Merge pull request #29 from bird-house/update-processes-20190416

updated processes

.travis.yml

@@ -1,10 +1,8 @@
+dist: xenial   # required for Python >= 3.7
 language: python
 python:
-  #- "2.7"
   - "3.6"
-# branches:
-#  only:
-#    - master
+  - "3.7"
 os:
   - linux
 #  - osx

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 hummingbird start -b 0.0.0.0 -c /opt/wps/etc/demo.cfg"]
 
 # docker build -t bird-house/hummingbird .
 # docker run -p 5000:5000 bird-house/hummingbird

Makefile

@@ -23,6 +23,7 @@ help:
 	@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 "  restart     to restart $(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 "\nTesting targets:"
@@ -31,8 +32,10 @@ help:
 	@echo "  pep8        to run pep8 code style checks."
 	@echo "\nSphinx targets:"
 	@echo "  docs        to generate HTML documentation with Sphinx."
+	@echo "\nDeployment targets:"
+	@echo "  spec        to generate Conda spec file."
 
-## Anaconda targets
+## Conda targets
 
 .PHONY: check_conda
 check_conda:
@@ -50,6 +53,11 @@ envclean: check_conda
 	@echo "Removing conda env $(CONDA_ENV)"
 	@-"$(CONDA)" remove -n $(CONDA_ENV) --yes --all
 
+.PHONY: spec
+spec: check_conda
+	@echo "Updating conda environment specification file ..."
+	@-"$(CONDA)" list -n $(CONDA_ENV) --explicit > spec-file.txt
+
 ## Build targets
 
 .PHONY: bootstrap
@@ -59,7 +67,7 @@ bootstrap: check_conda conda_env bootstrap_dev
 .PHONY: bootstrap_dev
 bootstrap_dev:
 	@echo "Installing development requirements for tests and docs ..."
-	@-bash -c "$(CONDA) install -y -n $(CONDA_ENV) -c conda-forge pytest flake8 sphinx bumpversion"
+	@-bash -c "$(CONDA) install -y -n $(CONDA_ENV) pytest flake8 sphinx gunicorn psycopg2"
 	@-bash -c "source $(ANACONDA_HOME)/bin/activate $(CONDA_ENV) && pip install -r requirements_dev.txt"
 
 .PHONY: install
@@ -78,6 +86,10 @@ stop: check_conda
 	@echo "Stopping application ..."
 	@-bash -c "source $(ANACONDA_HOME)/bin/activate $(CONDA_ENV) && $(APP_NAME) stop"
 
+.PHONY: restart
+restart: stop start
+	@echo "Restarting application ..."
+
 .PHONY: status
 status: check_conda
 	@echo "Show status ..."

README.rst

@@ -26,9 +26,9 @@ Hummingbird (the bird)
   *Hummingbirds are among the smallest of birds. They hover in mid-air at rapid wing flapping rates,
   typically around 50 times per second, but possibly as high as 200 times per second,
   allowing them also to fly at speeds exceeding 15 m/s (54 km/h; 34 mph),
-  backwards or upside down. [..].* (`Wikipedia https://en.wikipedia.org/wiki/Hummingbird`_).
+  backwards or upside down. [..].* (Wikipedia_).
 
-A Web Processing Service for general tools used in the climate science community like cdo and cfchecker.
+A Web Processing Service for metadata compliance checks used in the climate science community.
 
 Hummingbird is part of the `Birdhouse <http://bird-house.github.io>`_ project.
 
@@ -42,3 +42,4 @@ This package was created with Cookiecutter_ and the `bird-house/cookiecutter-bir
 
 .. _Cookiecutter: https://github.com/audreyr/cookiecutter
 .. _`bird-house/cookiecutter-birdhouse`: https://github.com/bird-house/cookiecutter-birdhouse
+.. _Wikipedia: https://en.wikipedia.org/wiki/Hummingbird

docker-compose.yml

@@ -1,6 +1,6 @@
 version: '3'
 services:
-  emu:
+  wps:
     build: .
     image: bird-house/hummingbird
     ports:

docs/source/conf.py

@@ -52,7 +52,7 @@
 
 # General information about the project.
 project = u'Hummingbird'
-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/dev_guide.rst

@@ -7,12 +7,14 @@ Developer Guide
     :local:
     :depth: 1
 
+.. WARNING:: To create new processes look at examples in Emu_.
+
 Building the docs
 -----------------
 
 First install dependencies for the documentation:
 
-.. code-block:: sh
+.. code-block:: console
 
   $ make bootstrap_dev
   $ make docs
@@ -26,26 +28,26 @@ Run tests using `pytest`_.
 
 First activate the ``hummingbird`` Conda environment and install ``pytest``.
 
-.. code-block:: sh
+.. code-block:: console
 
    $ source activate hummingbird
    $ conda install pytest flake8  # if not already installed
 
 Run quick tests (skip slow and online):
 
-.. code-block:: sh
+.. code-block:: console
 
     $ pytest -m 'not slow and not online'"
 
 Run all tests:
 
-.. code-block:: sh
+.. code-block:: console
 
     $ pytest
 
 Check pep8:
 
-.. code-block:: sh
+.. code-block:: console
 
     $ flake8
 
@@ -54,12 +56,28 @@ Run tests the lazy way
 
 Do the same as above using the ``Makefile``.
 
-.. code-block:: sh
+.. code-block:: console
 
     $ make test
     $ make testall
     $ make pep8
 
+Prepare a release
+-----------------
+
+Update the Conda specification file to build identical environments_ on a specific OS.
+
+.. note:: You should run this on your target OS, in our case Linux.
+
+.. code-block:: console
+
+  $ make clean
+  $ make install
+  $ make spec
+
+.. _`environments`: https://conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html#building-identical-conda-environments
+
+
 Bump a new version
 ------------------
 
@@ -77,3 +95,4 @@ See the bumpversion_ documentation for details.
 
 .. _bumpversion: https://pypi.org/project/bumpversion/
 .. _pytest: https://docs.pytest.org/en/latest/
+.. _Emu: https://github.com/bird-house/emu

docs/source/processes.rst

@@ -7,54 +7,6 @@ Processes
     :local:
     :depth: 1
 
-CDO BBox
---------
-
-.. autoprocess:: hummingbird.processes.wps_cdo_bbox.CDOBBox
-   :docstring:
-   :skiplines: 1
-
-CDO Copy
---------
-
-.. autoprocess:: hummingbird.processes.wps_cdo_copy.CDOCopy
-  :docstring:
-  :skiplines: 1
-
-CDO Ensembles
--------------
-
-.. autoprocess:: hummingbird.processes.wps_cdo_ensembles.CDOEnsembles
-   :docstring:
-   :skiplines: 1
-
-CDO Indices
------------
-
-.. autoprocess:: hummingbird.processes.wps_cdo_indices.CDOClimateIndices
-   :docstring:
-   :skiplines: 1
-
-CDO Remapping
--------------
-
-.. autoprocess:: hummingbird.processes.wps_cdo_remapping.CDOinter_MPI
-   :docstring:
-   :skiplines: 1
-
-CDO Operation
--------------
-
-.. autoprocess:: hummingbird.processes.wps_cdo_op.CDOOperation
-   :docstring:
-   :skiplines: 1
-
-CDO Info
---------
-
-.. autoprocess:: hummingbird.processes.wps_cdo_sinfo.CDOInfo
-   :docstring:
-   :skiplines: 1
 
 Compliance Checker
 ------------------

environment.yml

@@ -1,20 +1,19 @@
 name: hummingbird
 channels:
-- birdhouse
 - conda-forge
 - defaults
 dependencies:
 - python=3.6
-- six
+- pip
 # pywps
-- pywps=4.2
 - jinja2
 - click
 - psutil
-# cdo
-- cdo=1.9.4
-- python-cdo
 - xarray
-- netcdf4=1.4.1
+- netcdf4
 # compliance checker ioos
-- compliance-checker=4.1
+- compliance-checker
+# tests
+- pytest
+- pip:
+  - -e git+https://github.com/geopython/pywps@master#egg=pywps

etc/debug.cfg

@@ -1,2 +1,5 @@
 [logging]
 level = DEBUG
+
+[server]
+cleantempdir = false

etc/sample-custom.cfg

@@ -1,8 +1,6 @@
 [server]
 url = http://demo.org:5000/wps
 outputurl = http://demo.org:5000/outputs
-outputpath = /var/lib/pywps/outputs
-workdir = /var/lib/pywps/tmp
 
 [logging]
 level = DEBUG

hummingbird/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"))
 

hummingbird/default.cfg

@@ -10,7 +10,7 @@ provider_url=http://hummingbird.readthedocs.org/en/latest/
 url = http://localhost:5000/wps
 outputurl = http://localhost:5000/outputs
 allowedinputpaths = /
-maxsingleinputsize = 500mb
+maxsingleinputsize = 200mb
 maxprocesses = 10
 parallelprocesses = 2
 

hummingbird/processes/__init__.py

@@ -1,32 +1,10 @@
 from .wps_ncdump import NCDump
 from .wps_compliance_checker import CChecker
 from .wps_spotchecker import SpotChecker
-from .wps_cdo_sinfo import CDOInfo
-from .wps_cdo_op import CDOOperation
-from .wps_cdo_copy import CDOCopy
-from .wps_cdo_bbox import CDOBBox
-from .wps_cdo_indices import CDOClimateIndices
-from .wps_cdo_ensembles import CDOEnsembles
-from .wps_cdo_remapping import CDOinter_MPI
-from .wps_cfchecker import CFChecker
-from .wps_hdh_cfchecker import HDHCFChecker
-from .wps_hdh_qachecker import QualityChecker
-from .wps_cmor_checker import CMORChecker
 
 
 processes = [
     NCDump(),
     CChecker(),
     SpotChecker(),
-    # CFChecker(),
-    # CMORChecker(),
-    # HDHCFChecker(),
-    # QualityChecker(),
-    CDOInfo(),
-    CDOOperation(),
-    CDOCopy(),
-    CDOBBox(),
-    CDOClimateIndices(),
-    CDOEnsembles(),
-    CDOinter_MPI(),
 ]