Create python-app.yml (#4)

* Create python-app.yml

Add ci/cd

* Update ci cd.

* Fixes for mypy.

* Add a basic test.

* Add a basic test.

* Remove tests for now.

.github/workflows/ci.yml

@@ -1,53 +0,0 @@
-# This is a basic workflow to help you get started with Actions
-# some parts are taken from here: https://github.com/ternaus/iglovikov_helper_functions/blob/master/.github/workflows/ci.yml
-name: CI
-
-# Controls when the action will run. Triggers the workflow on push or pull request
-# events but only for the master branch
-on:
-  push:
-    branches: [ master ]
-  pull_request:
-    branches: [ master ]
-
-# A workflow run is made up of one or more jobs that can run sequentially or in parallel
-jobs:
-  # This workflow contains a single job called "build"
-  build:
-    # The type of runner that the job will run on
-    runs-on: ubuntu-latest
-
-    # Steps represent a sequence of tasks that will be executed as part of the job
-    steps:
-      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
-      - uses: actions/checkout@v2
-      - name: Set up Python
-        uses: actions/setup-python@v2
-        with:
-          python-version: '3.9.15'
-      - name: Cache pip
-        uses: actions/cache@v1
-        with:
-         path: ~/.cache/pip # This path is specific to Ubuntu
-         # Look to see if there is a cache hit for the corresponding requirements file
-         key: ${{ runner.os }}-pip-${{ hashFiles('requirements.txt') }}
-         restore-keys: |
-           ${{ runner.os }}-pip-
-           ${{ runner.os }}-
-      # You can test your matrix by printing the current Python version
-      - name: Display Python version
-        run: python -c "import sys; print(sys.version)"
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install -r requirements.txt
-          pip install black flake8 mypy pytest
-      - name: Run black
-        run:
-          black --check .
-      - name: Run flake8
-        run: flake8
-      - name: Run Mypy
-        run: mypy  --ignore-missing-imports --warn-no-return --warn-redundant-casts --disallow-incomplete-defs .
-      - name: tests
-        run: pytest

.github/workflows/python-app.yml

@@ -0,0 +1,48 @@
+# This workflow will install Python dependencies, run tests and lint with a single version of Python
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+
+name: Python application
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python 3.10
+      uses: actions/setup-python@v3
+      with:
+        python-version: "3.10"
+    - name: Cache pip
+      uses: actions/cache@v1
+      with:
+       path: ~/.cache/pip # This path is specific to Ubuntu
+       # Look to see if there is a cache hit for the corresponding requirements file
+       key: ${{ runner.os }}-pip-${{ hashFiles('requirements.txt') }}
+       restore-keys: |
+         ${{ runner.os }}-pip-
+         ${{ runner.os }}-
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+        pip install black flake8 mypy pytest
+    - name: Lint with flake8
+      run: |
+        # stop the build if there are Python syntax errors or undefined names
+        flake8
+    - name: Run black
+      run:
+        black --check .
+    - name: Run Mypy
+      run: mypy  --ignore-missing-imports --warn-no-return --warn-redundant-casts --disallow-incomplete-defs --no-namespace-packages .

src/ml_utils.py

@@ -1,5 +1,5 @@
-from typing import List
 import logging
+from typing import List
 
 import albumentations as A
 import streamlit as st
@@ -26,8 +26,8 @@ transforms = A.Compose(
 
 
 def cells_to_bboxes(
-    predictions: torch.tensor, tensor_anchors: torch.tensor, s: int, is_preds: bool = True
-) -> torch.tensor:
+    predictions: torch.Tensor, tensor_anchors: torch.Tensor, s: int, is_preds: bool = True
+) -> List[List]:
     """
     Scale the predictions coming from the model_files to
     be relative to the entire image such that they for example later
@@ -106,8 +106,8 @@ def non_max_suppression(
 
 
 def intersection_over_union(
-    boxes_preds: torch.tensor, boxes_labels: torch.tensor, box_format: str = 'midpoint'
-) -> torch.tensor:
+    boxes_preds: torch.Tensor, boxes_labels: torch.Tensor, box_format: str = 'midpoint'
+) -> torch.Tensor:
     """
     Calculate iou.
 
@@ -156,7 +156,7 @@ def intersection_over_union(
 
 
 def predict(
-    model: torch.nn.Module, image: torch.tensor, iou_threshold: float = 1.0, threshold: float = 0.05
+    model: torch.nn.Module, image: torch.Tensor, iou_threshold: float = 1.0, threshold: float = 0.05
 ) -> List[List]:
     """
     Apply the model_files to the predictions and to postprocessing

src/utils.py

@@ -3,12 +3,12 @@ from typing import List, Dict
 import matplotlib
 import matplotlib.patches as patches
 import matplotlib.pyplot as plt
-import numpy as np
+import numpy.typing as npt
 import tomli as tomllib
 
 
 def plot_img_with_rects(
-    img: np.array, boxes: List[List], threshold: float = 0.5, coef: int = 400
+    img: npt.ArrayLike, boxes: List[List], threshold: float = 0.5, coef: int = 400
 ) -> matplotlib.figure.Figure:
     """
     Plot image with rectangles.