[ENH] Make pip installable (#6)

* adding pip

* add tests

* fix test bug

* fix example

* change test name

.github/workflows/publish.yml

@@ -0,0 +1,31 @@
+name: Upload Python Package to PyPI when a Release is Created
+
+on:
+  release:
+    types: [created]
+
+jobs:
+  pypi-publish:
+    name: Publish release to PyPI
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/multi_comp_matrix
+    permissions:
+      id-token: write
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install setuptools wheel
+      - name: Build package
+        run: |
+          python -m pip install build
+          python -m build
+      - name: Publish package distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

.github/workflows/pytest.yml

@@ -0,0 +1,44 @@
+name: PR pytest
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+    paths:
+      - "multi_comp_matrix/**"
+      - ".github/workflows/**"
+      - "pyproject.toml"
+
+jobs:
+  test-mcm:
+
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ ubuntu-22.04, macOS-14, windows-2022 ]
+        python-version: [ "3.10" ]
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        uses: nick-fields/retry@v3
+        with:
+          timeout_minutes: 30
+          max_attempts: 3
+          command: python -m pip install .[dev]
+
+      - name: Show dependencies
+        run: python -m pip list
+
+      - name: Run tests
+        run: python -m pytest -n logical

MANIFEST.in

@@ -0,0 +1,9 @@
+recursive-include multi_comp_matrix *.py
+include LICENSE
+include MANIFEST.in
+include pyproject.toml
+include README.md
+include *.csv
+include *.pdf
+include *.png
+include *.tex

main.py

@@ -1,28 +1,31 @@
 import pandas as pd
 
-from MCM import MCM
+from multi_comp_matrix import MCM
 
 if __name__ == "__main__":
     path_res = "./results_example.csv"
-    output_dir = "./"
+    output_dir = "../"
 
     df_results = pd.read_csv(path_res)
 
     MCM.compare(
         df_results=df_results,
+        output_dir=output_dir,
         pdf_savename="heatmap",
         png_savename="heatmap",
     )
 
     MCM.compare(
         df_results=df_results,
+        output_dir=output_dir,
         excluded_col_comparates=["clf1", "clf3"],
         png_savename="heatline_vertical",
         include_ProbaWinTieLoss=True
     )
 
     MCM.compare(
         df_results=df_results,
+        output_dir=output_dir,
         excluded_row_comparates=["clf1", "clf3"],
         png_savename="heatline_horizontal",
         tex_savename="heatline_horizontal",

MCM/MCM.py → multi_comp_matrix/MCM.py

@@ -335,6 +335,7 @@ def get_analysis(
     re_order_comparates(df_results=df_results, analysis=analysis)
 
     if save_as_json:
+        print(save_file)
         with open(save_file, "w") as fjson:
             json.dump(analysis, fjson, cls=NpEncoder)
 
@@ -759,71 +760,67 @@ def draw(
         plt.savefig(
             os.path.join(output_dir + f"{pdf_savename}.pdf"), bbox_inches="tight"
         )
-        plt.cla()
-        plt.clf()
-        plt.close()
-    elif png_savename is not None:
+
+    if png_savename is not None:
         plt.savefig(
             os.path.join(output_dir + f"{png_savename}.png"), bbox_inches="tight"
         )
-        plt.cla()
-        plt.clf()
-
-    latex_string += (
-        f"\\begin{{tabular}}{{{'c' * (len(latex_table[0]) + 1)}}}\n"  # +1 for labels
-    )
-    for latex_row in latex_table:
-        latex_string += " & ".join(latex_row) + " \\\\[1ex]" + "\n"
 
-    if colorbar_orientation == "horizontal":
-        latex_string += "\\end{tabular}\\\\\n"
-    else:
-        latex_string += "\\end{tabular}\n"
+    if tex_savename is not None:
+        latex_string += (
+            f"\\begin{{tabular}}{{{'c' * (len(latex_table[0]) + 1)}}}\n"  # +1 for labels
+        )
+        for latex_row in latex_table:
+            latex_string += " & ".join(latex_row) + " \\\\[1ex]" + "\n"
 
-    latex_colorbar_0 = "\\begin{tikzpicture}[baseline=(current bounding box.center)]\\begin{axis}[hide axis,scale only axis,"
-    latex_colorbar_1 = f"colormap={{cm}}{{rgb255(1)=({','.join([str(int(_ * 255)) for _ in cm(cm_norm(min_value))[:-1]])}) rgb255(2)=(220,220,220) rgb255(3)=({','.join([str(int(_ * 255)) for _ in cm(cm_norm(max_value))[:-1]])})}},"
-    latex_colorbar_2 = (
-        f"colorbar horizontal,point meta min={_vmin:.02f},point meta max={_vmax:.02f},"
-    )
-    latex_colorbar_3 = "colorbar/width=1.0em"
-    latex_colorbar_4 = "}] \\addplot[draw=none] {0};\\end{axis}\\end{tikzpicture}"
+        if colorbar_orientation == "horizontal":
+            latex_string += "\\end{tabular}\\\\\n"
+        else:
+            latex_string += "\\end{tabular}\n"
 
-    if colorbar_orientation == "horizontal":
-        latex_string += (
-            latex_colorbar_0
-            + "width=0sp,height=0sp,colorbar horizontal,colorbar style={width=0.25\linewidth,"
-            + latex_colorbar_1
-            + latex_colorbar_2
-            + latex_colorbar_3
-            + ",scaled x ticks=false,xticklabel style={/pgf/number format/fixed,/pgf/number format/precision=3},"
-            + f"xlabel={{{_colorbar_value}}},"
-            + latex_colorbar_4
+        latex_colorbar_0 = "\\begin{tikzpicture}[baseline=(current bounding box.center)]\\begin{axis}[hide axis,scale only axis,"
+        latex_colorbar_1 = f"colormap={{cm}}{{rgb255(1)=({','.join([str(int(_ * 255)) for _ in cm(cm_norm(min_value))[:-1]])}) rgb255(2)=(220,220,220) rgb255(3)=({','.join([str(int(_ * 255)) for _ in cm(cm_norm(max_value))[:-1]])})}},"
+        latex_colorbar_2 = (
+            f"colorbar horizontal,point meta min={_vmin:.02f},point meta max={_vmax:.02f},"
         )
-    else:
+        latex_colorbar_3 = "colorbar/width=1.0em"
+        latex_colorbar_4 = "}] \\addplot[draw=none] {0};\\end{axis}\\end{tikzpicture}"
+
+        if colorbar_orientation == "horizontal":
+            latex_string += (
+                latex_colorbar_0
+                + "width=0sp,height=0sp,colorbar horizontal,colorbar style={width=0.25\linewidth,"
+                + latex_colorbar_1
+                + latex_colorbar_2
+                + latex_colorbar_3
+                + ",scaled x ticks=false,xticklabel style={/pgf/number format/fixed,/pgf/number format/precision=3},"
+                + f"xlabel={{{_colorbar_value}}},"
+                + latex_colorbar_4
+            )
+        else:
+            latex_string += (
+                latex_colorbar_0
+                + "width=1pt,colorbar right,colorbar style={height=0.25\linewidth,"
+                + latex_colorbar_1
+                + latex_colorbar_2
+                + latex_colorbar_3
+                + ",scaled y ticks=false,ylabel style={rotate=180},yticklabel style={/pgf/number format/fixed,/pgf/number format/precision=3},"
+                + f"ylabel={{{_colorbar_value}}},"
+                + latex_colorbar_4
+            )
+
+        latex_string += "\\end{center}\n"
         latex_string += (
-            latex_colorbar_0
-            + "width=1pt,colorbar right,colorbar style={height=0.25\linewidth,"
-            + latex_colorbar_1
-            + latex_colorbar_2
-            + latex_colorbar_3
-            + ",scaled y ticks=false,ylabel style={rotate=180},yticklabel style={/pgf/number format/fixed,/pgf/number format/precision=3},"
-            + f"ylabel={{{_colorbar_value}}},"
-            + latex_colorbar_4
+            "\\caption{[...] \\textbf{"
+            + f"{p_value_text}".replace("\n", " ")
+            + "} [...]}\n"
         )
+        latex_string += "\\end{table}\n"
+        latex_string += "\\end{document}\n"
 
-    latex_string += "\\end{center}\n"
-    latex_string += (
-        "\\caption{[...] \\textbf{"
-        + f"{p_value_text}".replace("\n", " ")
-        + "} [...]}\n"
-    )
-    latex_string += "\\end{table}\n"
-    latex_string += "\\end{document}\n"
-
-    latex_string = latex_string.replace(">", "$>$")
-    latex_string = latex_string.replace("<", "$<$")
-
-    if tex_savename is not None:
+        latex_string = latex_string.replace(">", "$>$")
+        latex_string = latex_string.replace("<", "$<$")
+
         with open(
             f"{output_dir}/{tex_savename}.tex", "w", encoding="utf8", newline="\n"
         ) as file:
@@ -837,3 +834,7 @@ def draw(
 
     if tex_savename is None and pdf_savename is None and png_savename is None:
         plt.show()
+
+    plt.cla()
+    plt.clf()
+    plt.close()

multi_comp_matrix/tests/test_mcm.py

@@ -0,0 +1,41 @@
+from multi_comp_matrix.MCM import compare
+import pandas as pd
+import tempfile
+import time
+import pytest
+
+@pytest.mark.parametrize("save_type", ["pdf", "png", "tex"])
+def test_all_type_saving(save_type):
+    """Test each of the save types."""
+    data = {
+        'clf1': [1, 2, 3, 4],
+        'clf2': [4.0, 6.0, 2.0, 1.0],
+        'clf3': [10.5, 20.5, 30.5, 40.5]
+    }
+    df = pd.DataFrame(data)
+    with tempfile.TemporaryDirectory() as tmp:
+        if save_type == "pdf":
+            curr_time = str(time.time_ns())
+
+            compare(df_results=df, output_dir=tmp, pdf_savename=curr_time+"test_pdf")
+            compare(df_results=df, output_dir=tmp, pdf_savename=curr_time+"test_vertical_pdf",
+                    excluded_col_comparates=["clf1", "clf3"],)
+            compare(df_results=df, output_dir=tmp, pdf_savename=curr_time+"test_horizontal_pdf",
+                    excluded_row_comparates=["clf1", "clf3"],)
+        elif save_type == "png":
+            curr_time = str(time.time_ns())
+
+            compare(df_results=df, output_dir=tmp, png_savename=curr_time+"test_png")
+            compare(df_results=df, output_dir=tmp, png_savename=curr_time+"test_vertical_png",
+                    excluded_col_comparates=["clf1", "clf3"],)
+            compare(df_results=df, output_dir=tmp, png_savename=curr_time+"test_horizontal_png",
+                    excluded_row_comparates=["clf1", "clf3"],)
+        elif save_type == "tex":
+            curr_time = str(time.time_ns())
+
+            compare(df_results=df, output_dir=tmp, tex_savename=curr_time+"test_tex")
+            compare(df_results=df, output_dir=tmp, tex_savename=curr_time+"test_vertical_tex",
+                    excluded_col_comparates=["clf1", "clf3"],)
+            compare(df_results=df, output_dir=tmp, tex_savename=curr_time+"test_horizontal_tex",
+                    excluded_row_comparates=["clf1", "clf3"],)
+

pyproject.toml

@@ -0,0 +1,77 @@
+[build-system]
+requires = ["setuptools>61", "wheel", "toml", "build"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "multi_comp_matrix"
+version = "0.0.1"
+description = "  Multi Comparison Matrix: A long term approach to benchmark evaluations  "
+readme = { file = "README.md", content-type = "text/markdown" }
+authors = [
+    {name = "Ali Ismail-Fawaz", email = "[email protected]"},
+    {name = "Maxime Devanne", email = "[email protected]"},
+    {name = "Stefano Berretti", email = "[email protected]"},
+    {name = "Jonathan Weber", email = "[email protected]"},
+    {name = "Germain Forestier", email = "[email protected]"}
+]
+maintainers = [
+    {name = "Ali Ismail-Fawaz", email = "[email protected]"}
+]
+requires-python = ">=3.10"
+license = {text = "GPL-3.0-only"}
+
+keywords = [
+    "data-science",
+    "machine-learning",
+    "data-mining",
+    "time-series",
+    "time-series-analysis",
+    "time-series-classification",
+    "time-series-regression",
+    "time-series-machine-learning",
+    "benchmarking",
+    "benchmarking-machine-learning"
+]
+
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Intended Audience :: Developers",
+    "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12"
+]
+
+dependencies = [
+    "numpy==1.24.4",
+    "pandas==2.0.3",
+    "matplotlib==3.7.4",
+    "scipy==1.10.0",
+    "baycomp==1.0",
+    "tqdm==4.66.1"
+]
+
+[project.optional-dependencies]
+dev = [
+    "black",
+    "flake8",
+    "mypy",
+    "pytest",
+    "pytest-cov",
+    "pytest-xdist",
+    "pytest-timeout",
+    "pytest-rerunfailures",
+    "pre-commit"
+]
+
+[tool.setuptools]
+packages = ["multi_comp_matrix"]
+
+[tool.setuptools.package-data]
+multi_comp_matrix = [
+    "*.png",
+    "*.csv",
+    "*.pdf",
+    "*.tex",
+]