Updates for SMRF

.gitignore

@@ -1,4 +1,6 @@
 # Eclipse files
+.venv
+.vscode
 .project
 .settings
 .pydevproject
@@ -10,6 +12,8 @@ test_data/stoporad.ip
 *.prof
 *.ipw
 
+output/*.png
+
 test_data/wrfout_d02_2016-03-10.nc
 test_data/stoporad*
 examples/*.nc

.travis.yml

@@ -1,15 +1,79 @@
-# Config file for automatic testing at travis-ci.org
-
-sudo: required
-
-language: python
+# test stage will test all branches against:
+#   - linux python 3.5, 3.6, 3.7, 3.8
+#   - osx python 3.7
+#
+# deploy stage builds and test the wheels when jobs is
+#   - pull request
+#   - master branch
+#   - tagged commit, only this will be uploaded to pypi
 
 services:
   - docker
 
-before_install:
-  - docker pull usdaarsnwrc/smrf:latest
-  - docker build --build-arg REQUIREMENTS=_dev -t usdaarsnwrc/awsm .
+stages:
+  - test
+  - name: deploy
+    if:  type = pull_request OR branch = master OR tag IS present AND repo = USDA-ARS-NWRC/awsm
+
+env:
+  global:
+    - TWINE_USERNAME=__token__
+    # Note: TWINE_PASSWORD is set to a PyPI API token in Travis settings
+
+# defining the unittest jobs
+unittest: &unittest
+  stage: test
+  os: linux
+  dist: bionic
+  language: python
+  cache: pip
+  addons:
+    apt:
+      packages:
+        - libeccodes-tools
+    homebrew:
+      packages:
+        - eccodes
+        - gcc@7
+  install: 
+    - python3 --version
+    - python3 -m pip install tox-travis cython
+  script: tox
+
+jobs:
+  include:
+    # test stage
+    - <<: *unittest
+      python: 3.6
+      env: TOXENV=py36
+
+    - <<: *unittest
+      python: 3.6
+      env: TOXENV=coverage
+
+    - <<: *unittest
+      python: 3.6
+      env: TOXENV=flake8
+
+    - <<: *unittest
+      python: 3.7
+      env: TOXENV=py37
+
+    - <<: *unittest
+      python: 3.8
+      env: TOXENV=py38
+
+    - <<: *unittest
+      os: osx
+      osx_image: xcode11.2  # Python 3.7.X running on macOS 10.14
+      language: shell
+      env:
+        - TOXENV=py37
+        - CC=gcc-7
+        - NOT_ON_GOLD_HOST=yup
 
-script:
-  docker run -it usdaarsnwrc/awsm test
+  allow_failures:
+    - python: 3.6
+      env: TOXENV=coverage
+    - python: 3.6
+      env: TOXENV=flake8

Dockerfile

@@ -1,51 +1,45 @@
-# AWSM is built on SMRF
-FROM usdaarsnwrc/smrf:latest
-
-MAINTAINER Scott Havens <[email protected]>
-
-ARG REQUIREMENTS=''
-
-####################################################
-# Software version
-####################################################
-ENV VPYSNOBAL "0.2.0"
-
-####################################################
-# Install dependencies
-####################################################
-
-RUN apt-get update \
-    && apt-get install -y --no-install-recommends curl \
-    && apt-get install -y gcc \
-    && cd /code \
-    && git clone --depth 1 https://github.com/USDA-ARS-NWRC/pysnobal.git \
+# Multi-stage AWSM docker build
+FROM python:3.6-slim-buster as builder
+
+RUN mkdir /install \
+    && mkdir /build \
+    && apt-get update -y \
+    && apt-get install -y --no-install-recommends \
+    gcc \
+    git \
+    libssl-dev \
+    libyaml-dev \
+    libhdf5-serial-dev \
+    curl \
+    libeccodes-tools \
     && rm -rf /var/lib/apt/lists/* \
-    && apt remove -y curl \
-    && apt autoremove -y
+    && apt-get autoremove -y curl
 
-####################################################
-# AWSM
-####################################################
+COPY . /build
+WORKDIR /build
 
-COPY . / /code/awsm/
+RUN python3 -m pip install --no-cache-dir --upgrade pip \
+    && python3 -m pip install --no-cache-dir setuptools wheel \
+    && python3 -m pip install --no-cache-dir --user 'numpy<1.19.0' cython \
+    && python3 -m pip install --no-cache-dir --user -r requirements.txt \
+    && python3 setup.py install --user
 
-#ENV PYTHONPATH=/code/awsm/
+##############################################
+# main image
+##############################################
+FROM python:3.6-slim-buster
 
-RUN cd /code/pysnobal \
-    && python3 -m pip install --upgrade pip \
-    && python3 setup.py install
+COPY --from=builder /root/.local /usr/local
 
-RUN cd /code/awsm \
-    && python3 -m pip install --no-cache-dir -r /code/awsm/requirements${REQUIREMENTS}.txt \
-    && python3 setup.py install \
-    && rm -r /root/.cache/pip
+RUN apt-get update -y \
+    && apt-get install -y --no-install-recommends libeccodes-tools \
+    # && python3 -m pip install --no-cache-dir nose \
+    # && nosetests -vv --exe awsm \
+    # && python3 -m pip uninstall -y nose \
+    && rm -rf /var/lib/apt/lists/*
 
+# Create a shared data volume
+VOLUME /data
 WORKDIR /data
 
-COPY ./docker-entrypoint.sh /
-RUN chmod +x /docker-entrypoint.sh
-RUN echo "umask 0002" >> /etc/bash.bashrc
-ENTRYPOINT ["/docker-entrypoint.sh"]
-#CMD ["python3", "/code/awsm/scripts/awsm"]
-
-#ENTRYPOINT ["python3", "/code/awsm/scripts/awsm"]
+CMD ["/bin/bash"]

Makefile

@@ -21,10 +21,10 @@ for line in sys.stdin:
 		print("%-20s %s" % (target, help))
 endef
 export PRINT_HELP_PYSCRIPT
-BROWSER := python -c "$$BROWSER_PYSCRIPT"
+BROWSER := python3 -c "$$BROWSER_PYSCRIPT"
 
 help:
-	@python -c "$$PRINT_HELP_PYSCRIPT" < $(MAKEFILE_LIST)
+	@python3 -c "$$PRINT_HELP_PYSCRIPT" < $(MAKEFILE_LIST)
 
 clean: clean-build clean-pyc clean-test ## remove all build, test, coverage and Python artifacts
 
@@ -47,19 +47,26 @@ clean-test: ## remove test and coverage artifacts
 	rm -f .coverage
 	rm -fr htmlcov/
 
+isort: ## using isort to sort imports
+	isort -rc -v .
+
 lint: ## check style with flake8
 	flake8 awsm tests
 
-test: ## run tests quickly with the default Python
-
-		python setup.py test
+test: ## run tests quickly with the default python3
+	python3 -m unittest -v
 
 test-all: ## run tests on every Python version with tox
 	tox
 
-coverage: ## check code coverage quickly with the default Python
+coverage: ## run coverage and submit
 	coverage run --source awsm setup.py test
-	coverage report -m
+	coverage report --fail-under=40
+
+coveralls: coverage ## run coveralls
+	coveralls
+
+coverage-html: coverage ## check code coverage quickly with the default Python
 	coverage html
 	$(BROWSER) htmlcov/index.html
 
@@ -75,13 +82,13 @@ servedocs: docs ## compile the docs watching for changes
 	watchmedo shell-command -p '*.rst' -c '$(MAKE) -C docs html' -R -D .
 
 release: clean ## package and upload a release
-	python setup.py sdist upload
-	python setup.py bdist_wheel upload
+	python3 setup.py sdist upload
+	python3 setup.py bdist_wheel upload
 
 dist: clean ## builds source and wheel package
-	python setup.py sdist
-	python setup.py bdist_wheel
+	python3 setup.py sdist
+	python3 setup.py bdist_wheel
 	ls -l dist
 
 install: clean ## install the package to the active Python's site-packages
-	python setup.py install
+	python3 setup.py install

awsm/__init__.py

@@ -1,33 +1,32 @@
-# -*- coding: utf-8 -*-
 
-"""Top-level package for awsm."""
-
-__author__ = """Micah Sandusky"""
-__email__ = '[email protected]'
 __version__ = '0.10.0'
-import matplotlib
-matplotlib.use('Agg')
+
+from . import framework
+from . import interface
+from . import convertFiles
+from . import utils
 import os
 
-__core_config__ = os.path.abspath(os.path.dirname(__file__) + '/framework/CoreConfig.ini')
-__recipes__ = os.path.abspath(os.path.dirname(__file__) + '/framework/recipes.ini')
+__core_config__ = os.path.abspath(
+    os.path.dirname(__file__) + '/framework/CoreConfig.ini')
+__recipes__ = os.path.abspath(os.path.dirname(
+    __file__) + '/framework/recipes.ini')
 
-__config_titles__ = {'awsm master': 'Configurations for AWSM Master section',
-                      'paths': 'Configurations for PATHS section'
-                               ' for rigid directory work',
-                      'grid': 'Configurations for GRID data to run iSnobal',
-                      'files': 'Input files to run AWSM',
-                      'awsm system': 'System parameters',
-                      'isnobal restart': 'Parameters for restarting'
-                                         ' from crash',
-                      'ipysnobal': 'Running Python wrapped iSnobal',
-                      'ipysnobal initial conditions': 'Initial condition'
-                                                      ' parameters for'
-                                                      ' PySnobal',
-                      'ipysnobal constants': 'Input constants for PySnobal'
-                      }
+__config_titles__ = {
+    'awsm master': 'Configurations for AWSM Master section',
+    'paths': 'Configurations for PATHS section'
+    ' for rigid directory work',
+    'grid': 'Configurations for GRID data to run iSnobal',
+    'files': 'Input files to run AWSM',
+    'awsm system': 'System parameters',
+    'isnobal restart': 'Parameters for restarting'
+    ' from crash',
+    'ipysnobal': 'Running Python wrapped iSnobal',
+    'ipysnobal initial conditions': 'Initial condition'
+    ' parameters for'
+    ' PySnobal',
+    'ipysnobal constants': 'Input constants for PySnobal'
+}
 
-from . import utils
 
 __config_header__ = utils.utilities.get_config_header()
-