Split from xclim

.flake8

@@ -12,6 +12,9 @@ ignore =
 	F,
 	W503
 per-file-ignores =
+rst-directives =
+	bibliography,
+	autolink-skip
 rst-roles =
 	doc,
 	mod,
@@ -25,3 +28,8 @@ rst-roles =
 	py:mod,
 	py:obj,
 	py:ref
+	ref,
+	cite:cts,
+	cite:p,
+	cite:t,
+	cite:ts

.github/workflows/main.yml

@@ -56,8 +56,6 @@ jobs:
       matrix:
         os: [ 'ubuntu-latest' ]
         python-version:
-          - "3.8"
-          - "3.9"
           - "3.10"
           - "3.11"
           - "3.12"
@@ -98,7 +96,7 @@ jobs:
     strategy:
       matrix:
         os: [ 'ubuntu-latest' ]
-        python-version: [ "3.9", "3.10", "3.11", "3.12" ]
+        python-version: [ "3.10", "3.11", "3.12" ]
     defaults:
       run:
         shell: bash -l {0}
@@ -118,6 +116,11 @@ jobs:
           create-args: >-
             python=${{ matrix.python-version }}
           micromamba-version: "1.5.10-0"  # pinned to avoid the breaking changes with mamba and micromamba (2.0.0).
+      - name: Install xclim development version
+        # FIXME: This is a workaround to install xclim v0.53, which is not released.
+        run: |
+          echo "Installing xclim from main branch until version 0.53.0+ is released"
+          python -m pip install git+https://github.com/Ouranosinc/xclim.git@main
       - name: Install xsdba
         run: |
           python -m pip install --no-deps .

.pre-commit-config.yaml

@@ -46,7 +46,7 @@ repos:
     hooks:
       - id: ruff
         args: [ '--fix' ]
-      - id: ruff-format
+#      - id: ruff-format
   - repo: https://github.com/pycqa/flake8
     rev: 7.1.1
     hooks:

.zenodo.json

@@ -5,6 +5,11 @@
       "name": "Smith, Trevor James",
       "affiliation": "Ouranos, Montréal, Québec, Canada",
       "orcid": "0000-0001-5393-8359"
+    },
+    {
+      "name": "Dupuis, Éric",
+      "affiliation": "Ouranos, Montréal, Québec, Canada",
+      "orcid": "0000-0001-7976-4596"
     }
   ],
   "keywords": [

AUTHORS.rst

@@ -5,12 +5,13 @@ Credits
 Development Lead
 ----------------
 
-* Trevor James Smith <smith.trevorj@ouranos.ca> `@Zeitsperre <https://github.com/Zeitsperre>`_
+* Éric Dupuis <dupuis.eric@ouranos.ca> `@coxipi <https://github.com/coxipi>`_
 
 Co-Developers
 -------------
 
-None yet. Why not be the first?
+* Pascal Bourgault <[email protected]> `@aulemahal <https://github.com/aulemahal>`_
+* Trevor James Smith <[email protected]> `@Zeitsperre <https://github.com/Zeitsperre>`_
 
 Contributors
 ------------

CHANGELOG.rst

@@ -5,22 +5,20 @@ Changelog
 `Unreleased <https://github.com/Ouranosinc/xsdba>`_ (latest)
 ------------------------------------------------------------
 
-Contributors:
+Contributors: Éric Dupuis (:user:`coxipi`), Trevor James Smith (:user:`Zeitsperre`).
 
 Changes
 ^^^^^^^
-* No change.
+* Split `sdba` from `xclim` and duplicate code where needed. (:pull:`8`)
+* `units` are a copy (or almost) of given modules in `xclim`. A lot of duplicated code from xclim's `calendar` is also in xsdba's `base`. (:pull:`8`)
 
-Fixes
-^^^^^
-* No change.
 
 .. _changes_0.1.0:
 
 `v0.1.0 <https://github.com/Ouranosinc/xsdba/tree/0.1.0>`_
 ----------------------------------------------------------
 
-Contributors: Trevor James Smith (:user:`Ouranosinc`)
+Contributors: Trevor James Smith (:user:`Zeitsperre`)
 
 Changes
 ^^^^^^^

README.rst

@@ -37,6 +37,11 @@ This package was created with Cookiecutter_ and the `Ouranosinc/cookiecutter-pyp
         :target: https://github.com/psf/black
         :alt: Python Black
 
+.. |logo| image:: https://raw.githubusercontent.com/Ouranosinc/xsdba/main/docs/logos/xsdba-logo-small-light.png
+        :target: https://github.com/Ouranosinc/xsdba
+        :alt: Xsdba
+        :class: xsdba-logo-small no-theme
+
 .. |build| image:: https://github.com/Ouranosinc/xsdba/actions/workflows/main.yml/badge.svg
         :target: https://github.com/Ouranosinc/xsdba/actions
         :alt: Build Status

docs/api.rst

@@ -0,0 +1,81 @@
+===
+API
+===
+
+.. _xsdba-user-api:
+
+xsdba Module
+============
+
+.. automodule:: xsdba.adjustment
+   :members:
+   :exclude-members: BaseAdjustment
+   :special-members:
+   :show-inheritance:
+   :noindex:
+
+.. automodule:: xsdba.processing
+   :members:
+   :noindex:
+
+.. automodule:: xsdba.detrending
+   :members:
+   :show-inheritance:
+   :exclude-members: BaseDetrend
+   :noindex:
+
+.. automodule:: xsdba.utils
+   :members:
+   :noindex:
+
+.. autoclass:: xsdba.base.Grouper
+   :members:
+   :class-doc-from: init
+   :noindex:
+
+.. automodule:: xsdba.nbutils
+   :members:
+   :noindex:
+
+.. automodule:: xsdba.loess
+   :members:
+   :noindex:
+
+.. automodule:: xsdba.properties
+   :members:
+   :exclude-members: StatisticalProperty
+   :noindex:
+
+.. automodule:: xsdba.measures
+   :members:
+   :exclude-members: StatisticalMeasure
+   :noindex:
+
+.. _`xsdba-developer-api`:
+
+xsdba Utilities
+---------------
+
+.. automodule:: xsdba.base
+   :members:
+   :show-inheritance:
+   :exclude-members: Grouper
+   :noindex:
+
+.. autoclass:: xsdba.detrending.BaseDetrend
+   :members:
+   :noindex:
+
+.. autoclass:: xsdba.adjustment.TrainAdjust
+   :members:
+   :noindex:
+
+.. autoclass:: xsdba.adjustment.Adjust
+   :members:
+   :noindex:
+
+.. autofunction:: xsdba.properties.StatisticalProperty
+   :noindex:
+
+.. autofunction:: xsdba.measures.StatisticalMeasure
+   :noindex:

docs/conf.py

@@ -22,8 +22,18 @@
 
 sys.path.insert(0, os.path.abspath('..'))
 
+import xarray
+from pybtex.plugin import register_plugin
+from pybtex.style.formatting.alpha import Style as AlphaStyle
+from pybtex.style.labels import BaseLabelStyle
+
+xarray.DataArray.__module__ = "xarray"
+xarray.Dataset.__module__ = "xarray"
+xarray.CFTimeIndex.__module__ = "xarray"
+
 import xsdba
 
+
 # -- General configuration ---------------------------------------------
 
 # If your documentation needs a minimal Sphinx version, state it here.
@@ -36,12 +46,21 @@
     'sphinx.ext.autodoc',
     'sphinx.ext.autosectionlabel',
     'sphinx.ext.extlinks',
-    'sphinx.ext.viewcode',
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.napoleon",
     'sphinx.ext.todo',
+    'sphinx.ext.viewcode',
+    "sphinxcontrib.bibtex",
     'sphinx_codeautolink',
     'sphinx_copybutton',
+    "nbsphinx",
+
 ]
 
+# suppress "duplicate citation for key" warnings
+suppress_warnings = ['bibtex.duplicate_citation']
+
+
 autosectionlabel_prefix_document = True
 autosectionlabel_maxdepth = 2
 
@@ -53,6 +72,29 @@
     "special-members": False,
 }
 
+
+# Bibliography stuff
+# a simple label style which uses the bibtex keys for labels
+class XCLabelStyle(BaseLabelStyle):
+    def format_labels(self, sorted_entries):
+        for entry in sorted_entries:
+            yield entry.key
+
+
+class XCStyle(AlphaStyle):
+    default_label_style = XCLabelStyle
+
+
+register_plugin("pybtex.style.formatting", "xcstyle", XCStyle)
+bibtex_bibfiles = ["references.bib"]
+bibtex_default_style = "xcstyle"
+bibtex_reference_style = "author_year"
+
+intersphinx_mapping = {
+    "scipy": ("https://docs.scipy.org/doc/scipy/", None),
+    "pandas": ("https://pandas.pydata.org/docs/", None),
+}
+
 extlinks = {
     "issue": ("https://github.com/Ouranosinc/xsdba/issues/%s", "GH/%s"),
     "pull": ("https://github.com/Ouranosinc/xsdba/pull/%s", "PR/%s"),
@@ -67,7 +109,9 @@
 source_suffix = {'.rst': 'restructuredtext'}
 
 # The master toctree document.
-master_doc = 'index'
+# master_doc = 'index'
+root_doc = "index"
+
 
 # General information about the project.
 project = 'xsdba'
@@ -157,7 +201,7 @@
 # (source start file, target name, title, author, documentclass
 # [howto, manual, or own class]).
 latex_documents = [
-    (master_doc, 'xsdba.tex',
+    (root_doc, 'xsdba.tex',
      'xsdba Documentation',
      'Trevor James Smith', 'manual'),
 ]
@@ -168,7 +212,7 @@
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
 man_pages = [
-    (master_doc, 'xsdba',
+    (root_doc, 'xsdba',
      'xsdba Documentation',
      [author], 1)
 ]
@@ -180,7 +224,7 @@
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-    (master_doc, 'xsdba',
+    (root_doc, 'xsdba',
      'xsdba Documentation',
      author,
      'xsdba',

docs/index.rst

@@ -1,24 +1,46 @@
 Welcome to xsdba's documentation!
 =================================
 
+.. toctree::
+   :hidden:
+
+   self
+
 .. toctree::
    :maxdepth: 2
-   :caption: Contents:
+   :caption: Table of Contents:
 
    readme
    installation
    usage
+   xsdba
    contributing
    releasing
+   notebooks/index
+   notebooks/example
+   notebooks/advanced_example
+
+
+.. toctree::
+   :titlesonly:
+
    authors
    changelog
+   references
 
 .. toctree::
    :maxdepth: 1
    :caption: All Modules
 
    apidoc/modules
 
+
+.. toctree::
+   :maxdepth: 2
+   :caption: User API
+
+   api
+
 Indices and tables
 ==================
 * :ref:`genindex`