Merge pull request #103 from ninahakansson/fix_ci_and_authors

Fix github tests

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,7 +1,7 @@
 <!-- Describe what your PR does, and why -->
 
- - [ ] Closes #xxxx <!-- remove if there is no corresponding issue, which should only be the case for minor changes -->
+ - [ ] Closes #xxxx <!-- remove if there is no corresponding issue
  - [ ] Tests added <!-- for all bug fixes or enhancements -->
  - [ ] Tests passed: Passes ``pytest level1c4pps`` <!-- for all non-documentation changes) -->
  - [ ] Passes ``flake8`` <!-- remove if you did not edit any Python files -->
- - [ ] Fully documented <!-- remove if this change should not be visible to users, e.g., if it is an internal clean-up, or if this is part of a larger project that will be documented later -->
+ - [ ] Add your name to `AUTHORS.md` if not there already

.github/workflows/ci.yaml

@@ -13,7 +13,7 @@ jobs:
         python-version: ["3.9", "3.11", "3.12"]
         experimental: [false]
         include:
-          - python-version: "3.12"
+          - python-version: "3.13"
             os: "ubuntu-latest"
             experimental: true
 
@@ -28,15 +28,15 @@ jobs:
         uses: actions/checkout@v3
 
       - name: Setup Conda Environment
-        uses: conda-incubator/setup-miniconda@v2
+        uses: conda-incubator/setup-miniconda@v3
         with:
-          miniforge-variant: Mambaforge
           miniforge-version: latest
-          use-mamba: true
           python-version: ${{ matrix.python-version }}
           environment-file: continuous_integration/environment.yaml
           activate-environment: test-environment
-          auto-update-conda: true
+          channels: conda-forge
+          conda-remove-defaults: true
+          channel-priority: strict
 
       - name: Install unstable dependencies
         if: matrix.experimental == true

.gitignore

@@ -1,5 +1,7 @@
 build
+dist
 *py~
 *pyc
 *~
-*.egg*
+*.egg*
+*#*

AUTHORS.md

@@ -0,0 +1,12 @@
+# Project Contributors
+
+- [Nina Håkansson] (https://github.com/ninahakansson)
+- [Bengt Rydberg] (BengtRydberg)](https://github.com/BengtRydberg)
+- [Sara Hörnquist] (shornqui)](https://github.com/shornqui)
+- [Inderpreet Kaur] (https://github.com/ikaur17)
+- [Salomon Eliasson] (https://github.com/salomoneliassonSMHI)
+- [Erik Johansson] (https://github.com/smhi-erik)
+- [Stephan Finkensieper] (https://github.com/sfinkens)
+- [Adam Dybbroe (adybbroe)] (https://github.com/adybbroe)
+- [Martin Raspaud (mraspaud)] (https://github.com/mraspaud)
+- [Panu Lahtinen (pnuu)] (https://github.com/pnuu)

bin/avhrr2pps.py

@@ -16,11 +16,6 @@
 #
 # You should have received a copy of the GNU General Public License
 # along with level1c4pps.  If not, see <http://www.gnu.org/licenses/>.
-# Author(s):
-
-#   Martin Raspaud <[email protected]>
-#   Nina Hakansson <[email protected]>
-#   Adam.Dybbroe <[email protected]>
 
 """Script to convert AVHRR level-1 to PPS level-1c format using Pytroll/Satpy."""
 

bin/eumgacfdr2pps.py

@@ -16,12 +16,6 @@
 #
 # You should have received a copy of the GNU General Public License
 # along with level1c4pps.  If not, see <http://www.gnu.org/licenses/>.
-# Author(s):
-
-#   Martin Raspaud <[email protected]>
-#   Nina Hakansson <[email protected]>
-#   Adam.Dybbroe <[email protected]>
-
 
 """Script to make EUMETSAT GAC level1c in PPS-format with pytroll."""
 
@@ -58,7 +52,7 @@
                         required=False, default=99999,
                         help="Orbit number (default is 99999).")
     options = parser.parse_args()
-    process_one_file(options.file, options.out_dir,  start_line=options.start_line,
+    process_one_file(options.file, options.out_dir, start_line=options.start_line,
                      end_line=options.end_line, engine=options.nc_engine,
                      remove_broken=not options.no_remove_bad,
                      orbit_n=options.orbit_number)

bin/gac2pps.py

@@ -16,12 +16,6 @@
 #
 # You should have received a copy of the GNU General Public License
 # along with level1c4pps.  If not, see <http://www.gnu.org/licenses/>.
-# Author(s):
-
-#   Martin Raspaud <[email protected]>
-#   Nina Hakansson <[email protected]>
-#   Adam.Dybbroe <[email protected]>
-
 
 """Script to make seviri level1c in PPS-format with pytroll."""
 

bin/mersi2pps.py

@@ -16,11 +16,6 @@
 #
 # You should have received a copy of the GNU General Public License
 # along with level1c4pps.  If not, see <http://www.gnu.org/licenses/>.
-# Author(s):
-
-#   Martin Raspaud <[email protected]>
-#   Nina Hakansson <[email protected]>
-#   Adam.Dybbroe <[email protected]>
 
 """Script to convert MERSI-2 level-1 to PPS level-1c format using Pytroll/Satpy."""
 

bin/metimage2pps.py

@@ -16,11 +16,6 @@
 #
 # You should have received a copy of the GNU General Public License
 # along with level1c4pps.  If not, see <http://www.gnu.org/licenses/>.
-# Author(s):
-
-#   Martin Raspaud <[email protected]>
-#   Nina Hakansson <[email protected]>
-#   Adam.Dybbroe <[email protected]>
 
 """Script to convert METIMAGE level-1 to PPS level-1c format using Pytroll/Satpy."""
 

bin/modis2pps.py

@@ -16,11 +16,6 @@
 #
 # You should have received a copy of the GNU General Public License
 # along with level1c4pps.  If not, see <http://www.gnu.org/licenses/>.
-# Author(s):
-
-#   Martin Raspaud <[email protected]>
-#   Nina Hakansson <[email protected]>
-#   Adam.Dybbroe <[email protected]>
 
 """Script to convert MODIS level-1 to PPS level-1c format using Pytroll/Satpy."""
 

bin/seviri2pps.py

@@ -16,12 +16,6 @@
 #
 # You should have received a copy of the GNU General Public License
 # along with level1c4pps.  If not, see <http://www.gnu.org/licenses/>.
-# Author(s):
-
-#   Martin Raspaud <[email protected]>
-#   Nina Hakansson <[email protected]>
-#   Adam.Dybbroe <[email protected]>
-#   Stephan Finkensieper <[email protected]>
 
 # This program was developed by CMSAF to be used for the processing of
 # CLAAS3.

bin/slstr2pps.py

@@ -16,11 +16,6 @@
 #
 # You should have received a copy of the GNU General Public License
 # along with level1c4pps.  If not, see <http://www.gnu.org/licenses/>.
-# Author(s):
-
-#   Martin Raspaud <[email protected]>
-#   Nina Hakansson <[email protected]>
-#   Adam.Dybbroe <[email protected]>
 
 """Script to convert SLSTR level-1 to PPS level-1c format using Pytroll/Satpy."""
 

bin/vgac2pps.py

@@ -16,12 +16,6 @@
 #
 # You should have received a copy of the GNU General Public License
 # along with level1c4pps.  If not, see <http://www.gnu.org/licenses/>.
-# Author(s):
-
-#   Martin Raspaud <[email protected]>
-#   Nina Hakansson <[email protected]>
-#   Adam.Dybbroe <[email protected]>
-#   Salomon.Eliasson <[email protected]>
 
 """Script to convert VIIRS level-1 to PPS level-1c format using Pytroll/Satpy."""
 

bin/viirs2pps.py

@@ -16,11 +16,6 @@
 #
 # You should have received a copy of the GNU General Public License
 # along with level1c4pps.  If not, see <http://www.gnu.org/licenses/>.
-# Author(s):
-
-#   Martin Raspaud <[email protected]>
-#   Nina Hakansson <[email protected]>
-#   Adam.Dybbroe <[email protected]>
 
 """Script to convert VIIRS level-1 to PPS level-1c format using Pytroll/Satpy."""
 
@@ -41,7 +36,7 @@
                         help="Output directory where to store the level1c file")
     parser.add_argument('--iband', action='store_true',
                         help="Iband resolution include I01-I03, M15-M16 and optional M09, M14")
-    parser.add_argument('--reader', type=str,  nargs='?',
+    parser.add_argument('--reader', type=str, nargs='?',
                         required=False, default="viirs_sdr",
                         help="VIIRS reader default: viirs_sdr")
     parser.add_argument('-ne', '--nc_engine', type=str, nargs='?',

continuous_integration/environment.yaml

@@ -2,15 +2,12 @@ name: test-environment
 channels:
   - conda-forge
 dependencies:
-  - tensorflow
-  - scikit-learn
   - sphinx
   - scipy
   - h5py
   - python-geotiepoints
-  - matplotlib
   - mock
-  - numpy<2.0.0
+  - numpy
   - satpy>0.41.1
   - pyspectral
   - h5netcdf
@@ -21,4 +18,3 @@ dependencies:
   - pip:
     - trollsift
     - pygac
-    - git+https://github.com/foua-pps/sbafs_ann@main

level1c4pps/__init__.py

@@ -16,10 +16,6 @@
 #
 # You should have received a copy of the GNU General Public License
 # along with level1c4pps.  If not, see <http://www.gnu.org/licenses/>.
-# Author(s):
-
-#   Adam.Dybbroe <[email protected]>
-#   Nina Hakansson <[email protected]>
 
 """Package Initializer for level1c4pps."""
 from importlib.metadata import version
@@ -184,12 +180,12 @@ def convert_angles(scene, delete_azimuth=False):
         'sunazimuth': np.array([-18000, 18000], dtype='int16'),
         'satazimuth': np.array([-18000, 18000], dtype='int16'),
     },
-    'mersi_file_key':  {
+    'mersi_file_key': {
         'sunzenith': 'Geolocation/SolarZenithAngle',
         'satzenith': 'Geolocation/SensorZenithAngle',
         'azimuthdiff': 'Geolocation/SensorSolarAzimuthDifference',
     },
-    'standard_name':  {
+    'standard_name': {
         'sunzenith': 'solar_zenith_angle',
         'satzenith': 'sensor_zenith_angle',  # platform in ppsv2018
         'azimuthdiff': 'absolute_angle_of_rotation_from_solar_azimuth_to_platform_azimuth',
@@ -211,12 +207,12 @@ def convert_angles(scene, delete_azimuth=False):
         'standard_name': "longitude",
         'units': 'degrees_east',
         'valid_range': np.array([-180, 180], dtype='float32')}
-    }
+}
 
 
 def make_azidiff_angle(sata, suna, divisor=360):
     """Calculate azimuth difference angle."""
-    daz = abs(sata-suna)
+    daz = abs(sata - suna)
     half_divisor = divisor / 2.0
     daz = daz % divisor
     if isinstance(daz, np.ndarray):
@@ -368,20 +364,21 @@ def adjust_lons_to_valid_range(scene):
     # scene['lon'] = centered_modulus(scene['lon']) # makes lon loose attrs satpy 0.24.0
     scene['lon'].values = centered_modulus(scene['lon'].values)
 
+
 def fix_sun_earth_distance_correction_factor(scene, band, start_time):
     from pyorbital.astronomy import sun_earth_distance_correction
     date_control = np.datetime64("2019-01-01T00:00:00")
     sun_earth_distance_20190409 = sun_earth_distance_correction(date_control)
     sun_earth_distance = sun_earth_distance_correction(start_time)
     if (np.abs(sun_earth_distance_20190409 - 0.9833280675966011) < 0.00001 and
-        np.abs(sun_earth_distance - scene[band].attrs['sun_earth_distance_correction_factor']) < 0.00001):
+            np.abs(sun_earth_distance - scene[band].attrs['sun_earth_distance_correction_factor']) < 0.00001):
         logger.info("The sun earth distance correction attribute contain the sun earth distance, not the square.")
         logger.info("Updating and adding sun earth distance correction attributes.")
         current_factor = scene[band].attrs['sun_earth_distance_correction_factor']
-        scene[band].attrs['satpy_sun_earth_distance_correction_factor'] =  current_factor
+        scene[band].attrs['satpy_sun_earth_distance_correction_factor'] = current_factor
         scene[band].attrs['pps_sun_earth_distance_correction_factor'] = sun_earth_distance * sun_earth_distance
         scene[band].attrs['sun_earth_distance'] = sun_earth_distance
-        scene[band].attrs['sun_earth_distance_correction_factor'] = sun_earth_distance * sun_earth_distance    
+        scene[band].attrs['sun_earth_distance_correction_factor'] = sun_earth_distance * sun_earth_distance
 
 
 def set_header_and_band_attrs_defaults(scene, BANDNAMES, PPS_TAGNAMES, REFL_BANDS, irch, orbit_n=0):
@@ -413,7 +410,7 @@ def set_header_and_band_attrs_defaults(scene, BANDNAMES, PPS_TAGNAMES, REFL_BAND
     sensor_name = (fix_too_great_attributes(sensor_name)).upper()
     scene.attrs['sensor'] = sensor_name.upper()
     scene.attrs['instrument'] = sensor_name.upper()
-    nowutc = datetime.utcnow()
+    nowutc = datetime.now(timezone.utc)
     scene.attrs['orbit_number'] = int(orbit_n)
     scene.attrs['date_created'] = nowutc.strftime("%Y-%m-%dT%H:%M:%SZ")
     scene.attrs['version_level1c4pps_satpy'] = satpy.__version__

level1c4pps/avhrr2pps_lib.py

@@ -16,11 +16,6 @@
 #
 # You should have received a copy of the GNU General Public License
 # along with level1c4pps.  If not, see <http://www.gnu.org/licenses/>.
-# Author(s):
-
-#   Martin Raspaud <[email protected]>
-#   Nina Hakansson <[email protected]>
-#   Adam.Dybbroe <[email protected]>
 
 """Functions to convert AVHRR AAPP or EPS l1b data to a NWCSAF/PPS level-1c formatet netCDF/CF file."""
 
@@ -50,9 +45,9 @@
 
 REFL_BANDS = ['1', '2', '3a']
 
-PPS_TAGNAMES = {'1':  'ch_r06',
-                '2':  'ch_r09',
-                '3a':  'ch_r16',
+PPS_TAGNAMES = {'1': 'ch_r06',
+                '2': 'ch_r09',
+                '3a': 'ch_r16',
                 '3b': 'ch_tb37',
                 '4': 'ch_tb11',
                 '5': 'ch_tb12'}
@@ -133,5 +128,5 @@ def process_one_scene(scene_files, out_path, engine='h5netcdf', orbit_n=0):
                        encoding=get_encoding_avhrr(scn_))
     print("Saved file {:s} after {:3.1f} seconds".format(
         os.path.basename(filename),
-        time.time()-tic))
+        time.time() - tic))
     return filename

level1c4pps/calibration_coefs.py

@@ -16,10 +16,6 @@
 #
 # You should have received a copy of the GNU General Public License
 # along with level1c4pps.  If not, see <http://www.gnu.org/licenses/>.
-# -*- coding: utf-8 -*-
-# Author(s):
-
-#  Nina.Hakansson
 
 """Module with calibration coefficients for SEVIRI."""
 

level1c4pps/eumgacfdr2pps_lib.py

@@ -16,11 +16,6 @@
 #
 # You should have received a copy of the GNU General Public License
 # along with level1c4pps.  If not, see <http://www.gnu.org/licenses/>.
-# Author(s):
-
-#   Martin Raspaud <[email protected]>
-#   Nina Hakansson <[email protected]>
-#   Adam.Dybbroe <[email protected]>
 
 """Utilities to convert AVHRR GAC formattet data to PPS level-1c format."""
 
@@ -249,5 +244,5 @@ def process_one_file(eumgacfdr_file, out_path='.', reader_kwargs=None,
 
     logger.info("Saved file {:s} after {:3.1f} seconds".format(
         os.path.basename(filename),
-        time.time()-tic))
+        time.time() - tic))
     return filename

level1c4pps/gac2pps_lib.py

@@ -16,11 +16,6 @@
 #
 # You should have received a copy of the GNU General Public License
 # along with level1c4pps.  If not, see <http://www.gnu.org/licenses/>.
-# Author(s):
-
-#   Martin Raspaud <[email protected]>
-#   Nina Hakansson <[email protected]>
-#   Adam.Dybbroe <[email protected]>
 
 """Utilities to convert AVHRR GAC formattet data to PPS level-1c format."""
 
@@ -39,11 +34,9 @@
                          get_header_attrs, convert_angles)
 import logging
 
-from packaging.version import Version
 logger = logging.getLogger('gac2pps')
 
 
-
 BANDNAMES = ['1', '2', '3', '3a', '3b', '4', '5']
 
 REFL_BANDS = ['1', '2', '3a']
@@ -171,5 +164,5 @@ def process_one_file(gac_file, out_path='.', reader_kwargs=None, engine='h5netcd
 
     print("Saved file {:s} after {:3.1f} seconds".format(
         os.path.basename(filename),
-        time.time()-tic))
+        time.time() - tic))
     return filename