Merge pull request #23 from andersy005/esmlab

Code Refactoring for newer version
NCAR · Jan 4, 2019 · 09cef9c · 09cef9c
2 parents b8c2cef + 14a7911
commit 09cef9c
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Showing 14 changed files with 182 additions and 234 deletions.
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -6,27 +6,8 @@ workflows:
     jobs:
       - "python-2.7"
       - "python-3.6"
-      - "deploy-pypi":
-          requires:
-            - "python-2.7"
-            - "python-3.6"
-          filters:
-            tags:
-              only: /^v.*/
-            branches:
-              ignore: /.*/
-
-      - "deploy-conda":
-          requires:
-            - "python-2.7"
-            - "python-3.6"
-          filters:
-            tags:
-              only: /^v.*/
-            branches:
-              ignore: /.*/
+      - "python-3.7"
 
-
 jobs:
   # Python 2.7 build
   "python-2.7":
@@ -82,6 +63,45 @@ jobs:
       - restore_cache:
           key: deps-{{ .Branch }}-3.6-{{ checksum "ci/environment-dev-3.6.yml" }}
 
+      - run: # install and activate conda environment
+          name: configure conda 
+          command: ./ci/install-circle.sh
+      - run:
+          command: |
+            source activate ${ENV_NAME}
+            pytest --junitxml=test-reports/junit.xml --cov=./
+     
+      # Cache some files for a speedup in subsequent builds
+      - save_cache:
+          key: deps-{{ .Branch }}-3.6-{{ checksum "ci/environment-dev-3.6.yml" }}
+          paths:
+            - "/opt/conda/envs/${ENV_NAME}/"
+            - "/opt/conda/pkgs"
+
+      - store_test_results:
+          path: test-reports
+
+      - store_artifacts:
+          path: test-reports
+
+
+  "python-3.7":
+    docker:
+      - image: continuumio/miniconda:latest
+
+    environment:
+      PYTHON: "3.7"
+      ENV_NAME: "esmlab-dev"
+
+    steps:
+
+      # Get our data and merge with upstream
+      - checkout
+
+      # Restore cached files to speed things up
+      - restore_cache:
+          key: deps-{{ .Branch }}-3.7-{{ checksum "ci/environment-dev-3.7.yml" }}
+
       - run: # install and activate conda environment
           name: configure conda 
           command: ./ci/install-circle.sh
@@ -117,7 +137,7 @@ jobs:
      
       # Cache some files for a speedup in subsequent builds
       - save_cache:
-          key: deps-{{ .Branch }}-3.6-{{ checksum "ci/environment-dev-3.6.yml" }}
+          key: deps-{{ .Branch }}-3.7-{{ checksum "ci/environment-dev-3.7.yml" }}
           paths:
             - "/opt/conda/envs/${ENV_NAME}/"
             - "/opt/conda/pkgs"
@@ -130,36 +150,4 @@ jobs:
       # Tell Circle to store the documentation output in a folder that we can access later
       - store_artifacts: 
           path: docs/_build/html
-          destination: html
-
-  "deploy-pypi":
-    # This is the base environment that Circle will use
-    docker:
-      - image: continuumio/miniconda:latest
-
-    steps:
-      # Get our data and merge with upstream
-      - checkout
-
-      - run:
-          name: Building and Deploying PyPI package
-          command: |
-            python setup.py sdist
-            pip wheel . -w dist
-      
-
-  "deploy-conda":
-    docker:
-      - image: continuumio/miniconda:latest
-
-    steps:
-      # Get our data and merge with upstream
-      - checkout
-
-      - run:
-          name: Deploy package release to Anaconda.org
-          command: |
-            conda install conda-build anaconda-client --yes --quiet
-            ./ci/upload-anaconda.sh
-
-            
+          destination: html
diff --git a/MANIFEST.in b/MANIFEST.in
@@ -0,0 +1,10 @@
+recursive-include esmlab *.py
+
+include LICENSE
+include README.rst
+include requirements.txt
+
+recursive-exclude * __pycache__
+recursive-exclude * *.py[co]
+include versioneer.py
+include esmlab/_version.py
diff --git a/README.rst b/README.rst
@@ -1,7 +1,7 @@
 Esmlab (Earth System Model Lab)
 ================================
 
-.. image:: https://img.shields.io/circleci/project/github/NCAR/esmlab/master.svg?style=for-the-badge
+.. image:: https://img.shields.io/circleci/project/github/NCAR/esmlab/master.svg?style=for-the-badge&logo=circleci
     :target: https://circleci.com/gh/NCAR/esmlab/tree/master
 
 .. image:: https://img.shields.io/codecov/c/github/NCAR/esmlab.svg?style=for-the-badge
@@ -12,6 +12,15 @@ Esmlab (Earth System Model Lab)
     :target: https://esmlab.readthedocs.io/en/latest/?badge=latest
     :alt: Documentation Status
 
+.. image:: https://img.shields.io/pypi/v/esmlab.svg?style=for-the-badge
+    :target: https://pypi.org/project/esmlab
+    :alt: Python Package Index
+
+.. image:: https://img.shields.io/conda/vn/conda-forge/esmlab.svg?style=for-the-badge
+    :target: https://anaconda.org/conda-forge/esmlab
+    :alt: Conda Version
+
+
 
 Tools for working with earth system multi-model analyses with xarray. See
 documentation_ for more information.

diff --git a/ci/environment-dev-2.7.yml b/ci/environment-dev-2.7.yml
@@ -10,20 +10,10 @@ dependencies:
   - zarr
   - dask
   - distributed
-  - autopep8
-  - flake8
   - pytest
   - coverage
   - pytest-cov
   - codecov
-  - sphinx>=1.6
-  - sphinx_rtd_theme
-  - recommonmark 
-  - numpydoc
-  - nbsphinx
-  - pandoc
-  - ipykernel
-  - six
-  - pip:
-    - sphinx_copybutton
+
+
 
diff --git a/ci/environment-dev-3.6.yml b/ci/environment-dev-3.6.yml
@@ -10,22 +10,7 @@ dependencies:
   - zarr
   - dask
   - distributed
-  - autopep8
-  - flake8
-  - black
-  - isort
   - pytest
   - coverage
   - pytest-cov
-  - codecov
-  - sphinx>=1.6
-  - sphinx_rtd_theme
-  - recommonmark 
-  - numpydoc
-  - nbsphinx
-  - pandoc
-  - ipykernel
-  - six
-  - pip:
-    - sphinx_copybutton
-
+  - codecov
diff --git a/ci/environment-dev-3.7.yml b/ci/environment-dev-3.7.yml
@@ -0,0 +1,31 @@
+name: esmlab-dev
+channels:
+  - conda-forge
+dependencies:
+  - python=3.7
+  - numpy
+  - xarray
+  - matplotlib
+  - netcdf4
+  - zarr
+  - dask
+  - distributed
+  - autopep8
+  - flake8
+  - black
+  - isort
+  - pytest
+  - coverage
+  - pytest-cov
+  - codecov
+  - sphinx>=1.6
+  - sphinx_rtd_theme
+  - recommonmark 
+  - numpydoc
+  - nbsphinx
+  - pandoc
+  - ipykernel
+  - six
+  - pip:
+    - sphinx_copybutton
+
diff --git a/ci/upload-anaconda.sh b/ci/upload-anaconda.sh
diff --git a/conda/meta.yaml b/conda/meta.yaml
diff --git a/docs/source/api.rst b/docs/source/api.rst
@@ -2,22 +2,41 @@ API reference
 =============
 
 
-Statistics functions
-"""""""""""""""""""""
-
 .. currentmodule:: esmlab
 
+Statistics functions
+~~~~~~~~~~~~~~~~~~~~~~~
+
 .. autosummary::
    statistics.weighted_sum
    statistics.weighted_mean
    statistics.weighted_std
    statistics.weighted_rmsd
    statistics.weighted_cov
    statistics.weighted_corr
+
+Climatogy functions
+~~~~~~~~~~~~~~~~~~~~~~~
+
+.. autosummary::
+   climatology.compute_mon_climatology
+   climatology.compute_mon_anomaly
+   climatology.compute_ann_climatology
+
+
+.. currentmodule:: esmlab.statistics
+
+.. autofunction:: weighted_sum
+.. autofunction:: weighted_mean
+.. autofunction:: weighted_std
+.. autofunction:: weighted_rmsd
+.. autofunction:: weighted_cov
+.. autofunction:: weighted_corr
+
+.. currentmodule:: esmlab.climatology
+
+.. autofunction:: compute_mon_climatology
+.. autofunction:: compute_mon_anomaly
+.. autofunction:: compute_ann_climatology
+
 
-.. autofunction:: esmlab.statistics.weighted_sum
-.. autofunction:: esmlab.statistics.weighted_mean
-.. autofunction:: esmlab.statistics.weighted_std
-.. autofunction:: esmlab.statistics.weighted_rmsd
-.. autofunction:: esmlab.statistics.weighted_cov
-.. autofunction:: esmlab.statistics.weighted_corr
diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -4,7 +4,7 @@
    :maxdepth: 2
    :caption: Contents:
 
-   installation
+   install
    api
    develop
    changelog