Merge pull request #411 from simontorres/packaging_updates

Update packaging to latest standard and to use vcs tags for versioning

.github/workflows/python-package.yml

@@ -10,23 +10,53 @@ on:
     branches: [ main ]
 
 jobs:
-  build:
-
-    runs-on: ubuntu-latest
+  tests:
+    name: ${{ matrix.name }}
+    runs-on: ${{ matrix.os }}
     strategy:
+      fail-fast: false
       matrix:
-        python-version: ['3.8', '3.9', '3.10', '3.11']
+        include:
+
+          - name: Python 3.12 with Coverage
+            os: ubuntu-latest
+            python: '3.12'
+            toxenv: py312-test-cov
+
+          - name: Python 3.12
+            os: ubuntu-latest
+            python: '3.12'
+            toxenv: py312-test
+
+          - name: Python 3.10
+            os: ubuntu-latest
+            python: '3.10'
+            toxenv: py310-test
+
+          - name: Python 3.9
+            os: ubuntu-latest
+            python: 3.9
+            toxenv: py39-test
+
+          - name: Python 3.8
+            os: ubuntu-latest
+            python: 3.8
+            toxenv: py38-test
 
     steps:
-    - uses: actions/checkout@v4
-    - name: Set up Python ${{ matrix.python-version }}
+    - name: Checkout code
+      uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
+
+    - name: Set up Python ${{ matrix.python }}
       uses: actions/setup-python@v5
       with:
-        python-version: ${{ matrix.python-version }}
+        python-version: ${{ matrix.python }}
     - name: Install dependencies
       run: |
-        python -m pip install --upgrade pip
-        pip install flake8 pytest-cov wheel
+        python -m pip install --upgrade tox
+        pip install flake8 pytest-cov wheel tox
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
     - name: Compile DCR Binaries
       run: |
@@ -40,13 +70,40 @@ jobs:
         flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
         # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
         flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-    - name: Test with pytest
+    - run: |
+        pwd
+        ls -la goodman_pipeline
+    - name: Run Tests
       run: |
-        pytest --cov=goodman_pipeline
+        tox ${{ matrix.toxargs }} -e ${{ matrix.toxenv }} -- ${{ matrix.toxposargs }}
+    - name: Upload coverage to artifacts
+      if: ${{ contains(matrix.toxenv,'-cov') }}
+      uses: actions/upload-artifact@v4
+      with:
+        name: coverage_${{ matrix.toxenv }}.xml
+        path: coverage.xml
+        if-no-files-found: error
 
-    - uses: codecov/codecov-action@v4
+  upload-coverage-report:
+    needs: ['tests']
+    permissions:
+      contents: none
+    runs-on: ubuntu-latest
+    name: Upload Coverage
+    steps:
+    - name: Download coverage artifacts
+      uses: actions/download-artifact@v4
+      with:
+        path: coverage
+        pattern: coverage_*
+        merge-multiple: true
+    - name: Upload to Codecov
+      if: ${{ hashFiles('coverage/') != ''}}
+      uses: codecov/codecov-action@v4
       with:
-        token: ${{ secrets.CODECOV_TOKEN }} # not required for public repos
+        token: ${{ secrets.CODECOV_TOKEN }}
+        directory: coverage
         fail_ci_if_error: true # optional (default = false)
+        verbose: true
 
 

.gitignore

@@ -14,5 +14,7 @@ goodman_pipeline/data/dcr_source/*.o
 .eggs/*
 .tmp/*
 .tox/*
-goodman_pipeline.egg-info/*
+*/goodman_pipeline.egg-info/*
+goodman_pipeline/version.py
+coverage.xml
 *.DS_Store

docs/conf.py

@@ -19,6 +19,7 @@
 # import os
 # import sys
 # sys.path.insert(0, os.path.abspath('.'))
+from importlib.metadata import version
 
 
 # -- General configuration ------------------------------------------------
@@ -31,7 +32,7 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 
-__version__ = __import__('goodman_pipeline').__version__
+__version__ = version('goodman_pipeline')
 
 extensions = ['sphinx.ext.todo',
               'sphinx.ext.coverage',

goodman_pipeline/__init__.py

@@ -1,9 +1,11 @@
 from __future__ import absolute_import
 
-from .version import __version__
+from importlib.metadata import version
 
 from . import spectroscopy
 from . import images
 from . import core
 
-from .core import setup_logging
+from .core import setup_logging
+
+__version__ = version('goodman_pipeline')

goodman_pipeline/core/check_version.py

@@ -7,25 +7,25 @@
 import requests
 import os
 
-from distutils.version import LooseVersion
+from packaging.version import Version
 
 logger = logging.getLogger(__name__)
 
 API_URL = 'https://api.github.com/repos/soar-telescope/goodman/releases/latest'
 
 
-def get_last(github_api_token='GITHUB_ACCESS_TOKEN'):
+def get_last(github_api_token: str = 'GITHUB_ACCESS_TOKEN') -> Version:
     """
     Returns the version of the last release on GitHub.
 
     Parameters
     ----------
         github_api_token (str, optional) : Name of the environment variable
-        holding the github access token for the API
+          holding the github access token for the API
 
     Returns
     -------
-        version (LooseVersion) : the last version of the pipeline.
+        version (object) : A :class:`pkg_resources.extern.packaging.version.Version` the last version of the pipeline.
     """
     try:
         access_token = os.environ[github_api_token]
@@ -39,14 +39,14 @@ def get_last(github_api_token='GITHUB_ACCESS_TOKEN'):
         raise ConnectionRefusedError('Number of tests reached maximum for now.')
 
     tag_name = response.json()['tag_name'].replace('v', '')
-    _version = LooseVersion(tag_name)
+    _version = Version(tag_name)
 
-    return _version.vstring
+    return _version
 
 
-def am_i_updated(version):
+def am_i_updated(version: str) -> bool:
 
-    version = LooseVersion(version.replace('v', ''))
+    version = Version(version)
     last_version = get_last()
 
     return last_version <= version

goodman_pipeline/core/core.py

@@ -29,13 +29,14 @@
 from astropy.stats import sigma_clip
 from astropy.time import Time
 from astroscrappy import detect_cosmics
+from importlib.metadata import version
 from matplotlib import pyplot as plt
 from scipy import signal, interpolate
 from threading import Timer
 
 from . import check_version
 
-__version__ = __import__('goodman_pipeline').__version__
+__version__ = version('goodman_pipeline')
 
 log = logging.getLogger(__name__)
 
@@ -3266,7 +3267,7 @@ def trace_targets(ccd, target_list, sampling_step=5, pol_deg=2, nfwhm=5,
     return all_traces
 
 
-def validate_ccd_region(ccd_region, regexp='^\[\d*:\d*,\d*:\d*\]$'):
+def validate_ccd_region(ccd_region, regexp=r'^\[\d*:\d*,\d*:\d*\]$'):
     compiled_reg_exp = re.compile(regexp)
     if not compiled_reg_exp.match(ccd_region):
         raise SyntaxError("ccd regions must be defined in the format "

goodman_pipeline/core/tests/test_check_version.py

@@ -3,20 +3,21 @@
 
 import os
 import unittest
-
 import requests
 
-from goodman_pipeline.core import check_version
+from importlib.metadata import version
+
+from ..core import check_version
 
-__version__ = __import__('goodman_pipeline').__version__
+__version__ = version('goodman_pipeline')
 
 
 class TestVersionChecker(unittest.TestCase):
 
     def test_get_last(self):
         try:
             v = check_version.get_last()
-            self.assertRegex(v, '^(\*|\d+(\.\d+){0,2}(\.\*)?)$')
+            self.assertRegex(v.base_version, '^(\*|\d+(\.\d+){0,2}(\.\*)?)$')
             # self.assertEqual(v, __version__)
         except ConnectionRefusedError:  # pragma: no cover
             pass
@@ -26,7 +27,7 @@ def test_get_last(self):
     def test_get_last_no_token(self):
         try:
             v = check_version.get_last(github_api_token='NONEXISTANTVAR')
-            self.assertRegex(v, '^(\*|\d+(\.\d+){0,2}(\.\*)?)$')
+            self.assertRegex(v.base_version, '^(\*|\d+(\.\d+){0,2}(\.\*)?)$')
             # self.assertEqual(v, __version__)
         except ConnectionRefusedError:  # pragma: no cover
             pass

goodman_pipeline/core/tests/test_core.py

@@ -232,8 +232,8 @@ class ClassifySpectroscopicData(TestCase):
 
     def setUp(self):
         self.path = os.path.join(
-            os.getcwd(),
-            'goodman_pipeline/data/test_data/test_classify_spectroscopic');
+            os.path.dirname(__file__),
+            '../../data/test_data/test_classify_spectroscopic');
         if not os.path.isdir(self.path):
             os.mkdir(self.path)
 
@@ -1366,7 +1366,7 @@ def setUp(self):
         # expected master flat to be retrieved by get_best_flat
         self.reference_flat_name = 'master_flat_1200m2_0.84_dome.fits'
         # location of sample flats
-        self.flat_path = 'goodman_pipeline/data/test_data/master_flat'
+        self.flat_path = os.path.join(os.path.dirname(__file__), '../../data/test_data/master_flat')
         slit = re.sub('[A-Za-z" ]',
                       '',
                       self.master_flat.header['SLIT'])
@@ -1761,8 +1761,8 @@ class ReferenceDataTest(TestCase):
 
     def setUp(self):
         self.rd = ReferenceData(
-            reference_dir=os.path.join(os.getcwd(),
-                                       'goodman_pipeline/data/ref_comp'))
+            reference_dir=os.path.join(os.path.dirname(__file__),
+                                       '../../data/ref_comp'))
         self.ccd = CCDData(data=np.ones((800, 2000)),
                            meta=fits.Header(),
                            unit='adu')
@@ -2037,8 +2037,8 @@ def setUp(self):
                        'FALSE']], columns=columns)]
 
         self.reference_data = ReferenceData(
-            reference_dir=os.path.join(os.getcwd(),
-                                       'goodman_pipeline/data/ref_comp'))
+            reference_dir=os.path.join(os.path.dirname(__file__),
+                                       '../../data/ref_comp'))
 
     def test_search_comp_group(self):
         result = search_comp_group(

goodman_pipeline/images/data_classifier.py

@@ -158,7 +158,3 @@ def _get_obs_technique(self):
         # inform the results, no need to return
         self.log.info('Detected {:s} Data from {:s} '
                       'Camera'.format(self.technique, self.instrument))
-
-
-if __name__ == '__main__':
-    pass

goodman_pipeline/images/goodman_ccd.py

@@ -1,9 +1,6 @@
 from __future__ import (absolute_import, division, print_function,
                         unicode_literals)
 
-from .data_classifier import DataClassifier
-from .night_organizer import NightOrganizer
-from .image_processor import ImageProcessor
 
 import os
 import sys
@@ -13,14 +10,20 @@
 import logging
 import matplotlib
 
+from importlib.metadata import version
+
+from .data_classifier import DataClassifier
+from .night_organizer import NightOrganizer
+from .image_processor import ImageProcessor
+
 log = logging.getLogger(__name__)
 
 try:
     matplotlib.use('Qt5Agg')
 except ImportError as error:
     log.warning(error)
 
-__version__ = __import__('goodman_pipeline').__version__
+__version__ = version('goodman_pipeline')
 
 
 def get_args(arguments=None):

goodman_pipeline/images/image_processor.py

@@ -587,7 +587,3 @@ def process_imaging_science(self, imaging_group):
                 log.info('Created science file: {:s}'.format(final_name))
         else:
             log.error('Can not process data without a master flat')
-
-
-if __name__ == '__main__':
-    pass

goodman_pipeline/images/tests/test_data_classifier.py

@@ -16,8 +16,8 @@ class DataClassifierTests(TestCase):
 
     def setUp(self):
         self.raw_path = os.path.join(
-            os.getcwd(),
-            'goodman_pipeline/data/test_data/classify-data')
+            os.path.dirname(__file__),
+            '../../data/test_data/classify-data')
 
         if not os.path.isdir(self.raw_path):
             os.mkdir(self.raw_path)

goodman_pipeline/images/tests/test_night_organizer.py

@@ -111,8 +111,8 @@ class NightOrganizerTest(TestCase):
 
     def setUp(self):
         self.full_path = os.path.join(
-            os.getcwd(),
-            'goodman_pipeline/data/test_data/night-organizer-test')
+            os.path.dirname(__file__),
+            '../../data/test_data/night-organizer-test')
 
         if not os.path.isdir(self.full_path):
             os.mkdir(self.full_path)

goodman_pipeline/scripts/redccd

@@ -12,6 +12,6 @@ if '-h' not in sys.argv and \
                 '--version' not in sys.argv:
     setup_logging()
 
-if __name__ == '__main__':
+if __name__ == '__main__':  # pragma: no cover
     GOODMAN_CCD = MainApp()
     GOODMAN_CCD()

goodman_pipeline/scripts/redspec

@@ -13,6 +13,6 @@ if '-h' not in sys.argv and \
     setup_logging()
 
 
-if __name__ == '__main__':
+if __name__ == '__main__':   # pragma: no cover
     GOODMAN_SPECTROSCOPY = MainApp()
     GOODMAN_SPECTROSCOPY()