Update docstrings

MANIFEST.in

@@ -5,8 +5,10 @@ include README.rst
 include requirements.txt
 
 recursive-include intake_esm *.yaml
-recursive-include tests
-recursive-include example_input
+recursive-include tests *.py
+recursive-include tests *.nc
+recursive-include tests *yml
+recursive-include tests *yaml
 recursive-include intake_esm *.py
 recursive-exclude * __pycache__
 recursive-exclude * *.py[co]

Makefile

@@ -24,33 +24,19 @@ clean-pyc:
 	find . -name '*~' -exec rm -f {} +
 
 lint:
-	flake8 intake_esm test
+	flake8 intake_esm
+	black --check --line-length=100 -S --exclude='intake_esm/_version.py|versioneer.py' intake_esm
+	isort --recursive -w 100 --check-only intake_esm
 
 test:
-	py.test
+	pytest -v
 
-test-all:
-	tox
 
 coverage:
-	coverage run --source intake_esm setup.py test
-	coverage report -m
-	coverage html
+	pytest --cov-report=html --cov=./ tests/ --verbose
 	open htmlcov/index.html
 
 docs:
-	rm -f docs/intake_esm.rst
-	rm -f docs/modules.rst
-	sphinx-apidoc -o docs/ intake_esm
 	$(MAKE) -C docs clean
 	$(MAKE) -C docs html
 	open docs/_build/html/index.html
-
-release: clean
-	python setup.py sdist upload
-	python setup.py bdist_wheel upload
-
-sdist: clean
-	python setup.py sdist
-	python setup.py bdist_wheel upload
-	ls -l dist

docs/source/api.rst

@@ -1,28 +1,6 @@
 API reference
 =============
 
-This is a reference API class listing, and modules.
-
-.. autosummary::
-   intake_esm.core.ESMMetadataStoreCatalog
-   intake_esm.cmip.CMIPSource
-   intake_esm.cmip.CMIPCollection
-   intake_esm.cesm.CESMSource
-   intake_esm.cesm.CESMCollection
-
-
-.. autoclass:: intake_esm.core.ESMMetadataStoreCatalog
-   :members: search, open_collection
-
-
-.. autoclass:: intake_esm.cesm.CESMSource
-   :members: to_xarray, results
-
-.. autoclass:: intake_esm.cesm.CESMCollection
-   :members:
-
-.. autoclass:: intake_esm.cmip.CMIPSource
-   :members: to_xarray, results
-
-.. autoclass:: intake_esm.cmip.CMIPCollection
-   :members:
+.. automodule:: intake_esm.core
+    :members:
+    :show-inheritance:

intake_esm/cesm.py

@@ -29,7 +29,8 @@ class CESMCollection(Collection):
     See Also
     --------
     intake_esm.core.ESMMetadataStoreCatalog
-    intake_esm.cmip.CMIPCollection
+    intake_esm.cmip.CMIP5Collection
+    intake_esm.cmip.CMIP6Collection
     """
 
     def __init__(self, collection_spec):

intake_esm/cmip.py

@@ -34,19 +34,22 @@ def __init__(self, collection_spec):
         self.root_dir = self.collection_spec['data_sources']['root_dir']['urlpath']
 
     def build(self):
-        """ Build collection and return a pandas Dataframe
+        """ Builds CMIP5 collection and returns a pandas Dataframe
+
+        Notes
+        ------
         Directory structure = <activity>/
                                 <product>/
                                     <institute>/
                                         <model>/
                                             <experiment>/
                                                 <frequency>/
-                                                <modeling_realm>/
-                                                    <MIP table>/
+                                                   <modeling_realm>/
+                                                     <MIP table>/
                                                         <ensemble member>/
                                                             <version number>/
                                                                 <variable name>
-        with ``depth=7``, we retrieve all directories up to ``realm`` level
+        With ``depth=7``, we retrieve all directories up to ``modeling_realm`` level
         Reference: CMIP5 DRS: https://cmip.llnl.gov/cmip5/docs/cmip5_data_reference_syntax_v1-00_clean.pdf
         """
         self.build_cmip(depth=7, exclude_dirs=['files', 'latest'])
@@ -127,6 +130,10 @@ def __init__(self, collection_spec):
 
     def build(self):
         """
+        Builds CMIP6 collection and returns a pandas Dataframe
+
+        Notes
+        -----
         Directory structure = <mip_era>/
                                 <activity_id>/
                                     <institution_id>/
@@ -137,8 +144,7 @@ def build(self):
                                                         <variable_id>/
                                                             <grid_label>/
                                                                 <version>
-
-        with ``depth=9``, we retrieve all directories up to ``grid_label`` level
+        With ``depth=9``, we retrieve all directories up to ``grid_label`` level
         Reference: CMIP6 DRS: http://goo.gl/v1drZl
         """
         self.build_cmip(depth=9, exclude_dirs=[])

intake_esm/core.py

@@ -31,7 +31,8 @@ class ESMMetadataStoreCatalog(Catalog):
                 Collection type. Accepted values include:
 
                 - `cesm`
-                - `cmip`
+                - `cmip5`
+                - `cmip6`
     overwrite_existing : bool,
             Whether to overwrite existing built collection catalog