Merge 0e556e4 into 2c26a11

conda-recipe/meta.yaml

@@ -32,16 +32,14 @@ requirements:
     - setuptools
     - h5py
     - lxml
-    - matplotlib
+    - matplotlib-base
     - numpy
-    - six
 
   run:
     - h5py
     - lxml
-    - matplotlib
+    - matplotlib-base
     - numpy
-    - six
 
 test:
 
@@ -50,7 +48,6 @@ test:
 
   commands:
     - spec2nexus --help
-    - python run_test.py
 
 extra:
   recipe-maintainers:

docs/source/_static/pv_plugin.py

@@ -1,11 +1,9 @@
 from collections import OrderedDict
-import six
 from spec2nexus.plugin import AutoRegister
 from spec2nexus.plugin import ControlLineHandler
 from spec2nexus.utils import strip_first_word
 
-@six.add_metaclass(AutoRegister)
-class PV_ControlLine(ControlLineHandler):
+class PV_ControlLine(ControlLineHandler, metaclass=AutoRegister):
     '''**#PV** -- EPICS PV associates mnemonic with PV'''
 
     key = '#PV'

docs/source/conf.py

@@ -198,4 +198,4 @@
 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
 
 # http://www.sphinx-doc.org/en/master/usage/extensions/autodoc.html#confval-autodoc_mock_imports
-autodoc_mock_imports = "h5py numpy matplotlib pyRestTable".split()
+autodoc_mock_imports = "h5py numpy matplotlib".split()

docs/source/how_to_write_plugin.rst

@@ -65,26 +65,18 @@ plugin manager to automatically register your new plugin.
 Write a plugin module
 *********************
 
-Give the custom plugin module a name ending with ``.py``.
-As with any Python module, the name must be unique within a directory.
-If the plugin is not in your working directory,
-there must be a ``__init__.py`` file in the same directory (even if 
-that file is empty) so that your plugin module can be loaded with ``import <MODULE>``.
-
-**Plugin module setup**
-
-.. sidebar:: The ``six`` package
-
-   The ``six`` package is used to make our plugins run with either
-   Python 2.7 or Python 3.5+.
-
-Please view the existing plugins in :mod:`~spec2nexus.plugins.spec_common`
-for examples.  The custom plugin module should contain, at minimum one subclass of  
-:class:`spec2nexus.plugin.ControlLineHandler` which is decorated
-with ``@six.add_metaclass(spec2nexus.plugin.AutoRegister)``.  
-The ``add_metaclass`` decorator allows our custom ControlLineHandlers 
-to register themselves when their module is imported.
-A custom plugin module can contain many such handlers, as needs dictate.
+Give the custom plugin module a name ending with ``.py``. As with any Python
+module, the name must be unique within a directory. If the plugin is not in your
+working directory, there must be a ``__init__.py`` file in the same directory
+(even if that file is empty) so that your plugin module can be loaded with
+``import <MODULE>``.
+
+Please view the existing plugins in :mod:`~spec2nexus.plugins.spec_common` for
+examples.  The custom plugin module should contain, at minimum one subclass of
+:class:`spec2nexus.plugin.ControlLineHandler` and the keyword argument
+``metaclass=AutoRegister``. The ``metaclass`` keyword argument allows our custom
+ControlLineHandlers to register themselves when their module is imported. A
+custom plugin module can contain many such handlers, as needs dictate.
 
 .. sidebar::  Useful ``import``
 
@@ -97,7 +89,6 @@ These imports are necessary to to write plugins for *spec2nexus*:
 .. code-block:: python
    :linenos:
 
-   import six
    from spec2nexus.plugin import AutoRegister
    from spec2nexus.plugin import ControlLineHandler
    from spec2nexus.utils import strip_first_word
@@ -253,12 +244,10 @@ we create one that ignores processing by doing nothing:
 .. code-block:: python
    :linenos:
 
-   import six
    from spec2nexus.plugin import AutoRegister
    from spec2nexus.plugin import ControlLineHandler
    
-   @six.add_metaclass(AutoRegister)
-   class Ignore_Y_ControlLine(ControlLineHandler):
+   class Ignore_Y_ControlLine(ControlLineHandler, metaclass=AutoRegister):
        '''
        **#Y** -- as in ``#Y 1 2 3 4 5``
        
@@ -338,13 +327,11 @@ Gathering all parts of the examples above, the custom plugin module is:
 .. code-block:: python
    :linenos:
 
-   import six
    from spec2nexus.plugin import AutoRegister
    from spec2nexus.plugin import ControlLineHandler
    from spec2nexus.utils import strip_first_word
    
-   @six.add_metaclass(AutoRegister)
-   class User_ControlLine(ControlLineHandler):
+   class User_ControlLine(ControlLineHandler, metaclass=AutoRegister):
        '''**#U** -- User data (#U user1 user2 user3)'''
    
        key = '#U'
@@ -367,8 +354,7 @@ Gathering all parts of the examples above, the custom plugin module is:
        scan.U_sum = sum(scan.U)
    
    
-   @six.add_metaclass(AutoRegister)
-   class Ignore_Y_ControlLine(ControlLineHandler):
+   class Ignore_Y_ControlLine(ControlLineHandler, metaclass=AutoRegister):
        '''**#Y** -- as in ``#Y 1 2 3 4 5``'''
    
        key = '#Y'
@@ -503,7 +489,7 @@ Summary Requirements for custom plugin
 * for each control line:
 
   * subclass :class:`spec2nexus.plugin.ControlLineHandler`
-  * add ``@six.add_metaclass(AutoRegister)`` decorator to auto-register the plugin
+  * add ``metaclass=AutoRegister`` keyword argument to auto-register the plugin
   * import the module you defined (FIXME:  check this and revise)
   * identify the control line pattern
   * define ``key`` with a regular expression to match [#]_

docs/source/unit_testing.rst

@@ -3,43 +3,39 @@
 Unit Testing
 ############
 
-Since release 2017.0201.0, this project relies on the Python *unittest* [#]_ 
-package to apply
-unit testing [#]_ to the source code.  The test code is in the `tests`
-directory.  Various tests have been developed starting with the *2017.0201.0* 
-release to provide features or resolve problems reported.  The tests are not 
-yet exhaustive yet the reported code coverage [#]_ is well over 80%.
+This project uses the Python *pytest* [#]_ package to apply unit testing [#]_ to
+the source code.  The test code is in the ``tests/`` directories.  Various tests
+have been developed starting to provide features or resolve problems reported.
 
 The unit tests are implemented in a standard manner such that independent
-review [#]_ can run the tests on this code based on the instructions provided 
-in a `.travis.yml` configuration file in the project directory.
+review [#]_ can run the tests on this code based on the instructions provided
+in ``.github/workflows`` configuration files in the project directory.
 
 This command will run the unit tests locally::
 
-    python tests
+    pytest -vvv .
 
 Additional information may be learned with a Python package to run the tests::
 
-    coverage run -a tests && coverage report -m
+    coverage run -m pytest --lf -vvv .
 
-The *coverage* command ([#]_), will run the tests and then prepare a report of 
-the percentage of the Python source code that has been executed during the
-unit tests.
+The *coverage* command ([#]_), will run the tests and create a report of the
+percentage of the Python source code that has been executed during the unit
+tests::
 
-.. note:: The number of lines reported by *coverage* may differ from that 
-   reported by *travis-ci*.  The primary reason is that certain tests involving
-   access to information from GitHub may succeed or not depending on the 
-   "Github API rate limit". [#]_
+    coverage report --precision 3
 
-.. [#] Python *unittest* package: 
-   https://docs.python.org/2/library/unittest.html
+The unit tests on GitHub automatically upload the coverage results to the
+*coveralls* [#]_ site [#]_ which tracks coverage over time.
 
-.. [#] unit testing: https://en.wikipedia.org/wiki/Unit_testing
+.. [#] Python *pytest* package: https://pytest.org
 
-.. [#] *coveralls* code coverage: https://coveralls.io/github/prjemian/spec2nexus
+.. [#] unit testing: https://en.wikipedia.org/wiki/Unit_testing
 
-.. [#] *travis-ci* continuous intregration: https://travis-ci.org/prjemian/spec2nexus
+.. [#] GitHub Actions workflow: https://github.com/prjemian/spec2nexus/actions
 
 .. [#] *coverage*: https://coverage.readthedocs.io
 
-.. [#] Github API rate limit: https://developer.github.com/v3/rate_limit/
+.. [#] *coveralls*: https://coveralls.io
+
+.. [#] *coveralls* code coverage: https://coveralls.io/github/prjemian/spec2nexus

environment.yml

@@ -1,12 +1,9 @@
-name: pyRestTable
+name: spec2nexus
 channels:
   - defaults
   - conda-forge
-  - prjemian
 dependencies:
   - h5py
   - lxml
-  - matplotlib
+  - matplotlib-base
   - numpy
-  - pyRestTable
-  - six

requirements-dev.txt

@@ -1,3 +1,4 @@
-versioneer
 coverage
 coveralls
+docopt
+versioneer

requirements.txt

@@ -1,8 +1,4 @@
-coverage
-docopt
 h5py
 lxml
-matplotlib
+matplotlib-base
 numpy
-pyRestTable
-six

src/spec2nexus/eznx.py

@@ -1,7 +1,6 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
-
 """
 (Easy NeXus) support reading & writing NeXus HDF5 files using h5py
 
@@ -59,10 +58,8 @@
 
 """
 
-
 import h5py  # HDF5 support
 import numpy
-import six
 
 
 def makeFile(filename, **attr):
@@ -140,7 +137,7 @@ def makeDataset(parent, name, data=None, **attr):
         # https://stackoverflow.com/questions/23220513/
         # [n.encode("ascii", "ignore") for n in data]
         def encoder(value):
-            if isinstance(value, six.string_types):
+            if isinstance(value, str):
                 return value.encode("ascii", "ignore")
             return value
 

src/spec2nexus/plugins/XPCS.py

@@ -10,16 +10,13 @@
 SPEC data file control lines unique to the APS XPCS instrument
 """
 
-import six
-
 from ..eznx import makeGroup
 from ..plugin import AutoRegister, ControlLineHandler
 from ..spec import SpecDataFileHeader, SpecDataFileScan
 from ..utils import strip_first_word
 
 
-@six.add_metaclass(AutoRegister)
-class XPCS_VA(ControlLineHandler):
+class XPCS_VA(ControlLineHandler, metaclass=AutoRegister):
     """**#VA**"""
 
     key = r"#VA\d+"
@@ -43,8 +40,7 @@ def writer(self, h5parent, writer, scan, nxclass=None, *args, **kws):
         writer.save_dict(group, dd)
 
 
-@six.add_metaclass(AutoRegister)
-class XPCS_VD(ControlLineHandler):
+class XPCS_VD(ControlLineHandler, metaclass=AutoRegister):
     """**#VD** """
 
     key = r"#VD\d+"
@@ -69,8 +65,7 @@ def writer(self, h5parent, writer, scan, nxclass=None, *args, **kws):
         writer.save_dict(group, dd)
 
 
-@six.add_metaclass(AutoRegister)
-class XPCS_VE(ControlLineHandler):
+class XPCS_VE(ControlLineHandler, metaclass=AutoRegister):
     """**#VE** """
 
     key = r"#VE\d+"
@@ -95,8 +90,7 @@ def writer(self, h5parent, writer, scan, nxclass=None, *args, **kws):
         writer.save_dict(group, dd)
 
 
-@six.add_metaclass(AutoRegister)
-class XPCS_XPCS(ControlLineHandler):
+class XPCS_XPCS(ControlLineHandler, metaclass=AutoRegister):
     """#XPCS"""
 
     key = r"#XPCS"
@@ -114,8 +108,7 @@ def writer(self, h5parent, writer, scan, nxclass=None, *args, **kws):
         pass
 
 
-@six.add_metaclass(AutoRegister)
-class XPCS_CCD(ControlLineHandler):
+class XPCS_CCD(ControlLineHandler, metaclass=AutoRegister):
     """#CCD"""
 
     key = r"#CCD"

src/spec2nexus/plugins/apstools_specwriter.py

@@ -22,14 +22,12 @@
 """
 
 from collections import OrderedDict
-import six
 
 from .. import eznx
 from ..plugin import AutoRegister, ControlLineHandler
 
 
-@six.add_metaclass(AutoRegister)
-class MD_apstools(ControlLineHandler):
+class MD_apstools(ControlLineHandler, metaclass=AutoRegister):
 
     """**#MD** -- Bluesky metadata from apstools SpecWriterCallback"""
 

src/spec2nexus/plugins/fallback.py

@@ -6,15 +6,13 @@
 """
 
 from collections import OrderedDict
-import six
 
 from ..eznx import makeGroup
 from ..plugin import AutoRegister, ControlLineHandler
 from ..spec import UNRECOGNIZED_KEY, SpecDataFileHeader, SpecDataFileScan
 
 
-@six.add_metaclass(AutoRegister)
-class UnrecognizedControlLine(ControlLineHandler):
+class UnrecognizedControlLine(ControlLineHandler, metaclass=AutoRegister):
 
     """unrecognized control line"""