cerfacs-globc · bzah · Dec 21, 2023 · Dec 15, 2023 · Dec 15, 2023 · Dec 18, 2023
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -20,11 +20,16 @@ repos:
     -   id: end-of-file-fixer
         language_version: python3
     -   id: check-yaml
+    -   id: check-toml
         language_version: python3
     -   id: debug-statements
         language_version: python3
     -   id: requirements-txt-fixer
         language_version: python3
+-   repo: https://github.com/pappasam/toml-sort
+    rev: v0.23.1
+    hooks:
+     - id: toml-sort-fix
 -   repo: https://github.com/psf/black
     rev: 23.11.0
     hooks:

diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -7,7 +7,3 @@ build:
   os: "ubuntu-20.04"
   tools:
     python: "3.9"
-
-python:
-   install:
-   - requirements: requirements_dev.txt
diff --git a/README.rst b/README.rst
@@ -15,7 +15,7 @@ From conda-forge: ``conda install -c conda-forge icclim``.
 
 From sources:
     - Clone the repository ``git clone https://github.com/cerfacs-globc/icclim.git``
-    - Install icclim ``python -m setup install``
+    - Install icclim ``pip install .``
 
 How to use icclim
 -----------------

diff --git a/doc/source/dev/release_process.rst b/doc/source/dev/release_process.rst
@@ -1,23 +1,18 @@
 Release process
 ===============
 
+
 #. Make sure all tests pass.
 #. Create and checkout a release branch.
 #. Update version number of ICCLIM_VERSION in ``icclim/models/constants.py`` and in ``setup.py``.
 #. Update release notes in ``doc/source/references/release_notes.rst``.
 #. Merge release branch to master with a PR.
 #. Clean dist directory content.
-#. Create wheel file on master.
-
-    .. code-block:: sh
-
-        python3 -m setup bdist_wheel
-
-#. Create source archive.
+#. Create wheel file on master and source archive.
 
     .. code-block:: sh
 
-        python3 -m setup sdist
+        python3 -m build
 
 #. Try to upload on testpypi first. ``twine`` must be installed in your env beforehand.
 

diff --git a/doc/source/references/release_notes.rst b/doc/source/references/release_notes.rst
@@ -259,7 +259,7 @@ Release candidates for 5.0 change logs
 * [maint] Refactored ecad_functions (removed duplicated code, simplified function signatures...)
 * [maint] Refactored IndexConfig to hide some technical knowledge which was leaked to other modules.
 * [enh] Made a basic integration of clix-meta yaml to populate the generated docstring for c3s.
-* [maint] This makes pyyaml an required dependency of icclim.
+* [maint] This makes pyyaml a required dependency of icclim.
 * [fix] Fixed an issue with aliasing of "icclim" module and "icclim" package
 * [maint] Added some metadata to qualify the ecad_indices and recognize the arguments necessary to compute them.
 * [maint] Added readthedocs CI configuration. This is necessary to use python 3.8.

diff --git a/environment.yml b/environment.yml
@@ -13,7 +13,6 @@ dependencies:
  - dask[array]
  - netCDF4>=1.5.7
  - cftime>=1.5.0
- - pyyaml>=6.0
  - rechunker>=0.3.3
  - psutil
  - zarr
@@ -34,6 +33,8 @@ dependencies:
  - setuptools
  - twine
  - flake8-rst-docstrings
+ - build
+ - flit
  # Extra dependencies
  - matplotlib
  - cartopy

diff --git a/pyproject.toml b/pyproject.toml
@@ -0,0 +1,84 @@
+[build-system]
+requires = ["flit_core >=3.2,<4"]
+build-backend = "flit_core.buildapi"
+
+[project]
+name = "icclim"
+authors = [
+  {name = "Christian Page", email = "[email protected]"}
+]
+maintainers = [
+  {name = "Christian Page", email = "[email protected]"},
+  {name = "Abel Aoun", email = "[email protected]"}
+]
+readme = "README.rst"
+license = {file = "LICENSE"}
+classifiers = [
+  "Programming Language :: Python",
+  "Development Status :: 4 - Beta",
+  "Intended Audience :: Science/Research",
+  "License :: OSI Approved :: Apache Software License",
+  "Natural Language :: English",
+  "Operating System :: OS Independent",
+  "Programming Language :: Python :: 3.9",
+  "Topic :: Scientific/Engineering :: Atmospheric Science"
+]
+dynamic = ["version", "description"]
+requires-python = ">=3.9"
+keywords = ["netcdf", "climate", "climate-indices", "climate-indicators", "xarray"]
+dependencies = [
+  "numpy>=1.16",
+  "xarray>=2022.6",
+  "xclim>=0.45, <=0.47",
+  "cf_xarray>=0.7.4",
+  "cftime>=1.4.1",
+  "dask[array]",
+  "netCDF4>=1.5.7",
+  "psutil",
+  "zarr",
+  "rechunker>=0.3, !=0.4",
+  "fsspec",
+  "pandas>=1.3",
+  "dateparser",
+  "pint",
+  "jinja2"
+]
+
+[project.optional-dependencies]
+dev = [
+  "black",
+  "build",
+  "cf_xarray>=0.7.4",
+  "cftime~=1.5.0",
+  "dask",
+  "dateparser",
+  "flake8",
+  "flake8-rst-docstrings",
+  "flit",
+  "isort",
+  "netCDF4~=1.5.7",
+  "numpy~=1.22",
+  "pandas>=1.3",
+  "pint<0.20",
+  "pip",
+  "pre-commit>=2.9",
+  "psutil",
+  "pydata-sphinx-theme",
+  "pylint",
+  "pytest",
+  "pytest-cov",
+  "rechunker>=0.3.3",
+  "setuptools>=49.6.0",
+  "sphinx",
+  "sphinx_codeautolink",
+  "sphinx_copybutton",
+  "sphinx_lfs_content",
+  "twine",
+  "xarray>=2022.6",
+  "xclim>=0.45",
+  "zarr"
+]
+
+[project.urls]
+Documentation = "https://icclim.readthedocs.io/en/latest/how_to/index.html"
+Source = "https://github.com/cerfacs-globc/icclim/"
diff --git a/requirements.txt b/requirements.txt
diff --git a/requirements_dev.txt b/requirements_dev.txt
diff --git a/setup.cfg b/setup.cfg
diff --git a/setup.py b/setup.py
diff --git a/icclim/.gitignore → src/icclim/.gitignore b/icclim/.gitignore → src/icclim/.gitignore
diff --git a/icclim/__init__.py → src/icclim/__init__.py b/icclim/__init__.py → src/icclim/__init__.py
@@ -1,7 +1,8 @@
+"""Python library for climate indices calculation"""
+
 from icclim._generated_api import *  # noqa
 from icclim.generic_indices.threshold import build_threshold
 from icclim.main import index, indice, indices
-from icclim.models.constants import ICCLIM_VERSION
 from icclim.pre_processing.rechunk import create_optimized_zarr_store
 
 __all__ = [
@@ -15,4 +16,4 @@
     "build_threshold",
 ]
 
-__version__ = ICCLIM_VERSION
+__version__ = "6.5.0"
diff --git a/icclim/_generated_api.py → src/icclim/_generated_api.py b/icclim/_generated_api.py → src/icclim/_generated_api.py
diff --git a/icclim/ecad/__init__.py → src/icclim/ecad/__init__.py b/icclim/ecad/__init__.py → src/icclim/ecad/__init__.py
diff --git a/icclim/ecad/ecad_indices.py → src/icclim/ecad/ecad_indices.py b/icclim/ecad/ecad_indices.py → src/icclim/ecad/ecad_indices.py
diff --git a/icclim/ecad/xclim_binding.py → src/icclim/ecad/xclim_binding.py b/icclim/ecad/xclim_binding.py → src/icclim/ecad/xclim_binding.py
diff --git a/icclim/generic_indices/__init__.py → src/icclim/generic_indices/__init__.py b/icclim/generic_indices/__init__.py → src/icclim/generic_indices/__init__.py
diff --git a/icclim/generic_indices/generic_indicators.py → ...lim/generic_indices/generic_indicators.py b/icclim/generic_indices/generic_indicators.py → ...lim/generic_indices/generic_indicators.py
diff --git a/icclim/generic_indices/generic_templates.py → ...clim/generic_indices/generic_templates.py b/icclim/generic_indices/generic_templates.py → ...clim/generic_indices/generic_templates.py
diff --git a/icclim/generic_indices/standard_variable.py → ...clim/generic_indices/standard_variable.py b/icclim/generic_indices/standard_variable.py → ...clim/generic_indices/standard_variable.py
diff --git a/icclim/generic_indices/threshold.py → src/icclim/generic_indices/threshold.py b/icclim/generic_indices/threshold.py → src/icclim/generic_indices/threshold.py
diff --git a/...im/generic_indices/threshold_templates.py → ...im/generic_indices/threshold_templates.py b/...im/generic_indices/threshold_templates.py → ...im/generic_indices/threshold_templates.py
diff --git a/icclim/icclim_exceptions.py → src/icclim/icclim_exceptions.py b/icclim/icclim_exceptions.py → src/icclim/icclim_exceptions.py
diff --git a/icclim/icclim_logger.py → src/icclim/icclim_logger.py b/icclim/icclim_logger.py → src/icclim/icclim_logger.py
diff --git a/icclim/icclim_types.py → src/icclim/icclim_types.py b/icclim/icclim_types.py → src/icclim/icclim_types.py
diff --git a/icclim/main.py → src/icclim/main.py b/icclim/main.py → src/icclim/main.py
diff --git a/icclim/models/__init__.py → src/icclim/models/__init__.py b/icclim/models/__init__.py → src/icclim/models/__init__.py
diff --git a/icclim/models/cf_calendar.py → src/icclim/models/cf_calendar.py b/icclim/models/cf_calendar.py → src/icclim/models/cf_calendar.py
diff --git a/icclim/models/climate_variable.py → src/icclim/models/climate_variable.py b/icclim/models/climate_variable.py → src/icclim/models/climate_variable.py
diff --git a/icclim/models/constants.py → src/icclim/models/constants.py b/icclim/models/constants.py → src/icclim/models/constants.py
diff --git a/icclim/models/frequency.py → src/icclim/models/frequency.py b/icclim/models/frequency.py → src/icclim/models/frequency.py
diff --git a/icclim/models/global_metadata.py → src/icclim/models/global_metadata.py b/icclim/models/global_metadata.py → src/icclim/models/global_metadata.py
diff --git a/icclim/models/index_config.py → src/icclim/models/index_config.py b/icclim/models/index_config.py → src/icclim/models/index_config.py
diff --git a/icclim/models/index_group.py → src/icclim/models/index_group.py b/icclim/models/index_group.py → src/icclim/models/index_group.py
diff --git a/icclim/models/logical_link.py → src/icclim/models/logical_link.py b/icclim/models/logical_link.py → src/icclim/models/logical_link.py
diff --git a/icclim/models/netcdf_version.py → src/icclim/models/netcdf_version.py b/icclim/models/netcdf_version.py → src/icclim/models/netcdf_version.py
diff --git a/icclim/models/operator.py → src/icclim/models/operator.py b/icclim/models/operator.py → src/icclim/models/operator.py
diff --git a/icclim/models/quantile_interpolation.py → src/icclim/models/quantile_interpolation.py b/icclim/models/quantile_interpolation.py → src/icclim/models/quantile_interpolation.py
diff --git a/icclim/models/registry.py → src/icclim/models/registry.py b/icclim/models/registry.py → src/icclim/models/registry.py
diff --git a/icclim/models/standard_index.py → src/icclim/models/standard_index.py b/icclim/models/standard_index.py → src/icclim/models/standard_index.py
diff --git a/icclim/models/user_index_dict.py → src/icclim/models/user_index_dict.py b/icclim/models/user_index_dict.py → src/icclim/models/user_index_dict.py
diff --git a/icclim/pre_processing/__init__.py → src/icclim/pre_processing/__init__.py b/icclim/pre_processing/__init__.py → src/icclim/pre_processing/__init__.py
diff --git a/icclim/pre_processing/in_file_dictionary.py → ...clim/pre_processing/in_file_dictionary.py b/icclim/pre_processing/in_file_dictionary.py → ...clim/pre_processing/in_file_dictionary.py
diff --git a/icclim/pre_processing/input_parsing.py → src/icclim/pre_processing/input_parsing.py b/icclim/pre_processing/input_parsing.py → src/icclim/pre_processing/input_parsing.py
diff --git a/icclim/pre_processing/rechunk.py → src/icclim/pre_processing/rechunk.py b/icclim/pre_processing/rechunk.py → src/icclim/pre_processing/rechunk.py
diff --git a/icclim/tests/__init__.py → src/icclim/user_indices/__init__.py b/icclim/tests/__init__.py → src/icclim/user_indices/__init__.py
diff --git a/icclim/user_indices/calc_operation.py → src/icclim/user_indices/calc_operation.py b/icclim/user_indices/calc_operation.py → src/icclim/user_indices/calc_operation.py
diff --git a/icclim/utils.py → src/icclim/utils.py b/icclim/utils.py → src/icclim/utils.py
diff --git a/icclim/user_indices/__init__.py → tests/__init__.py b/icclim/user_indices/__init__.py → tests/__init__.py
diff --git a/icclim/tests/test_cf_calendar.py → tests/test_cf_calendar.py b/icclim/tests/test_cf_calendar.py → tests/test_cf_calendar.py
diff --git a/icclim/tests/test_ecad_indices.py → tests/test_ecad_indices.py b/icclim/tests/test_ecad_indices.py → tests/test_ecad_indices.py
diff --git a/icclim/tests/test_frequency.py → tests/test_frequency.py b/icclim/tests/test_frequency.py → tests/test_frequency.py
@@ -7,7 +7,7 @@
 
 from icclim.icclim_exceptions import InvalidIcclimArgumentError
 from icclim.models.frequency import FrequencyRegistry, get_seasonal_time_updater
-from icclim.tests.testing_utils import stub_tas
+from tests.testing_utils import stub_tas
 
 
 class Test_build_frequency_over_frequency:

diff --git a/icclim/tests/test_generated_api.py → tests/test_generated_api.py b/icclim/tests/test_generated_api.py → tests/test_generated_api.py
@@ -17,8 +17,8 @@
 from icclim.models.netcdf_version import NetcdfVersionRegistry
 from icclim.models.quantile_interpolation import QuantileInterpolationRegistry
 from icclim.models.standard_index import StandardIndex
-from icclim.tests.testing_utils import stub_tas
 from icclim.user_indices.calc_operation import CalcOperation, CalcOperationRegistry
+from tests.testing_utils import stub_tas
 
 DEFAULT_ARGS = dict(
     in_files="pouet.nc",

diff --git a/icclim/tests/test_index_group.py → tests/test_index_group.py b/icclim/tests/test_index_group.py → tests/test_index_group.py
diff --git a/icclim/tests/test_input_parsing.py → tests/test_input_parsing.py b/icclim/tests/test_input_parsing.py → tests/test_input_parsing.py
diff --git a/icclim/tests/test_main.py → tests/test_main.py b/icclim/tests/test_main.py → tests/test_main.py
@@ -23,7 +23,7 @@
 )
 from icclim.models.frequency import FrequencyRegistry
 from icclim.models.index_group import IndexGroupRegistry
-from icclim.tests.testing_utils import K2C, stub_pr, stub_tas
+from tests.testing_utils import K2C, stub_pr, stub_tas
 
 
 @patch("icclim.main.index")

diff --git a/icclim/tests/test_rechunk.py → tests/test_rechunk.py b/icclim/tests/test_rechunk.py → tests/test_rechunk.py
diff --git a/icclim/tests/test_threshold.py → tests/test_threshold.py b/icclim/tests/test_threshold.py → tests/test_threshold.py
diff --git a/icclim/tests/test_user_index.py → tests/test_user_index.py b/icclim/tests/test_user_index.py → tests/test_user_index.py
@@ -9,7 +9,7 @@
     USER_INDEX_TEMPERATURE_STAMP,
 )
 from icclim.models.operator import OperatorRegistry
-from icclim.tests.testing_utils import stub_tas
+from tests.testing_utils import stub_tas
 
 
 class Test_max:

diff --git a/icclim/tests/testing_utils.py → tests/testing_utils.py b/icclim/tests/testing_utils.py → tests/testing_utils.py