
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python src/main.py -m STree -P iMac27 -n 7
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be_main -m STree -P iMac27 -n 7
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# 5 Fold 10 seeds with STree and best results hyperparams
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python src/main.py -m STree -P iMac27 -f 1
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be_main -m STree -P iMac27 -f 1
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# 5 Fold 10 seeds with STree and same hyperparameters
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python src/main.py -m STree -P iMac27 -p '{"kernel": "rbf", "gamma": 0.1}'
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be_main -m STree -P iMac27 -p '{"kernel": "rbf", "gamma": 0.1}'
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```
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## Best Results
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```python
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# Build best results of STree model and print report
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python src/build_best.py -m STree -r 1
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be_build_best -m STree -r 1
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# Report of STree best results
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python src/report.py -b STree
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be_report -b STree
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```
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## Reports
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```python
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# Datasets list
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python src/report.py
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be_report
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# Report of given experiment
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python src/report.py -f results/results_STree_iMac27_2021-09-22_17:13:02.json
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be_report -f results/results_STree_iMac27_2021-09-22_17:13:02.json
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# Report of given experiment building excel file and compare with best results
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python src/report.py -f results/results_STree_iMac27_2021-09-22_17:13:02.json -x 1 -c 1
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be_report -f results/results_STree_iMac27_2021-09-22_17:13:02.json -x 1 -c 1
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# Report of given experiment building sql file
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python src/report.py -f results/results_STree_iMac27_2021-09-22_17:13:02.json -q 1
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be_report -f results/results_STree_iMac27_2021-09-22_17:13:02.json -q 1
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```
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## Benchmark
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```python
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# Do benchmark and print report
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python src/benchmark.py
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be_benchmark
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# Do benchmark, print report and build excel file with data
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python src/benchmark.py -x 1
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be_benchmark -x 1
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# Do benchmark, print report and build tex table with results
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be_benchmark -t 1
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```
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## List
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```python
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# List of results of given model
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python src/list.py -m ODTE
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be_list -m ODTE
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# List of results of given model and score
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python src/list.py -m STree -s f1-macro
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be_list -m STree -s f1-macro
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# List all results
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python src/list.py
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be_list
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```
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@@ -1,10 +1,9 @@
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from .Experiments import Experiment, Datasets, DatasetsSurcov, DatasetsTanveer
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from .Results import Report, Summary
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from .Arguments import EnvDefault
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__author__ = "Ricardo Montañana Gómez"
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__copyright__ = "Copyright 2020-2022, Ricardo Montañana Gómez"
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__license__ = "MIT License"
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__author_email__ = "ricardo.montanana@alu.uclm.es"
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__all__ = ["Experiment", "Datasets", "Report", "Summary", "EnvDefault"]
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__all__ = ["Experiment", "Datasets", "Report", "Summary"]
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55
setup.py
55
setup.py
@@ -7,9 +7,8 @@ def readme():
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return f.read()
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def get_data(field):
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def get_data(field, file_name="__init__.py"):
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item = ""
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file_name = "_version.py" if field == "version" else "__init__.py"
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with open(os.path.join("benchmark", file_name)) as f:
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for line in f.readlines():
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if line.startswith(f"__{field}__"):
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@@ -21,17 +20,34 @@ def get_data(field):
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return item
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def import_scripts():
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def get_requirements():
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with open("requirements.txt") as f:
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return f.read().splitlines()
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def script_names():
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scripts = [
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"benchmark",
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"best",
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"build_best",
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"build_grid",
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"grid",
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"list",
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"main",
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"pair_check",
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"print_strees",
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"report",
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"summary",
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]
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result = []
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names = os.listdir(os.path.join("benchmark", "scripts"))
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for name in names:
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result.append(os.path.join("benchmark", "scripts", name))
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for script in scripts:
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result.append(f"be_{script}=benchmark.scripts.be_{script}:main")
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return result
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setuptools.setup(
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name="benchmark",
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version=get_data("version"),
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version=get_data("version", "_version.py"),
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license=get_data("license"),
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description="Oblique decision tree with svm nodes",
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long_description=readme(),
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@@ -46,32 +62,15 @@ setuptools.setup(
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"Development Status :: 4 - Beta",
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"License :: OSI Approved :: " + get_data("license"),
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"Programming Language :: Python :: 3.8",
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"Programming Language :: Python :: 3.9",
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"Programming Language :: Python :: 3.10",
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"Natural Language :: English",
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"Topic :: Scientific/Engineering :: Artificial Intelligence",
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"Intended Audience :: Science/Research",
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],
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install_requires=[
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"scikit-learn",
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"odte",
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"pandas",
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"mufs",
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"xlsxwriter",
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"tqdm",
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],
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install_requires=get_requirements(),
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zip_safe=False,
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entry_points={
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"console_scripts": [
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"be_list=benchmark.scripts.be_list:main",
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"be_report=benchmark.scripts.be_report:main",
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"be_main=benchmark.scripts.be_main:main",
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"be_benchmark=benchmark.scripts.be_benchmark:main",
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"be_best=benchmark.scripts.be_best:main",
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"be_build_best=benchmark.scripts.be_build_best:main",
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"be_build_grid=benchmark.scripts.be_build_grid:main",
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"be_grid=benchmark.scripts.be_grid:main",
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"be_pair_check=benchmark.scripts.be_pair_check:main",
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"be_print_strees=benchmark.scripts.be_print_strees:main",
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"be_summary=benchmark.scripts.be_summary:main",
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],
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"console_scripts": script_names(),
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},
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)
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