Add patch CLI (#258)

adds a --patch flag to pyhf cls and tests

Additionally adds jsonpatch as a core dependency

c.f. https://github.com/stefankoegl/python-json-patch

pyhf/commandline.py

@@ -5,12 +5,14 @@
 import click
 import json
 import os
+import jsonpatch
 
 from . import readxml
 from . import writexml
 from .utils import runOnePoint
 from .pdf import Model
 
+
 @click.group(context_settings=dict(help_option_names=['-h', '--help']))
 def pyhf():
     pass
@@ -45,8 +47,9 @@ def json2xml(workspace,xmlfile,specroot,dataroot):
 @click.argument('workspace', default = '-')
 @click.option('--output-file', help='The location of the output json file. If not specified, prints to screen.', default=None)
 @click.option('--measurement', default=None)
+@click.option('-p','--patch', multiple = True)
 @click.option('--qualify-names/--no-qualify-names', default=False)
-def cls(workspace, output_file, measurement, qualify_names):
+def cls(workspace, output_file, measurement, qualify_names, patch):
     specstream = click.open_file(workspace)
     d = json.load(specstream)
     measurements = d['toplvl']['measurements']
@@ -63,7 +66,11 @@ def cls(workspace, output_file, measurement, qualify_names):
             measurement_index = measurement_names.index(measurement)
 
         log.debug('calculating CLs for measurement {0:s}'.format(measurements[measurement_index]['name']))
-        p = Model({'channels':d['channels']}, poiname=measurements[measurement_index]['config']['poi'], qualify_names=qualify_names)
+        spec = {'channels':d['channels']}
+        for p in patch:
+            p = jsonpatch.JsonPatch(json.loads(click.open_file(p).read()))
+            spec = p.apply(spec)
+        p = Model(spec, poiname=measurements[measurement_index]['config']['poi'], qualify_names=qualify_names)
         result = runOnePoint(1.0, sum((d['data'][c['name']] for c in d['channels']),[]) + p.config.auxdata, p)
         result = {'CLs_obs': result[-2].tolist()[0], 'CLs_exp': result[-1].ravel().tolist()}
         if output_file is None:

setup.py

@@ -14,6 +14,7 @@
     'tqdm',  # for readxml
     'six',  # for modifiers
     'jsonschema>=v3.0.0a2',  # for utils, alpha-release for draft 6
+    'jsonpatch'
   ],
   extras_require = {
     'xmlimport': [

tests/test_scripts.py

@@ -68,3 +68,42 @@ def test_import_and_export(tmpdir, script_runner):
 
     command = 'pyhf json2xml {0:s} --specroot {1:s} --dataroot {1:s}'.format(temp.strpath,str(tmpdir))
     ret = script_runner.run(*shlex.split(command))
+    assert ret.success
+
+def test_patch(tmpdir, script_runner):
+    patch = tmpdir.join('patch.json')
+
+    patchcontent = u'''
+[{"op": "replace", "path": "/channels/0/samples/0/data", "value": [5,6]}]
+    '''
+    patch.write(patchcontent)
+
+    temp = tmpdir.join("parsed_output.json")
+    command = 'pyhf xml2json validation/xmlimport_input/config/example.xml --basedir validation/xmlimport_input/ --output-file {0:s}'.format(temp.strpath)
+    ret = script_runner.run(*shlex.split(command))
+
+    command = 'pyhf cls {0:s} --patch {1:s}'.format(temp.strpath,patch.strpath)
+    ret = script_runner.run(*shlex.split(command))
+    assert ret.success
+    import io
+    command = 'pyhf cls {0:s} --patch -'.format(temp.strpath,patch.strpath)
+
+    pipefile = io.StringIO(patchcontent) #python 2.7 pytest-files are not file-like enough
+    ret = script_runner.run(*shlex.split(command), stdin = pipefile)
+    print(ret.stderr)
+    assert ret.success
+
+
+def test_patch_fail(tmpdir, script_runner):
+    patch = tmpdir.join('patch.json')
+
+    patch.write('''not,json''')
+
+    temp = tmpdir.join("parsed_output.json")
+    command = 'pyhf xml2json validation/xmlimport_input/config/example.xml --basedir validation/xmlimport_input/ --output-file {0:s}'.format(temp.strpath)
+    ret = script_runner.run(*shlex.split(command))
+
+    command = 'pyhf cls {0:s} --patch {1:s}'.format(temp.strpath,patch.strpath)
+    ret = script_runner.run(*shlex.split(command))
+    assert not ret.success
+