Allow custom Rivet identifier, fix ErrorBreakdown, improve PyPI release

* Fix check for non-numeric independent variables in ObjectWrapper.
* Define bin number excluding non-numeric y values in ErrorBreakdown.
* Allow custom Rivet identifier as YAML qualifier for YODA export.
* Build wheel archive on Travis CI to push to PyPI for tagged release.
* Change PyPI authentication to use (encrypted) API token not password.
* Add badge to README showing latest version available from PyPI.
* Specify recommended ROOT and YODA versions in README.
* Add long description to setup.cfg as contents of README.
* Bump version to 0.1.35 in preparation for tagged release.

Signed-off-by: Graeme Watt <Graeme.Watt@durham.ac.uk>

.travis.yml

@@ -17,16 +17,17 @@ install:
 script:
   - export CURRENT_PATH=`pwd`
   - docker run -v $CURRENT_PATH:$CURRENT_PATH hepdata/hepdata-converter:0.1.35 /bin/bash -c "cd  $CURRENT_PATH && coverage run -m unittest discover hepdata_converter/testsuite 'test_*'"
-  - docker run -v $CURRENT_PATH:$CURRENT_PATH hepdata/hepdata-converter:0.1.35 /bin/bash -c "cd  $CURRENT_PATH && python setup.py install sdist && hepdata-converter -v"
+  - docker run -v $CURRENT_PATH:$CURRENT_PATH hepdata/hepdata-converter:0.1.35 /bin/bash -c "cd  $CURRENT_PATH && python setup.py install sdist bdist_wheel && hepdata-converter -v"
 after_success:
   - coveralls
 
 deploy:
   skip_cleanup: true
   provider: pypi
-  user: hepdata
+  user: "__token__"
   password:
-    secure: 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
+    secure: "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"
+  distributions: "sdist bdist_wheel"
   on:
     tags: true
     repo: HEPData/hepdata-converter

README.rst

@@ -19,6 +19,10 @@ HEPData Converter
    :target: https://github.com/HEPData/hepdata-converter/releases
    :alt: GitHub Releases
 
+.. image:: https://img.shields.io/pypi/v/hepdata-converter
+   :target: https://pypi.org/project/hepdata-converter/
+   :alt: PyPI Version
+
 .. image:: https://img.shields.io/github/issues/hepdata/hepdata-converter.svg?maxAge=2592000
    :target: https://github.com/HEPData/hepdata-converter/issues
    :alt: GitHub Issues
@@ -33,8 +37,8 @@ This Python library provides support for converting:
 * Old HepData input format (`sample <https://github.com/HEPData/hepdata-submission/blob/master/examples/oldhepdata/sample.oldhepdata>`_) to `YAML <https://github.com/HEPData/hepdata-submission>`_
 * `YAML <https://github.com/HEPData/hepdata-submission>`_ to:
 
-  * `ROOT <https://root.cern.ch>`_
-  * `YODA <https://yoda.hepforge.org>`_
+  * `ROOT <https://root.cern.ch>`_ (tested with v6.20.00)
+  * `YODA <https://yoda.hepforge.org>`_  (tested with v1.7.7)
   * `CSV <https://en.wikipedia.org/wiki/Comma-separated_values>`_
 
 Documentation: http://hepdata-converter.readthedocs.io

hepdata_converter/version.py

@@ -1,3 +1,3 @@
 # this file ideally should only contain __version__ declaration, as anything else
 # may break setup.py and PyPI uploads
-__version__ = '0.1.34'
+__version__ = '0.1.35'

hepdata_converter/writers/array_writer.py

@@ -71,8 +71,8 @@ def __init__(self, independent_variable_map, dependent_variable, dependent_varia
     def match(cls, independent_variables_map, dependent_variable):
         if not cls.accept_alphanumeric:
             # don't match if any independent or dependent variable values are non-numeric
-            for var in independent_variables_map:
-                if False in cls.is_number_var(dependent_variable):
+            for independent_variable in independent_variables_map:
+                if False in cls.is_number_var(independent_variable):
                     return False
             if False in cls.is_number_var(dependent_variable):
                 return False
@@ -119,13 +119,14 @@ def get_next_object(self):
             for class_wrapper in self.class_list:
                 # if auxiliary object was already created for this variable, don't create more
                 # (eg. after creating TH3 (which does not consume variables) don't create TH2 & TH1,
-                # but go for best fit of "core" objects eg. TGraph
+                # but go for best fit of "core" objects eg. TGraph)
 
                 if not class_wrapper.core_object and auxiliary_object_created:
                     continue
 
                 objects = class_wrapper.match_and_create(self.map[dependent_variable_index],
-                                                         self.dependent_variables[dependent_variable_index], dependent_variable_index)
+                                                         self.dependent_variables[dependent_variable_index],
+                                                         dependent_variable_index)
                 if objects and not class_wrapper.core_object:
                     auxiliary_object_created = True
 
@@ -161,27 +162,31 @@ def process_error_labels(value):
 
     @staticmethod
     def calculate_total_errors(variable, is_number_list, min_errs, max_errs, values, err_breakdown={}):
+        i_numeric = -1  # bin number excluding non-numeric y values
         for i, entry in enumerate(variable['values']):
-            if not is_number_list[i]: continue # skip non-numeric y values
+            if not is_number_list[i]:
+                continue  # skip non-numeric y values
+            else:
+                i_numeric += 1
             if 'value' in entry:
                 values.append(entry['value'])
                 if 'errors' in entry:
                     errors_min = 0.0
                     errors_max = 0.0
-                    err_breakdown[i] = {}
+                    err_breakdown[i_numeric] = {}
                     # process the error labels to ensure uniqueness
                     ArrayWriter.process_error_labels(entry)
                     for error in entry['errors']:
                         label = error.get('label', 'error')
-                        err_breakdown[i][label] = {}
+                        err_breakdown[i_numeric][label] = {}
                         if 'asymerror' in error:
                             try:
                                 err_minus = error_value_processor(entry['value'], error['asymerror']['minus'])
                                 err_plus = error_value_processor(entry['value'], error['asymerror']['plus'])
                                 errors_min += pow(min(err_plus, err_minus, 0.0), 2)
                                 errors_max += pow(max(err_plus, err_minus, 0.0), 2)
-                                err_breakdown[i][label]['up'] = err_plus # want to maintain directionality of errors
-                                err_breakdown[i][label]['dn'] = err_minus # want to maintain directionality of errors
+                                err_breakdown[i_numeric][label]['up'] = err_plus # want to maintain directionality of errors
+                                err_breakdown[i_numeric][label]['dn'] = err_minus # want to maintain directionality of errors
                             except TypeError:
                                 log.error('TypeError encountered when parsing {0} and {1}'.format(
                                     unicode(error['asymerror']['minus']).encode('utf8', 'replace'),
@@ -191,8 +196,8 @@ def calculate_total_errors(variable, is_number_list, min_errs, max_errs, values,
                                 err = error_value_processor(entry['value'], error['symerror'])
                                 errors_min += pow(err, 2)
                                 errors_max += pow(err, 2)
-                                err_breakdown[i][label]['up'] = err
-                                err_breakdown[i][label]['dn'] = -err
+                                err_breakdown[i_numeric][label]['up'] = err
+                                err_breakdown[i_numeric][label]['dn'] = -err
                             except TypeError:
                                 log.error('TypeError encountered when parsing {0}'.format(
                                     unicode(error['symerror']).encode('utf8', 'replace'))

hepdata_converter/writers/yoda_writer.py

@@ -113,9 +113,17 @@ def _write_table(self, data_out, table):
             table_doi = table.name
         f = ObjectFactory(self.class_list, table.independent_variables, table.dependent_variables)
         for idep, graph in enumerate(f.get_next_object()):
-            graph.title = table_doi
-            graph.path = '/REF/' + self.rivet_analysis_name + '/' \
-                         + 'd' + table_num.zfill(2) + '-x01-y' + str(idep + 1).zfill(2)
+            rivet_identifier = 'd' + table_num.zfill(2) + '-x01-y' + str(idep + 1).zfill(2)
+            # Allow the standard Rivet identifier to be overridden by a custom value specified in the qualifiers.
+            if 'qualifiers' in table.dependent_variables[idep]:
+                for qualifier in table.dependent_variables[idep]['qualifiers']:
+                    if qualifier['name'] == 'Custom Rivet identifier':
+                        rivet_identifier = qualifier['value']
+            rivet_path = '/REF/' + self.rivet_analysis_name + '/' + rivet_identifier
+            graph.title = table_doi  # use for YODA 1.7.7
+            graph.path = rivet_path  # use for YODA 1.7.7
+#            graph.setTitle(table_doi)  # use for YODA 1.8.1
+#            graph.setPath(rivet_path)  # use for YODA 1.8.1
             graph.setAnnotation('IsRef', '1')
             yoda.core.writeYODA(graph, data_out)
             data_out.write('\n')

setup.cfg

@@ -1,2 +1,3 @@
 [metadata]
-description-file = README.md
+long_description = file: README.rst
+long_description_content_type = text/x-rst

setup.py

@@ -1,4 +1,7 @@
 # -*- coding: utf-8 -*-
+
+"Library providing means of conversion between oldhepdata format to new one, and new one to csv / yoda / root etc."
+
 import os
 from setuptools import setup
 import re
@@ -42,11 +45,10 @@ def get_version():
     packages=['hepdata_converter', 'hepdata_converter.parsers', 'hepdata_converter.writers', 'hepdata_converter.testsuite'],
     package_data={'hepdata_converter': get_all_datafiles(package='hepdata_converter/testsuite', path='testdata')},
     include_package_data=True,
-
-    url='https://github.com/HEPData/hepdata-converter/',
+    url='https://github.com/HEPData/hepdata-converter',
     license='GPL',
     author='HEPData Team',
     author_email='info@hepdata.net',
-    description='Library providing means of conversion between oldhepdata format to new one, and new one to csv / yoda / root etc.',
-    download_url='https://github.com/HEPData/hepdata-converter/tarball/%s' % get_version(),
+    description=__doc__,
+    download_url='https://github.com/HEPData/hepdata-converter/tarball/%s' % get_version()
 )