Release 0.4.3

README.md

@@ -84,6 +84,14 @@ all existing files. We apologize for the inconveniences it incurs.
 
 ## Change Log
 
+### 0.4.3
+
+- Issue #94 revisited.
+- [minor] Fix syntax incompatibility with earlier versions of `msgpack`.
+- [minor] Fix a bug of not updating meta-database when `-s existing` is used.
+
+**A file signature clean up is required after this upgrade.**
+
 ### 0.4.2
 
 - Issue #214 for container support.

dscrutils/DESCRIPTION

@@ -1,7 +1,7 @@
 Package: dscrutils
 Encoding: UTF-8
 Type: Package
-Version: 0.4.2
+Version: 0.4.3
 Date: 2019-12-03
 Title: Dynamic Statistical Comparisons R Interface
 Authors@R: c(person("Gao","Wang",role=c("aut","cre"),

release.sos

@@ -15,7 +15,7 @@ sh: workdir = '.'
  pandoc --from=markdown --to=rst --output=README.rst README.md
 
 [pip]
-depends: "README.rst"
+depends: "README.rst", Py_Module('twine')
 parameter: version = str
 # check the version of the latest version
 cur_ver = get_output(f"pip{py} show dsc | grep Version | cut -d' ' -f2").strip()
@@ -25,13 +25,7 @@ stop_if(cur_ver == version)
 
 sh: workdir = '.', expand = True 
  python{py} setup.py sdist && \
- rm -rf /tmp/release_dsc && \
- mkdir /tmp/release_dsc && \
- cp dist/dsc-{version}.tar.gz /tmp/release_dsc && \
- cd /tmp/release_dsc && \
- tar zxf dsc-{version}.tar.gz && \
- cd dsc-{version} && \
- python{py} setup.py sdist bdist_wheel upload && \
+ twine upload dist/dsc-{version}.tar.gz && \
  pip{py} install -U --upgrade-strategy only-if-needed .
 
 [upgrade]

setup.py

@@ -53,7 +53,7 @@ def run(self):
  cmdclass = cmdclass,
  package_dir = {'dsc': 'src'},
  install_requires = ['numpy', 'pandas>=0.24.1', 'sympy', 'numexpr',
- 'sos>=0.21.5', 'sos-pbs>=0.20.3', 'h5py', 'PTable',
+ 'sos>=0.21.6', 'sos-pbs>=0.20.3', 'h5py', 'PTable',
  'pyarrow>=0.5.0', 'sqlalchemy', 'tzlocal',
  'msgpack-python']
  )

src/utils.py

@@ -8,7 +8,7 @@
 from itertools import cycle, chain, islice
 from fnmatch import fnmatch
 from difflib import SequenceMatcher
-from collections.abc import MutableMapping
+from collections.abc import Mapping, MutableMapping
 try:
  from xxhash import xxh32 as xxh
 except ImportError:
@@ -151,7 +151,7 @@ def lower_keys(x, level_start=0, level_end=2, mapping=dict):
  return x
  if isinstance(x, list):
  return [lower_keys(v, level_start, level_end) for v in x]
- elif isinstance(x, collections.Mapping):
+ elif isinstance(x, Mapping):
  return mapping((k.lower(), lower_keys(v, level_start, level_end))
  for k, v in x.items())
  else:
@@ -164,7 +164,7 @@ def is_null(var):
  if isinstance(var, str):
  if var.lower() in ['na', 'nan', 'null', 'none', '']:
  return True
- if isinstance(var, (list, tuple, collections.Mapping)):
+ if isinstance(var, (list, tuple, Mapping)):
  return True if len(var) == 0 else False
  return False
 
@@ -217,11 +217,11 @@ def flatten_list(lst):
 
 
 def flatten_dict(d, mapping=dict):
- if not isinstance(d, collections.Mapping):
+ if not isinstance(d, Mapping):
  return d
  items = []
  for k, v in d.items():
- if isinstance(v, collections.Mapping):
+ if isinstance(v, Mapping):
  items.extend(flatten_dict(v).items())
  else:
  items.append((k, v))
@@ -371,19 +371,19 @@ def find_nested_key(key, dictionary):
  for k, v in dictionary.items():
  if k == key:
  yield [k]
- elif isinstance(v, collections.Mapping):
+ elif isinstance(v, Mapping):
  for result in find_nested_key(key, v):
  yield [k] + result
  elif isinstance(v, list):
  for d in v:
- if isinstance(d, collections.Mapping):
+ if isinstance(d, Mapping):
  for result in find_nested_key(key, d):
  yield [k] + result
 
 
 def recursive_items(dictionary):
  for key, value in dictionary.items():
- if isinstance(value, collections.Mapping):
+ if isinstance(value, Mapping):
  yield (key, value)
  yield from recursive_items(value)
  else:
@@ -402,7 +402,7 @@ def dict2str(value):
 
 def update_nested_dict(d, u, mapping=dict):
  for k, v in u.items():
- if isinstance(v, collections.Mapping):
+ if isinstance(v, Mapping):
  r = update_nested_dict(d.get(k, mapping()), v)
  d[k] = r
  else:
@@ -411,7 +411,7 @@ def update_nested_dict(d, u, mapping=dict):
 
 
 def strip_dict(data, mapping=dict, into_list=False, skip_keys=None):
- if not isinstance(data, collections.Mapping):
+ if not isinstance(data, Mapping):
  return data
  skip_keys = skip_keys or []
  mapping_null = [dict()]
@@ -420,7 +420,7 @@ def strip_dict(data, mapping=dict, into_list=False, skip_keys=None):
  if k in skip_keys:
  new_data[k] = v
  continue
- if isinstance(v, collections.Mapping):
+ if isinstance(v, Mapping):
  v = strip_dict(v, mapping, into_list)
  if isinstance(v, list) and into_list:
  v = [strip_dict(x, mapping, into_list) for x in v]

src/version.py

@@ -1 +1 @@
-__version__ = '0.4.2'
+__version__ = '0.4.3'

test/test_interface.sos

@@ -13,5 +13,6 @@ bash: expand = True, workdir = f'{_input:d}'
  fi
 
 [default_2]
+input: group_by = 'all'
 R: workdir = '../dscrutils'
  devtools::test('tests')

test/test_parser.py

@@ -55,7 +55,7 @@
  @simulate:
  x: 1
  y: 2
- @ALIAS: 
+ @ALIAS:
  simulate: x_1 = x
  $out: x
 '''
@@ -72,7 +72,7 @@
  @simulate:
  x: 1
  y: 2
- @ALIAS: 
+ @ALIAS:
  *: x_1 = x
  $out: x
 '''
@@ -147,9 +147,9 @@ def testBasicSyntaxPass(self):
  self.assertEqual(list(res.modules['simulate'].plugin.alias_map.items()), [('x', 'x_1')])
  # use global variable
  res = DSC_Script(text11)
- self.assertEqual(list(res.modules['simulate'].dump()['input'].items()), [('x', [2]), ('y', [2])])
+ self.assertEqual(list(res.modules['simulate'].dump()['input'].items()), [('x', [1]), ('y', [2])])
  res = DSC_Script(text12)
- self.assertEqual(list(res.modules['simulate'].dump()['input'].items()), [('x', [4,3,2,1]), ('y', [2])])
+ self.assertEqual(list(res.modules['simulate'].dump()['input'].items()), [('x', [1]), ('y', [2])])
  # alias partial list / dict
  res = DSC_Script(text13)
  self.assertEqual(list(res.modules['simulate'].plugin.dump()['container_variables'].items()), [('x', [None, 'xvar']), ('y', [None, 'yy'])])
@@ -188,7 +188,7 @@ def testLegalNamesFail(self):
  text = '''
 simulate: R()
  .x: 1
-DSC: 
+DSC:
  run: simulate
 '''
  self.assertRaises(FormatError, DSC_Script, text)
@@ -244,7 +244,7 @@ def testModuleDerivationPass(self):
 base: R(base=1)
  x: 2
  $out: x
-simulate(base): 
+simulate(base):
  x: R(1:5)
 '''
  res = DSC_Script(text)
@@ -266,7 +266,7 @@ def testModuleDerivationPass(self):
  y: 5
  n: 6
  $x: x
- 
+
 simulate(normal):
  mu: 1
 '''
@@ -277,7 +277,7 @@ def testModuleDerivationPass(self):
  def testModuleDerivationFail(self):
  # missing executable
  text = text0 + '''
-simulate: 
+simulate:
  x: R{1:5}
  $out: x
 '''
@@ -290,8 +290,8 @@ def testModuleDerivationFail(self):
  y: 5
  n: 6
  $x: x
- 
-simulate(normal, t): 
+
+simulate(normal, t):
  mu: 1
 DSC:
  run: test
@@ -305,17 +305,17 @@ def testModuleDerivationFail(self):
  y: 5
  n: 6
  $x: x
- 
+
 shifted_normal(normal):
  mu: 1
-''' 
+'''
  self.assertRaises(FormatError, DSC_Script, text)
  # non-existing base
  text = text0 + '''
 base: R()
  x: 2
  $out: x
-simulate(base1): 
+simulate(base1):
  x: R(1:5)
 '''
  self.assertRaises(FormatError, DSC_Script, text)
@@ -409,7 +409,7 @@ def testDuplicatesFail(self):
 
 simulate: R()
  $x: 7
-''' 
+'''
  self.assertWarns(UserWarning, DSC_Script, text)
  text = text0 + '''
 simulate: R()
@@ -472,7 +472,7 @@ def testFilterPass(self):
 simulate, t: R(), R()
  n: 100, 200, 300, 400, 500
  k: 0, 1
- @FILTER: 
+ @FILTER:
  *: n in [100,200,300]
  t: n = 300
  $x: x