Merge pull request #34 from andersy005/rename-package

Rename package

Author: andersy005

.circleci/config.yml

@@ -16,7 +16,7 @@ jobs:
 
     environment:
       PYTHON: "3.6"
-      ENV_NAME: "intake-cesm-dev"
+      ENV_NAME: "intake-esm-dev"
 
     steps:
       - checkout
@@ -61,7 +61,7 @@ jobs:
 
     environment:
       PYTHON: "3.7"
-      ENV_NAME: "intake-cesm-dev"
+      ENV_NAME: "intake-esm-dev"
 
     steps:
 
@@ -110,7 +110,7 @@ jobs:
 
     environment:
       PYTHON: "3.7"
-      ENV_NAME: "intake-cesm-dev"
+      ENV_NAME: "intake-esm-dev"
 
     steps:
 

.coveragerc

@@ -1,6 +1,6 @@
 [run]
 omit = 
     tests/*.py
-    intake_cesm/_version.py
+    intake_esm/_version.py
     versioneer.py
     setup.py

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,8 +1,6 @@
 Thanks for submitting a PR, your contribution is really appreciated!
 
-Here's a quick checklist that should be present in PRs (you can delete this text from the final description, this is
-just a guideline):
+Here's a quick checklist that should be present in PRs (you can delete this text from the final description, this is just a guideline):
 
-- [ ] Create a new changelog file in the `changelog` folder, with a name like `<ISSUE NUMBER>.<TYPE>.rst`. See [CHANGELOG.rst](https://github.com/NCAR/intake-cesm/blob/master/CHANGELOG.rst) for details.
 - [ ] Include documentation when adding new features.
 - [ ] Include new tests or update existing tests when applicable.

CONTRIBUTING.rst

@@ -1,5 +1,5 @@
 ============================
-Contribution getting started
+Contributing to intake-esm
 ============================
 
 Contributions are highly welcomed and appreciated.  Every little help counts,
@@ -14,10 +14,10 @@ so do not hesitate!
 Feature requests and feedback
 -----------------------------
 
-Do you like intake-cesm?  Share some love on Twitter or in your blog posts!
+Do you like intake-esm?  Share some love on Twitter or in your blog posts!
 
 We'd also like to hear about your propositions and suggestions.  Feel free to
-`submit them as issues <https://github.com/NCAR/intake-cesm>`_ and:
+`submit them as issues <https://github.com/NCAR/intake-esm>`_ and:
 
 * Explain in detail how they should work.
 * Keep the scope as narrow as possible.  This will make it easier to implement.
@@ -28,13 +28,13 @@ We'd also like to hear about your propositions and suggestions.  Feel free to
 Report bugs
 -----------
 
-Report bugs for intake-cesm in the `issue tracker <https://github.com/NCAR/intake-cesm>`_.
+Report bugs for intake-esm in the `issue tracker <https://github.com/NCAR/intake-esm>`_.
 
 If you are reporting a bug, please include:
 
 * Your operating system name and version.
 * Any details about your local setup that might be helpful in troubleshooting,
-  specifically the Python interpreter version, installed libraries, and intake-cesm
+  specifically the Python interpreter version, installed libraries, and intake-esm
   version.
 * Detailed steps to reproduce the bug.
 
@@ -48,15 +48,15 @@ fix the bug itself.
 Fix bugs
 --------
 
-Look through the `GitHub issues for bugs <https://github.com/NCAR/intake-cesm/labels/type:%20bug>`_.
+Look through the `GitHub issues for bugs <https://github.com/NCAR/intake-esm/labels/type:%20bug>`_.
 
 Talk to developers to find out how you can fix specific bugs.
 
 
 Write documentation
 -------------------
 
-intake-cesm could always use more documentation.  What exactly is needed?
+intake-esm could always use more documentation.  What exactly is needed?
 
 * More complementary documentation.  Have you perhaps found something unclear?
 * Docstrings.  There can never be too many of them.
@@ -69,11 +69,14 @@ without using a local copy.  This can be convenient for small fixes.
     Build the documentation locally with the following command:
 
     .. code:: bash
-
-        $ tox -e docs
+        
+        $ conda env update -f ci/environment-dev-3.7.yml
+        $ cd docs
+        $ make html
 
     The built documentation should be available in the ``docs/_build/``.
 
+
 
  .. _`pull requests`:
 .. _pull-requests:
@@ -83,22 +86,21 @@ Preparing Pull Requests
 
 
 #. Fork the
-   `intake-cesm GitHub repository <https://github.com/NCAR/intake-cesm>`__.  It's
-   fine to use ``intake-cesm`` as your fork repository name because it will live
+   `intake-esm GitHub repository <https://github.com/NCAR/intake-esm>`__.  It's
+   fine to use ``intake-esm`` as your fork repository name because it will live
    under your user.
 
 #. Clone your fork locally using `git <https://git-scm.com/>`_ and create a branch::
 
-    $ git clone [email protected]:YOUR_GITHUB_USERNAME/intake-cesm.git
-    $ cd intake-cesm
+    $ git clone [email protected]:YOUR_GITHUB_USERNAME/intake-esm.git
+    $ cd intake-esm
+
     # now, to fix a bug or add feature create your own branch off "master":
 
-        $ git checkout -b your-bugfix-feature-branch-name master
+    $ git checkout -b your-bugfix-feature-branch-name master
 
-   If you need some help with Git, follow this quick start
-   guide: https://git.wiki.kernel.org/index.php/QuickStart
 
-#. Install `pre-commit <https://pre-commit.com>`_ and its hook on the intake-cesm repo::
+#. Install `pre-commit <https://pre-commit.com>`_ and its hook on the intake-esm repo::
 
      $ pip install --user pre-commit
      $ pre-commit install
@@ -107,24 +109,20 @@ Preparing Pull Requests
 
    https://pre-commit.com/ is a framework for managing and maintaining multi-language pre-commit hooks
    to ensure code-style and code formatting is consistent.
+#. Install dependencies into a new conda environment::
 
-#. Install tox
-
-   Tox is used to run all the tests and will automatically setup virtualenvs
-   to run the tests in.
-   (will implicitly use http://www.virtualenv.org/en/latest/)::
-
-    $ pip install tox
+    $ conda env update -f ci/environment-dev-3.7.yml
 
+   
 #. Run all the tests
 
-   You need to have Python 3.6 and 3.7 available in your system.  Now
-   running tests is as simple as issuing this command::
+   Now running tests is as simple as issuing this command::
+
+    $ conda activate intake-esm-dev
+    $ pytest --junitxml=test-reports/junit.xml --cov=./ --verbose
 
-    $ tox -e linting,py36,py37
 
-   This command will run tests via the "tox" tool against Python 3.6 and 3.7
-   and also perform "lint" coding-style checks.
+   This command will run tests via the "pytest" tool against Python 3.7.
 
 #. You can now edit your local working copy and run the tests again as necessary. Please follow PEP-8 for naming.
 
@@ -135,16 +133,12 @@ Preparing Pull Requests
     $ git commit -a -m "<commit message>"
     $ git push -u
 
-#. Create a new changelog entry in ``changelog``. The file should be named ``<issueid>.<type>``,
-   where *issueid* is the number of the issue related to the change and *type* is one of
-   ``bugfix``, ``removal``, ``feature``, ``vendor``, ``doc`` or ``trivial``.
-
-#. Add yourself to ``AUTHORS`` file if not there yet, in alphabetical order.
 
 #. Finally, submit a pull request through the GitHub website using this data::
 
-    head-fork: YOUR_GITHUB_USERNAME/intake-cesm
+    head-fork: YOUR_GITHUB_USERNAME/intake-esm
     compare: your-branch-name
 
-    base-fork: NCAR/intake-cesm
-    base: master          # if it's a bugfix or feature
+    base-fork: NCAR/intake-esm
+    base: master         
+

MANIFEST.in

@@ -5,8 +5,8 @@ include README.rst
 include requirements.txt
 
 recursive-include example_input
-recursive-include intake_cesm *.py
+recursive-include intake_esm *.py
 recursive-exclude * __pycache__
 recursive-exclude * *.py[co]
 include versioneer.py
-include intake_cesm/_version.py
+include intake_esm/_version.py

Makefile

@@ -24,7 +24,7 @@ clean-pyc:
 	find . -name '*~' -exec rm -f {} +
 
 lint:
-	flake8 intake_cesm test
+	flake8 intake_esm test
 
 test:
 	py.test
@@ -33,15 +33,15 @@ test-all:
 	tox
 
 coverage:
-	coverage run --source intake_cesm setup.py test
+	coverage run --source intake_esm setup.py test
 	coverage report -m
 	coverage html
 	open htmlcov/index.html
 
 docs:
-	rm -f docs/intake_cesm.rst
+	rm -f docs/intake_esm.rst
 	rm -f docs/modules.rst
-	sphinx-apidoc -o docs/ intake_cesm
+	sphinx-apidoc -o docs/ intake_esm
 	$(MAKE) -C docs clean
 	$(MAKE) -C docs html
 	open docs/_build/html/index.html

README.rst

@@ -1,123 +1,28 @@
 ===============================
-Intake-cesm
+Intake-esm
 ===============================
 
-.. image:: https://img.shields.io/circleci/project/github/NCAR/intake-cesm/master.svg?style=for-the-badge&logo=circleci
-    :target: https://circleci.com/gh/NCAR/intake-cesm/tree/master
+.. image:: https://img.shields.io/circleci/project/github/NCAR/intake-esm/master.svg?style=for-the-badge&logo=circleci
+    :target: https://circleci.com/gh/NCAR/intake-esm/tree/master
 
-.. image:: https://img.shields.io/codecov/c/github/NCAR/intake-cesm.svg?style=for-the-badge
-    :target: https://codecov.io/gh/NCAR/intake-cesm
+.. image:: https://img.shields.io/codecov/c/github/NCAR/intake-esm.svg?style=for-the-badge
+    :target: https://codecov.io/gh/NCAR/intake-esm
 
 
-.. image:: https://img.shields.io/readthedocs/intake-cesm/latest.svg?style=for-the-badge
-    :target: https://intake-cesm.readthedocs.io/en/latest/?badge=latest
+.. image:: https://img.shields.io/readthedocs/intake-esm/latest.svg?style=for-the-badge
+    :target: https://intake-esm.readthedocs.io/en/latest/?badge=latest
     :alt: Documentation Status
 
-.. image:: https://img.shields.io/pypi/v/intake-cesm.svg?style=for-the-badge
-    :target: https://pypi.org/project/intake-cesm
+.. image:: https://img.shields.io/pypi/v/intake-esm.svg?style=for-the-badge
+    :target: https://pypi.org/project/intake-esm
     :alt: Python Package Index
 
-.. image:: https://img.shields.io/conda/vn/conda-forge/intake-cesm.svg?style=for-the-badge
-    :target: https://anaconda.org/conda-forge/intake-cesm
+.. image:: https://img.shields.io/conda/vn/conda-forge/intake-esm.svg?style=for-the-badge
+    :target: https://anaconda.org/conda-forge/intake-esm
     :alt: Conda Version
 
 
-Intake-cesm provides a plug for reading CESM Large Ensemble data sets using intake.
+Intake-esm provides a plug for reading esm Large Ensemble data sets using intake.
 See documentation_ for more information.
 
-.. _documentation: https://intake-cesm.readthedocs.io/en/latest/
-
-
-An example of using intake-cesm:
-
-.. code-block:: python
-
-    >>> import intake
-    >>> 'cesm_metadatastore' in intake.registry
-    True
-    >>> from intake_cesm.config import set_options
-    >>> set_options(database_directory="./tests/test_collections")
-    <intake_cesm.config.set_options object at 0x10349efd0>
-
-    >>> build_args = {"collection_input_file" : "./tests/collection_input_test.yml", "collection_type_def_file" : "intake_cesm/cesm_definitions.yml", 
-    ... "overwrite_existing" : True}
-    >>> col = intake.open_cesm_metadatastore(collection="cesm_dple_test_collection", build_args=build_args)
-    INFO:root:Active collection : cesm_dple_test_collection
-    INFO:root:Active database: /Users/abanihi/devel/ncar/intake-cesm/tests/test_collections/cesm_dple_test_collection.csv
-    INFO:root:calling build
-    INFO:root:working on experiment: g.e11_LENS.GECOIAF.T62_g16.009
-    INFO:root:getting file listing: TEST-LIST:input-file:tests/intake-cesm-test-filelist
-    INFO:root:building file database: TEST-LIST:input-file:tests/intake-cesm-test-filelist
-    100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████| 3/3 [00:00<00:00, 12052.60it/s]
-    1it [00:00, 112.32it/s]
-    INFO:root:working on experiment: g.e11_LENS.GECOIAF.T62_g16.009-copy
-    INFO:root:getting file listing: SAMPLE-DATA:posix:tests/sample_data
-    INFO:root:building file database: SAMPLE-DATA:posix:tests/sample_data
-    100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████| 3/3 [00:00<00:00, 23215.70it/s]
-    1it [00:00, 71.65it/s]
-    Active collection: cesm_dple_test_collection
-    >>> col.df
-                                                resource resource_type direct_access  ... sequence_order has_ocean_bgc       grid
-    0                SAMPLE-DATA:posix:tests/sample_data         posix          True  ...              0           NaN  POP_gx1v6
-    1                SAMPLE-DATA:posix:tests/sample_data         posix          True  ...              0           NaN  POP_gx1v6
-    2                SAMPLE-DATA:posix:tests/sample_data         posix          True  ...              0           NaN  POP_gx1v6
-    3  TEST-LIST:input-file:tests/intake-cesm-test-fi...    input-file         False  ...              0           NaN  POP_gx1v6
-    4  TEST-LIST:input-file:tests/intake-cesm-test-fi...    input-file         False  ...              0           NaN  POP_gx1v6
-    5  TEST-LIST:input-file:tests/intake-cesm-test-fi...    input-file         False  ...              0           NaN  POP_gx1v6
-
-    [6 rows x 18 columns]
-    >>> cat = col.search(variable='O2', direct_access=True)
-    >>> print(cat.yaml(True))
-    plugins:
-    source:
-    - module: intake_cesm.core
-    sources:
-    cesm_dple_test_collection-26a47333-f124-4b88-a235-020a731c2509:
-        args:
-        chunks:
-            time: 1
-        collection: cesm_dple_test_collection
-        concat_dim: time
-        decode_coords: false
-        decode_times: false
-        engine: netcdf4
-        query:
-            case: null
-            component: null
-            ctrl_branch_year: null
-            date_range: null
-            direct_access: true
-            ensemble: null
-            experiment: null
-            files: null
-            files_basename: null
-            files_dirname: null
-            grid: null
-            has_ocean_bgc: null
-            resource: null
-            resource_type: null
-            sequence_order: null
-            stream: null
-            variable: O2
-            year_offset: null
-        description: Catalog from cesm_dple_test_collection collection
-        driver: cesm
-        metadata:
-        cache: {}
-        catalog_dir: ''
-
-    >>> ds = cat.to_xarray()
-    >>> ds
-    <xarray.Dataset>
-    Dimensions:  (ens: 1, nlat: 5, nlon: 5, sigma: 5, time: 12)
-    Coordinates:
-    * sigma    (sigma) float64 23.4 23.45 23.5 23.55 23.6
-    * time     (time) float64 9.092e+04 9.094e+04 ... 9.122e+04 9.125e+04
-    Dimensions without coordinates: ens, nlat, nlon
-    Data variables:
-        TLAT     (nlat, nlon) float64 dask.array<shape=(5, 5), chunksize=(5, 5)>
-        ULONG    (nlat, nlon) float64 dask.array<shape=(5, 5), chunksize=(5, 5)>
-        ULAT     (nlat, nlon) float64 dask.array<shape=(5, 5), chunksize=(5, 5)>
-        TLONG    (nlat, nlon) float64 dask.array<shape=(5, 5), chunksize=(5, 5)>
-        O2       (ens, time, sigma, nlat, nlon) float32 dask.array<shape=(1, 12, 5, 5, 5), chunksize=(1, 1, 5, 5, 5)>
-    >>> 
+.. _documentation: https://intake-esm.readthedocs.io/en/latest/

ci/environment-dev-3.6.yml

@@ -1,4 +1,4 @@
-name: intake-cesm-dev
+name: intake-esm-dev
 channels:
   - conda-forge
 dependencies:

ci/environment-dev-3.7.yml

@@ -1,4 +1,4 @@
-name: intake-cesm-dev
+name: intake-esm-dev
 channels:
   - conda-forge
 dependencies:
@@ -31,5 +31,6 @@ dependencies:
   - tqdm
   - xarray
   - pip=18.1
+  - make
   - pip:
     - sphinx_copybutton