Merge branch 'master' into 534_pjg_mfw_extremes

.circleci/config.yml

@@ -0,0 +1,218 @@
+version: 2
+
+checkout:
+ post:
+ - ./ci-support/checkout_merge_commit.sh
+
+aliases:
+
+ - &setup_miniconda
+ name: setup_miniconda
+ command: |
+ mkdir -p workspace
+ git clone -b validateNightly [email protected]:CDAT/cdat workspace/cdat --depth=1
+ python workspace/cdat/scripts/install_miniconda.py -w $WORKDIR -p 'py3.6'
+ 
+ - &create_conda_env
+ name: create_conda_env
+ environment:
+ PKGS: "vcs vcsaddons mesalib matplotlib scipy cia testsrunner 'proj4<5' 'vtk-cdat>8.1' libnetcdf=4.6.2"
+ CHANNELS: "-c cdat/label/nightly -c conda-forge -c pcmdi"
+ command: |
+ if [ -d ${HOME}/miniconda ]; then
+ export PATH=$HOME/miniconda/bin:$PATH
+ echo "Found miniconda directory"
+ else
+ mkdir -p workspace
+ git clone -b validateNightly [email protected]:CDAT/cdat workspace/cdat --depth=1
+ python workspace/cdat/scripts/install_miniconda.py -w ${HOME} -p 'py3.7'
+ echo "miniconda directory not found, installing conda"
+ export PATH=${HOME}/miniconda/bin:$PATH
+ conda config --set always_yes yes --set changeps1 no
+ conda update -y -q conda
+ conda config --set anaconda_upload no
+ if [[ $PY_VER = "py2" ]]; then
+ conda create -q -n cdat $CHANNELS "python<3" $PKGS $FFMPEG
+ else
+ conda create -q -n cdat $CHANNELS "python=3.7" $PKGS $FFMPEG $COVERAGE_PKGS
+ fi
+ fi
+
+ - &setup_pmp
+ name: setup_pmp
+ command: |
+ export PATH=${HOME}/miniconda/bin:$PATH
+ source activate cdat
+ python setup.py install
+
+ - &run_pmp_tests
+ name: run_pmp_tests
+ command: |
+ export PATH=${HOME}/miniconda/bin:$PATH
+ export CDAT_ANONYMOUS_LOG=False
+ export CDAT_SETUP_PATH=${HOME}
+ source activate cdat
+ python run_tests.py -H -v2 $COVERAGE
+ RESULT=$?
+ echo "*** $PY_VER test result: ${RESULT}"
+
+ - &run_coveralls
+ name: run_coveralls
+ command: |
+ export PATH=${HOME}/miniconda/bin:$PATH
+ source activate cdat
+ coveralls
+ source deactivate
+
+ - &conda_upload
+ name: conda_upload
+ environment:
+ CHANNELS: "-c cdat/label/nightly -c conda-forge -c pcmdi"
+ PKG_NAME: "pcmdi_metrics"
+ LABEL: "nightly"
+ command: |
+ if [[ $CIRCLE_BRANCH != 'master' ]]; then
+ exit 0
+ fi
+ export PATH=${HOME}/miniconda/bin:$PATH
+ mkdir conda-bld
+ cd conda-bld
+ conda install conda-build anaconda-client
+ conda config --set anaconda_upload no
+ export CONDA_BLD_PATH=`pwd`/build_conda
+ mkdir build_conda
+ git clone git:https://github.com/cdat/conda-recipes
+ cd conda-recipes
+ rm -rf cdp
+ cp -r ../../recipes/pcmdi_metrics .
+ python ./prep_for_build.py -l 1.2
+ conda build $PKG_NAME $CHANNELS --python=37
+ conda build $PKG_NAME $CHANNELS --python=27
+ anaconda -t $CONDA_UPLOAD_TOKEN upload -u pcmdi -l $LABEL $CONDA_BLD_PATH/noarch/$PKG_NAME-*tar.bz2 --force
+
+
+jobs:
+ macos_pmp_py2:
+ macos:
+ xcode: "9.2.0"
+ environment:
+ WORKDIR: "test_macos_pmp_py2"
+ OS: "osx-64"
+ PY_VER: "py2"
+ FFMPEG: "'ffmpeg>4' 'libpng>1.6.34'"
+ steps:
+ - checkout
+ - restore_cache:
+ keys:
+ - macos_py2_2019-06-01
+ - run: *create_conda_env
+ - save_cache:
+ key: macos_py2_2019-06-01
+ paths: /Users/distiller/miniconda
+ - run: *setup_pmp
+ - run: *run_pmp_tests
+ - store_artifacts:
+ path: tests_html
+ destination: tests_html
+ - store_artifacts:
+ path: tests_png
+ destination: tests_png
+
+ macos_pmp_py3:
+ macos:
+ xcode: "9.2.0"
+ environment:
+ WORKDIR: "test_macos_pmp_py3"
+ OS: "osx-64"
+ PY_VER: "py3"
+ FFMPEG: "'ffmpeg>4' 'libpng>1.6.34'"
+ COVERAGE: "-c tests/coverage.json --coverage-from-egg"
+ COVERAGE_PKGS: "coverage coveralls"
+ steps:
+ - checkout
+ - restore_cache:
+ keys:
+ - macos_py3_2019-06-01
+ - run: *create_conda_env
+ - save_cache:
+ key: macos_py3_2019-06-01
+ paths: /Users/distiller/miniconda
+ - run: *setup_pmp
+ - run: *run_pmp_tests
+ - run: *run_coveralls
+ - store_artifacts:
+ path: tests_html
+ destination: tests_html
+ - store_artifacts:
+ path: tests_png
+ destination: tests_png
+
+ linux_pmp_py2:
+ machine:
+ image: circleci/classic:latest
+ environment:
+ WORKDIR: "test_linux_pmp_py2"
+ OS: "linux-64"
+ PY_VER: "py2"
+ FFMPEG: "ffmpeg"
+ steps:
+ - checkout
+ - restore_cache:
+ keys:
+ - linux_py2_2019-06-01
+ - run: *create_conda_env
+ - save_cache:
+ key: linux_py2_2019-06-01
+ paths: /home/circleci/miniconda
+ - run: *setup_pmp
+ - run: *run_pmp_tests
+ - store_artifacts:
+ path: tests_html
+ destination: tests_html
+ - store_artifacts:
+ path: tests_png
+ destination: tests_png
+
+ linux_pmp_py3:
+ machine:
+ image: circleci/classic:latest
+ environment:
+ WORKDIR: "test_linux_pmp_py3"
+ OS: "linux-64"
+ PY_VER: "py3"
+ FFMPEG: "ffmpeg"
+ COVERAGE: "-c tests/coverage.json --coverage-from-egg"
+ COVERAGE_PKGS: "coverage coveralls"
+ steps:
+ - checkout
+ - restore_cache:
+ keys:
+ - linux_py3_2019-06-01
+ - run: *create_conda_env
+ - save_cache:
+ key: linux_py3_2019-06-01
+ paths: /home/circleci/miniconda
+ - run: *setup_pmp
+ - run: *run_pmp_tests
+ - run: *conda_upload
+ - run: *run_coveralls
+ - store_artifacts:
+ path: tests_html
+ destination: tests_html
+ - store_artifacts:
+ path: tests_png
+ destination: tests_png
+
+
+workflows:
+ version: 2
+ pcmdi_metrics:
+ jobs:
+ - macos_pmp_py2
+ - macos_pmp_py3:
+ requires:
+ - macos_pmp_py2
+ - linux_pmp_py2
+ - linux_pmp_py3:
+ requires:
+ - linux_pmp_py2

README.md

@@ -1,36 +1,41 @@
+<img src="share/pcmdi/PMPLogo_1359x1146px_300dpi.png" width="15%" height="15%" align="right" />
+<h5 align="right"></h5> 
+
 PCMDI metrics package (PMP)
 ======
-[![stable version](https://img.shields.io/badge/stable%20version-1.1.2-brightgreen.svg)](https://github.com/PCMDI/pcmdi_metrics/releases/tag/1.1.2)
-![repo size](https://reposs.herokuapp.com/?path=PCMDI/pcmdi_metrics)
+[![stable version](https://img.shields.io/badge/stable%20version-1.2-brightgreen.svg)](https://github.com/PCMDI/pcmdi_metrics/releases/tag/1.2)
 ![platforms](https://img.shields.io/badge/platforms-linux%20|%20osx-lightgrey.svg)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.809463.svg)](https://doi.org/10.5281/zenodo.809463)
 [![Anaconda-Server Badge](https://anaconda.org/pcmdi/pcmdi_metrics/badges/installer/conda.svg)](https://conda.anaconda.org/pcmdi)
 [![Anaconda-Server Badge](https://anaconda.org/pcmdi/pcmdi_metrics/badges/downloads.svg)](https://anaconda.org/pcmdi/pcmdi_metrics)
-
+[![CircleCI](https://circleci.com/gh/PCMDI/pcmdi_metrics.svg?style=svg)](https://circleci.com/gh/PCMDI/pcmdi_metrics)
+[![Coverage Status](https://coveralls.io/repos/github/PCMDI/pcmdi_metrics/badge.svg)](https://coveralls.io/github/PCMDI/pcmdi_metrics)
 
 The PCMDI metrics package is used to objectively compare results from climate models with observations using well-established statistical tests. Results are produced in the context of all model simulations contributed to CMIP5 and earlier CMIP phases. Among other purposes, this enables modeling groups to evaluate changes during the development cycle in the context of the structural error distribution of the multi-model ensemble. Currently, the comparisons emphasize large- to global-scale annual cycle performance metrics. Current work in v1.x development branches include established statistics for ENSO, regional monsoon precipitation, and the diurnal cycle of precipitation. These diagnostics will be included in a future PMP release.
 
 The metrics package consists of four parts: 1) Analysis software, 2) an observationally-based database of global (or near global, land or ocean) annual cycle climatologies, 3) a database of performance metrics computed for CMIP models and 4) package documentation.
 The package expects model data to be [CF-compliant](http:https://cfconventions.org/). To successfully use the package some input data "conditioning" may be required. We provide several demo scripts within the package to facilitate new users.
 
-**Users of the current release (v1.1.2) will need to contact the PMP developers ([email protected]) to obtain supporting datasets and get started using the package.**
+**Users of the current release (v1.2) will need to contact the PMP developers ([email protected]) to obtain supporting datasets and get started using the package.**
 
 
 GETTING STARTED
 ----------------
 
-Installation requirements and instructions are available on the [Install](https://github.com/PCMDI/pcmdi_metrics/wiki/Install) page
+Installation requirements and instructions are available on the [Install](https://github.com/PCMDI/pcmdi_metrics/wiki/Install-using-Anaconda) page
 
 An overview for using the package and template scripts are detailed on the [Using-the-package](https://github.com/PCMDI/pcmdi_metrics/wiki/Using-the-package) page
 
 Some installation support for CMIP participating modeling groups is available: [email protected]
 
-
 PMP versions
 ------------
 
-v1.0 - Prototype version of the PMP
+v1.2 - Tied to CDAT 8.0. Now includes extensive regression testing. New metrics: Diurnal cycle and intermittency of precipitation, Sperber and Wang Monsoon metrics
+
+v1.1.2 - Now managed through Anaconda, and tied to UV-CDAT 2.10. Weights on bias statistic added. Extensive provenance information incorporated into json files.
 
 v1.1 - First public release, emphasizing climatological statistics, with development branches for ENSO and regional monsoon precipitation indices
 
-v1.1.2 - Now managed through Anaconda, and tied to UV-CDAT 2.10. Weights on bias statistic added. Extensive provenance information incorporated into json files.
+v1.0 - Prototype version of the PMP
+

ci-support/checkout_merge_commit.sh

@@ -0,0 +1,29 @@
+#!/bin/bash
+
+
+# Add `master` branch to the update list.
+# Otherwise CircleCI will give us a cached one.
+FETCH_REFS="+master:master"
+
+# Update PR refs for testing.
+if [[ -n "${CIRCLE_PR_NUMBER}" ]]
+then
+ FETCH_REFS="${FETCH_REFS} +refs/pull/${CIRCLE_PR_NUMBER}/head:pr/${CIRCLE_PR_NUMBER}/head"
+ FETCH_REFS="${FETCH_REFS} +refs/pull/${CIRCLE_PR_NUMBER}/merge:pr/${CIRCLE_PR_NUMBER}/merge"
+fi
+
+# Retrieve the refs.
+git fetch -u origin ${FETCH_REFS}
+
+# Checkout the PR merge ref.
+if [[ -n "${CIRCLE_PR_NUMBER}" ]]
+then
+ git checkout -qf "pr/${CIRCLE_PR_NUMBER}/merge"
+fi
+
+# Check for merge conflicts.
+if [[ -n "${CIRCLE_PR_NUMBER}" ]]
+then
+ git branch --merged | grep master > /dev/null
+ git branch --merged | grep "pr/${CIRCLE_PR_NUMBER}/head" > /dev/null
+fi