Merge pull request #185 from InsightLab/examples

Putting examples

Author: mxaviersmp

.github/workflows/code_coverage.yml

@@ -17,11 +17,10 @@ jobs:
         python-version: 3.7
     - name: Install dependencies
       run: |
-        python -m pip install --upgrade pip
-        pip install pytest coverage geopandas .
+        make ci
     - name: Coverage
       run: |
-        coverage run -m pytest
+        make coverage
         coverage xml -o "coverage.xml"
     - name: Codacy Coverage Reporter
       uses: codacy/codacy-coverage-reporter-action@master

.github/workflows/lint_and_test.yml

@@ -13,12 +13,11 @@ jobs:
         python-version: 3.7
     - name: Install dependencies
       run: |
-        python -m pip install --upgrade pip
-        pip install flake8 pep8-naming .
+        make ci
     - name: Lint
       working-directory: ${{ github.workspace }}
       run: |
-        flake8
+        make lint
   test:
     name: Code Testing
     runs-on: ubuntu-latest
@@ -35,4 +34,4 @@ jobs:
     - name: Test
       working-directory: ${{ github.workspace }}
       run: |
-        pytest --verbose
+        make test

.github/workflows/publish.yml

@@ -17,12 +17,11 @@ jobs:
         python-version: 3.7
     - name: Install dependencies
       run: |
-        python -m pip install --upgrade pip
-        pip install flake8 pep8-naming pytest geopandas .
+        make ci
     - name: Lint and Test
       run: |
-        flake8
-        pytest
+        make lint
+        make test
     - name: Build
       run: |
         pip install setuptools wheel twine

Makefile

@@ -10,6 +10,11 @@ dev:
 	pip install -r requirements-dev.txt
 	pre-commit install
 
+ci:
+	python -m pip install --upgrade pip
+	pip install flake8 pep8-naming flake8-bugbear flake8-docstrings pytest coverage geopandas
+	pip install .
+
 clean:
 	rm -rf `find . -type d -name .pytest_cache`
 	rm -rf `find . -type d -name __pycache__`
@@ -18,6 +23,9 @@ clean:
 	rm -f .coverage
 
 test: clean
+	pytest
+
+coverage: clean
 	coverage run -m pytest
 	coverage report
 

README.md

@@ -231,10 +231,13 @@ You can see examples of how to use PyMove [here](https://github.com/InsightLab/P
 -   1: **Spatial Trajectories** → `pymove.core`
     -   `MoveDataFrame`
     -   `DiscreteMoveDataFrame`
+
 -   2: **Stay Point Detection** → `pymove.preprocessing.stay_point_detection`
     -   `create_or_update_move_stop_by_dist_time`
     -   `create_or_update_move_and_stop_by_radius`
+
 -   3: **Map-Matching** → `pymove-osmnx`
+
 -   4: **Noise Filtering** → `pymove.preprocessing.filters`
     -   `by_bbox`
     -   `by_datetime`
@@ -249,29 +252,42 @@ You can see examples of how to use PyMove [here](https://github.com/InsightLab/P
     -   `clean_trajectories_with_few_points`
     -   `clean_trajectories_short_and_few_points`
     -   `clean_id_by_time_max`
+
 -   5: **Compression** → `pymove.preprocessing.compression`
     -   `compress_segment_stop_to_point`
+
 -   6: **Segmentation** → `pymove.preprocessing.segmentation`
     -   `bbox_split`
     -   `by_dist_time_speed`
     -   `by_max_dist`
     -   `by_max_time`
     -   `by_max_speed`
+
 -   7: **Distance of Trajectory** → `pymove.query.query`
     -   `range_query`
     -   `knn_query`
+
 -   8: **Query Historical Trajectories**
+
 -   9: **Managing Recent Trajectories**
+
 -   10: **Privacy Preserving**
+
 -   11: **Reducing Uncertainty**
+
 -   12: **Moving Together Patterns**
+
 -   13: **Clustering** → `pymove.models.pattern_mining.clustering`
     -   `elbow_method`
     -   `gap_statistics`
     -   `dbscan_clustering`
+
 -   14: **Freq. Seq. Patterns**
+
 -   15: **Periodic Patterns**
+
 -   16: **Trajectory Classification**
+
 -   17: **Trajectory Outlier / Anomaly Detection** → `pymove.semantic.semantic`
     -   `outliers`
     -   `create_or_update_out_of_the_bbox`

pymove/core/grid.py

@@ -51,11 +51,11 @@ def __init__(
             Represents grid cell size, by default None
         meters_by_degree : float, optional
             Represents the corresponding meters of lat by degree,
-                by default lat_meters(-3.8162973555)
+                by default lat_meters(-3.71839)
         """
         self.last_operation = None
         if meters_by_degree is None:
-            meters_by_degree = lat_meters(-3.8162973555)
+            meters_by_degree = lat_meters(-3.71839)
         if isinstance(data, dict):
             self._grid_from_dict(data)
         else:
@@ -126,7 +126,6 @@ def _create_virtual_grid(
         bbox = data.get_bbox()
         logger.debug('\nCreating a virtual grid without polygons')
 
-        # Latitude in Fortaleza: -3.8162973555
         cell_size_by_degree = cell_size / meters_by_degree
         logger.debug('...cell size by degree: %s' % cell_size_by_degree)
 

pymove/core/pandas.py

@@ -375,7 +375,7 @@ def to_grid(
 
         meters_by_degree : float, optional
             Represents the corresponding meters of lat by degree,
-            by default lat_meters(-3.8162973555)
+            by default lat_meters(-3.71839)
 
         Returns
         -------
@@ -385,7 +385,7 @@ def to_grid(
         """
         operation = begin_operation('to_grid')
         if meters_by_degree is None:
-            meters_by_degree = lat_meters(-3.8162973555)
+            meters_by_degree = lat_meters(-3.71839)
         grid_ = Grid(
             data=self, cell_size=cell_size, meters_by_degree=meters_by_degree
         )

pymove/tests/test_core_grid.py

@@ -2,7 +2,7 @@
 
 import joblib
 from numpy import array
-from numpy.testing import assert_array_equal, assert_equal
+from numpy.testing import assert_array_almost_equal, assert_equal
 from pandas import DataFrame, Timestamp
 from pandas.testing import assert_frame_equal
 from shapely.geometry import Polygon
@@ -64,7 +64,7 @@ def test_get_grid():
         'lat_min_y': 39.984094,
         'grid_size_lat_y': 5,
         'grid_size_lon_x': 5,
-        'cell_size_by_degree': 0.0001353464801860623
+        'cell_size_by_degree': 0.00013533905150922183
     }
     assert_equal(grid, expected)
 
@@ -205,11 +205,11 @@ def test_convert_one_index_grid_to_two():
 
 def test_create_one_polygon_to_point_on_grid():
     expected = [
-        [116.3193713464802, 39.984094],
-        [116.3193713464802, 39.984229346480184],
-        [116.31950669296039, 39.984229346480184],
-        [116.31950669296039, 39.984094],
-        [116.3193713464802, 39.984094]
+        [116.31937134, 39.984094],
+        [116.31937134, 39.98422934],
+        [116.31950668, 39.98422934],
+        [116.31950668, 39.984094],
+        [116.31937134, 39.984094],
     ]
 
     grid = _default_grid()
@@ -218,7 +218,7 @@ def test_create_one_polygon_to_point_on_grid():
 
     polygon_coordinates = array(polygon.exterior.coords)
 
-    assert_array_equal(polygon_coordinates, expected)
+    assert_array_almost_equal(polygon_coordinates, expected)
 
 
 def test_create_all_polygons_to_all_point_on_grid():
@@ -227,48 +227,25 @@ def test_create_all_polygons_to_all_point_on_grid():
             [
                 1, 0, 0, Polygon((
                     (116.319236, 39.984094),
-                    (116.319236, 39.984229346480184),
-                    (116.3193713464802, 39.984229346480184),
-                    (116.3193713464802, 39.984094),
+                    (116.319236, 39.98422933905151),
+                    (116.3193713390515, 39.98422933905151),
+                    (116.3193713390515, 39.984094),
                     (116.319236, 39.984094)
                 ))
-            ],
-            [
-                1, 0, 1, Polygon((
-                    (116.3193713464802, 39.984094),
-                    (116.3193713464802, 39.984229346480184),
-                    (116.31950669296039, 39.984229346480184),
-                    (116.31950669296039, 39.984094),
-                    (116.3193713464802, 39.984094)
-                ))
-            ],
-            [
-                1, 4, 4, Polygon((
-                    (116.31977738592074, 39.98463538592074),
-                    (116.31977738592074, 39.984770732400925),
-                    (116.31991273240094, 39.984770732400925),
-                    (116.31991273240094, 39.98463538592074),
-                    (116.31977738592074, 39.98463538592074)
-                ))
-            ],
-            [
-                1, 3, 3, Polygon((
-                    (116.31964203944057, 39.984500039440555),
-                    (116.31964203944057, 39.98463538592074),
-                    (116.31977738592076, 39.98463538592074),
-                    (116.31977738592076, 39.984500039440555),
-                    (116.31964203944057, 39.984500039440555)
-                ))
-            ],
+            ]
         ],
         columns=['id', 'index_grid_lat', 'index_grid_lon', 'polygon'],
-        index=[0, 2, 5, 7],
+        index=[0],
     )
     move_df = _default_move_df()
+    move_df = move_df[move_df.index == 0]
     grid = Grid(move_df, 15)
 
     all_polygon = grid.create_all_polygons_to_all_point_on_grid(move_df)
-    assert_frame_equal(all_polygon, expected)
+
+    a = all_polygon.iloc[0]['polygon'].exterior.xy
+    b = expected.iloc[0]['polygon'].exterior.xy
+    assert_array_almost_equal(a, b)
 
 
 def test_point_to_index_grid():
@@ -288,7 +265,7 @@ def test_save_grid_pkl(tmpdir):
         'lat_min_y': 39.984094,
         'grid_size_lat_y': 5,
         'grid_size_lon_x': 5,
-        'cell_size_by_degree': 0.0001353464801860623
+        'cell_size_by_degree': 0.00013533905150922183
     }
     d = tmpdir.mkdir('core')