Add github ci and badges

refactor setup

.github/workflows/codeql-analysis.yml

@@ -0,0 +1,56 @@
+name: "CodeQL"
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    # The branches below must be a subset of the branches above
+    branches: [ master ]
+  schedule:
+    - cron: '16 17 * * 3'
+
+jobs:
+  analyze:
+    name: Analyze
+    runs-on: ubuntu-latest
+
+    strategy:
+      fail-fast: false
+      matrix:
+        language: [ 'python' ]
+        # CodeQL supports [ 'cpp', 'csharp', 'go', 'java', 'javascript', 'python' ]
+        # Learn more:
+        # 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
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v2
+
+    # Initializes the CodeQL tools for scanning.
+    - name: Initialize CodeQL
+      uses: github/codeql-action/init@v1
+      with:
+        languages: ${{ matrix.language }}
+        # If you wish to specify custom queries, you can do so here or in a config file.
+        # By default, queries listed here will override any specified in a config file.
+        # Prefix the list here with "+" to use these queries and those in the config file.
+        # queries: ./path/to/local/query, your-org/your-repo/queries@main
+
+    # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
+    # If this step fails, then you should remove it and run the build manually (see below)
+    - name: Autobuild
+      uses: github/codeql-action/autobuild@v1
+
+    # ℹ️ Command-line programs to run using the OS shell.
+    # 📚 https://git.io/JvXDl
+
+    # ✏️ If the Autobuild fails above, remove it and uncomment the following three lines
+    #    and modify them (or add more) to build your code if your project
+    #    uses a compiled language
+
+    #- run: |
+    #   make bootstrap
+    #   make release
+
+    - name: Perform CodeQL Analysis
+      uses: github/codeql-action/analyze@v1

.github/workflows/main.yml

@@ -0,0 +1,41 @@
+name: CI
+
+on:
+  push:
+    branches: [master]
+  pull_request:
+    branches: [master]
+  workflow_dispatch:
+
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [macos-latest, ubuntu-latest, windows-latest]
+        python: [3.8]
+
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python ${{ matrix.python }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python }}
+      - name: Install dependencies
+        run: |
+          pip install -q --upgrade pip
+          pip install -q -r requirements.txt
+          pip install -q --upgrade codecov coverage black flake8
+      - name: Lint
+        run: |
+          black --check --diff stree
+          flake8 --count stree
+      - name: Tests
+        run: |
+          coverage run -m unittest -v stree.tests
+          coverage xml
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v1
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          files: ./coverage.xml

README.md

@@ -1,3 +1,7 @@
+![CI](https://github.com/Doctorado-ML/benchmark/workflows/CI/badge.svg)
+[![codecov](https://codecov.io/gh/doctorado-ml/benchmark/branch/master/graph/badge.svg)](https://codecov.io/gh/doctorado-ml/benchmark)
+[![Language grade: Python](https://img.shields.io/lgtm/grade/python/g/Doctorado-ML/STree.svg?logo=lgtm&logoWidth=18)](https://lgtm.com/projects/g/Doctorado-ML/STree/context:python)
+![https://img.shields.io/badge/python-3.8%2B-blue](https://img.shields.io/badge/python-3.8%2B-brightgreen)
 # benchmark
 
 Benchmarking models
@@ -6,53 +10,55 @@ Benchmarking models
 
 ```python
 # 5 Fold 10 seeds with STree with default hyperparameters and report
-python src/main.py -m STree -P iMac27 -r 1
+be_main -m STree -P iMac27 -r 1
 # Setting number of folds, in this case 7
-python src/main.py -m STree -P iMac27 -n 7
+be_main -m STree -P iMac27 -n 7
 # 5 Fold 10 seeds with STree and best results hyperparams
-python src/main.py -m STree -P iMac27 -f 1
+be_main -m STree -P iMac27 -f 1
 # 5 Fold 10 seeds with STree and same hyperparameters
-python src/main.py -m STree -P iMac27 -p '{"kernel": "rbf", "gamma": 0.1}'
+be_main -m STree -P iMac27 -p '{"kernel": "rbf", "gamma": 0.1}'
 ```
 
 ## Best Results
 
 ```python
 # Build best results of STree model and print report
-python src/build_best.py -m STree -r 1
+be_build_best -m STree -r 1
 # Report of STree best results
-python src/report.py -b STree
+be_report -b STree
 ```
 
 ## Reports
 
 ```python
 # Datasets list
-python src/report.py
+be_report
 # Report of given experiment
-python src/report.py -f results/results_STree_iMac27_2021-09-22_17:13:02.json
+be_report -f results/results_STree_iMac27_2021-09-22_17:13:02.json
 # Report of given experiment building excel file and compare with best results
-python src/report.py -f results/results_STree_iMac27_2021-09-22_17:13:02.json -x 1 -c 1
+be_report -f results/results_STree_iMac27_2021-09-22_17:13:02.json -x 1 -c 1
 # Report of given experiment building sql file
-python src/report.py -f results/results_STree_iMac27_2021-09-22_17:13:02.json -q 1
+be_report -f results/results_STree_iMac27_2021-09-22_17:13:02.json -q 1
 ```
 
 ## Benchmark
 
 ```python
 # Do benchmark and print report
-python src/benchmark.py
+be_benchmark
 # Do benchmark, print report and build excel file with data
-python src/benchmark.py -x 1
+be_benchmark -x 1
+# Do benchmark, print report and build tex table with results
+be_benchmark -t 1
 ```
 
 ## List
 
 ```python
 # List of results of given model
-python src/list.py -m ODTE
+be_list -m ODTE
 # List of results of given model and score
-python src/list.py -m STree -s f1-macro
+be_list -m STree -s f1-macro
 # List all results
-python src/list.py
+be_list
 ```

benchmark/__init__.py

@@ -1,10 +1,9 @@
 from .Experiments import Experiment, Datasets, DatasetsSurcov, DatasetsTanveer
 from .Results import Report, Summary
-from .Arguments import EnvDefault
 
 __author__ = "Ricardo Montañana Gómez"
 __copyright__ = "Copyright 2020-2022, Ricardo Montañana Gómez"
 __license__ = "MIT License"
 __author_email__ = "ricardo.montanana@alu.uclm.es"
 
-__all__ = ["Experiment", "Datasets", "Report", "Summary", "EnvDefault"]
+__all__ = ["Experiment", "Datasets", "Report", "Summary"]

setup.py

@@ -7,9 +7,8 @@ def readme():
         return f.read()
 
 
-def get_data(field):
+def get_data(field, file_name="__init__.py"):
     item = ""
-    file_name = "_version.py" if field == "version" else "__init__.py"
     with open(os.path.join("benchmark", file_name)) as f:
         for line in f.readlines():
             if line.startswith(f"__{field}__"):
@@ -21,17 +20,34 @@ def get_data(field):
     return item
 
 
-def import_scripts():
+def get_requirements():
+    with open("requirements.txt") as f:
+        return f.read().splitlines()
+
+
+def script_names():
+    scripts = [
+        "benchmark",
+        "best",
+        "build_best",
+        "build_grid",
+        "grid",
+        "list",
+        "main",
+        "pair_check",
+        "print_strees",
+        "report",
+        "summary",
+    ]
     result = []
-    names = os.listdir(os.path.join("benchmark", "scripts"))
+    for script in scripts:
-    for name in names:
+        result.append(f"be_{script}=benchmark.scripts.be_{script}:main")
-        result.append(os.path.join("benchmark", "scripts", name))
     return result
 
 
 setuptools.setup(
     name="benchmark",
-    version=get_data("version"),
+    version=get_data("version", "_version.py"),
     license=get_data("license"),
     description="Oblique decision tree with svm nodes",
     long_description=readme(),
@@ -46,32 +62,15 @@ setuptools.setup(
         "Development Status :: 4 - Beta",
         "License :: OSI Approved :: " + get_data("license"),
         "Programming Language :: Python :: 3.8",
+        "Programming Language :: Python :: 3.9",
+        "Programming Language :: Python :: 3.10",
         "Natural Language :: English",
         "Topic :: Scientific/Engineering :: Artificial Intelligence",
         "Intended Audience :: Science/Research",
     ],
-    install_requires=[
+    install_requires=get_requirements(),
-        "scikit-learn",
-        "odte",
-        "pandas",
-        "mufs",
-        "xlsxwriter",
-        "tqdm",
-    ],
     zip_safe=False,
     entry_points={
-        "console_scripts": [
+        "console_scripts": script_names(),
-            "be_list=benchmark.scripts.be_list:main",
-            "be_report=benchmark.scripts.be_report:main",
-            "be_main=benchmark.scripts.be_main:main",
-            "be_benchmark=benchmark.scripts.be_benchmark:main",
-            "be_best=benchmark.scripts.be_best:main",
-            "be_build_best=benchmark.scripts.be_build_best:main",
-            "be_build_grid=benchmark.scripts.be_build_grid:main",
-            "be_grid=benchmark.scripts.be_grid:main",
-            "be_pair_check=benchmark.scripts.be_pair_check:main",
-            "be_print_strees=benchmark.scripts.be_print_strees:main",
-            "be_summary=benchmark.scripts.be_summary:main",
-        ],
     },
 )