Merge pull request #136 from phovea/release-7.0.0

Release 7.0.0

.circleci/config.yml

@@ -1,9 +1,13 @@
-version: 2
-jobs:
-  build:
+version: 2.1
+
+executors:
+  python-executor:
     working_directory: ~/phovea
     docker:
       - image: circleci/python:3.7-buster-node-browsers # for node version see Dockerfile on https://hub.docker.com/r/circleci/python
+jobs:
+  build:
+    executor: python-executor
     steps:
       - checkout
       - run:
@@ -48,8 +52,34 @@ jobs:
             npm run dist
       - store_artifacts:
           path: dist
+          destination: dist
+      - persist_to_workspace:
+          root: ~/phovea
+          paths: .
+  publish:
+    executor: python-executor
+    steps:
+      - attach_workspace:
+          at: ~/phovea
+      - run:
+          name: Install twine
+          command: |
+            . ~/venv/bin/activate \
+            pip install twine \
+      - run:
+          name: Authentication
+          command:  |
+            echo -e "[pypi]" >> ~/.pypirc
+            echo -e "repository = $PYPI_REPOSITORY" >> ~/.pypirc
+            echo -e "username = $PYPI_USERNAME" >> ~/.pypirc
+            echo -e "password = $PYPI_PASSWORD" >> ~/.pypirc
+      - run:
+          name: Publish package
+          command: |
+            . venv/bin/activate
+            twine upload dist/*
 workflows:
-  version: 2
+  version: 2.1
 #  build-nightly:
 #    triggers:
 #      - schedule:
@@ -60,17 +90,27 @@ workflows:
 #                - develop
 #    jobs:
 #      - build
-  build-branch:
+  build-branches-only:
     jobs:
       - build:
           filters:
             tags:
-              ignore: /^v.*/
-  build-tag:
+              ignore: /.*/
+  build-publish-tag:
     jobs:
       - build:
           filters:
             branches:
               ignore: /.*/
             tags:
               only: /^v.*/
+      - publish:
+          context:
+              - org-public
+          requires:
+              - build
+          filters:
+            branches:
+              ignore: /.*/
+            tags:
+              only: /^v.*/

deploy/docker-compose.partial.yml

@@ -15,3 +15,6 @@ services:
     - '9000:80'
     volumes:
     - .:/phovea
+    # Add support for PDB debugger
+    # stdin_open: true
+    # tty: true

package.json

@@ -1,7 +1,7 @@
 {
   "name": "phovea_server",
   "description": "Python server implementation of Phovea",
-  "version": "6.0.1",
+  "version": "7.0.0",
   "author": {
     "name": "The Caleydo Team",
     "email": "[email protected]",

phovea_server/launch.py

@@ -3,10 +3,13 @@
 # Copyright (c) The Caleydo Team. All rights reserved.
 # Licensed under the new BSD license, available at http://caleydo.org/license
 ###############################################################################
+from gevent import monkey
+monkey.patch_all()
 
-import logging.config
-import logging
-from . import config
+
+import logging.config  # noqa: E402
+import logging  # noqa: E402
+from . import config  # noqa: E402
 
 
 # set configured registry

phovea_server/mainapp.py

@@ -126,6 +126,11 @@ def _build_info():
   return ns.jsonify(build_info)
 
 
+# health check for docker-compose, kubernetes
+def _health():
+    return 'ok', 200
+
+
 def default_app():
   # from .config import view, _initialize
   from phovea_server import config
@@ -141,4 +146,5 @@ def default_app():
   else:
     app.add_url_rule('/<path:path>', 'deliver', _deliver_production)
   app.add_url_rule('/api/buildInfo.json', 'build_info', _build_info)
+  app.add_url_rule('/health', 'health', _health)
   return app

phovea_server/plugin.py

@@ -85,12 +85,10 @@ def __init__(self, desc):
   def load(self):
     if self._impl is None:
       import importlib
-      import gevent.monkey
       _log = logging.getLogger(__name__)
       _log.info('importing %s', self.module)
 
       m = importlib.import_module(self.module)
-      gevent.monkey.patch_all()  # ensure the standard libraries are patched
       if hasattr(m, '_plugin_initialize'):  # init method
         # import inspect
         # inspect.getcallargs()

phovea_server/server.py

@@ -194,6 +194,10 @@ def create(parser):
                       help='server port')
   parser.add_argument('--address', '-a', default=cc.get('address'),  # get default value from config.json
                       help='server address')
+  parser.add_argument('--certfile', '-c', default=cc.get('certfile'),  # get default value from config.json
+                      help='ssl certificate')
+  parser.add_argument('--keyfile', '-k', default=cc.get('keyfile'),  # get default value from config.json
+                      help='keyfile for ssl certificate')
 
   def _launcher(args):
     """
@@ -202,12 +206,26 @@ def _launcher(args):
     """
     from geventwebsocket.handler import WebSocketHandler
     from gevent.pywsgi import WSGIServer
+    from flask.logging import default_handler
+    import logging
+    # from gevent import monkey
 
     # create phovea server application
     application = create_application()
 
-    _log.info('prepare server that will listen on %s:%s', args.address, args.port)
-    http_server = WSGIServer((args.address, args.port), application, handler_class=WebSocketHandler)
+    # add handler for wsgi's logger
+    logger = logging.getLogger('wsgi')
+    logger.setLevel(logging.INFO)
+    _log.addHandler(default_handler)
+
+    _log.info('prepare server that will listen on %s:%s [cert=%s, key=%s]', args.address, args.port, args.certfile, args.keyfile)
+    # Test whether monkey.patch_all() has been used correctly,
+    # keys have to be set
+    # _log.warn(monkey.saved.keys())
+    if args.certfile and args.keyfile:
+      http_server = WSGIServer((args.address, args.port), application, keyfile=args.keyfile, certfile=args.certfile, handler_class=WebSocketHandler)
+    else:
+      http_server = WSGIServer((args.address, args.port), application, handler_class=WebSocketHandler)
 
     server = http_server.serve_forever  # return function name only; initialization will be done later
 

requirements.txt

@@ -1,14 +1,11 @@
-Flask==1.1.1
+Flask==1.1.2
 flask-restplus==0.13.0
 Flask-Sockets==0.2.1
-gevent==1.4.0
+gevent==20.9.0
 gevent-websocket==0.10.1
-numpy==1.18.1
-scipy==1.4.1
-pandas==1.0.1
-matplotlib==3.1.3
-Pillow==7.0.0
-json-cfg==0.4.2
-
-# pin greenlet version (see https://github.com/phovea/phovea_server/issues/130)
-greenlet==0.4.16
+numpy==1.19.4
+scipy==1.5.4
+pandas==1.1.4
+matplotlib==3.3.3
+Pillow==8.0.1
+json-cfg==0.4.2

requirements_dev.txt

@@ -1,6 +1,6 @@
-flake8==3.7.9
-pep8-naming==0.9.1
-pytest==5.3.5
+flake8==3.8.4
+pep8-naming==0.11.1
+pytest==6.1.2
 pytest-runner==5.2
-Sphinx==2.4.2
+Sphinx==3.3.1
 recommonmark==0.6.0