Merge branch 'main' into translation

Ouranosinc · Sep 15, 2023 · 9b17a6f · 9b17a6f
2 parents 5bac82f + adafdbe
commit 9b17a6f
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diff --git a/.cruft.json b/.cruft.json
@@ -11,7 +11,7 @@
       "project_slug": "xscen",
       "project_short_description": "A climate change scenario-building analysis framework, built with xclim/xarray.",
       "pypi_username": "RondeauG",
-      "version": "0.7.4-beta",
+      "version": "0.7.5-beta",
       "use_pytest": "y",
       "use_black": "y",
       "add_pyup_badge": "n",

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -6,7 +6,7 @@ repos:
     rev: v3.10.1
     hooks:
     -   id: pyupgrade
-        args: [--py39-plus]
+        args: [ '--py39-plus' ]
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.4.0
     hooks:
@@ -27,8 +27,8 @@ repos:
     rev: v1.10.0
     hooks:
       - id: rst-inline-touching-normal
-  - repo: https://github.com/psf/black
-    rev: 23.7.0
+  - repo: https://github.com/psf/black-pre-commit-mirror
+    rev: 23.9.1
     hooks:
       - id: black
         exclude: ^docs/
@@ -53,7 +53,7 @@ repos:
     rev: v0.3.8
     hooks:
       - id: blackdoc
-        additional_dependencies: [ 'black==23.3.0' ]
+        additional_dependencies: [ 'black==23.9.1' ]
         exclude: config.py
   - repo: https://github.com/adrienverge/yamllint.git
     rev: v1.32.0

diff --git a/CONTRIBUTING.rst b/CONTRIBUTING.rst
@@ -114,9 +114,14 @@ Ready to contribute? Here's how to set up `xscen` for local development.
     # or to simply generate the html
     $ cd docs/
     $ make html
+    
+.. note::
 
-9. Submit a pull request through the GitHub website.
+    When building the documentation, the default behaviour is to evaluate notebooks ('nbsphinx_execute = "always"'), rather than simply parse the content ('nbsphinx_execute = "never"'). Due to their complexity, this can sometimes be a very computationally demanding task and should only be performed when necessary (i.e.: when the notebooks have been modified).
+
+    In order to speed up documentation builds, setting a value for the environment variable "SKIP_NOTEBOOKS" (e.g. "$ export SKIP_NOTEBOOKS=1") will prevent the notebooks from being evaluated on all subsequent "$ tox -e docs" or "$ make docs" invocations.
 
+9. Submit a pull request through the GitHub website.
 
 Translating xscen
 ~~~~~~~~~~~~~~~~~

diff --git a/HISTORY.rst b/HISTORY.rst
@@ -12,18 +12,20 @@ Announcements
 
 New features and enhancements
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-* N/A
+* Added the ability to search for simulations that reach a given warming level. (:pull:`251`).
 
 Breaking changes
 ^^^^^^^^^^^^^^^^
 * N/A
 
 Bug fixes
 ^^^^^^^^^
-* N/A
+* Fixed a bug in ``xs.search_data_catalogs`` when searching for fixed fields and specific experiments/members. (:pull:`251`).
+* Fixed a bug in the documentation build configuration that prevented stable/latest and tagged documentation builds from resolving on ReadTheDocs. (:pull:`256`).
 
 Internal changes
 ^^^^^^^^^^^^^^^^
+* Continued work on adding tests. (:pull:`251`).
 * Fixed pre-commit's pretty-format-json so it ignores notebooks. (:pull:`254`).
 * Fixed the labeler so docs/CI isn't automatically added for contributions by new collaborators. (:pull:`254`).
 * Made it so that `tests` are no longer treated as an installable package. (:pull:`248`).

diff --git a/docs/conf.py b/docs/conf.py
@@ -21,14 +21,15 @@
 import os
 import sys
 import warnings
+from datetime import datetime
 from pathlib import Path
 
-sys.path.insert(0, os.path.abspath('..'))
-if os.environ.get('READTHEDOCS') and 'ESMFMKFILE' not in os.environ:
+sys.path.insert(0, os.path.abspath(".."))
+if os.environ.get("READTHEDOCS") and "ESMFMKFILE" not in os.environ:
     # RTD doesn't activate the env, and esmpy depends on a env var set there
     # We assume the `os` package is in {ENV}/lib/pythonX.X/os.py
     # See conda-forge/esmf-feedstock#91 and readthedocs/readthedocs.org#4067
-    os.environ['ESMFMKFILE'] = str(Path(os.__file__).parent.parent / 'esmf.mk')
+    os.environ["ESMFMKFILE"] = str(Path(os.__file__).parent.parent / "esmf.mk")
 
 import xscen  # noqa
 import xarray  # noqa
@@ -53,7 +54,7 @@
     "sphinx.ext.viewcode",
     "nbsphinx",
     "sphinx_codeautolink",
-    "sphinx_copybutton"
+    "sphinx_copybutton",
 ]
 
 # To ensure that underlined fields (e.g. `_field`) are shown in the docs.
@@ -68,25 +69,29 @@
 autosectionlabel_maxdepth = 2
 
 autosummary_generate = True
-nbsphinx_execute = "always"
 
-# To avoid running notebooks on linkcheck
+nbsphinx_execute = "always"
+# To avoid running notebooks on linkcheck and when building PDF.
 try:
     skip_notebooks = int(os.getenv("SKIP_NOTEBOOKS"))
 except TypeError:
     skip_notebooks = False
 if skip_notebooks:
-    warnings.warn("Not executing notebooks.")
+    warnings.warn("SKIP_NOTEBOOKS is set. Not executing notebooks.")
     nbsphinx_execute = "never"
+elif os.getenv("READTHEDOCS_VERSION_NAME") in ["latest", "stable"] or os.getenv(
+    "READTHEDOCS_VERSION_TYPE"
+) in ["tag"]:
+    if os.getenv("READTHEDOCS_OUTPUT") in ["pdf"]:
+        warnings.warn("Generating PDF version. Not executing notebooks.")
+        nbsphinx_execute = "never"
 
 # if skip_notebooks or os.getenv("READTHEDOCS_VERSION_TYPE") in [
 #     "branch",
 #     "external",
 # ]:
-# elif os.getenv("READTHEDOCS_VERSION_NAME") in ["latest", "stable"]:
-#     nbsphinx_execute = "always"
-# else:
-#     nbsphinx_execute = "auto"
+#     warnings.warn("Not executing notebooks.")
+#     nbsphinx_execute = "never"
 
 # To avoid having to install these and burst memory limit on ReadTheDocs.
 # autodoc_mock_imports = [
@@ -136,14 +141,14 @@
 # You can specify multiple suffix as a list of string:
 #
 # source_suffix = ['.rst', '.md']
-source_suffix = ['.rst']
+source_suffix = [".rst"]
 
 # The master toctree document.
-master_doc = 'index'
+master_doc = "index"
 
 # General information about the project.
-project = 'xscen'
-copyright = "2022, Ouranos Inc., Gabriel Rondeau-Genesse, and contributors"
+project = "xscen"
+copyright = f"2022-{datetime.now().year}, Ouranos Inc., Gabriel Rondeau-Genesse, and contributors"
 author = "Gabriel Rondeau-Genesse"
 
 # The version info for the project you're documenting, acts as replacement
@@ -172,7 +177,7 @@
 ]
 
 # The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
+pygments_style = "sphinx"
 
 # If true, `todo` and `todoList` produce output, else they produce nothing.
 todo_include_todos = False
@@ -201,13 +206,13 @@
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+html_static_path = ["_static"]
 
 
 # -- Options for HTMLHelp output ---------------------------------------
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'xscendoc'
+htmlhelp_basename = "xscendoc"
 
 
 # -- Options for LaTeX output ------------------------------------------
@@ -216,15 +221,12 @@
     # The paper size ('letterpaper' or 'a4paper').
     #
     # 'papersize': 'letterpaper',
-
     # The font size ('10pt', '11pt' or '12pt').
     #
     # 'pointsize': '10pt',
-
     # Additional stuff for the LaTeX preamble.
     #
     # 'preamble': '',
-
     # Latex figure (float) alignment
     #
     # 'figure_align': 'htbp',
@@ -234,21 +236,21 @@
 # (source start file, target name, title, author, documentclass
 # [howto, manual, or own class]).
 latex_documents = [
-    (master_doc, 'xscen.tex',
-     'xscen Documentation',
-     'Gabriel Rondeau-Genesse', 'manual'),
+    (
+        master_doc,
+        "xscen.tex",
+        "xscen Documentation",
+        "Gabriel Rondeau-Genesse",
+        "manual",
+    ),
 ]
 
 
 # -- Options for manual page output ------------------------------------
 
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
-man_pages = [
-    (master_doc, 'xscen',
-     'xscen Documentation',
-     [author], 1)
-]
+man_pages = [(master_doc, "xscen", "xscen Documentation", [author], 1)]
 
 
 # -- Options for Texinfo output ----------------------------------------
@@ -257,10 +259,13 @@
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-    (master_doc, 'xscen',
-     'xscen Documentation',
-     author,
-     'xscen',
-     'One line description of project.',
-     'Miscellaneous'),
+    (
+        master_doc,
+        "xscen",
+        "xscen Documentation",
+        author,
+        "xscen",
+        "One line description of project.",
+        "Miscellaneous",
+    ),
 ]
diff --git a/docs/notebooks/1_catalog.ipynb b/docs/notebooks/1_catalog.ipynb
@@ -254,7 +254,7 @@
     "- `allow_conversion` is used to allow searching for calculable variables, in the case where the requested variable would not be available.\n",
     "- `restrict_resolution` is used to limit the results to the finest or coarsest resolution available for each source.\n",
     "- `restrict_members` is used to limit the results to a maximum number of realizations for each source.\n",
-    "- `restrict_warming_level` is used to limit the results to only datasets that are present in the csv used for calculating warming levels.\n",
+    "- `restrict_warming_level` is used to limit the results to only datasets that are present in the csv used for calculating warming levels. You can also pass a dict to verify that a given warming level is reached.\n",
     "\n",
     "Note that compared to `search`, the result of `search_data_catalog` is a dictionary with one entry per unique ID. A given unique ID might contain multiple datasets as per `intake-esm`'s definition, because it groups catalog lines per *id - domain - processing_level - xrfreq*. Thus, it would separate model data that exists at different frequencies.\n",
     "\n",
@@ -390,7 +390,9 @@
     "    data_catalogs=[f\"{Path().absolute()}/samples/pangeo-cmip6.json\"],\n",
     "    variables_and_freqs=variables_and_freqs,\n",
     "    match_hist_and_fut=True,\n",
-    "    restrict_warming_level=True,  # In this case all models exist in our database, so nothing gets eliminated.\n",
+    "    restrict_warming_level={\n",
+    "        \"wl\": 2\n",
+    "    },  # SSP126  gets eliminated, since it doesn't reach +2°C by 2100.\n",
     ")\n",
     "\n",
     "cat_sim"

diff --git a/setup.cfg b/setup.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.7.4-beta
+current_version = 0.7.5-beta
 commit = True
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+).(?P<patch>\d+)(\-(?P<release>[a-z]+))?

diff --git a/setup.py b/setup.py
@@ -102,6 +102,6 @@ def run(self):
     test_suite="tests",
     extras_require={"dev": dev_requirements},
     url="https://github.com/Ouranosinc/xscen",
-    version="0.7.4-beta",
+    version="0.7.5-beta",
     zip_safe=False,
 )
diff --git a/tests/conftest.py b/tests/conftest.py
@@ -26,7 +26,7 @@ def remove_data_folder():
     request.addfinalizer(remove_data_folder)
 
 
-@pytest.mark.requires_docs
+@pytest.mark.requires_netcdf
 @pytest.fixture(scope="session")
 def samplecat():
     """Generate a sample catalog with the tutorial netCDFs."""