Merge pull request #147 from tsjackson-noaa/develop

v3.0 beta 3 release: merge feature/v3alpha3 into NOAA-GFDL:main.

.gitignore

@@ -38,11 +38,13 @@ wheels/
 *.tmp
 MANIFEST
 
-# Sphinx intermediate files
+# Sphinx intermediate files - all autogenerated
 doc/_build
 doc/sphinx/pod_toc.rst
 doc/sphinx/src.*
 doc/sphinx_pods
+doc/sphinx/site_toc.rst
+doc/sphinx_sites
 
 # Byte-compiled / optimized / DLL files
 __pycache__/

.travis.yml

@@ -4,22 +4,23 @@
 
 # Config validator: https://config.travis-ci.com/explore 
 
-os: linux
-dist: xenial # default
-language: shell # synonym for "minimal". Use instead of "python" to save disk space; all software installed through conda
-# sudo: false # deprecated in Travis
-python: '3.7' # doesn't matter, conda python used instead of system
-
-branches:
-  only:
-    - main
-    - develop
-    - /^feature/ 
+jobs:
+  include:
+    - os: linux
+      dist: xenial # default
+      language: shell # synonym for "minimal". Use instead of "python" to save disk space; all software installed through conda
+      python: '3.7' # doesn't matter, conda python used instead of system
+      env:
+        - MINICONDA_INSTALLER="https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh"
+    - os: osx
+      osx_image: xcode12.2
+      env:
+        - MINICONDA_INSTALLER="https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh"
 
 before_install: 
   # TRAVIS_BUILD_DIR = abs path to checked-out repo
   - BUILD_PARENT="$( cd "$( dirname "$TRAVIS_BUILD_DIR" )" >/dev/null 2>&1 && pwd )"
-  - POD_OUTPUT="${BUILD_PARENT}/wkdir/MDTF_NCAR-CAM5.timeslice_2000_2004"
+  - POD_OUTPUT="${BUILD_PARENT}/wkdir/MDTF_NCAR-CAM5.timeslice_2000_2003"
   - echo "$TRAVIS_BUILD_DIR" # debug
   - echo "$BUILD_PARENT"
   - echo "$POD_OUTPUT"
@@ -29,13 +30,7 @@ install:
 # miniconda setup taken from official guide at 
 # https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/use-conda-with-travis-ci.html
   # - sudo apt update
-  # We do this conditionally because it saves us some downloading if the
-  # version is the same.
-  - if [[ "$TRAVIS_PYTHON_VERSION" == "2.7" ]]; then
-      wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh -O miniconda.sh;
-    else
-      wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
-    fi
+  - wget $MINICONDA_INSTALLER -O miniconda.sh;
   - bash miniconda.sh -b -p $HOME/miniconda
   - source "$HOME/miniconda/etc/profile.d/conda.sh"
   - hash -r
@@ -54,22 +49,27 @@ install:
   - curl --verbose --ipv4 --connect-timeout 8 --max-time 1200 --retry 128 --ftp-ssl --disable-epsv --ftp-pasv -u "anonymous:anonymous" ftp://ftp.gfdl.noaa.gov/pub/thomas.jackson/travis_test.tar --output travis_test.tar
   - tar -xvf travis_test.tar
   - mkdir wkdir
+  - pwd # debug
   - ls # debug
+  - ls -R travis_test
 
   - df -h # Log space remaining
 
 before_script:
   - cd "$TRAVIS_BUILD_DIR"
   - pwd # debug
   - ls #debug
-  - cat ./mdtf
 
 script:
   # trivial check that install script worked
   - ./mdtf --version
 
+  # run unit tests
+  - conda activate _MDTF_base
+  - python -m unittest discover
+
   # try running EOF_500hPa and example PODs
-  - ./mdtf -f "${TRAVIS_BUILD_DIR}/tests/travis_test.jsonc"
+  - ./mdtf -v -f "${TRAVIS_BUILD_DIR}/tests/travis_test.jsonc"
   # EOF_500hPa 
   - ls "${POD_OUTPUT}/EOF_500hPa/obs"
   - ls "${POD_OUTPUT}/EOF_500hPa/model"
@@ -78,7 +78,3 @@ script:
   - ls "${POD_OUTPUT}/example/obs"
   - ls "${POD_OUTPUT}/example/model"
   - cat "${POD_OUTPUT}/example/example.log"
-
-  # run unit tests
-  - conda activate _MDTF_base
-  - python -m unittest discover

LICENSE.txt

@@ -10,8 +10,6 @@ This file is part of the MDTF code package, version 2.0, which includes the foll
 
 The MDTF code package and individual PODs are made available under the version 3 of the GNU Lesser General Public License, which is provided below. 
 
-The 'six' compatbility library (src/six.py) is copyright (c) 2010-2020 Benjamin Peterson and provided in accordance with the terms of its MIT license. See the header of src/six.py for license information.
-
 The intent of this license is to ensure free and unrestricted access to the MDTF code package and individual PODs, and to pass on those rights to modified versions this code package.
 
 GNU LESSER GENERAL PUBLIC LICENSE

SECURITY.md

@@ -16,6 +16,7 @@ and climate model analysis code from the community, we adopt the following secur
 
 | Version    | Supported          |
 | ---------- | ------------------ |
+| 3.0 beta 3 | :white_check_mark: |
 | 3.0 beta 2 | :white_check_mark: |
 | 3.0 beta 1 | :x:                |
 | 2.0        | :x:                |

data/cmip6-cmor-tables/.circleci/config.yml

@@ -0,0 +1,93 @@
+version: 2
+
+checkout:
+  post:
+    - ./ci-support/checkout_merge_commit.sh
+
+aliases:
+
+  - &setup_miniconda
+    name: setup_miniconda
+    command: |
+      mkdir -p $WORKDIR
+      if [[ $OS == 'osx-64' ]]; then
+        curl -L https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -o miniconda.sh
+      else
+        curl -L https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -o miniconda.sh
+      fi
+      bash miniconda.sh -b -p $WORKDIR/miniconda
+      
+  - &create_conda_env
+    name: create_conda_env
+    command: |
+       export PATH=$WORKDIR/miniconda/bin:$PATH
+       conda config --set always_yes yes --set changeps1 no
+       conda update -y -q conda
+       conda config --set anaconda_upload no
+       conda create -q -n py3 -c cdat/label/nightly -c pcmdi/label/nightly -c conda-forge -c cdat lazy-object-proxy cmor=3.6.0 python=3.8 testsrunner
+
+  - &setup_cmor
+    name: setup_cmor
+    command: |
+       export PATH=$WORKDIR/miniconda/bin:$PATH
+       set +e
+       source activate py3
+       echo "ACTIVATE RETURN CODE $?"
+       set -e
+       git clone https://github.com/PCMDI/cmor
+       cd cmor
+       # update cmip6-cmor-tables submodule with the current branch
+       git submodule init
+       git submodule update
+       cd cmip6-cmor-tables
+       git checkout $CIRCLE_BRANCH
+       exit 0
+
+  - &run_prepare_tests
+    name: run_prepare_tests
+    command: |
+       export PATH=$WORKDIR/miniconda/bin:$PATH
+       export UVCDAT_ANONYMOUS_LOG=False
+       set +e
+       source activate py3
+       set -e
+       cp Tables/* cmor/Tables
+       cd cmor
+       export PYTHONPATH=Test
+       python run_tests.py -v2 -H -n1 Test/test_python_CMIP6_CV*.py
+
+jobs:
+  macos_cmip6:
+    macos:
+      xcode: "11.1.0"
+    environment:
+      WORKDIR: "workspace/test_macos_cmor"
+      UVCDAT_ANONYMOUS_LOG: "False"
+      OS: "osx-64"
+    steps:
+      - checkout
+      - run: *setup_miniconda
+      - run: *create_conda_env
+      - run: *setup_cmor
+      - run: *run_prepare_tests
+
+  linux_cmip6:
+    machine:
+      image: circleci/classic:latest
+    environment:
+      WORKDIR: "workspace/test_linux_cmor"
+      UVCDAT_ANONYMOUS_LOG: "False"
+      OS: "linux-64"
+    steps:
+      - checkout
+      - run: *setup_miniconda
+      - run: *create_conda_env
+      - run: *setup_cmor
+      - run: *run_prepare_tests
+
+workflows:
+  version: 2
+  nightly:
+    jobs:
+      - macos_cmip6
+      - linux_cmip6

data/cmip6-cmor-tables/README.md

@@ -0,0 +1,9 @@
+# cmip6-cmor-tables
+
+Note:
+----
+Only `CMOR` and `PrePARE` should use the `JSON` file of concatenated `CMIP6` Control Vocabulary [CMIP6_CV.json](https://github.com/PCMDI/cmip6-cmor-tables/blob/master/Tables/CMIP6_CV.json) found in this repository.  
+
+All other software should get the CV's directly from the [WCRP](https://github.com/WCRP-CMIP/CMIP6_CVs) repository. 
+
+CMIP6 Data Request can be found in the following [mip tables](http://clipc-services.ceda.ac.uk/dreq/index/miptable.html).