updating submodules

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 2.2.6dev
+current_version = 2.3.0dev
 commit = True
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(?P<release>[a-z]+)?

.github/ISSUE_TEMPLATE.md

@@ -0,0 +1,25 @@
+<!-- **NEVER INCLUDE PLAINTEXT PASSWORDS OR PRIVATE INFORMATION IN THE BUG REPORT** -->
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behaviour:
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+
+**Expected behaviour**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Desktop (please complete the following information):**
+ - OS: [e.g. iOS]
+ - Browser [e.g. chrome, safari] (if the issue is related to Marvin Web)
+ - Version of Marvin [e.g. 2.0.2]
+
+**Additional context**
+Add any other context about the problem here.

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,31 @@
+---
+name: Bug report
+about: Create a report to help us improve
+
+---
+
+<!-- **NEVER INCLUDE PLAINTEXT PASSWORDS OR PRIVATE INFORMATION IN THE BUG REPORT** -->
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior:
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Desktop (please complete the following information):**
+ - OS: [e.g. iOS]
+ - Browser [e.g. chrome, safari]
+ - Version [e.g. 22]
+
+**Additional context**
+Add any other context about the problem here.

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,17 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,10 @@
+Fixes #
+
+This pull request:
+- [ ] Has a title that summarises what is changing.
+- [ ] Updates the documentation accordingly.
+- [ ] Has unit tests & [code coverage](https://coveralls.io/github/sdss/marvin) is not adversely affected (within reason).
+- [ ] Works with Python 2.7 and 3.6 (and ideally with Python 3.7).
+- [ ] Updates the [CHANGELOG](https://github.com/sdss/marvin/blob/master/CHANGELOG.rst).
+- [ ] Removes more lines of code than it adds.
+- [ ] If relevant, adds a new entry to the [What's new?](https://github.com/sdss/marvin/blob/master/docs/sphinx/whats-new.rst) page.

.travis.yml

@@ -37,6 +37,7 @@ matrix:
 notifications:
   slack:
     secure: 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
+  email: false
 branches:
   except:
   - mpl6

CHANGELOG.rst

@@ -1,7 +1,7 @@
 Marvin's Change Log
 ===================
 
-[2.2.6] - 2018/?/?
+[2.3.0] - 2018/?/?
 --------------------
 
 Changed
@@ -28,6 +28,11 @@ Fixed
 - Issue `#421 <https://github.com/sdss/marvin/issues/421>`_ - query returning spaxel props returns wrong total count
 - Bugfix - Python 3 xrange syntax bug in buildImageDict
 
+Changed
+^^^^^^^
+- Extra keyword arguments passed to ``Spectrum.plot`` are now forwarded to ``Axes.plot``.
+- Tools (e.g., ``Cube``, ``Maps``) can now be accessed from the ``marvin`` namespace (e.g., ``marvin.tools.Cube`` or ``marvin.tools.cube.Cube``).
+
 
 [2.2.5] - 2018/04/26
 --------------------

CODE_OF_CONDUCT.md

@@ -0,0 +1,84 @@
+# Code of Conduct
+
+## 1. Purpose
+
+A primary goal of Marvin is to be inclusive to the largest number of contributors, with the most varied and diverse backgrounds possible. As such, we are committed to providing a friendly, safe and welcoming environment for all, regardless of gender, sexual orientation, ability, ethnicity, socioeconomic status, and religion (or lack thereof).
+
+This code of conduct outlines our expectations for all those who participate in our community, as well as the consequences for unacceptable behavior.
+
+We invite all those who participate in Marvin to help us create safe and positive experiences for everyone.
+
+## 2. Open Source Citizenship
+
+A supplemental goal of this Code of Conduct is to increase open source citizenship by encouraging participants to recognize and strengthen the relationships between our actions and their effects on our community.
+
+Communities mirror the societies in which they exist and positive action is essential to counteract the many forms of inequality and abuses of power that exist in society.
+
+If you see someone who is making an extra effort to ensure our community is welcoming, friendly, and encourages all participants to contribute to the fullest extent, we want to know.
+
+## 3. Expected Behavior
+
+The following behaviors are expected and requested of all community members:
+
+*   Participate in an authentic and active way. In doing so, you contribute to the health and longevity of this community.
+*   Exercise consideration and respect in your speech and actions.
+*   Attempt collaboration before conflict.
+*   Refrain from demeaning, discriminatory, or harassing behavior and speech.
+*   Be mindful of your surroundings and of your fellow participants. Alert community leaders if you notice a dangerous situation, someone in distress, or violations of this Code of Conduct, even if they seem inconsequential.
+*   Remember that community event venues may be shared with members of the public; please be respectful to all patrons of these locations.
+
+## 4. Unacceptable Behavior
+
+The following behaviors are considered harassment and are unacceptable within our community:
+
+*   Violence, threats of violence or violent language directed against another person.
+*   Sexist, racist, homophobic, transphobic, ableist or otherwise discriminatory jokes and language.
+*   Posting or displaying sexually explicit or violent material.
+*   Posting or threatening to post other people’s personally identifying information ("doxing").
+*   Personal insults, particularly those related to gender, sexual orientation, race, religion, or disability.
+*   Inappropriate photography or recording.
+*   Inappropriate physical contact. You should have someone’s consent before touching them.
+*   Unwelcome sexual attention. This includes, sexualized comments or jokes; inappropriate touching, groping, and unwelcomed sexual advances.
+*   Deliberate intimidation, stalking or following (online or in person).
+*   Advocating for, or encouraging, any of the above behavior.
+*   Sustained disruption of community events, including talks and presentations.
+
+## 5. Consequences of Unacceptable Behavior
+
+Unacceptable behavior from any community member, including sponsors and those with decision-making authority, will not be tolerated.
+
+Anyone asked to stop unacceptable behavior is expected to comply immediately.
+
+If a community member engages in unacceptable behavior, the community organizers may take any action they deem appropriate, up to and including a temporary ban or permanent expulsion from the community without warning (and without refund in the case of a paid event).
+
+## 6. Reporting Guidelines
+
+If you are subject to or witness unacceptable behavior, or have any other concerns, please notify a community organizer as soon as possible. ombuds@sdss.org.
+
+[Reporting Guidelines](https://www.sdss.org/collaboration/the-sloan-digital-sky-survey-code-of-conduct/)
+
+Additionally, community organizers are available to help community members engage with local law enforcement or to otherwise help those experiencing unacceptable behavior feel safe. In the context of in-person events, organizers will also provide escorts as desired by the person experiencing distress.
+
+## 7. Addressing Grievances
+
+If you feel you have been falsely or unfairly accused of violating this Code of Conduct, you should notify SDSS with a concise description of your grievance. Your grievance will be handled in accordance with our existing governing policies.
+
+[Policy](https://www.sdss.org/collaboration/the-sloan-digital-sky-survey-code-of-conduct/)
+
+## 8. Scope
+
+We expect all community participants (contributors, paid or otherwise; sponsors; and other guests) to abide by this Code of Conduct in all community venues–online and in-person–as well as in all one-on-one communications pertaining to community business.
+
+This code of conduct and its related procedures also applies to unacceptable behavior occurring outside the scope of community activities when such behavior has the potential to adversely affect the safety and well-being of community members.
+
+## 9. Contact info
+
+ombuds@sdss.org
+
+## 10. License and attribution
+
+This Code of Conduct is distributed under a [Creative Commons Attribution-ShareAlike license](http://creativecommons.org/licenses/by-sa/3.0/).
+
+Portions of text derived from the [Django Code of Conduct](https://www.djangoproject.com/conduct/) and the [Geek Feminism Anti-Harassment Policy](http://geekfeminism.wikia.com/wiki/Conference_anti-harassment/Policy).
+
+Retrieved on November 22, 2016 from [http://citizencodeofconduct.org/](http://citizencodeofconduct.org/)

docs/sphinx/tutorials/plotting-tutorial.rst

@@ -72,9 +72,10 @@ Quick Model Fit Plot
     # must use Maps.getSpaxel() to get modelcube
     # (the bracket slicing of Maps does not return the modelcube)
     spax = maps.getSpaxel(x=17, y=17, xyorig='lower', model=True)
-    ax = spax.flux.plot()
-    ax.plot(spax.full_fit.wavelength, spax.full_fit.value)
-    ax.legend(list(ax.get_lines()), ['observed', 'model'])
+    # extra arguments to plot are passed to the matplotlib routine
+    ax = spax.flux.plot(label='observed)
+    ax.plot(spax.full_fit.wavelength, spax.full_fit.value, label='model')
+    ax.legend()
 
 .. image:: ../_static/quick_model_plot.png
 

docs/sphinx/whats-new.rst

@@ -1,5 +1,9 @@
 .. _whats-new:
 
+What's New in Marvin 2.3.0 (unreleased)
+=======================================
+
+
 What's New in Marvin 2.2 (January 2018)
 =======================================
 

python/marvin/__init__.py

@@ -15,6 +15,9 @@
 import six
 from collections import OrderedDict
 
+# Set the Marvin version
+__version__ = '2.3.0dev'
+
 # Does this so that the implicit module definitions in extern can happen.
 from marvin import extern
 
@@ -42,14 +45,17 @@
 log = initLog(logFilePath)
 
 warnings.simplefilter('once')
-warnings.filterwarnings('ignore', 'Skipped unsupported reflection of expression-based index')
-warnings.filterwarnings('ignore', '(.)+size changed, may indicate binary incompatibility(.)+')
+# warnings.filterwarnings('ignore', 'Skipped unsupported reflection of expression-based index')
+# warnings.filterwarnings('ignore', '(.)+size changed, may indicate binary incompatibility(.)+')
 warnings.filterwarnings('ignore', category=FITSFixedWarning)
 
-# Filters for PY3
-# TODO: undestand why these warnings are issued and fix the root of the problem (JSG)
+# This warning seems harmless (see https://github.com/astropy/astropy/issues/6025) so
+# will ignore it for now.
 warnings.filterwarnings('ignore', 'can\'t resolve package(.)+')
-warnings.filterwarnings('ignore', 'unclosed file <_io.TextIOWrapper+')
+
+# Ignore DeprecationWarnings that are not Marvin's
+warnings.filterwarnings('ignore', category=DeprecationWarning)
+warnings.filterwarnings('once', category=DeprecationWarning, module='marvin')
 
 
 class MarvinConfig(object):
@@ -677,3 +683,7 @@ def login(self, refresh=None):
 from marvin.api.api import Interaction
 from marvin.api.base import arg_validate
 
+# Provide access to base submodules from the marvin namespace
+from . import tools
+from . import db
+from . import utils

python/marvin/core/core.py

@@ -225,9 +225,9 @@ def _parse_input(value):
 
         return_dict = {'plate': None, 'ifu': None, 'mangaid': None}
 
-        plateifu_pattern = re.compile('([0-9]{4,5})\-([0-9]{4,9})')
+        plateifu_pattern = re.compile(r'([0-9]{4,5})-([0-9]{4,9})')
         ifu_pattern = re.compile('(7|127|[0-9]{2})([0-9]{2})')
-        mangaid_pattern = re.compile('[0-9]{1,3}\-[0-9]+')
+        mangaid_pattern = re.compile(r'[0-9]{1,3}-[0-9]+')
         plateid_pattern = re.compile('([0-9]{4,})(?!-)(?<!-)')
 
         plateid_match = re.match(plateid_pattern, value)

python/marvin/db/database.py

@@ -4,21 +4,24 @@
 
     The example given is for a PostgreSQL database, but can be modified for any other.
 '''
-from __future__ import print_function
-from __future__ import division
+from __future__ import division, print_function
 
+import os
+
+import yaml
+from marvin import config
 from marvin.db.DatabaseConnection import DatabaseConnection
 from pgpasslib import getpass
-from marvin import config
-import yaml
-import os
+
 
 # Read in the db connection configuration
 dbconfigfile = 'dbconfig.ini'
 dbconfigfile = os.path.join(os.path.dirname(os.path.abspath(__file__)), dbconfigfile)
 
 try:
-    rawfile = open(dbconfigfile, 'r').read()
+    with open(dbconfigfile, 'r') as ff:
+        rawfile = ff.read()
+
 except IOError as e:
     raise RuntimeError('IOError: Could not open dbconfigfile {0}:{1}'.format(dbconfigfile, e))
 dbdict = yaml.load(rawfile)

python/marvin/tests/test_imports.py

@@ -0,0 +1,33 @@
+#!/usr/bin/env python
+# -*- coding:utf-8 -*-
+#
+# @Author: José Sánchez-Gallego (gallegoj@uw.edu)
+# @Date: 2018-07-09
+# @Filename: test_imports.py
+# @License: BSD 3-clause (http://www.opensource.org/licenses/BSD-3-Clause)
+#
+# @Last modified by: José Sánchez-Gallego
+# @Last modified time: 2018-07-09 12:11:48
+
+import marvin
+
+
+class TestImports(object):
+
+    def test_access_tools_full_path(self):
+
+        assert marvin.tools.plate.Plate is not None
+        assert marvin.tools.cube.Cube is not None
+        assert marvin.tools.maps.Maps is not None
+        assert marvin.tools.modelcube.ModelCube is not None
+        assert marvin.tools.spaxel.Spaxel is not None
+        assert marvin.tools.spaxel.Bin is not None
+
+    def test_access_tools_from_root(self):
+
+        assert marvin.tools.Plate is not None
+        assert marvin.tools.Cube is not None
+        assert marvin.tools.Maps is not None
+        assert marvin.tools.ModelCube is not None
+        assert marvin.tools.Spaxel is not None
+        assert marvin.tools.Bin is not None

python/marvin/tools/__init__.py

@@ -0,0 +1,6 @@
+from . import cube, maps, modelcube, spaxel
+from .cube import Cube
+from .maps import Maps
+from .modelcube import ModelCube
+from .plate import Plate
+from .spaxel import Bin, Spaxel

python/marvin/tools/quantities/spectrum.py

@@ -133,7 +133,8 @@ def std(self):
 
     def plot(self, xlim=None, ylim=None, show_std=True, use_mask=True,
              n_sigma=1, xlabel='Wavelength', ylabel='Flux', show_units=True,
-             plt_style='seaborn-darkgrid', figure=None, return_figure=False):
+             plt_style='seaborn-darkgrid', figure=None, return_figure=False,
+             **kwargs):
         """Plots the spectrum.
 
         Displays the spectrum showing, optionally, the :math:`n\\sigma` region,
@@ -171,6 +172,8 @@ def plot(self, xlim=None, ylim=None, show_std=True, use_mask=True,
             return_figure (bool):
                 If ``True``, the matplotlib `~matplotlib.figure.Figure` object
                 used will be returned along with the axes object.
+            kwargs (dict):
+                Keyword arguments to be passed to `~matplotlib.axes.Axes.plot`.
 
         Returns:
             axes:
@@ -202,7 +205,7 @@ def plot(self, xlim=None, ylim=None, show_std=True, use_mask=True,
             value = self.value
             wave = self.wavelength.value
 
-        ax.plot(wave, value)
+        ax.plot(wave, value, **kwargs)
 
         if show_std and self.std is not None:
             if use_mask is False: