Merge pull request #12 from phovea/release_0.1.0

Release 0.1.0

.gitattributes

@@ -67,6 +67,7 @@
 # build config
 *.npmignore text
 *.bowerrc text
+Dockerfile text eof=LF
 
 # Heroku
 Procfile text
@@ -123,4 +124,4 @@ AUTHORS text
 # Note: .db, .p, and .pkl files are associated
 # with the python modules ``pickle``, ``dbm.*``,
 # ``shelve``, ``marshal``, ``anydbm``, & ``bsddb``
-# (among others).
+# (among others).

.travis.yml

@@ -1,27 +1,33 @@
 language: python
 sudo: required
 env:
-  - TOXENV=py27
-  - TOXENV=py34
-
+- TOXENV=py27
+- TOXENV=py34
 install:
-  - (!(test -f docker_packages.txt) || (cat docker_packages.txt | xargs sudo apt-get install -y))
-  - pip install -r requirements_dev.txt
-  - pip install -r requirements.txt
-
+- "(!(test -f docker_packages.txt) || (cat docker_packages.txt | xargs sudo apt-get
+  install -y))"
+- pip install -r requirements_dev.txt
+- pip install -r requirements.txt
 script: npm run dist
-
+notifications:
+  slack:
+    secure: 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
+    on_success: change
+    on_failure: always
 deploy:
-  provider: releases
+- provider: releases
   api_key:
-    secure: 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
+    secure: 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
   file_glob: true
   file: dist/phovea_data_mongo*.egg
   on:
     tags: true
-
-notifications:
-  slack:
-    secure: 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
-    on_success: change
-    on_failure: always
+    repo: phovea/phovea_data_mongo
+- provider: pypi
+  user: caleydo-bot
+  password:
+    secure: e4v7ObSMoIejma3OSmJWvSKq74ejA2tnXgi4/3+rGwmVSe0S6LRkOT5bT/p4ZMYbnJFH4i83Y7RVtt61OA3EFxUiWxXg7MQ7FgvD4eHVbQeIiYbSbvkRImjz+kvlTT9+Jp6nq3/H5YoUKZ3uP+8Pk2XSX/vB7Aak60FNdi36TJRK4vfkeb3fVQ89OsJfMnHVJgHaphnAAMvodSBwOP+Y641QQTnVMcKxJwkIZUqXWHv7fl99ib0rDQ5AEJbvs+T1gLUaBANYe7OKkybkB496a4rnwUCKnZLVxAxhMSkf0lhGaA5F5iXXnnrHXFTTjMU/5NNdjiMfZKvT9IVJWw6cxA5euBY6OLedJiZUOhUSz0pK99hpsuiYrE2L+1gn6VIEUUEcJpkpYuDtfGqqbO2veOFrp6v/AxMKMpxGs5mXZl4dmOMmG4iGJnYu3CSX3iH/heAS3NgFCnI9CxfrhSXnXTdyUv1Gx5klhs7eysdcnE2tguZ+3/acrB9uVXQfs1iMNFc4130/Apkomk/TmlXQiYGWmMUqFnmGFzFA67XPx3G84SgelV/+5GeLQKln8+5SSNeLxDF9ya1JnfDnmRo7cTD1e4c60TeCI0Itv2+nrMtG9Cq4J1emeM8CsGG/TteydwHtQUEyBug+8mvFFuq0AFenY4OJiba8RAwgF3ik2Ok=
+  on:
+    tags: true
+    distributions: sdist bdist_wheel
+    repo: phovea/phovea_data_mongo

README.md

@@ -31,7 +31,7 @@ npm run build
 ***
 
 <a href="https://caleydo.org"><img src="http://caleydo.org/assets/images/logos/caleydo.svg" align="left" width="200px" hspace="10" vspace="6"></a>
-This repository is part of **[Phovea](http://phovea.caleydo.org/)**, a platform for developing web-based visualization applications. For tutorials, API docs, and more information about the build and deployment process, see the [documentation page](http://caleydo.org/documentation/).
+This repository is part of **[Phovea](http://phovea.caleydo.org/)**, a platform for developing web-based visualization applications. For tutorials, API docs, and more information about the build and deployment process, see the [documentation page](http://phovea.caleydo.org).
 
 
 [phovea-image]: https://img.shields.io/badge/Phovea-Server%20Plugin-10ACDF.svg
@@ -40,5 +40,5 @@ This repository is part of **[Phovea](http://phovea.caleydo.org/)**, a platform
 [npm-url]: https://npmjs.org/package/phovea_data_mongo
 [travis-image]: https://travis-ci.org/phovea/phovea_data_mongo.svg?branch=master
 [travis-url]: https://travis-ci.org/phovea/phovea_data_mongo
-[daviddm-image]: https://david-dm.org/phovea/phovea_data_mongo.svg?theme=shields.io
+[daviddm-image]: https://david-dm.org/phovea/phovea_data_mongo/status.svg
 [daviddm-url]: https://david-dm.org/phovea/phovea_data_mongo

build.py

@@ -0,0 +1,51 @@
+import shutil
+from codecs import open
+import json
+
+__author__ = 'Samuel Gratzl'
+
+
+def _git_head(cwd):
+  import subprocess
+  try:
+    output = subprocess.check_output(['git', 'rev-parse', '--verify', 'HEAD'], cwd=cwd)
+    return output.strip()
+  except subprocess.CalledProcessError:
+    return 'error'
+
+
+def _resolve_plugin(repo, version):
+  import os.path
+  if os.path.isdir('.git') and repo:
+    if repo.endswith('.git'):
+      repo = repo[0:-4]
+    return repo + '/commit/' + _git_head('.')
+  # not a git repo
+  return version
+
+
+def to_version(v):
+  import datetime
+  now = datetime.datetime.utcnow()
+  return v.replace('SNAPSHOT', now.strftime('%Y%m%d-%H%M%S'))
+
+
+with open('package.json', 'r', encoding='utf-8') as f:
+  pkg = json.load(f)
+
+name = pkg['name']
+version = to_version(pkg['version'])
+resolved = _resolve_plugin(pkg.get('repository', {}).get('url'), version)
+
+# copy source code
+shutil.rmtree('build/source/' + name, ignore_errors=True)
+shutil.copytree(name, 'build/source/' + name, symlinks=False, ignore=shutil.ignore_patterns('*.pyc'))
+
+# create buildInfo.json
+build_info = dict(name=name, version=version, resolved=resolved, description=pkg['description'],
+                  homepage=pkg.get('homepage'), repository=pkg.get('repository', {}).get('url'))
+
+# TODO create build Info
+
+with open('build/source/' + name + '/buildInfo.json', 'w', encoding='utf-8') as f:
+  json.dump(build_info, f, indent=2)

deploy/docker-compose.partial.yml

@@ -6,4 +6,8 @@ services:
     links:
     - db_mongo:mongo
   db_mongo:
-    image: mongo:3.2
+    image: mongo:3.2
+    volumes:
+    - db_mongo_data:/data/db
+volumes:
+  db_mongo_data:

docs/.gitignore

@@ -0,0 +1,3 @@
+/modules.rst
+/phovea_server.rst
+

docs/conf.py

@@ -0,0 +1,126 @@
+# -*- coding: utf-8 -*-
+#
+# This file is execfile()d with the current directory set to its
+# containing dir.
+#
+# Note that not all possible configuration values are present in this
+# autogenerated file.
+#
+# All configuration values have a default; values that are commented out
+# serve to show the default.
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+import sys
+import os
+import json
+from codecs import open
+
+sys.path.insert(0, os.path.abspath('..'))
+
+with open('../package.json', encoding='utf-8') as json_data:
+  import json
+
+  pkg = json.load(json_data)
+
+# -- General configuration ------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#
+# needs_sphinx = '1.0'
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = ['sphinx.ext.autodoc',
+              'sphinx.ext.intersphinx',
+              'sphinx.ext.todo']
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The suffix(es) of source filenames.
+# You can specify multiple suffix as a list of string:
+#
+source_parsers = {
+  '.md': 'recommonmark.parser.CommonMarkParser',
+}
+source_suffix = ['.rst', '.md']
+
+# The master toctree document.
+master_doc = 'index'
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This patterns also effect to html_static_path and html_extra_path
+exclude_patterns = ['build', 'tests']
+
+# General information about the project.
+project = pkg['name']
+copyright = pkg['license']
+author = pkg['author']['name']
+
+# The version info for the project you're documenting, acts as replacement for
+# |version| and |release|, also used in various other places throughout the
+# built documents.
+#
+# The short X.Y version.
+version = pkg['version']
+# The full version, including alpha/beta/rc tags.
+release = pkg['version']
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#
+# This is also used if you do content translation via gettext catalogs.
+# Usually you set "language" from the command line for these cases.
+language = None
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+# If true, `todo` and `todoList` produce output, else they produce nothing.
+todo_include_todos = True
+
+# -- Options for HTML output ----------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = 'alabaster'
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further.  For a list of options available for each theme, see the
+# documentation.
+#
+# html_theme_options = {}
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']
+
+# -- Options for HTMLHelp output ------------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = pkg['name'] + 'doc'
+
+# Sort members by type
+autodoc_member_order = 'groupwise'
+
+
+# Ensure that the __init__ method gets documented.
+def skip(app, what, name, obj, skip, options):
+  if name == '__init__':
+    return False
+  return skip
+
+
+def setup(app):
+  app.connect('autodoc-skip-member', skip)
+
+
+# Example configuration for intersphinx: refer to the Python standard library.
+intersphinx_mapping = {'https://docs.python.org/': None}

docs/index.rst

@@ -0,0 +1,20 @@
+.. phovea_data_mongo documentation master file, created by
+   sphinx-quickstart on Tue Feb  7 19:42:32 2017.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to phovea_data_mongo's documentation!
+=========================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   modules
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

package.json

@@ -1,4 +1,21 @@
 {
+  "name": "phovea_data_mongo",
+  "description": "Data provider plugin for loading graph data stored in a MongoDB.",
+  "homepage": "https://phovea.caleydo.org",
+  "version": "0.1.0",
+  "author": {
+    "name": "The Caleydo Team",
+    "email": "[email protected]",
+    "url": "https://caleydo.org"
+  },
+  "license": "BSD-3-Clause",
+  "bugs": {
+    "url": "https://github.com/phovea/phovea_data_mongo/issues"
+  },
+  "repository": {
+    "type": "git",
+    "url": "https://github.com/phovea/phovea_data_mongo.git"
+  },
   "files": [
     "phovea_data_mongo",
     "__init__.py",
@@ -14,26 +31,9 @@
     "pretest": "npm run check",
     "test": "test ! -d tests || python setup.py test",
     "predist": "npm run build && npm run docs",
-    "dist": "python setup.py bdist_egg",
-    "docs": "echo todo creating docs...",
+    "dist": "python setup.py bdist_egg && cd build && tar cvzf ../dist/phovea_data_mongo.tar.gz *",
+    "docs": "sphinx-apidoc -o docs -f ./phovea_data_mongo && sphinx-build ./docs build/docs",
     "prebuild": "node -e \"process.exit(process.env.PHOVEA_SKIP_TESTS === undefined?1:0)\" || npm run test",
-    "build": "python -c \"from distutils.dir_util import mkpath ; mkpath('./build/source')\" && (tar -c ./phovea_data_mongo --exclude '*.pyc' | tar -xC build/source)"
-  },
-  "name": "phovea_data_mongo",
-  "description": "Data provider plugin for loading graph data stored in a MongoDB.",
-  "homepage": "https://phovea.caleydo.org",
-  "version": "0.0.5",
-  "author": {
-    "name": "The Caleydo Team",
-    "email": "[email protected]",
-    "url": "https://caleydo.org"
-  },
-  "license": "BSD-3-Clause",
-  "bugs": {
-    "url": "https://github.com/phovea/phovea_data_mongo/issues"
-  },
-  "repository": {
-    "type": "git",
-    "url": "https://github.com/phovea/phovea_data_mongo.git"
+    "build": "python build.py"
   }
 }

phovea_data_mongo/config.json

@@ -1,4 +1,5 @@
 {
   "host": "mongo",
-  "port": 27017
+  "port": 27017,
+  "db": "graph"
 }