Merge pull request #26 from cp4cds/update-template-20190911

updated from template

.gitignore

@@ -4,7 +4,7 @@
 # Docker
 #Dockerfile
 
-# PyWPS
+# PyWPS 
 custom.cfg
 .custom.cfg
 *.pid

.travis.yml

@@ -1,7 +1,11 @@
+dist: xenial   # required for Python >= 3.7
 language: python
 python:
-  - "2.7"
   - "3.6"
+  - "3.7"
+branches:
+  only:
+    - master
 os:
   - linux
 #  - osx
@@ -23,7 +27,7 @@ install:
   - source activate c4cds
   # Packages for testing
   - conda install pytest flake8
-  # Install Emu WPS
+  # Install WPS
   - python setup.py install
 before_script:
   # Start WPS service on port 5000 on 0.0.0.0

Dockerfile

@@ -25,7 +25,7 @@ RUN ["/bin/bash", "-c", "source activate wps && python setup.py develop"]
 # Start WPS service on port 5000 on 0.0.0.0
 EXPOSE 5000
 ENTRYPOINT ["/bin/bash", "-c"]
-CMD ["source activate wps && exec emu start -b 0.0.0.0 -config /opt/wps/etc/demo.cfg"]
+CMD ["source activate wps && exec c4cds start -b 0.0.0.0 -c /opt/wps/etc/demo.cfg"]
 
 # docker build -t cp4cds/c4cds-wps .
 # docker run -p 5000:5000 cp4cds/c4cds-wps

LICENSE.txt

@@ -1,6 +1,6 @@
 Apache Software License 2.0
 
-Copyright (c) 2018, Carsten Ehbrecht
+Copyright (c) 2019, Carsten Ehbrecht
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.

Makefile

@@ -1,127 +1,129 @@
-# Application
-APP_ROOT := $(CURDIR)
+# Configuration
+APP_ROOT := $(abspath $(lastword $(MAKEFILE_LIST))/..)
 APP_NAME := c4cds
 
-# Anaconda
-CONDA := $(shell command -v conda 2> /dev/null)
-ANACONDA_HOME := $(shell conda info --base 2> /dev/null)
-CONDA_ENV := $(APP_NAME)
-
-TEMP_FILES := *.egg-info *.log *.sqlite
-
 # end of configuration
 
-.DEFAULT_GOAL := all
+.DEFAULT_GOAL := help
 
 .PHONY: all
 all: help
 
 .PHONY: help
 help:
-	@echo "Please use \`make <target>' where <target> is one of"
-	@echo "  help        to print this help message. (Default)"
-	@echo "  install     to install $(APP_NAME) by running 'python setup.py develop'."
-	@echo "  start       to start $(APP_NAME) service as daemon (background process)."
-	@echo "  stop        to stop $(APP_NAME) service."
-	@echo "  status      to show status of $(APP_NAME) service."
-	@echo "  clean       to remove *all* files that are not controlled by 'git'. WARNING: use it *only* if you know what you do!"
+	@echo "Please use 'make <target>' where <target> is one of:"
+	@echo "  help              to print this help message. (Default)"
+	@echo "  install           to install app by running 'pip install -e .'"
+	@echo "  develop           to install with additional development requirements."
+	@echo "  start             to start $(APP_NAME) service as daemon (background process)."
+	@echo "  stop              to stop $(APP_NAME) service."
+	@echo "  restart           to restart $(APP_NAME) service."
+	@echo "  status            to show status of $(APP_NAME) service."
+	@echo "  clean             to remove all files generated by build and tests."
 	@echo "\nTesting targets:"
-	@echo "  test        to run tests (but skip long running tests)."
-	@echo "  testall     to run all tests (including long running tests)."
-	@echo "  pep8        to run pep8 code style checks."
+	@echo "  test              to run tests (but skip long running tests)."
+	@echo "  test-all          to run all tests (including long running tests)."
+	@echo "  lint              to run code style checks with flake8."
 	@echo "\nSphinx targets:"
-	@echo "  docs        to generate HTML documentation with Sphinx."
-
-## Anaconda targets
-
-.PHONY: check_conda
-check_conda:
-ifndef CONDA
-		$(error "Conda is not available. Please install miniconda: https://conda.io/miniconda.html")
-endif
-
-.PHONY: conda_env
-conda_env: check_conda
-	@echo "Updating conda environment $(CONDA_ENV) ..."
-	"$(CONDA)" env update -n $(CONDA_ENV) -f environment.yml
-
-.PHONY: envclean
-envclean: check_conda
-	@echo "Removing conda env $(CONDA_ENV)"
-	@-"$(CONDA)" remove -n $(CONDA_ENV) --yes --all
+	@echo "  docs              to generate HTML documentation with Sphinx."
+	@echo "\nDeployment targets:"
+	@echo "  dist              to build source and wheel package."
 
 ## Build targets
 
-.PHONY: bootstrap
-bootstrap: check_conda conda_env bootstrap_dev
-	@echo "Bootstrap ..."
-
-.PHONY: bootstrap_dev
-bootstrap_dev:
-	@echo "Installing development requirements for tests and docs ..."
-	@-bash -c "$(CONDA) install -y -n $(CONDA_ENV) -c conda-forge pytest flake8 sphinx bumpversion"
-	@-bash -c "source $(ANACONDA_HOME)/bin/activate $(CONDA_ENV) && pip install -r requirements_dev.txt"
-
 .PHONY: install
-install: bootstrap
+install:
 	@echo "Installing application ..."
-	@-bash -c "source $(ANACONDA_HOME)/bin/activate $(CONDA_ENV) && python setup.py develop"
+	@-bash -c 'pip install -e .'
 	@echo "\nStart service with \`make start'"
 
+.PHONY: develop
+develop:
+	@echo "Installing development requirements for tests and docs ..."
+	@-bash -c 'pip install -e ".[dev]"'
+
 .PHONY: start
-start: check_conda
+start:
 	@echo "Starting application ..."
-	@-bash -c "source $(ANACONDA_HOME)/bin/activate $(CONDA_ENV) && $(APP_NAME) start -d"
+	@-bash -c "$(APP_NAME) start -d"
 
 .PHONY: stop
-stop: check_conda
+stop:
 	@echo "Stopping application ..."
-	@-bash -c "source $(ANACONDA_HOME)/bin/activate $(CONDA_ENV) && $(APP_NAME) stop"
+	@-bash -c "$(APP_NAME) stop"
+
+.PHONY: restart
+restart: stop start
+	@echo "Restarting application ..."
 
 .PHONY: status
-status: check_conda
+status:
 	@echo "Show status ..."
-	@-bash -c "source $(ANACONDA_HOME)/bin/activate $(CONDA_ENV) && $(APP_NAME) status"
+	@-bash -c "$(APP_NAME) status"
 
 .PHONY: clean
-clean: srcclean envclean
-	@echo "Cleaning generated files ..."
-	@-for i in $(TEMP_FILES); do \
-  	test -e $$i && rm -v -rf $$i; \
-  done
-
-.PHONY: srcclean
-srcclean:
-	@echo "Removing *.pyc files ..."
-	@-find $(APP_ROOT) -type f -name "*.pyc" -print | xargs rm
-
-.PHONY: distclean
-distclean: clean
-	@echo "Cleaning ..."
+clean: clean-build clean-pyc clean-test ## remove all build, test, coverage and Python artifacts
+
+.PHONY: clean-build
+clean-build:
+	@echo "Remove build artifacts ..."
+	@-rm -fr build/
+	@-rm -fr dist/
+	@-rm -fr .eggs/
+	@-find . -name '*.egg-info' -exec rm -fr {} +
+	@-find . -name '*.egg' -exec rm -f {} +
+	@-find . -name '*.log' -exec rm -fr {} +
+	@-find . -name '*.sqlite' -exec rm -fr {} +
+
+.PHONY: clean-pyc
+clean-pyc:
+	@echo "Remove Python file artifacts ..."
+	@-find . -name '*.pyc' -exec rm -f {} +
+	@-find . -name '*.pyo' -exec rm -f {} +
+	@-find . -name '*~' -exec rm -f {} +
+	@-find . -name '__pycache__' -exec rm -fr {} +
+
+.PHONY: clean-test
+clean-test:
+	@echo "Remove test artifacts ..."
+	@-rm -fr .pytest_cache
+
+.PHONY: clean-dist
+clean-dist: clean
+	@echo "Run 'git clean' ..."
 	@git diff --quiet HEAD || echo "There are uncommited changes! Not doing 'git clean' ..."
-	@-git clean -dfx -e *.bak -e custom.cfg
+	@-git clean -dfx
 
 ## Test targets
 
 .PHONY: test
-test: check_conda
-	@echo "Running tests (skip slow, online and data tests) ..."
-	@-bash -c "source $(ANACONDA_HOME)/bin/activate $(CONDA_ENV);pytest -v -m 'not slow and not online and not data'"
+test:
+	@echo "Running tests (skip slow and online tests) ..."
+	@bash -c 'pytest -v -m "not slow and not online" tests/'
 
-.PHONY: testall
-testall: check_conda
+.PHONY: test-all
+test-all:
 	@echo "Running all tests (including slow and online tests) ..."
-	@-bash -c "source $(ANACONDA_HOME)/bin/activate $(CONDA_ENV) && pytest -v"
+	@bash -c 'pytest -v tests/'
 
-.PHONY: pep8
-pep8: check_conda
-	@echo "Running pep8 code style checks ..."
-	@-bash -c "source $(ANACONDA_HOME)/bin/activate $(CONDA_ENV) && flake8"
+.PHONY: lint
+lint:
+	@echo "Running flake8 code style checks ..."
+	@bash -c 'flake8'
 
-##  Sphinx targets
+## Sphinx targets
 
 .PHONY: docs
-docs: check_conda
+docs:
 	@echo "Generating docs with Sphinx ..."
-	@-bash -c "source $(ANACONDA_HOME)/bin/activate $(CONDA_ENV);$(MAKE) -C $@ clean html"
-	@echo "open your browser: firefox docs/build/html/index.html"
+	@-bash -c '$(MAKE) -C $@ clean html'
+	@echo "open your browser: open file://$(APP_ROOT)/docs/build/html/index.html"
+
+## Deployment targets
+
+.PHONY: dist
+dist: clean
+	@echo "Builds source and wheel package ..."
+	@-python setup.py sdist
+	@-python setup.py bdist_wheel
+	ls -l dist

c4cds/__init__.py

@@ -2,8 +2,6 @@
 
 """Top-level package for c4cds-wps."""
 
-from .wsgi import application
+from .__version__ import __author__, __email__, __version__  # noqa: F401
 
-__author__ = """Carsten Ehbrecht"""
-__email__ = 'ehbrecht@dkrz.de'
-__version__ = '0.2.0'
+from .wsgi import application  # noqa: F401

c4cds/__version__.py

@@ -0,0 +1,9 @@
+# -*- coding: utf-8 -*-
+
+# This information is located in its own file so that it can be loaded
+# without importing the main package when its dependencies are not installed.
+# See: https://packaging.python.org/guides/single-sourcing-package-version
+
+__author__ = """Carsten Ehbrecht"""
+__email__ = 'ehbrecht@dkrz.de'
+__version__ = '0.2.0'

c4cds/cli.py

@@ -12,7 +12,7 @@
 from pywps import configuration
 
 from . import wsgi
-from six.moves.urllib.parse import urlparse
+from urllib.parse import urlparse
 
 PID_FILE = os.path.abspath(os.path.join(os.path.curdir, "pywps.pid"))
 

c4cds/ncdump.py

@@ -1,6 +1,5 @@
-import six
 import os
-from subprocess import check_output, CalledProcessError
+from subprocess import check_output
 
 import logging
 LOGGER = logging.getLogger('PYWPS')
@@ -15,7 +14,7 @@ def ncdump(dataset):
 
     try:
         output = check_output(['ncdump', '-h', dataset])
-        if not isinstance(output, six.string_types):
+        if not isinstance(output, str):
             output = output.decode('utf-8')
         lines = output.split('\n')
         # replace the filename for safety

c4cds/plotter.py

@@ -1,15 +1,16 @@
 import os
 
-import matplotlib
-matplotlib.use('agg')
-import matplotlib.pyplot as plt
 import cartopy.crs as ccrs
 from cartopy import config
 
 from netCDF4 import Dataset
 
 from c4cds.util import guess_variable_name
 
+import matplotlib
+matplotlib.use('agg')
+import matplotlib.pyplot as plt  # noqa: E402
+
 
 class Plotter(object):
     def __init__(self, output_dir=None):

c4cds/regridder.py

@@ -6,15 +6,15 @@
 
 from c4cds import util
 
+import logging
+LOGGER = logging.getLogger('PYWPS')
+
 # domain types
 GLOBAL = 'global'
 REGIONAL = 'regional'
 
 GRID_FILES_DIR = os.path.join(os.path.dirname(__file__), 'resources', 'grid_files')
 
-import logging
-LOGGER = logging.getLogger('PYWPS')
-
 
 class Regridder(object):
     def __init__(self, output_dir=None, archive_base=None):

c4cds/search.py

@@ -1,5 +1,4 @@
 import os
-import tempfile
 import glob
 
 from c4cds import util

c4cds/subsetter.py

@@ -1,5 +1,4 @@
 import os
-import tempfile
 
 from cdo import Cdo
 

docker-compose.yml

@@ -1,6 +1,6 @@
 version: '3'
 services:
-  emu:
+  wps:
     build: .
     image: cp4cds/c4cds-wps
     ports:

docs/source/conf.py

@@ -52,7 +52,7 @@
 
 # General information about the project.
 project = u'c4cds-wps'
-copyright = u"2018, Carsten Ehbrecht"
+copyright = u"2019, Carsten Ehbrecht"
 author = u"Carsten Ehbrecht"
 
 # The version info for the project you're documenting, acts as replacement

docs/source/configuration.rst

@@ -31,7 +31,7 @@ Use one of the existing ``sample-*.cfg`` files as example and copy them to ``etc
 
 For example change the hostname (*demo.org*) and logging level:
 
-.. code-block:: sh
+.. code-block:: console
 
    $ cd c4cds
    $ vim etc/custom.cfg
@@ -51,7 +51,7 @@ For example change the hostname (*demo.org*) and logging level:
 
 Start the service with your custom configuration:
 
-.. code-block:: sh
+.. code-block:: console
 
    # start the service with this configuration
    $ c4cds start -c etc/custom.cfg