Merge pull request NSLS-II#43 from awalter-bnl/add-travis-yml

Adding .yml file and enc file for Travis integration and doc creation

.travis.yml

@@ -0,0 +1,29 @@
+language: python
+python:
+  - 3.6
+cache:
+  directories:
+    - $HOME/.cache/pip
+    - $HOME/.ccache  # https://github.com/travis-ci/travis-ci/issues/5853
+
+install:
+  # Install this package and the packages listed in requirements.txt.
+  - pip install .
+  # Install extra requirements for running tests and building docs.
+  - pip install -r requirements-dev.txt
+
+env:
+   global:
+    # Doctr deploy key for NSLS-II/nslsii
+    - secure: "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"
+
+script:
+  - coverage run -m pytest  # Run the tests and check for test coverage.
+  - coverage report -m  # Generate test coverage report.
+  - codecov  # Upload the report to codecov.
+  - flake8 --max-line-length=79
+  - set -e  # Stop here if anything fails above
+#commenting out the lines below until there are docs to build.
+#  - make -C docs html  # Build the documentation
+#  - pip install doctr
+#  - doctr deploy --built-docs docs/build/html .  # Publish the documentation

github_deploy_key_nsls_ii_nslsii.enc

@@ -0,0 +1 @@
+gAAAAABbxz01GnyDC8lnHpPlT8i32N3mm2qpw6kSutu50zS_DzikWfBA2IdZtNwROhcddRSgExw8Mr0u254TMM_2jgN_c4GnMar40MjLD_sogS0ZF82vB0p_UTJqzAwimo1euMPalDqBvkoNasnRBz5mCIsrNsbE2QF3zuXqNM0EzTfgcie4f6xGo6C3PfNrxaZUqmlvt4GV5nle4wm7pD58BGiFwkXBqYB8uC6YC4NvkR-iR7jJonldxvcuspM6VZRlPAV7oIG2XTgouY0N3vIRaDpc595xqQwqooHGN9b-dWKWPU7q1dLbrz9SNuqJNtZaP0Q3md5eXdw_6rw9Lbq5GjEsSqhi1PRT8lQFByPNBnfZWGcNkMubjaMwq9psOQwl3dXdLHH-tGBnyB2DSRDdiyZ4nWgVt9SmHvnmvcapZUOjEStLjHkSjQBVb3lfIs7HamuU2TUMPJAUIRmvzKpmVX8m98A1seFlapJSU-6f23nJjAabHBnpJjSvw8ifuR2qWaNgBlVZrNs2neMpP7DgYdNAK-iE-inoDx3KsHb2ZidebxTLsS74ZifCWNA_Oz0QJLOuym2yYrKfdIde3VKnP20lHVYXyqcaBWcgOS70G33C-_vpm6fMnXx5uuRpnDi8bAoZI8IEd7Dq709VJ0YKVV32PYPfr6bjUdE64rdXn2Txl-7dtgV3OweivHqH63AoQ87-bl-uqFj81tVRmix-4WoHyEGMwhOW7ZkJcuDa0FwnS6Wg7NMBY2AbhcIDIq5p7wl-0oAtP9YCOG0gjPIn_L2SHWzFR_iNDbKvlHcucLjwczQOnWm9FSnldE0u3-tHJ8PSE9xhsuUGndT8bVTXE7q-GVmBFUsD9BxwfrOkeASmTd7TclxqSM-5OMRaAGF6_giqXLKrlREL-RihQRPreVpzEL9F25qczepGAjpA6GJ6j4WHDJR8UnXIZLoscieTuFzVrvbhcP0aMpSuNP6UaMrsiN1vNM72WDJuATkHiPyzwnWbUc-nIXUv5LO-ejTruO60YhmZRdRnvrstAFYHQyzJqkiEeeHSKVwIBOci2m60C0-5-5VvbkHXhAAtocqWeyS8xLVr2cSYuS3bZfHzK-GEizGsDFgVj4KIV4xxDeXEUxSdclQ933lw4kfr_IuvXIqgexhBvu9MLThLRAh0nDS_zFN4VyLXfGtg-0RuAtYbK7XQo-M9Dq4s3nDhHnDaPhN0KU617nDSJXIp-N0t4QR-W373QWo4EoVGSC0STD2leqB3atf8c1MNheix97ssqxfs9VX_1RJFtR4v8pXHyekGfqbmQllPBuTu8UH89Larjquo7ABUtGUriB2gm9ag8DjP5xf23hz-Ab9SJD0CBKMwb9H7U4K08pLv6JbcsGhbbqG6_erQYlNWYoI7kKgIT_5BmUFKaFt5mmC-a84XaegF2njZuls3k-z8Yp79yWQvEyPv9w0HJXurYeHzZL1NiF8Am-GKNpcSTa3U_sIG-VxjzBW-Q8pC1mRqTFkTXGTJ6rYSKXlN0VzWvn86ixILAbyF-tbvw9SOK8RdmNy4maqVubWXf_ojpKl7cq3TSAsK-TjntgFbCUz5XjsH57Aq4dzztBlIdXl7P_65ujlgqqq1nl7DvZX5Z50vPNFXukfgvixjH9qO-wiXE1Iy65IntINZb4CAbGwWWkftVbBaaooFW7O8ZJoQ66yM7psP0Ex-F2gDYWFX7QNRpPtTccoAoOfL23_PjVDMHp1kyRD3mha6yF4n4hBQ5JHtGg9nKQlZlED9zSL-Tf-dRJ_j1MGVdgrPJf09Uu7IMNE8-G_ULQz2cLuPrTHKdAFskeiJ6jeUfCtG-TorVetqwrjM2rfuTZHYnR1hBhn6sHk1PB0T-3N-XWwrKApdBFFiGYqN3ErT_7E5MS6QxyoX0Bonjm1vIUSVq0Jzdz3tBLOGecTkKGWi6jFC420Mw4M-SZtUFi3tQ8Hc2SNpmmHyq2GGqEQEklcXqoo69U_zzzQqyDLzOfCVDSoVBEzB6zR6CeWAhwICo0OVA2uLKWeKPp3_oe74TLzIgwVwbHJXGFPyI5MUFHAJL2Vjys-LB_kds4Ar5cOIoBbhfb2CoTn88M5nsu1LJbjjacBwmlCvcqyNhMngf6wxVr6PFDQsEmY1Fk_OS7cnAmdtM9OTkMhdV4o02v78VJD47tNT9J4BaGmwunxEygQHy5pnPqrfjnbdFXpV56Pa-yc_glwhd3NJsk5ZWAQVCZWQtuR6b-nLRO3r0fQo5ROpuTCidRhGgh7w7WTzcdDnPygdMBchaBzBj6TiWOKadJzhORKBKLiOdHlcircJeg1naraFkkp6hf0yaTZ-d3IMz69mS5BmLw4evkbHkG8h6w2dQFUMBRrc5a3A8Wp79IGxvoyOws7oTbad7ZwQn-dEWvILaNEBARK0hopOa8q2pOGLJcvkc_GtvE4ddWo_69q7-KhtN4gKfYLlWnOQryHouqVrt1FXge6qDRRalGMJADrFJdeHsCcbarV16K6tPzyXK87XyW1GoJC6fLToFXcU4G4RxB4QKyYbwWbYs4jc4VSD1lBuobDIYy0blFYoCay5OmPAAZGYbStB11C2s28cXCL_BouwsI2_V6HrDBtNy1xYV_IUIuUkNJtEMR3RVGpq_yPpaIENqDcUCFqXUE6h4HZ1dklFxSjBHLUX39tAAs7rE-CxTXcQkjFevXaSw2dLLMEFHk0OIdCUu10RmG2GPSatLzjsgjfcvSGvj1lt-Tu3SZxnZxGJitEKHCh923QHHfvLqRAEqybJV4pxnq2VsFtsfdtJPUH6zWAEnDjKI5bz9YyCDYQhI0AobvfMPDGz_t8VTREYMb1FXqYMZdGb3s_9o6skkz4McziyKhvq2_bWfmcwD5MN7TNUIX8ATHq7NWQUvQFDedbkE7ju5jDe3CvzLAbidpkfDDKhlAnLh46PN_wDk_xWnID46-aMiCNgYZOYUn59uiq6mgnnMYpPWAAbRpMsRlYWN-l3qXQB82RoiM_OhbOne7co39swWxnjWDRS9vahAcAVE_olQ-HGQRkRjH7kWI4uXjEejn6JT_s-3-MKB8GSkyNn0_RZAFlJiD042ZAd1zrwS-ZXGkDTwA48yNtbDkrfGcUhttM3ZKdV5SSQG19UnjxE6o8uHIPWPyvsW4TYjHJlTXc09jZA4ueUO71G2j9pVZIGU4nyDux2TXsgePQPNdL04zB4MUjEVX5mbfYWQceMassn_iTldJZrZtJEfEJvUl3mESlyA21ryy7TI2u8GKL8Mic4JkbEgBDTk0p4PohxIlyorEbO_7g7E4MUhqE9Qh1Sta-flBAD0iehcTJ8Yoekb2tDDpTRhTN-25m0zqR8mjTI4KvYsH4QJObfATsTGYyBHi7QJNmuNlw6601PoL8gf0RWMQGDjp5qjba-2y3l2fjBy1wAQj29ltY4rqpT5McUu1UDVOoR9hByvZH4vLA1eLdAPTqE_IaFXfGVqIHyovTPWfJUweWzqrj0g0gV1LQr-9UvofFWPX5ngGumzsXtLY-TQa9J7N9C-jkVRUIh9n0VHxm-w1INF0QVkqtBSgpE-BK6pU_-lhoMdyfMtVIRA_Z1ieikX2xtb2zNuUj0mqqumYjNSDoFfLEvzSX847lzVUNUqkyIBCi5R5g6Vu8kdIXsO6Wyb89QIuRWZu-mnLOtAi7ebnNurjpQXL9LQLmOkOmrNonKUH6e4IeJNscPl3dffnyjCZxYx3z4Xtjh4mLn6n50lnEBu2X28X_elyni3OgnnwOnmgGmKMKlCmVJ6_yciNx5SBxH3GScyminSSNoeLTmlHjjxeP2NZx8fYrwgf5j2gj8rYSkHYL2CiTtLN-mK-DbCkja8f7MivR-5onIwTtG6Jmh_H_80HCcGSOWHTEyfJD7DhhdKhJyMTq9xp-B6ZCS3bz7AhXEbvVtuMYBIPbxjdrhdv5uctQ3GYB72DJfKoaiCUnfvy_HRxayed1UswYDT6eA55BZHLC9gFAHMt1pmqV2bqxooDxfpTlPXBdfvHqphI3CVz4qIPK5chsdVC19aOh3pQrximlB_5qJAcNCZ3xtqyPO1Rf3sh53elsXW7gwhgzbPLe0opjexYDAC0OMiH_YJOZ4QVhu69SLc_jjfBH3D55qEg6r_AVETCCnNfF3iZwagkj75_aT24kr-W9vBVOctn3RngoKGsCYQvqZDTPSHjRpbsXe2pd7-a8tMRMXFaar7rBiXkeRjMkUxQuA5uxDKG1Fh-fpLmJU9haNmOL3xSysFu2Ep6eNbGYZ3djHKoHOL2kQYPEBIZ17R1tcO5DWgIxo0AQN4WOW5JkJh1s4CMtQAmDa7yRhDI49nQ8UByC1BIKgP1NJ99kD4wxS0IUHZ90zPcDq59UhtI1Xkr8J99Enp6u5Y1Qnhaf0l1WBo8O4qvHkRQl9oP8KfUz642S46w==

nslsii/__init__.py

@@ -1,12 +1,14 @@
+from IPython import get_ipython
 from ._version import get_versions
 __version__ = get_versions()['version']
 del get_versions
 
 
 def import_star(module, ns):
-    public = lambda name: not name.startswith('_')
+    def public(name):
+        return not name.startswith('_')
     ns.update({name: getattr(module, name)
-                        for name in dir(module) if public(name)})
+               for name in dir(module) if public(name)})
 
 
 def configure_base(user_ns, broker_name, *,

nslsii/common/ipynb/info.py

@@ -3,10 +3,9 @@
 import platform
 from IPython.display import HTML
 
+
 def get_sys_info():
     """Display info on system and output as nice HTML"""
-    spacer = "<tr><td>&nbsp;</td><td>&nbsp;</td></tr>"
-
     html = '<h3>System Information for {}</h3>'.format(platform.node())
     html += '<table>'
 
@@ -31,6 +30,7 @@ def get_sys_info():
     html += '</table>'
     return HTML(html)
 
+
 def show_kernels():
     """Show all IPython Kernels on System"""
 
@@ -56,12 +56,12 @@ def show_kernels():
                 p = psutil.Process(pinfo['pid']).cpu_percent(0.1)
                 html += '<td>{}%</td>'.format(p)
                 html += '<td>{:.4} Mb</td>'.format(pinfo['memory_info'].vms /
-                                                1024**3)
-                html += '<td>{:.3}%</td>'.format(100 *pinfo['memory_info'].vms /
-                                                total_mem)
+                                                   1024**3)
+                html += '<td>{:.3}%</td>'.format(100 *
+                                                 pinfo['memory_info'].vms /
+                                                 total_mem)
                 html += '<td>{}</td>'.format(pinfo['status'])
                 html += '</tr>'
 
     html += '</table>'
     return HTML(html)
-

nslsii/detectors/trigger_mixins.py

@@ -147,7 +147,7 @@ def trigger_external(self):
         self._status._finished()
         # TODO this timestamp is inaccurate!
         if self.mode_settings.scan_type.get() != 'fly':
-            # Don't dispatch images for fly-scans - they are bulk read at the end
+            # Don't dispatch images for fly-scans-they are bulk read at the end
             self.dispatch(self._image_name, ttime.time())
         return self._status
 
@@ -173,7 +173,8 @@ def _reset_data(self):
     def bulk_read(self, timestamps):
         image_name = self.image_name
 
-        uids = [self.generate_datum(self.image_name, ts, {}) for ts in timestamps]
+        uids = [self.generate_datum(self.image_name, ts, {})
+                for ts in timestamps]
 
         # clear so unstage will not save the images twice:
         self._reset_data()

nslsii/detectors/utils.py

@@ -1,6 +1,5 @@
 from __future__ import print_function
 import os
-from ophyd import Signal
 
 
 def makedirs(path, mode=0o777):

nslsii/detectors/xspress3.py

@@ -2,7 +2,6 @@
 import time
 import time as ttime
 import logging
-import uuid
 
 from pathlib import PurePath
 from .utils import makedirs
@@ -95,7 +94,7 @@ def read(self):
         timestamp = time.time()
 
         uids = [self._reg.register_datum(
-            self._filestore_res, {'frame': self.parent._abs_trigger_count -1,
+            self._filestore_res, {'frame': self.parent._abs_trigger_count - 1,
                                   'channel': chan})
                 for chan in self.channels]
 

requirements-dev.txt

@@ -0,0 +1,11 @@
+# These are required for developing the package (running the tests, building
+# the documentation) but not necessarily required for _using_ it.
+codecov
+coverage
+flake8
+ipython
+matplotlib
+numpydoc
+pytest
+sphinx
+sphinx_rtd_theme

setup.py

@@ -7,13 +7,13 @@
     requirements = f.read().splitlines()
 
 setuptools.setup(
-	name='nslsii',
+    name='nslsii',
     version=versioneer.get_version(),
-	cmdclass=versioneer.get_cmdclass(),
+    cmdclass=versioneer.get_cmdclass(),
     license="BSD (3-clause)",
     packages=setuptools.find_packages(),
     description='Tools for data collection and analysis at NSLS-II',
-	author='Stuart B. Wilkins',
+    author='Stuart B. Wilkins',
     author_email='[email protected]',
     install_requires=requirements,
 )