Merge branch 'release/6.7.0'

.gitignore

@@ -70,3 +70,6 @@ docs/api
 
 # jupyter files
 .ipynb_checkpoints/
+
+# 
+junit.xml

.rtd-environment.yml

@@ -11,7 +11,7 @@ dependencies:
   - numpy
   - pandas
   - matplotlib
-  - scipy
+  - scipy>=0.19
   - cython
   - pillow
   - pytables

CHANGELOG.rst

@@ -1,6 +1,12 @@
 Unreleased changes
 ------------------
 
+
+6.7.0 / 2017-05-08
+------------------
+* ``totmonitor`` command line utility added
+* bump library versions (scipy >=0.19)
+
 6.6.6 / 2017-04-03
 ------------------
 * change blosc compression -> zlib compression

MANIFEST.in

@@ -5,6 +5,7 @@ recursive-include km3pipe *.pyxbld
 recursive-include docs *
 recursive-include km3pipe/tests *.py
 recursive-include km3pipe/io/tests *.py
+recursive-include km3pipe/style *.py
 recursive-include km3pipe/kp-data *
 
 recursive-exclude docs *.pyc

docs/conf.py

@@ -15,6 +15,7 @@
 import sys
 import os
 from datetime import date
+import sphinx_rtd_theme
 
 # what is this?
 #sys.path.append('../')
@@ -112,12 +113,10 @@
 
 # -- Options for HTML output ----------------------------------------------
 
-html_theme = 'alabaster'
-html_theme_options = {
-    'font_family': "'Open Sans', sans",
-    'head_font_family': "'Lato', sans",
-    'code_font_family': "'Roboto Mono', monospace",
-}
+html_theme = 'sphinx_rtd_theme'
+html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
+#html_theme_options = {
+#}
 
 
 # The name for this set of Sphinx documents.  If None, it defaults to

docs/index.rst

@@ -24,6 +24,7 @@
 
     install
     user_guide
+    logging
     examples
     api
     contribute

docs/logging.rst

@@ -0,0 +1,49 @@
+Logging
+=======
+
+
+.. contents:: :local:
+
+
+Introduction
+------------
+KM3Pipe uses a module based logging system which can individually be configured to
+provide information needed to understand the underlying mechanisms.
+
+You can also easily create your own logger.
+
+
+Accessing a Logger
+------------------
+To access a modules logger, you need to::
+
+    from km3pipe.logger import logging
+    log = logging.getLogger("module.path")
+
+where ``module.path`` is the Python import path of the module, like ``km3pipe.core``.
+
+To set a desired logging level, use the keywords ``DEBUG``, ``INFO``, ``WARNING``,
+``ERROR`` or ``CRITICAL``. For example::
+
+    log.setLevel("DEBUG")
+
+Creating your own Logger
+------------------------
+
+To create your own logger, use the same procedure as described above::
+
+    from km3pipe.logger import logging
+    log = logging.getLogger("your.desired.logger.name")
+
+After that, you can use it to log anywhere::
+
+    log.debug("A debug message")
+    log.info("An info message")
+    log.warn("A warning")
+    log.error("An error")
+    log.critical("A critical think")
+
+and set its debug level::
+
+    log.setLevel("WARN")
+

docs/version.txt

@@ -1,2 +1,2 @@
-KM3Pipe 6.6.6
+KM3Pipe 6.7.0
 =============

km3pipe/__version__.py

@@ -28,7 +28,7 @@
 
 log = logging.getLogger(__name__)  # pylint: disable=C0103
 
-version_info = (6, 6, 6, 'final', 0)
+version_info = (6, 7, 0, 'final', 0)
 
 
 def _get_version(version_info):
@@ -73,4 +73,7 @@ def check_for_update():
 version = _get_version(version_info)
 if config is not None:
     if config.check_for_updates:
-        check_for_update()
+        try:
+            check_for_update()
+        except (ValueError, TypeError, OSError):
+            pass

km3pipe/core.pyx

@@ -386,7 +386,7 @@ class Geometry(Module):
 
     Parameters
     ----------
-    should_apply: bool, optional [default=False]
+    apply: bool, optional [default=False]
         Apply the geometry to the hits (add position/direction/t0)?
     filename: str, optional [default=None]
         DetX file with detector description.

km3pipe/db.py

@@ -171,6 +171,7 @@ def _add_datetime(self, dataframe, timestamp_key='UNIXTIME'):
         def convert_data(timestamp):
             return datetime.fromtimestamp(float(timestamp) / 1e3, UTC_TZ)
         try:
+            log.debug("Adding DATETIME column to the data")
             converted = dataframe[timestamp_key].apply(convert_data)
             dataframe['DATETIME'] = converted
         except KeyError:
@@ -180,6 +181,7 @@ def _add_converted_units(self, dataframe, parameter, key='VALUE'):
         """Add an additional DATA_VALUE column with converted VALUEs"""
         convert_unit = self.parameters.get_converter(parameter)
         try:
+            log.debug("Adding unit converted DATA_VALUE to the data")
             dataframe[key] = dataframe['DATA_VALUE'].apply(convert_unit)
         except KeyError:
             log.warn("Missing 'VALUE': no unit conversion.")
@@ -322,45 +324,59 @@ def _get_content(self, url):
     def opener(self):
         "A reusable connection manager"
         if self._opener is None:
+            log.debug("Creating connection handler")
             opener = build_opener()
+            if self._cookies:
+                log.debug("Appending cookies")
+            else:
+                log.debug("No cookies to append")
             for cookie in self._cookies:
                 cookie_str = cookie.name + '=' + cookie.value
                 opener.addheaders.append(('Cookie', cookie_str))
             self._opener = opener
+        else:
+            log.debug("Reusing connection manager")
         return self._opener
 
     def request_sid_cookie(self, username, password):
         """Request cookie for permanent session token."""
+        log.debug("Requesting SID cookie")
         target_url = self._login_url + '?usr={0}&pwd={1}&persist=y' \
                                       .format(username, password)
         cookie = urlopen(target_url).read()
         return cookie
 
     def restore_session(self, cookie):
         """Establish databse connection using permanent session cookie"""
+        log.debug("Restoring session from cookie")
         opener = build_opener()
         opener.addheaders.append(('Cookie', cookie))
         self._opener = opener
 
     def request_permanent_session(self, username=None, password=None):
+        log.debug("Requesting permanent session")
         config = Config()
         if username is None and password is None:
+            log.debug("Checking configuration file for DB credentials")
             username, password = config.db_credentials
         cookie = self.request_sid_cookie(username, password)
         try:
             cookie_str = str(cookie, 'utf-8')  # Python 3
         except TypeError:
             cookie_str = str(cookie)  # Python 2
         log.debug("Session cookie: {0}".format(cookie_str))
+        log.debug("Storing cookie in configuration file")
         config.set('DB', 'session_cookie', cookie_str)
         self.restore_session(cookie)
 
     def login(self, username, password):
-        "Login to the databse and store cookies for upcoming requests."
+        "Login to the database and store cookies for upcoming requests."
+        log.debug("Logging in to the DB")
         opener = self._build_opener()
         values = {'usr': username, 'pwd': password}
         req = self._make_request(self._login_url, values)
         try:
+            log.debug("Sending login request")
             f = opener.open(req)
         except URLError as e:
             log.error("Failed to connect to the database -> probably down!")