Merge branch 'master' into inspections

.github/workflows/PackageTest.yml

@@ -0,0 +1,49 @@
+name: Test Package
+
+on:
+  workflow_dispatch:
+  workflow_call:
+  push:
+
+jobs:
+  run-tests:
+    name: Run Tests
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: [ "3.8", "3.9", "3.10", "3.11" ]
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+
+      - name: Setup Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install poetry
+        run: |
+          pip install poetry
+          poetry env use python${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: poetry install --with tests
+
+      - name: Run tests with coverage
+        run: |
+          poetry run coverage run -m unittest discover 
+          poetry run coverage report --omit="tests/*"
+          poetry run coverage xml --omit="tests/*" -o coverage.xml
+
+  # Use this job for branch protection rules
+  report-test-status:
+    name: Report Test Status
+    if: always()
+    needs: run-tests
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check build status
+        if: ${{ contains(needs.*.result, 'failure') }}
+        run: exit 1

pyproject.toml

@@ -0,0 +1,57 @@
+[build-system]
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"
+
+[tool.poetry]
+name = "sndata"
+version = "0.0.0"  # Version is set dynamically by the CI tool on publication
+authors = ["Daniel Perrefort"]
+readme = "README.md"
+description = "A Python interface for data published by various supernova surveys."
+homepage = "http://sndata.readthedocs.io/"
+repository = "https://github.com/sncosmo/SNData/"
+documentation = "http://sndata.readthedocs.io/"
+keywords = ["astronomy", "supernova", "data"]
+packages = [{ include = "sndata" }]
+include = [
+    "sndata/sdss/Spectra_txt.zip",
+    "sndata/loss/sndb_meta.csv"
+]
+classifiers = [
+    "Development Status :: 5 - Production/Stable",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)",
+    "Natural Language :: English",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python :: 3",
+    "Topic :: Scientific/Engineering :: Astronomy",
+    "Topic :: Scientific/Engineering :: Physics",
+    "Typing :: Typed"
+]
+
+[tool.poetry.dependencies]
+python = ">=3.8"
+beautifulsoup4 = "*"
+astropy = "*"
+cython = "*"
+numpy = ">=1.17.0"
+pandas = "*"
+pyyaml = "*"
+requests = "*"
+tqdm = "*"
+sncosmo = "*"
+pytz = "*"
+
+[tool.poetry.group.tests]
+optional = true
+
+[tool.poetry.group.tests.dependencies]
+coverage = "*"
+
+[tool.poetry.group.docs]
+optional = true
+
+[tool.poetry.group.docs.dependencies]
+sphinx = "*"
+sphinx-copybutton = "*"
+sphinx_rtd_theme = "*"

sndata/sweetspot/_dr1.py

@@ -163,15 +163,12 @@ def _get_data_for_id(self, obj_id: str, format_table: bool = True) -> Table:
     def _decompress_filters(self):
         """Decompress filter files into the filter directory"""
 
-        print(self._filter_zip_path)
         with tarfile.open(self._filter_zip_path) as data_archive:
             for ffile in data_archive:
                 path = self._filter_dir / ffile.name
                 if path.exists():
                     continue
 
-                print(f'Unzipping {ffile.name}')
-
                 try:
                     data_archive.extract(ffile, path=self._filter_dir)
 

sndata/utils/downloads.py

@@ -43,11 +43,11 @@ def download_file(
     if verbose:
         tqdm.write(f'Fetching {url}', file=sys.stdout)
         response = requests.get(url, stream=True, timeout=timeout)
+        response.raise_for_status()
 
         total = int(response.headers.get('content-length', 0))
         chunk_size = 1024
-        with tqdm(total=total, unit='B', unit_scale=True,
-                  unit_divisor=chunk_size, file=sys.stdout) as pbar:
+        with tqdm(total=total, unit='B', unit_scale=True, unit_divisor=chunk_size, file=sys.stdout) as pbar:
             for data in response.iter_content(chunk_size=chunk_size):
                 pbar.update(destination.write(data))
 

tests/common_tests/__init__.py

@@ -0,0 +1,20 @@
+"""This module defines reusable setup and testing logic for streamlining the
+creation of downstream tests.
+"""
+
+from unittest import SkipTest
+
+import requests
+
+from .data_parsing_tests import *
+from .ui_tests import *
+
+
+def download_data_or_skip(release):
+    """Download data for the given data release. Skip any further tests if the download fails"""
+
+    try:
+        release.download_module_data()
+
+    except requests.exceptions.ConnectionError:
+        raise SkipTest('Could not connect to one or more remote servers.')

tests/data_parsing_template_tests.py → tests/common_tests/data_parsing_tests.py

@@ -1,6 +1,4 @@
-"""This module provides template testing classes for spectroscopic and
-photometric data parsing.
-"""
+"""Template test classes for spectroscopic and photometric data parsing."""
 
 import numpy as np
 import sncosmo
@@ -27,9 +25,7 @@ def test_no_empty_data_tables(self, lim: int = 25):
                 return
 
             obj_id = input_table.meta['obj_id']
-            self.assertTrue(
-                input_table,
-                msg=f'Empty table for obj_id {obj_id}.')
+            self.assertTrue(input_table, msg=f'Empty table for obj_id {obj_id}.')
 
         if i < 0:
             self.fail('No data yielded')

tests/standard_ui_template_tests.py → tests/common_tests/ui_tests.py

@@ -1,6 +1,4 @@
-"""This module provides template testing classes for the user interface of
-spectroscopic and photometric data releases.
-"""
+"""Template test classes for high level data release class behavior."""
 
 
 class SpectroscopicDataUI:

tests/test_combined_datasets.py

@@ -1,6 +1,4 @@
-"""Test that survey data is accessed and served correctly for combined data
-sets
-"""
+"""Test that survey data is accessed and served correctly for combined data sets."""
 
 from unittest import TestCase
 
@@ -9,7 +7,7 @@
 from sndata import CombinedDataset
 from sndata import csp, des
 from sndata._combine_data import reduce_id_mapping
-from .data_parsing_template_tests import PhotometricDataParsing
+from .common_tests import PhotometricDataParsing
 from .test_exceptions import InvalidTableId
 
 

tests/test_csp/test_dr1.py

@@ -0,0 +1,24 @@
+"""Tests for the ``csp.DR1`` class."""
+
+from unittest import TestCase
+
+from sndata.csp import DR1
+from ..common_tests import SpectroscopicDataParsing, SpectroscopicDataUI, download_data_or_skip
+
+download_data_or_skip(DR1())
+
+
+class DR1Parsing(TestCase, SpectroscopicDataParsing):
+    """Data parsing tests for the DR1 release"""
+
+    @classmethod
+    def setUpClass(cls):
+        cls.test_class = DR1()
+
+
+class DR1UI(TestCase, SpectroscopicDataUI):
+    """UI tests for the DR1 release"""
+
+    @classmethod
+    def setUpClass(cls):
+        cls.test_class = DR1()