Merge pull request #19 from ML-KULeuven/develop

Mainly bugfixes, but we also changed the Term's hashing method. If this proofs to be worse, we may reconsider switching back later.

* Bugfix library/string.py::str2lst (public issue #84)
* Bugfix return exit code instead of result - only for probability task atm (public issue #82)
* Critical Bugfix in dSharp library (compiled CNF theory with too long clauses could yield wrong result)
* Bugfix in pypl related to lists (private issue #16)
* Minor improvements to LFI
* Changed Term's hashing method

INSTALL

@@ -13,7 +13,7 @@ For better performance you can also run ProbLog with PyPy:
     http://pypy.org/download.html
 
 ProbLog's evaluation is based on knowledge compilation tools.
-By default it uses dsharp [https://bitbucket.org/haz/dsharp].
+By default it uses dsharp [https://github.com/QuMuLab/dsharp/].
 
 It also supports two other tools:
     * C2D Compiler (NNF) [http://reasoning.cs.ucla.edu/c2d/]
@@ -88,10 +88,30 @@ C2D is automatically used instead of dsharp when detected.
 Licenses of included third-party software
 -----------------------------------------
 
-DSharp [https://bitbucket.org/haz/dsharp]
+DSharp [https://github.com/QuMuLab/dsharp/]
 +++++++++++++++++++++++++++++++++++++++++
 
-GPLv2
+MIT License
+
+Copyright (c) 2022 Christian Muise
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
 
 SDD [http://reasoning.cs.ucla.edu/sdd/]
 +++++++++++++++++++++++++++++++++++++++

KNOWN_ISSUES

@@ -33,6 +33,7 @@ There are two possible solutions:
 
     - Use a different knowledge compiler that does not have this issue (c2d or SDD).
 
-    - Compile a dSharp 32-bit version (dSharp source: https://bitbucket.org/haz/dsharp/src/default/) 
+    - Compile a dSharp 32-bit version (dSharp source: https://github.com/QuMuLab/dsharp/)
     and replace the original dSharp file with it. The path can be found in the OSError message.
     Alternatively, use the 32-bit version in this zip: https://github.com/ML-KULeuven/problog/files/3448011/dsharp.zip
+    Note: the .zip version is outdated and needs to be replaced (that binary has a limit on CNF clause length).

README.md

@@ -23,10 +23,6 @@ tested on *Mac OSX*, *Linux* and *Windows*.
 
 [![CircleCI](https://circleci.com/gh/ML-KULeuven/problog/tree/master.svg?style=svg)](https://circleci.com/gh/ML-KULeuven/problog/tree/master)
 [![codecov](https://codecov.io/gh/ML-KULeuven/problog/branch/master/graph/badge.svg)](https://codecov.io/gh/ML-KULeuven/problog/branch/master)
-dev:
-[![CircleCI](https://circleci.com/gh/ML-KULeuven/problog/tree/develop.svg?style=svg)](https://circleci.com/gh/ML-KULeuven/problog/tree/develop)
-[![codecov](https://codecov.io/gh/ML-KULeuven/problog/branch/develop/graph/badge.svg)](https://codecov.io/gh/ML-KULeuven/problog/branch/develop)
-
 
 ProbLog supports optional components which can be installed separately.
 See the file [INSTALL](https://github.com/ML-KULeuven/problog/blob/develop/INSTALL) for detailed installation instructions.

conversions/bn2problog.py

@@ -9,7 +9,6 @@
 import sys
 import os
 import argparse
-import itertools
 import logging
 import abc
 
@@ -77,13 +76,13 @@ def add_parser_arguments(parser):
             "--valueinatomname",
             action="store_false",
             help="Add value to atom name instead as a term (this removes invalid characters, "
-            "be careful that clean values do not overlap)",
+                 "be careful that clean values do not overlap)",
         )
         parser.add_argument(
             "--adisfunction",
             action="store_true",
             help="Consider all ADs to represent functions of mutual exclusive conditions (like "
-            "in a Bayesian net)",
+                 "in a Bayesian net)",
         )
         parser.add_argument("--compress", action="store_true", help="Compress tables")
         parser.add_argument(

conversions/pyparsing.py

@@ -872,7 +872,7 @@ def dump(self, indent="", depth=0):
     def pprint(self, *args, **kwargs):
         """Pretty-printer for parsed results as a list, using the C{pprint} module.
            Accepts additional positional or keyword args as defined for the 
-           C{pprint.pprint} method. (U{http://docs.python.org/3/library/pprint.html#pprint.pprint})"""
+           C{pprint.pprint} method. (U{https://docs.python.org/3/library/pprint.html#pprint.pprint})"""
         pprint.pprint(self.asList(), *args, **kwargs)
 
     # add support for pickle protocol

problog-cli.py

@@ -8,7 +8,7 @@
 you may not use this file except in compliance with the License.
 You may obtain a copy of the License at
 
-    http://www.apache.org/licenses/LICENSE-2.0
+    https://www.apache.org/licenses/LICENSE-2.0
 
 Unless required by applicable law or agreed to in writing, software
 distributed under the License is distributed on an "AS IS" BASIS,

problog/clausedb.py

@@ -875,13 +875,18 @@ def _create_alias(
 
     def load_external_module(self, filename):
         from .extern import problog_export
-        import imp
 
         problog_export.database = self
-
         module_name = os.path.splitext(os.path.split(filename)[-1])[0]
-        with open(filename, "r") as extfile:
-            imp.load_module(module_name, extfile, filename, (".py", "U", 1))
+
+        # Replaced deprecated imp.load_module()
+        # source: https://stackoverflow.com/a/19011259
+        import importlib.machinery
+        import importlib.util
+        loader = importlib.machinery.SourceFileLoader(module_name, filename)
+        module_spec = importlib.util.spec_from_loader(loader.name, loader)
+        new_module = importlib.util.module_from_spec(module_spec)
+        loader.exec_module(new_module)
 
         return module_name, self.__extern[module_name]
 

problog/dd_formula.py

@@ -443,9 +443,13 @@ def _initialize(self, with_evidence=True):
 
     def propagate(self):
         self._initialize()
+        # if (
+        #     type(self.semiring) == SemiringLogProbability
+        #     or type(self.semiring) == SemiringProbability
+        # ):
         if (
-            type(self.semiring) == SemiringLogProbability
-            or type(self.semiring) == SemiringProbability
+                isinstance(self.semiring, SemiringLogProbability)
+                or isinstance(self.semiring, SemiringProbability)
         ):
             self.normalization = self._get_manager().wmc_true(
                 self.weights, self.semiring
@@ -462,9 +466,13 @@ def _evaluate_evidence(self, recompute=False):
                 constraint_inode, *evidence_nodes
             )
 
+            # if (
+            #     type(self.semiring) == SemiringLogProbability
+            #     or type(self.semiring) == SemiringProbability
+            # ):
             if (
-                type(self.semiring) == SemiringLogProbability
-                or type(self.semiring) == SemiringProbability
+                    isinstance(self.semiring, SemiringLogProbability)
+                    or isinstance(self.semiring, SemiringProbability)
             ):
                 result = self._get_manager().wmc(
                     self.evidence_inode, self.weights, self.semiring
@@ -499,9 +507,13 @@ def evaluate_evidence(self, recompute=False):
         )
 
     def evaluate(self, node):
+        # if (
+        #     type(self.semiring) == SemiringLogProbability
+        #     or type(self.semiring) == SemiringProbability
+        # ):
         if (
-            type(self.semiring) == SemiringLogProbability
-            or type(self.semiring) == SemiringProbability
+                isinstance(self.semiring, SemiringLogProbability)
+                or isinstance(self.semiring, SemiringProbability)
         ):
             return self.evaluate_standard(node)
         else:

problog/extern.py

@@ -13,7 +13,7 @@
     you may not use this file except in compliance with the License.
     You may obtain a copy of the License at
 
-        http://www.apache.org/licenses/LICENSE-2.0
+        https://www.apache.org/licenses/LICENSE-2.0
 
     Unless required by applicable law or agreed to in writing, software
     distributed under the License is distributed on an "AS IS" BASIS,
@@ -142,8 +142,8 @@ def _wrapped_function(*args, **kwdargs):
             )
             converted_args = self._convert_inputs(args)
 
-            argspec = inspect.getargspec(func)
-            if argspec.keywords is not None:
+            argspec = inspect.getfullargspec(func)
+            if argspec.varkw is not None:
                 result = func(*converted_args, **kwdargs)
             else:
                 result = func(*converted_args)
@@ -272,8 +272,8 @@ def _wrapped_function(*args, **kwdargs):
             )
             converted_args = self._convert_inputs(args)
             results = []
-            argspec = inspect.getargspec(func)
-            if argspec.keywords is not None:
+            argspec = inspect.getfullargspec(func)
+            if argspec.varkw is not None:
                 func_result = func(*converted_args, **kwdargs)
             else:
                 func_result = func(*converted_args)