Update docs and meta package

.github/workflows/ci.yml

@@ -56,9 +56,7 @@ jobs:
       - name: Install dependencies and package
         shell: bash -l {0}
         run: |
-          # conda install -c conda-forge pyresample netCDF4
           pip install -e .[testing]
-          pip install git+https://github.com/TUW-GEO/repurpose@9e233bacd8989b4fa6f7eebb699025ffd231b8e9  # todo delete
       - name: Run all tests
         shell: bash -l {0}
         run: |      

.readthedocs.yml

@@ -13,7 +13,7 @@ build:
 python:
   install:
     - method: pip
-      path: .
+      path: .[docs]
 
 sphinx:
   configuration: docs/conf.py

docker/Dockerfile

@@ -23,9 +23,7 @@ ARG MAMBA_DOCKERFILE_ACTIVATE=1
 
 RUN micromamba install -y -n base -c conda-forge python=3.12
 RUN cd c3s_sm &&  \
-    pip install . &&\
-    pip uninstall repurpose --yes && \
-    pip install git+https://github.com/TUW-GEO/repurpose@9e233bacd8989b4fa6f7eebb699025ffd231b8e9
+    pip install .
 
 RUN micromamba clean --all --yes
 

docker/build.sh

@@ -12,8 +12,7 @@ fi
 # Tag/branch/commit in https://git.eodc.eu/cci-sm-work/cci_sm_ecvps_py_src
 GIT_BRANCH_TAG_COMMIT=$1
 
-# TODO: Change to upstream repo
-GIT_URL="https://github.com/wpreimes/c3s_sm.git"
+GIT_URL="https://github.com/TUW-GEO/c3s_sm.git"
 
 echo "Calling Dockerfile at $this_dir/docker/Dockerfile"
 echo "Checking out source tag $GIT_BRANCH_TAG_COMMIT"

docs/env.yml

@@ -4,16 +4,4 @@ channels:
 - conda-forge
 - defaults
 dependencies:
-- python=3.10
-- ipykernel
-- nbsphinx
-- mock
-- pillow
-- sphinx<7
-- sphinx_rtd_theme
-- pip
-- pip:
-  - recommonmark
-  - readthedocs-sphinx-ext
-  - myst_parser
-
+- python=3.10

setup.cfg

@@ -38,7 +38,7 @@ install_requires =
     netCDF4
     xarray
     pynetcf>=0.2.2
-    repurpose>=0.11
+    repurpose>=0.12
     parse
     cadati
     smecv_grid>=0.3
@@ -62,9 +62,17 @@ exclude =
 # PDF = ReportLab; RXP
 # Add here test requirements (semicolon/line-separated)
 docs =
-    xarray
-    dask
     matplotlib
+    jupyter
+    dask
+    sphinx<7
+    sphinx_rtd_theme
+    mock
+    pillow
+    recommonmark
+    readthedocs-sphinx-ext
+    myst_parser
+    nbsphinx
 
 testing =
     pytest

src/c3s_sm/download.py

@@ -13,7 +13,7 @@
 import pandas as pd
 from dateutil.relativedelta import relativedelta
 from cadati.dekad import day2dekad
-from repurpose.process import parallel_process_async
+from repurpose.process import parallel_process
 import traceback
 
 from c3s_sm.const import variable_lut, freq_lut, check_api_read
@@ -285,12 +285,12 @@ def download_and_extract(target_path,
 
             curr_year += 1
 
-    results = parallel_process_async(download_c3ssm, STATIC_KWARGS=STATIC_KWARGS,
-                                     ITER_KWARGS=ITER_KWARGS, n_proc=1,
-                                     log_path=os.path.join(target_path, '000_log'),
-                                     loglevel='INFO', backend='threading',
-                                     logger_name='dl_logger',
-                                     show_progress_bars=True)
+    results = parallel_process(download_c3ssm, STATIC_KWARGS=STATIC_KWARGS,
+                               ITER_KWARGS=ITER_KWARGS, n_proc=1,
+                               log_path=os.path.join(target_path, '000_log'),
+                               loglevel='INFO', backend='threading',
+                               logger_name='dl_logger',
+                               show_progress_bars=True)
 
     try:
         update_image_summary_file(target_path)

src/c3s_sm/misc.py

@@ -6,7 +6,7 @@
 from parse import parse
 from c3s_sm.const import fntempl as _default_template
 import xarray as xr
-from repurpose.process import parallel_process_async
+from repurpose.process import parallel_process
 
 def collect_ts_cov(data_path: str, n_proc=1, progressbar=False):
     """
@@ -41,9 +41,9 @@ def _func(f: str) -> tuple:
 
         return start, end, cell, parameters
 
-    se = parallel_process_async(_func, ITER_KWARGS=dict(f=fl),
-                                show_progress_bars=progressbar,
-                                backend='threading', n_proc=n_proc)
+    se = parallel_process(_func, ITER_KWARGS=dict(f=fl),
+                          show_progress_bars=progressbar,
+                          backend='threading', n_proc=n_proc)
 
     periods = {}
     parameters = None

src/c3s_sm/reshuffle.py

@@ -9,6 +9,7 @@
 import warnings
 from datetime import datetime
 import pandas as pd
+import pygeogrids
 from smecv_grid.grid import SMECV_Grid_v052
 from parse import parse
 from netCDF4 import Dataset
@@ -23,7 +24,11 @@
 from c3s_sm.const import fntempl as _default_template
 import c3s_sm.metadata as metadata
 from c3s_sm.metadata import C3S_daily_tsatt_nc, C3S_dekmon_tsatt_nc
-from c3s_sm.misc import update_ts_summary_file, collect_ts_cov, read_summary_yml, update_image_summary_file
+from c3s_sm.misc import (
+    update_ts_summary_file,
+    read_summary_yml,
+    update_image_summary_file,
+)
 
 def reshuffle(*args, **kwargs):
     warnings.warn("`c3s_sm.reshuffle.reshuffle` is deprecated, "
@@ -251,10 +256,15 @@ def img2ts(img_path, ts_path, startdate, enddate, parameters=None,
     else:
         input_dataset = ImageBaseConnection(input_dataset)
 
+    if isinstance(grid, pygeogrids.CellGrid):
+        _cellsize = None
+    else:
+        _cellsize = 5
+
     reshuffler = Img2Ts(input_dataset=input_dataset, outputpath=ts_path,
                         startdate=startdate, enddate=enddate, input_grid=grid,
-                        imgbuffer=imgbuffer, cellsize_lat=5.0,
-                        cellsize_lon=5.0, global_attr=global_attributes,
+                        imgbuffer=imgbuffer, cellsize_lat=_cellsize,
+                        cellsize_lon=_cellsize, global_attr=global_attributes,
                         zlib=True, unlim_chunksize=1000,
                         ts_attributes=ts_attributes, n_proc=n_proc,
                         backend='multiprocessing')