Merge pull request #20 from UTAustin-SwarmLab/adding_ci

Added ci

.github/workflows/ruff.yml

@@ -0,0 +1,19 @@
+name: Ruff
+on: [push, pull_request]
+
+jobs:
+  ruff:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v4
+      with:
+        python-version: "3.9"
+    - name: Run Ruff with auto-fix
+      uses: chartboost/ruff-action@v1
+      with:
+        args: --fix  # Automatically apply safe fixes
+    - uses: stefanzweifel/git-auto-commit-action@v4
+      with:
+        commit_message: 'style fixes by ruff'
+        file_pattern: '*.py'  # Ensure only Python files are committed

.github/workflows/unittest.yml

@@ -0,0 +1,19 @@
+name: Python Unit Tests
+on: [push, pull_request]
+
+jobs:
+  unit-tests:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v4
+      with:
+        python-version: '3.9'
+    - name: Install Dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -e ."[dev, test]"
+    - name: Run Unit Tests
+      run: |
+        python -m unittest discover

.gitignore

@@ -136,3 +136,8 @@ dmypy.json
 *.jpg
 *.jpeg
 *.png
+
+# don't ignore github workflow
+!/.github/
+!/.github/workflows/
+!/.github/workflows/*.yml

pyproject.toml

@@ -20,7 +20,8 @@ dependencies = [
     "numpy",
     "pandas",
     "seaborn",
-    "statannot"
+    "statannot",
+    "scipy"
 ]
 
 [project.urls]

ruff.toml

@@ -0,0 +1,61 @@
+# Exclude a variety of commonly ignored directories.
+exclude = [
+    ".bzr",
+    ".direnv",
+    ".eggs",
+    ".git",
+    ".git-rewrite",
+    ".hg",
+    ".mypy_cache",
+    ".nox",
+    ".pants.d",
+    ".pytype",
+    ".ruff_cache",
+    ".svn",
+    ".tox",
+    ".venv",
+    "__pypackages__",
+    "_build",
+    "buck-out",
+    "build",
+    "dist",
+    "node_modules",
+    "venv",
+]
+
+# Same as Black.
+line-length = 80
+indent-width = 4
+
+# Assume Python 3.9
+target-version = "py39"
+
+[lint]
+# Enable Pyflakes (`F`) and a subset of the pycodestyle (`E`)  codes by default.
+# Unlike Flake8, Ruff doesn't enable pycodestyle warnings (`W`) or
+# McCabe complexity (`C901`) by default.
+select = ["E4", "E7", "E9", "F"]
+ignore = []
+
+# Allow fix for all enabled rules (when `--fix`) is provided.
+fixable = ["ALL"]
+unfixable = []
+
+# Allow unused variables when underscore-prefixed.
+dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"
+
+[format]
+# Like Black, use double quotes for strings.
+quote-style = "double"
+
+# Like Black, indent with spaces, rather than tabs.
+indent-style = "space"
+
+# Like Black, respect magic trailing commas.
+skip-magic-trailing-comma = false
+
+# Like Black, automatically detect the appropriate line ending.
+line-ending = "auto"
+
+[lint.pydocstyle]
+convention = "google"

swarm_visualizer/barplot.py

@@ -1,4 +1,3 @@
-import numpy as np
 import seaborn as sns
 
 from swarm_visualizer.utility.general_utils import set_axis_infos

swarm_visualizer/lineplot.py

@@ -38,7 +38,6 @@ def plot_overlaid_ts(
     title_str: str = None,
     ylabel: str = None,
     xlabel: str = "time",
-    fontsize: float = 30,
     xticks=None,
     ylim=None,
     DEFAULT_ALPHA: float = 1.0,
@@ -53,7 +52,6 @@ def plot_overlaid_ts(
     :param title_str: title of the plot
     :param ylabel: y-axis label
     :param xlabel: x-axis label
-    :param fontsize: font size
     :param xticks: x-axis ticks
     :param ylim: y-axis limits
     :param DEFAULT_ALPHA: default alpha value

swarm_visualizer/scatterplot.py

@@ -55,7 +55,6 @@ def plot_scatter_pdf_plot(
     ts_y=None,
     title_str: str = None,
     ylabel: str = None,
-    lw: float = 3.0,
     ylim=None,
     xlabel: str = "time",
     xlim=None,

swarm_visualizer/utility/textfile_utils.py

@@ -15,7 +15,6 @@
 import os
 import pickle
 
-import numpy as np
 from scipy.ndimage import shift
 
 """

tests/test_lineplot.py

@@ -101,7 +101,6 @@ def test_overlaid_ts_plot(normalized_ts_dict) -> None:
         title_str="Overlaid Time Series Plot",
         ylabel="$y$",
         xlabel="$x$",
-        fontsize=30,
         xticks=None,
         ylim=None,
         DEFAULT_ALPHA=1.0,

tests/test_scatterplot.py

@@ -71,7 +71,6 @@ def test_scatter_pdf_plot(x_data, y_data) -> None:
         ts_y=y_data,
         title_str="Scatter Plot with CDFs",
         ylabel="$y$",
-        lw=3.0,
         ylim=None,
         xlabel="$x$",
         xlim=None,