Enh/setup cleanup

.github/workflows/ci.yml

@@ -9,22 +9,22 @@ jobs:
   # lint is handled by pre-commit ci conf
   generate-api:
     runs-on: ubuntu-latest
+    env:
+      FLIT_ROOT_INSTALL: 1
     steps:
       - uses: actions/checkout@v3
       - name: Set up Python 3.9
         uses: actions/setup-python@v2
         with:
           python-version: 3.9
-      - name: Install requirements
-        run: pip install -r requirements.txt
-      - name: Install icclim
-        run: python -m pip install -e .
-      - name: install black
-        run: pip install black
+      - name: Install build tools
+        run: pip install --upgrade pip flit
+      - name: Install icclim and dev requirements (dev, test and doc)
+        run: flit install --deps develop
       - name: call fun extractor
-        run: python ./tools/extract-icclim-funs.py icclim/_generated_api.py
-      - name: run black on generated module
-        run: black icclim/_generated_api.py
+        run: python ./tools/extract_icclim_funs.py src/icclim/_generated_api.py
+      - name: run ruff format on generated module
+        run: ruff format src/icclim/_generated_api.py
       - name: create local ref
         run: |
           git fetch origin ${{ github.head_ref }}
@@ -37,29 +37,28 @@ jobs:
       - name: commit
         run: |
           # Stage the file, commit and push
-          git add icclim/_generated_api.py
+          git add src/icclim/_generated_api.py
           # Ignore error cases
           git commit -m "MAINT: Update generated API" || true
           git push origin ${{ github.head_ref }}
 
   test:
     runs-on: ubuntu-latest
+    env:
+      FLIT_ROOT_INSTALL: 1
     steps:
        # actions/checkout@v2 checkouts to a new merge commit
       - uses: actions/checkout@v3
       - name: Set up Python 3.9
         uses: actions/setup-python@v2
         with:
           python-version: 3.9
-      - name: Install requirements
-        run: pip install -r requirements.txt
-      - name: Install pytest-cov
-        run: pip install pytest-cov
-      - name: Install icclim
-        run: python -m pip install -e .
+      - name: Install build tools
+        run: pip install --upgrade pip flit
+      - name: Install icclim and dev requirements (dev, test and doc)
+        run: flit install --deps develop
       - name: Build coverage file
-        run: |
-            pytest --junitxml=pytest.xml --cov-report=term-missing:skip-covered --cov=icclim icclim/tests | tee pytest-coverage.txt; ( exit ${PIPESTATUS[0]} )
+        run: pytest --junitxml=pytest.xml --cov-report=term-missing:skip-covered --cov=icclim tests/ | tee pytest-coverage.txt; ( exit ${PIPESTATUS[0]} )
       - name: Pytest coverage comment
         id: coverageComment
         uses: MishaKav/pytest-coverage-comment@main
@@ -96,6 +95,8 @@ jobs:
 
   logo-update:
     runs-on: ubuntu-latest
+    env:
+      FLIT_ROOT_INSTALL: 1
     steps:
       - uses: actions/checkout@v3
         with:
@@ -104,12 +105,10 @@ jobs:
         uses: actions/setup-python@v2
         with:
           python-version: 3.9
-      - name: Install requirements
-        run: pip install -r requirements.txt
-      - name: Install pytest-cov
-        run: pip install pytest-cov
-      - name: Install icclim
-        run: python -m pip install -e .
+      - name: Install build tools
+        run: pip install --upgrade pip flit
+      - name: Install icclim and dev requirements (dev, test and doc)
+        run: flit install --deps develop
       - name: Generate logos
         run: |
           python ./tools/update_logo_version.py ./doc/source/_static/logo_icclim_colored__base.svg ./doc/source/_static/logo_icclim_colored__displayed.svg

.pre-commit-config.yaml

@@ -7,11 +7,6 @@ repos:
     hooks:
     -   id: absolufy-imports
         name: absolufy-imports
--   repo: https://github.com/asottile/pyupgrade
-    rev: v3.15.0
-    hooks:
-    -   id: pyupgrade
-        language_version: python3
 -   repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.5.0
     hooks:
@@ -20,61 +15,23 @@ 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/psf/black
-    rev: 23.11.0
-    hooks:
-    -   id: black
-        language_version: python3
-        args: ["--target-version", "py37"]
--   repo: https://github.com/pycqa/flake8
-    rev: 6.1.0
+-   repo: https://github.com/pappasam/toml-sort
+    rev: v0.23.1
     hooks:
-    -   id: flake8
-        language_version: python3
-        additional_dependencies: ['flake8-rst-docstrings']
-        args: ['--config=setup.cfg']
--   repo: https://github.com/PyCQA/isort
-    rev: 5.13.0
-    hooks:
-    -   id: isort
-        language_version: python3
-        args: ['--profile', 'black']
--   repo: https://github.com/pycqa/pydocstyle
-    rev: 6.3.0
+     - id: toml-sort-fix
+-   repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.1.8
     hooks:
-    -   id: pydocstyle
-        language_version: python3
-        args: ['--convention=numpy', '--match="(?!test_).*\.py"']
+      -  id: ruff
+      -  id: ruff-format
 -   repo: meta
     hooks:
     -   id: check-hooks-apply
     -   id: check-useless-excludes
--   repo: https://github.com/keewis/blackdoc
-    rev: v0.3.9
-    hooks:
-      - id: blackdoc
-        additional_dependencies: [ 'black==22.3.0' ]
-#-   repo: https://github.com/pre-commit/mirrors-mypy
-#    rev: v0.910
-#    hooks:
-#    -   id: mypy
-#        additional_dependencies: [
-#            # Type stubs
-#            types-python-dateutil,
-#            types-pkg_resources,
-#            types-PyYAML,
-#            types-pytz,
-#            # Dependencies that are typed
-#            numpy,
-#            xarray,
-#            xclim,
-#            typing-extensions==3.10.0.0,
-#          ]
 
 ci:
     autofix_commit_msg: |

.readthedocs.yml

@@ -2,12 +2,16 @@ version: 2
 
 sphinx:
   configuration: doc/source/conf.py
+  fail_on_warning: true
 
 build:
-  os: "ubuntu-20.04"
+  os: "ubuntu-22.04"
   tools:
     python: "3.9"
 
 python:
-   install:
-   - requirements: requirements_dev.txt
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - "doc"

README.rst

@@ -1,7 +1,7 @@
 |logo|
 ======
 
-|build| |pypi| |black| |docs| |conda| |coverage| |doi|
+|build| |pypi| |ruff| |docs| |conda| |coverage| |doi|
 
 icclim is a Python library to compute climate indices.
 icclim name stands for index, calculation, climate.
@@ -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
 -----------------
@@ -68,7 +68,7 @@ For a detailed description of each ECA&D index, please visit: https://www.ecad.e
 ..
   Pytest Coverage Comment:Begin
 
-.. |coverage| image:: https://img.shields.io/badge/Coverage-91%25-brightgreen.svg
+.. |coverage| image:: https://img.shields.io/badge/Coverage-86%25-green.svg
         :target: https://github.com/cerfacs-globc/icclim/blob/master/README.rst#code-coverage
         :alt: Code coverage
 
@@ -80,10 +80,6 @@ For a detailed description of each ECA&D index, please visit: https://www.ecad.e
         :target: https://icclim.readthedocs.io/en/latest/?badge=latest
         :alt: Documentation Status
 
-.. |black| image:: https://img.shields.io/badge/code%20style-black-000000.svg
-        :target: https://github.com/python/black
-        :alt: Python Black
-
 .. |pypi| image:: https://img.shields.io/pypi/v/icclim.svg
         :target: https://pypi.python.org/pypi/icclim
         :alt: Python Package Index Build
@@ -104,3 +100,7 @@ For a detailed description of each ECA&D index, please visit: https://www.ecad.e
         :target: https://github.com/cerfacs-globc/icclim
         :alt: icclim
         :width: 200px
+
+.. |ruff| image:: https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json
+        :target: https://github.com/astral-sh/ruff
+        :alt: Ruff

doc/source/conf.py

@@ -1,3 +1,4 @@
+# noqa: INP001
 # Configuration file for the Sphinx documentation builder.
 #
 # This file only contains a selection of the most common options. For a full
@@ -10,15 +11,15 @@
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 #
-import os
 import sys
+from pathlib import Path
 
-sys.path.insert(0, os.path.abspath("../.."))
-import icclim
+sys.path.insert(0, Path("../..").resolve())
+import icclim  # noqa: E402 (import need to be after path update)
 
 # -- Project information -----------------------------------------------------
 project = "icclim"
-copyright = "2021, CERFACS"
+copyright = "2021, CERFACS"  # noqa: A001
 author = "Christian P."
 version = icclim.__version__
 release = icclim.__version__

doc/source/dev/release_process.rst

@@ -1,49 +1,24 @@
 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 version number of icclim in ``src/icclim/__init__.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.
-
-    .. code-block:: sh
-
-        python3 -m setup sdist
-
-#. Try to upload on testpypi first. ``twine`` must be installed in your env beforehand.
-
-    .. code-block:: sh
-
-        python3 -m twine upload --repository testpypi dist/*
-
-#. Try to install testpypi version on a clean virtual environment.
+#. Create wheel file on master and source archive.
 
     .. code-block:: sh
 
-        python3 -m pip install --index-url https://test.pypi.org/simple/ icclim
-
-    .. note::
-
-        It may fail due to missing dependencies in test.pypi.
-        In that case, create the environment from icclim environment.yml file to
-        pull all needed dependencies from conda.
-
-#. Test basic index such as `icclim.su("simple-tasmax-data.nc")`
+        python3 -m build
 
-#. Upload to pypi for real.
+#. Upload to pypi.
 
     .. code-block:: sh
 
-        python3 -m twine upload dist/*
+       flit publish
 
 #. Update conda-forge feedstock at https://github.com/conda-forge/icclim-feedstock
 

doc/source/references/ecad_functions_api.rst

@@ -16,11 +16,12 @@ For example to use this new API with the index `su` you can do:
 
     summer_days = icclim.su(in_files=glob.glob("netcdf_files/tasmax*.nc"))
 
-Generated API
--------------
+ECAD Generated Functions
+------------------------
 
 .. automodule:: icclim._generated_api
     :members:
+    :no-index:
 
     .. rubric:: Functions
 

doc/source/references/generic_functions_api.rst

@@ -4,7 +4,7 @@ Generic indices/indicators
 ==========================
 
 icclim 6.0 introduced the concept of generic indices.
-This document present the auto-generated functions that were built base on :ref:`GenericIndicatorRegistry`.
+This document present the auto-generated functions that were built base on :py:class:`icclim.generic_indices.GenericIndicatorRegistry`.
 The are accessible directly from `icclim` namespace.
 
 As an example, you can compute the number of days where a threshold is reached with:

doc/source/references/release_notes.rst

@@ -1,6 +1,21 @@
 Release history
 ===============
 
+6.6.0 (unreleased)
+------------------
+
+* [maint] Migrate from [black, blackdoc, flake8, isort, pyupgrade, pydocstyle] to ruff
+* [maint] Migrate from setup.py to pyproject.toml
+* [maint] Make readthedocs build fail when there are warnings
+* [maint] Fix warnings in doc build
+* [maint] Update architecture to have a `src/` and a `tests/` directory at root level
+* [maint] Migrate build toolchain from setuptools to flit
+* [maint] Remove version number from `constants` module as it was causing the build process to import icclim.
+          The version number is now statically set in src/icclim/__init__.py
+* [maint] Lint code using the more restrictive rules from ruff
+* [fix]   Force xarray to read dataset sequentially to avoid a netcdf-c threading issue causing seg faults.
+
+
 6.5.0
 -----
 
@@ -259,7 +274,7 @@ 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.