PEP8 and test suite

.github/workflows/linter.yml

@@ -0,0 +1,36 @@
+name: PEP8
+
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.11]
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install ruff
+    - name: Lint
+      run: |
+        ruff check --statistics *.py 
+        ruff check --statistics apps/
+        ruff check --ignore D205 tests/
+    - name: Format
+      run: |
+        ruff format --check *.py
+        ruff format --check apps/
+        ruff format --check tests/

.github/workflows/run_test.yml

@@ -0,0 +1,28 @@
+name: Sentinel
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+
+jobs:
+  test-suite:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.11]
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install Python dependencies
+      run: |
+        pip install --upgrade pip setuptools wheel
+        pip install -r requirements.txt
+        cd ..
+    - name: Run test suites
+      run: |
+        ./run_tests.sh --url ${{ secrets.APIURLDEV }}

apps/routes/objects/api.py

@@ -20,6 +20,7 @@
 
 bp = Blueprint("objects", __name__)
 
+
 # Enable CORS for this blueprint
 @bp.after_request
 def after_request(response):
@@ -53,7 +54,7 @@ def after_request(response):
     {
         "name": "columns",
         "required": False,
-        "description": f"Comma-separated data columns to transfer. Default is all columns.",
+        "description": "Comma-separated data columns to transfer. Default is all columns.",
     },
     {
         "name": "output-format",
@@ -62,6 +63,7 @@ def after_request(response):
     },
 ]
 
+
 @bp.route("/api/v1/objects", methods=["GET"])
 def return_object_arguments():
     """Obtain information about retrieving object data"""

apps/routes/objects/utils.py

@@ -13,9 +13,10 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 import pandas as pd
+from numpy import array as nparray
 from apps.utils.utils import download_cutout
 from apps.utils.client import connect_to_hbase_table
-from apps.utils.decoding import format_hbase_output
+from apps.utils.decoding import format_hbase_output, hbase_to_dict
 
 
 def extract_object_data(payload: dict) -> pd.DataFrame:
@@ -101,9 +102,9 @@ def extract_object_data(payload: dict) -> pd.DataFrame:
         else:
             colname = "b:cutout{}_stampData".format(cutout_kind)
             pdf[colname] = pdf[["i:objectId", "i:candid"]].apply(
-                lambda x: pd.Series(
-                    [download_cutout(x.iloc[0], x.iloc[1], cutout_kind)]
-                ),
+                lambda x: pd.Series([
+                    download_cutout(x.iloc[0], x.iloc[1], cutout_kind)
+                ]),
                 axis=1,
             )
 
@@ -145,12 +146,10 @@ def extract_object_data(payload: dict) -> pd.DataFrame:
 
         if "i:jd" in pdfUP.columns:
             # workaround -- see https://github.com/astrolabsoftware/fink-science-portal/issues/216
-            mask = np.array(
-                [
-                    False if float(i) in pdf["i:jd"].to_numpy() else True
-                    for i in pdfUP["i:jd"].to_numpy()
-                ]
-            )
+            mask = nparray([
+                False if float(i) in pdf["i:jd"].to_numpy() else True
+                for i in pdfUP["i:jd"].to_numpy()
+            ])
             pdfUP = pdfUP[mask]
 
         # Hacky way to avoid converting concatenated column to float
@@ -171,4 +170,4 @@ def extract_object_data(payload: dict) -> pd.DataFrame:
 
     client.close()
 
-    return pdf
+    return pdf

apps/routes/template/api.py

@@ -1,12 +1,12 @@
 # Copyright 2024 AstroLab Software
 # Author: Julien Peloton
-#   
+#
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
 #
 #     http://www.apache.org/licenses/LICENSE-2.0
-#   
+#
 # Unless required by applicable law or agreed to in writing, software
 # distributed under the License is distributed on an "AS IS" BASIS,
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
@@ -20,6 +20,7 @@
 
 bp = Blueprint("template", __name__)
 
+
 # Enable CORS for this blueprint
 @bp.after_request
 def after_request(response):
@@ -42,6 +43,7 @@ def after_request(response):
     },
 ]
 
+
 @bp.route("/api/v1/template", methods=["GET"])
 def return_template_arguments():
     """Obtain information about retrieving object data"""
@@ -51,6 +53,7 @@ def return_template_arguments():
     else:
         return jsonify({"args": ARGS})
 
+
 @bp.route("/api/v1/template", methods=["POST"])
 def return_template(payload=None):
     """Retrieve object data"""
@@ -70,5 +73,3 @@ def return_template(payload=None):
 
     output_format = payload.get("output-format", "json")
     return send_tabular_data(out, output_format)
-
-

apps/routes/template/utils.py

@@ -14,5 +14,6 @@
 # limitations under the License.
 import pandas as pd
 
+
 def my_function(payload):
     return pd.DataFrame({payload["arg1"]: [1, 2, 3]})

apps/utils/utils.py

@@ -13,6 +13,7 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 """Various utilities"""
+
 import io
 import json
 import yaml
@@ -23,6 +24,7 @@
 from astropy.table import Table
 from astropy.io import votable
 
+
 def extract_configuration(filename):
     """Extract user defined configuration
 
@@ -43,6 +45,7 @@ def extract_configuration(filename):
         config["APIURL"] = "http://" + config["HOST"] + ":" + str(config["PORT"])
     return config
 
+
 def download_cutout(objectId, candid, kind):
     """ """
     config = extract_configuration("config.yml")

run_tests.sh

@@ -0,0 +1,50 @@
+#!/bin/bash
+# Copyright 2024 AstroLab Software
+# Author: Julien Peloton
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+set -e
+message_help="""
+Run the test suite of the modules\n\n
+Usage:\n
+    \t./run_tests.sh [--url]\n\n
+
+--url is the Science Portal URL you would like to test against.
+"""
+# Grab the command line arguments
+while [ "$#" -gt 0 ]; do
+  case "$1" in
+    --url)
+        URL="$2"
+        shift 2
+        ;;
+    -h)
+        echo -e $message_help
+        exit
+        ;;
+  esac
+done
+
+if [[ -f $URL ]]; then
+  echo "You need to specify an URL" $URL
+  exit
+fi
+
+# Run the test suite on the utilities
+cd tests
+for filename in ./*.py
+do
+  echo $filename
+  # Run test suite
+  python $filename $URL
+done