Fix tests failures (#280)

intake · Aug 27, 2020 · 2b147ab · 2b147ab
1 parent 5b81bad
commit 2b147ab
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Showing 27 changed files with 591 additions and 641 deletions.
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -5,22 +5,22 @@ workflows:
   nightly:
     triggers:
       - schedule:
-          cron: "0 0 * * *"
+          cron: '0 0 * * *'
           filters:
             branches:
               only:
                 - master
     jobs:
-      - "upstream-dev"
-      - "python-3.6"
-      - "python-3.7"
-      - "python-3.8"
+      - 'upstream-dev'
+      - 'python-3.6'
+      - 'python-3.7'
+      - 'python-3.8'
   default:
     jobs:
-      - "upstream-dev"
-      - "python-3.6"
-      - "python-3.7"
-      - "python-3.8"
+      - 'upstream-dev'
+      - 'python-3.6'
+      - 'python-3.7'
+      - 'python-3.8'
 
 shared: &shared
   steps:
@@ -56,34 +56,33 @@ shared: &shared
     - save_cache:
         key: deps-{{ checksum "./ci/environment.yml" }}
         paths:
-          - "/opt/conda/pkgs"
-
+          - '/opt/conda/pkgs'
 
 jobs:
-  "upstream-dev":
+  'upstream-dev':
     <<: *shared
     docker:
       - image: ncarxdev/miniconda:3.7
     environment:
-      ENV_FILE: "./ci/environment-upstream-dev.yml"
+      ENV_FILE: './ci/environment-upstream-dev.yml'
 
-  "python-3.6":
+  'python-3.6':
     <<: *shared
     docker:
       - image: ncarxdev/miniconda:3.6
     environment:
-      ENV_FILE: "./ci/environment.yml"
+      ENV_FILE: './ci/environment.yml'
 
-  "python-3.7":
+  'python-3.7':
     <<: *shared
     docker:
       - image: ncarxdev/miniconda:3.7
     environment:
-      ENV_FILE: "./ci/environment.yml"
+      ENV_FILE: './ci/environment.yml'
 
-  "python-3.8":
+  'python-3.8':
     <<: *shared
     docker:
       - image: ncarxdev/miniconda:3.8
     environment:
-      ENV_FILE: "./ci/environment.yml"
+      ENV_FILE: './ci/environment.yml'
diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md
@@ -4,7 +4,6 @@ about: Create a report to help us improve
 title: ''
 labels: ''
 assignees: ''
-
 ---
 
 <!--
@@ -18,14 +17,13 @@ Here's a quick checklist in what to include:
 - [ ] Include a detailed description of the bug or suggestion
 - [ ] `conda list` of the conda environment you are using
 - [ ] Minimal, self-contained copy-pastable example that generates the issue if possible. Please be concise with code posted. See guidelines below on how to provide a good bug report:
+
   - [Minimal Complete Verifiable Examples](https://stackoverflow.com/help/mcve)
   - [Craft Minimal Bug Reports](http://matthewrocklin.com/blog/work/2018/02/28/minimal-bug-reports)
 
     Bug reports that follow these guidelines are easier to diagnose,
     and so are often handled much more quickly.
 
-
-
 ### Description
 
 ```
@@ -40,11 +38,12 @@ Paste the command(s) you ran and the output.
 If there was a crash, please include the traceback here.
 ```
 
-### Output of ``intake_esm.__version__``
+### Output of `intake_esm.__version__`
 
 <details>
 
 ```
 Paste the output of `intake_esm.__version__` here
 ```
+
 </details>
diff --git a/.github/ISSUE_TEMPLATE/feature_request.md b/.github/ISSUE_TEMPLATE/feature_request.md
@@ -4,7 +4,6 @@ about: Suggest an idea for this project
 title: ''
 labels: ''
 assignees: ''
-
 ---
 
 **Is your feature request related to a problem? Please describe.**

diff --git a/.github/workflows/linting.yaml b/.github/workflows/linting.yaml
@@ -0,0 +1,15 @@
+name: linting
+
+on:
+  push:
+    branches: '*'
+  pull_request:
+    branches: '*'
+
+jobs:
+  linting:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v2
+      - uses: pre-commit/[email protected]
diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,31 +1,51 @@
 repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v3.2.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-docstring-first
+      - id: check-json
+      - id: check-yaml
+      - id: double-quote-string-fixer
 
--   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v3.1.0
-    hooks:
-    -   id: trailing-whitespace
-    -   id: end-of-file-fixer
-    -   id: check-docstring-first
-    -   id: check-json
-    -   id: check-yaml
-    -   id: double-quote-string-fixer
+  - repo: https://github.com/ambv/black
+    rev: 20.8b1
+    hooks:
+      - id: black
 
--   repo: https://github.com/ambv/black
-    rev: 19.10b0
+  - repo: https://github.com/keewis/blackdoc
+    rev: v0.1.1
     hooks:
-    - id: black
-      args: ["--line-length", "100", "--skip-string-normalization"]
+      - id: blackdoc
 
--   repo: https://gitlab.com/pycqa/flake8
+  - repo: https://gitlab.com/pycqa/flake8
     rev: 3.8.3
     hooks:
-    - id: flake8
+      - id: flake8
 
--   repo: https://github.com/asottile/seed-isort-config
+  - repo: https://github.com/asottile/seed-isort-config
     rev: v2.2.0
     hooks:
-    -   id: seed-isort-config
--   repo: https://github.com/pre-commit/mirrors-isort
-    rev: v5.0.4
+      - id: seed-isort-config
+  - repo: https://github.com/pre-commit/mirrors-isort
+    rev: v5.4.2
+    hooks:
+      - id: isort
+
+  - repo: https://github.com/prettier/prettier
+    rev: 2.1.1
+    hooks:
+      - id: prettier
+
+  - repo: https://github.com/deathbeds/prenotebook
+    rev: f5bdb72a400f1a56fe88109936c83aa12cc349fa
     hooks:
-    -   id: isort
+      - id: prenotebook
+        args:
+          [
+            '--keep-output',
+            '--keep-metadata',
+            '--keep-execution-count',
+            '--keep-empty',
+          ]
diff --git a/.prettierrc.toml b/.prettierrc.toml
@@ -0,0 +1,3 @@
+tabWidth = 2
+semi = false
+singleQuote = true
diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -224,42 +224,6 @@ Features
   With `netCDF`, we can record very useful information into the global attributes of the netCDF dataset.
   (:pr:`119`) `Anderson Banihirwe`_
 
-  .. code-block:: python
-
-    >>> import intake
-    >>> col = intake.open_esm_metadatastore(collection_input_definition="GLADE-CMIP5")
-    >>> col.ds
-    <xarray.Dataset>
-    Dimensions:          (index: 615296)
-    Coordinates:
-    * index            (index) int64 0 1 2 3 4 ... 615292 615293 615294 615295
-    Data variables:
-        resource         (index) object ...
-        resource_type    (index) object ...
-        direct_access    (index) bool True True True True ... True True True True
-        activity         (index) object ...
-        ensemble_member  (index) object ...
-        experiment       (index) object ...
-        file_basename    (index) object ...
-        file_fullpath    (index) object ...
-        frequency        (index) object ...
-        institute        (index) object ...
-        mip_table        (index) object ...
-        model            (index) object ...
-        modeling_realm   (index) object ...
-        product          (index) object ...
-        temporal_subset  (index) object ...
-        variable         (index) object ...
-        version          (index) object ...
-    Attributes:
-        created_at:             2019-08-07T18:05:09.371259
-        intake_esm_version:     2019.5.11.post153
-        intake_version:         0.5.2
-        intake_xarray_version:  0.3.1
-        collection_spec:        {"name": "GLADE-CMIP5", "collection_type": "cmip5...
-        name:                   GLADE-CMIP5
-        collection_type:        cmip5
-
 - Add string representation of `ESMMetadataStoreCatalog`` object (:pr:`122`) `Anderson Banihirwe`_
 
 
@@ -269,10 +233,13 @@ Features
 
   .. code-block:: python
 
-    >>> import intake
-    >>> col = intake.open_esm_metadatastore(collection_name="GLADE-CMIP5")
-    >>> # if "GLADE-CMIP5" collection isn't built already, the above is equivalent to:
-    >>> col = intake.open_esm_metadatastore(collection_input_definition="GLADE-CMIP5")
+    In [1]: import intake
+
+    In [2]: col = intake.open_esm_metadatastore(collection_name="GLADE-CMIP5")
+
+    In [3]: # if "GLADE-CMIP5" collection isn't built already, the above is equivalent to:
+
+    In [4]: col = intake.open_esm_metadatastore(collection_input_definition="GLADE-CMIP5")
 
 - Revert back to using official DRS attributes when building CMIP5 and CMIP6 collections.
   (:pr:`126`) `Anderson Banihirwe`_
@@ -285,10 +252,12 @@ Features
 
   .. code-block:: python
 
-    >>> import intake
-    >>> col = intake.open_esm_metadatastore(collection_name="GLADE-CMIP5")
-    >>> col
-    GLADE-CMIP5 collection catalogue with 615853 entries:
+    In [1]: import intake
+
+    In [2]: col = intake.open_esm_metadatastore(collection_name="GLADE-CMIP5")
+
+    In [3]: col
+    Out[3]: GLADE-CMIP5 collection catalogue with 615853 entries:
             > 3 resource(s)
 
             > 1 resource_type(s)
@@ -323,7 +292,8 @@ Features
 
             > 489 version(s)
 
-    >>> col.nunique()
+    In[4]: col.nunique()
+
     resource                3
     resource_type           1
     direct_access           1
@@ -342,7 +312,9 @@ Features
     variable              454
     version               489
     dtype: int64
-    >>> col.unique(columns=['frequency', 'modeling_realm'])
+
+    In[4]: col.unique(columns=['frequency', 'modeling_realm'])
+
     {'frequency': {'count': 6, 'values': ['mon', 'day', '6hr', 'yr', '3hr', 'fx']},
     'modeling_realm': {'count': 7, 'values': ['atmos', 'land', 'ocean', 'seaIce', 'ocnBgchem',
     'landIce', 'aerosol']}}