Merge pull request #6 from sdss/codehealth

code health and pypi release

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.1.5dev
+current_version = 0.2.0
 commit = True
 tag = False
 tag_name = {new_version}
@@ -14,5 +14,5 @@ values =
 	dev
 	alpha
 
-[bumpversion:file:python/brain/__init__.py]
+[bumpversion:file:setup.cfg]
 

.gitignore

@@ -0,0 +1,110 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+*.DS_Store
+
+# C extensions
+*.so
+*.o
+*.a
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage*
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+docs/sphinx/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# dotenv
+.env
+
+# virtualenv
+.venv
+venv/
+ENV/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+
+.vscode
+
+.pytest_cache

CHANGELOG.rst

@@ -1,6 +1,13 @@
 Marvin's Brain Change Log
 =========================
 
+[0.2.0] - 2020/09/20
+--------------------
+- refactoring for code health
+- added setup.py and cfg
+- moved to sdsstools for logging and config
+- moved tests to top level
+
 [0.1.4] - 2020/08/31
 --------------------
 - Syntax change to accommodate networkx 2.4.x deprecations

LICENSE.md

@@ -0,0 +1,31 @@
+BSD 3-Clause License
+
+Copyright (c) 2020, SDSS
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+

README.md

@@ -1 +1,9 @@
-This repository has moved to https://github.com/sdss/marvin_brain
+This repository is mainly a dependency for https://github.com/sdss/marvin, containing some core
+logic and functions pertaining to Flask API infrastructure for the Marvin API.  It is not useable as a product or python package by itself.  The original ideas behind ``marvin_brain`` has largely been expanded into [sdss_brain](https://github.com/sdss/sdss_brain) and [valis](https://github.com/sdss/valis).
+
+
+Useful links
+------------
+
+- GitHub: https://github.com/sdss/marvin_brain
+- Issues: https://github.com/sdss/marvin_brain/issues

python/brain/__init__.py

@@ -11,12 +11,21 @@
 import os
 import netrc
 import warnings
-import yaml
 from brain.core.exceptions import BrainError, BrainUserWarning
-from brain.utils.general.general import merge, get_yaml_loader
+from sdsstools import get_config, get_logger, get_package_version
+
+NAME = 'marvin-brain'
+
+# Loads config
+curdir = os.path.dirname(os.path.abspath(__file__))
+cfg_params = get_config('brain', config_file=os.path.join(curdir, 'data/brain.yml'))
+
+# Inits the logging system. Only shell logging, and exception and warning catching.
+# File logging can be started by calling log.start_file_logger(path).
+log = get_logger(NAME)
 
 # Set the Brain version
-__version__ = '0.1.5dev'
+__version__ = get_package_version(path=__file__, package_name=NAME)
 
 
 class BrainConfig(object):
@@ -99,17 +108,8 @@ def has_netrc(self):
     def _load_defaults(self):
         ''' Load the Brain config yaml file '''
 
-        config = yaml.load(open(os.path.join(os.path.dirname(__file__), 'data/brain.yml')), Loader=get_yaml_loader())
-        user_config_path = os.path.expanduser('~/.brain/brain.yml')
-        if os.path.exists(user_config_path):
-            config = merge(yaml.load(open(user_config_path), Loader=get_yaml_loader()), config)
-
-        # update any matching Config values
-        for key, value in config.items():
-            if hasattr(self, key):
-                self.__setattr__(key, value)
-
-        self._custom_config = config
+        #self._custom_config = config
+        self._custom_config = cfg_params
 
     def _check_paths(self):
         ''' Check the paths in the custom config '''

python/brain/api/api.py

@@ -38,7 +38,8 @@ def __init__(self, route, params=None, request_type='post', auth='token',
         self.statuscodes = {200: 'Ok', 401: 'Authentication Required', 404: 'URL Not Found',
                             500: 'Internal Server Error', 405: 'Method Not Allowed',
                             400: 'Bad Request', 502: 'Bad Gateway', 504: 'Gateway Timeout',
-                            422: 'Unprocessable Entity', 429: 'Rate Limit Exceeded'}
+                            422: 'Unprocessable Entity', 429: 'Rate Limit Exceeded',
+                            409: 'Conflict'}
         self.compression = self.params['compression'] if self.params and \
             'compression' in self.params else bconfig.compression
 
@@ -225,10 +226,10 @@ def _checkResponse(self, response):
                 raise BrainError('Requests Http Status Error: {0}\nValidation Errors:\n{1}'.format(http, json_data))
             else:
                 self._closeRequestSession()
-                if b'api_error' in json_data:
+                if str('api_error') in json_data:
                     apijson = json_data['api_error']
-                    errmsg = '{0}\n{1}'.format(apijson['message'], apijson['traceback']) if 'message' in apijson else '{0}'.format(apijson['traceback'])
-                elif b'error' in json_data:
+                    errmsg = '{0}'.format(apijson['message']) if 'message' in apijson else '{0}'.format(apijson['traceback'])
+                elif str('error') in json_data:
                     err = json_data['error']
                     errmsg = '{0}'.format(err)
                 raise BrainError('Requests Http Status Error: {0}\n{1}'.format(http, errmsg))