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test: add test suite (#7)

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* add pre-commit hook
* improve logging of inconsistent data
This commit is contained in:
Felix Spöttel
2022-07-04 13:54:07 +02:00
committed by GitHub
parent 1c5d0f649e
commit d252c6b8f3
17 changed files with 435 additions and 72 deletions
Download Patch File Download Diff File Expand all files Collapse all files

4
.github/workflows/main.yml vendored
View File

@@ -42,6 +42,10 @@ jobs:
name: "Style"
run: |
black --check .
- python: "3.10"
task:
name: "Test"
run: pytest --exitfirst --failed-first
steps:
- uses: actions/checkout@v3

10
.pre-commit-config.yaml Normal file
View File

@@ -0,0 +1,10 @@
repos:
- repo: https://github.com/psf/black
rev: 22.3.0
hooks:
- id: black
# It is recommended to specify the latest version of Python
# supported by your project here, or alternatively use
# pre-commit's default_language_version, see
# https://pre-commit.com/#top_level-default_language_version
language_version: python3.9

2
Pipfile
View File

@@ -13,6 +13,8 @@ scikit-learn = "*"
[dev-packages]
black = "*"
pre-commit = "*"
pytest = "*"
wheel = "*"
[requires]

311
Pipfile.lock generated
View File

@@ -1,7 +1,7 @@
{
"_meta": {
"hash": {
"sha256": "2c871d34049ba57c71502528723f7a03014d0bf5c768f77704cf13ef88215378"
"sha256": "5f06b83fcb7ea20fc04cdfdf3da353a1f003ea441738f7615cc3f789877a60bf"
},
"pipfile-spec": 6,
"requires": {
@@ -16,6 +16,14 @@
]
},
"default": {
"appnope": {
"hashes": [
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"sha256:265a455292d0bd8a72453494fa24df5a11eb18373a60c7c0430889f22548605e"
],
"markers": "platform_system == 'Darwin'",
"version": "==0.1.3"
},
"argon2-cffi": {
"hashes": [
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@@ -99,58 +107,72 @@
},
"cffi": {
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"version": "==1.15.1"
},
"click": {
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@@ -440,11 +462,11 @@
},
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"version": "==0.6.6"
},
"nbconvert": {
"hashes": [
@@ -1037,6 +1059,14 @@
}
},
"develop": {
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"version": "==21.4.0"
},
"black": {
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@@ -1066,6 +1096,14 @@
"index": "pypi",
"version": "==22.6.0"
},
"cfgv": {
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"click": {
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@@ -1074,6 +1112,36 @@
"index": "pypi",
"version": "==8.1.3"
},
"distlib": {
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"markers": "python_version >= '3.7'",
"version": "==3.7.1"
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"identify": {
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"iniconfig": {
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},
"mypy-extensions": {
"hashes": [
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@@ -1081,6 +1149,22 @@
],
"version": "==0.4.3"
},
"nodeenv": {
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],
"markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4, 3.5, 3.6'",
"version": "==1.7.0"
},
"packaging": {
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"version": "==21.3"
},
"pathspec": {
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@@ -1096,6 +1180,109 @@
"markers": "python_version >= '3.7'",
"version": "==2.5.2"
},
"pluggy": {
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"version": "==1.0.0"
},
"pre-commit": {
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"setuptools": {
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],
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"version": "==1.16.0"
},
"toml": {
"hashes": [
"sha256:806143ae5bfb6a3c6e736a764057db0e6a0e05e338b5630894a5f779cabb4f9b",
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@@ -1106,11 +1293,19 @@
},
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36
geoclustering/io.py
View File

@@ -1,3 +1,4 @@
import math
from keplergl import KeplerGl
from pathlib import Path
from pkg_resources import resource_filename
@@ -38,23 +39,32 @@ def is_valid_lon(val: str) -> bool:
return False
def is_not_none(val: any) -> bool:
return val is not None
def read_csv_file(filename):
"""Read input csv file, dropping rows that don't have valid location data."""
df = pd.read_csv(filename)
initial_rows = len(df)
# replace NaN for all fields not to break kepler parsing.
df = pd.read_csv(filename).replace({np.nan: None})
df = df.dropna(subset=["lat", "lon"])
df = df.replace(
{np.nan: None}
) # replace for other fields not to break kepler parsing
print(f"Ignored {initial_rows - len(df)} coordinates with NaN")
# construct an index of values with valid lat & lon.
valid_index = df.lat.apply(is_valid_lat) & df.lon.apply(is_valid_lon)
df_invalid = df[~valid_index]
if count_invalid := len(df_invalid):
df_not_empty = df_invalid[
(df_invalid.lat.apply(is_not_none) | df_invalid.lon.apply(is_not_none))
]
count_not_empty = len(df_not_empty)
if count_empty := count_invalid - count_not_empty:
print(f"Removed {count_empty} empty coordinate pairs.")
if count_not_empty:
print(f"Removed {count_not_empty} invalid coordinate pairs:")
print(df_not_empty[["lat", "lon"]].to_string())
valid_index = df.lat.astype(str).apply(is_valid_lat) & df.lon.astype(str).apply(
is_valid_lon
)
if len(df_invalid := df[~valid_index]):
print(f"Found {len(df_invalid)} invalid coordinate pairs, ignoring:")
print(df_invalid[["lat", "lon"]].to_string())
return df[valid_index]

3
pytest.ini Normal file
View File

@@ -0,0 +1,3 @@
[pytest]
testpaths = tests/
python_files = *.py

4
setup.py
View File

@@ -33,7 +33,9 @@ setup(
"pandas",
"scikit-learn",
],
extras_require={"dev": ["black", "wheel"]},
extras_require={
"dev": ["black", "wheel", "pre-commit", "pytest"],
},
include_package_data=True,
zip_safe=False,
)

0
tests/__init__.py Normal file
View File

42
tests/clustering.py Normal file
View File

@@ -0,0 +1,42 @@
from geoclustering.clustering import cluster_locations
from geoclustering.io import read_csv_file
from tests.helpers import get_fixture_path, read_fixture_csv
df = read_fixture_csv("clustering.csv")
def has_member(list, name):
return any(x for x in list if x["name"] == name)
def test_clustering_all():
# there should be one cluster with all members but Erin.
res = cluster_locations(
df=df, algorithm="dbscan", radius_km=1.97, min_cluster_size=4
)
assert len(res.values()) == 1
assert len(res[0]) == 4
def test_clustering_split():
res = cluster_locations(
df=df, algorithm="dbscan", radius_km=0.5, min_cluster_size=2
)
# there should be two cluster: Alice & Bob and Carol & Dan
assert len(res.values()) == 2
cluster_one = res[0]
cluster_two = res[1]
assert len(cluster_one) == 2
assert has_member(cluster_one, "Alice")
assert has_member(cluster_one, "Bob")
assert has_member(cluster_two, "Carol")
assert has_member(cluster_two, "Dan")
def test_clustering_none():
# there should be no clusters now.
res = cluster_locations(
df=df, algorithm="dbscan", radius_km=0.5, min_cluster_size=3
)
assert len(res.values()) == 0

30
tests/encoding.py Normal file
View File

@@ -0,0 +1,30 @@
from geoclustering.clustering import cluster_locations
from geoclustering.encoding import encode_clusters
from tests.helpers import read_fixture_csv, read_fixture_content
df = read_fixture_csv("clustering.csv")
def test_encoders():
clusters = {
0: [
{"id": 1, "name": "Alice", "lat": 52.523955, "lon": 13.442362},
{"id": 2, "name": "Bob", "lat": 52.526659, "lon": 13.448097},
],
1: [
{"id": 3, "name": "Carol", "lat": 52.525626, "lon": 13.419246},
{
"id": 4,
"name": "Dan",
"lat": 52.52443559865125,
"lon": 13.41261723049818,
},
],
}
res = encode_clusters(clusters)
assert res["string"] == read_fixture_content("snapshots/result.txt")
assert res["json"] == read_fixture_content("snapshots/result.json")
assert res["geojson"] == read_fixture_content("snapshots/result.geojson")

6
tests/fixtures/clustering.csv vendored Normal file
View File

@@ -0,0 +1,6 @@
id,name,lat,lon
1,Alice,52.523955,13.442362
2,Bob,52.526659,13.448097
3,Carol,52.525626,13.419246
4,Dan,52.52443559865125,13.41261723049818
5,Erin,52.524838991760774,13.383188597040382
1 id name lat lon
2 1 Alice 52.523955 13.442362
3 2 Bob 52.526659 13.448097
4 3 Carol 52.525626 13.419246
5 4 Dan 52.52443559865125 13.41261723049818
6 5 Erin 52.524838991760774 13.383188597040382

9
tests/fixtures/io.csv vendored Normal file
View File

@@ -0,0 +1,9 @@
id,name,lat,lon
1,Alice,,
2,,52.523955,13.442362
,,-90.12,132.23
4,,78.234,-180.1212
5,Bob,52.524838991760774,13.383188597040382
6,Peter,91.234,
7,Horst,,23.23
7,Erin,foo,bar
1 id name lat lon
2 1 Alice
3 2 52.523955 13.442362
4 -90.12 132.23
5 4 78.234 -180.1212
6 5 Bob 52.524838991760774 13.383188597040382
7 6 Peter 91.234
8 7 Horst 23.23
9 7 Erin foo bar

1
tests/fixtures/snapshots/result.geojson vendored Normal file
View File

@@ -0,0 +1 @@
{"type": "FeatureCollection", "features": [{"type": "Feature", "geometry": {"type": "Point", "coordinates": [13.442362, 52.523955]}, "properties": {"id": 1, "name": "Alice", "cluster_id": 0}}, {"type": "Feature", "geometry": {"type": "Point", "coordinates": [13.448097, 52.526659]}, "properties": {"id": 2, "name": "Bob", "cluster_id": 0}}, {"type": "Feature", "geometry": {"type": "Point", "coordinates": [13.419246, 52.525626]}, "properties": {"id": 3, "name": "Carol", "cluster_id": 1}}, {"type": "Feature", "geometry": {"type": "Point", "coordinates": [13.412617, 52.524436]}, "properties": {"id": 4, "name": "Dan", "cluster_id": 1}}]}

1
tests/fixtures/snapshots/result.json vendored Normal file
View File

@@ -0,0 +1 @@
[{"cluster_id": 0, "points": [{"id": 1, "name": "Alice", "lat": 52.523955, "lon": 13.442362}, {"id": 2, "name": "Bob", "lat": 52.526659, "lon": 13.448097}]}, {"cluster_id": 0, "points": [{"id": 1, "name": "Alice", "lat": 52.523955, "lon": 13.442362}, {"id": 2, "name": "Bob", "lat": 52.526659, "lon": 13.448097}]}, {"cluster_id": 1, "points": [{"id": 3, "name": "Carol", "lat": 52.525626, "lon": 13.419246}, {"id": 4, "name": "Dan", "lat": 52.52443559865125, "lon": 13.41261723049818}]}, {"cluster_id": 1, "points": [{"id": 3, "name": "Carol", "lat": 52.525626, "lon": 13.419246}, {"id": 4, "name": "Dan", "lat": 52.52443559865125, "lon": 13.41261723049818}]}]

7
tests/fixtures/snapshots/result.txt vendored Normal file
View File

@@ -0,0 +1,7 @@
Cluster 0
id 1, name Alice, lat 52.523955, lon 13.442362
id 2, name Bob, lat 52.526659, lon 13.448097
Cluster 1
id 3, name Carol, lat 52.525626, lon 13.419246
id 4, name Dan, lat 52.52443559865125, lon 13.41261723049818

16
tests/helpers.py Normal file
View File

@@ -0,0 +1,16 @@
import os
from geoclustering.io import read_csv_file
def get_fixture_path(filename):
dir_path = os.path.dirname(os.path.realpath(__file__))
return os.path.join(dir_path, "fixtures", filename)
def read_fixture_csv(filename):
return read_csv_file(get_fixture_path(filename))
def read_fixture_content(filename):
with open(get_fixture_path(filename)) as f:
return f.read()

25
tests/io.py Normal file
View File

@@ -0,0 +1,25 @@
from pathlib import Path
import shutil
from geoclustering.io import write_output_file
from tests.helpers import read_fixture_csv
def test_csv_filters():
df = read_fixture_csv("io.csv")
# entries 2 & 5 in fixture are valid.
assert len(df) == 2
assert df.iloc[0]["name"] == None
assert df.iloc[1]["name"] == "Bob"
def test_write_output_file():
p = "./this/dir/does/not/exist"
f = "test.txt"
write_output_file(p, f, "test")
path = Path(p) / f
with open(path) as f:
assert f.read() == "test"
shutil.rmtree(Path("./this"))