Fix unit tests

abipy/abio/abivars.py

@@ -129,7 +129,7 @@ def expand_star_syntax(s):
         assert tokens[1] != "*"
         return " ".join(tokens)
 
-    #print(s)
+    #print(s, tokens)
     l = []
     while tokens:
         c = tokens.pop(0)
@@ -375,10 +375,13 @@ def parse_abinit_string(s):
     #
     # Step 3 is needed because we are gonna use python to evaluate the operators and
     # in abinit `2*sqrt(0.75)` means `sqrt(0.75) sqrt(0.75)` and not math multiplication!
-    tokens = []
+    #tokens = []
-    for t in " ".join(lines).split():
+    #for t in " ".join(lines).split():
-        tokens.extend(expand_star_syntax(t).split())
+    #    tokens.extend(expand_star_syntax(t).split())
-    tokens = eval_abinit_operators(tokens)
+    #tokens = eval_abinit_operators(tokens)
+    # The code above does not work everywhere e.g. typat 2 * 1
+    # I think this section should be performed afterwards when we have already constructed the dictionary
+    tokens = " ".join(lines).split()
 
     # Get value of ndtset.
     #try:

abipy/abio/inputs.py

@@ -314,13 +314,26 @@ class AbinitInput(six.with_metaclass(abc.ABCMeta, AbstractInput, MSONable, Has_S
         of the input objects. Note, indeed, that AbintInput is mutable and therefore
         should not be used as keyword in dictionaries.
         """
-        # todo add the decorators, do we need to add them ?
-        s = str(sorted([(unicode(i[0]), i[1]) for i in self.as_dict()['abi_args']]))
         # Use sha1 from hashlib because python builtin hash is not deterministic
         # (hash is version- and machine-dependent)
         import hashlib
         sha1 = hashlib.sha1()
-        sha1.update(s)
+
+        # Add abi_args to sha1
+        # (not sure this is code is portable: roundoff errors and conversion to string)
+        # We could just compute the hash from the keys (hash equality does not necessarily imply eq!)
+        for key in sorted(self.keys()):
+            value = self[key]
+            if isinstance(value, np.ndarray): value = value.tolist()
+            sha1.update(unicode(key))
+            sha1.update(unicode(value))
+
+        sha1.update(str(self.comment))
+        # add pseudos (this is easy because we have md5)
+        sha1.update(str([p.md5 for p in self.pseudos]))
+        # add the decorators, do we need to add them ?
+        sha1.update(str([dec.__class__.__name__ for dec in self.decorators]))
+
         return sha1.hexdigest()
 
     @pmg_serialize
@@ -330,7 +343,6 @@ class AbinitInput(six.with_metaclass(abc.ABCMeta, AbstractInput, MSONable, Has_S
         abi_args = []
         for key, value in self.items():
             if isinstance(value, np.ndarray): value = value.tolist()
-            #vars[key] = value
             abi_args.append((key, value))
 
         return dict(structure=self.structure.as_dict(),

abipy/abio/tests/test_factories.py

@@ -104,13 +104,12 @@ class FactoryTest(AbipyTest):
         self.assertIsInstance(inputs[2][0], AbinitInput)
         self.assertIsInstance(inputs[3][0], AbinitInput)
 
-        self.assertEqual(inputs[0][0].variable_checksum(), "6cf6121967a3cd08cc85efde3b50188df0b8067c")
+        self.assertEqual(inputs[0][0].variable_checksum(), "4b724717b4f39cf99e390e0e836c7c6df3738f0c")
-        self.assertEqual(inputs[1][0].variable_checksum(), "d1e2639f848204359e01a03d11e2dac146c7dbc6")
+        self.assertEqual(inputs[1][0].variable_checksum(), "e79dbacccf019d59ab87f66599b89f808333064e")
-        self.assertEqual(inputs[2][0].variable_checksum(), "fe1b410583611ce1ba799765f9182a9e6be6e822")
+        self.assertEqual(inputs[2][0].variable_checksum(), "569ca521b0207f77fdbb9e4f6e1a7295273b7e5a")
-        self.assertEqual(inputs[3][0].variable_checksum(), "d2ff935446e01d7af344e21c2fc7e0a9db201ce7")
+        self.assertEqual(inputs[3][0].variable_checksum(), "77f4e676b1532d517c562da4e7cc792b21c2b2eb")
 
         #for input in [inputs[0][0], inputs[1][0], inputs[2][0], inputs[3][0]]:
-
         for inp in [item for sublist in inputs for item in sublist]:
             val = inp.abivalidate()
             if val.retcode != 0:

abipy/dev_scripts/test_abinit_parser.py

@@ -1,61 +0,0 @@
-#!/usr/bin/env python
-# coding: utf-8
-"""
-This script tests the parser implemented in AbinitInputFile.
-It tries to read and parse all the input files of the Abinit test suite."""
-from __future__ import print_function, division, unicode_literals, absolute_import
-
-import os
-import numpy as np
-
-from abipy import abilab
-
-def is_abinit_input(path):
-    """True if path is one of the input files used in the Test suite."""
-    #beg = "#%%<BEGIN TEST_INFO>"
-    #end = "#%%<END TEST_INFO>"
-    if not path.endswith(".in"): return False
-
-    with open(path, "rt") as fh:
-        for line in fh:
-            if "executable" in line and "abinit" in line: return True
-        return False
-
-
-def test_abinit_input_parser(top):
-
-    inputs = []
-    nfiles, retcode = 0, 0
-    for dirpath, dirnames, filenames in os.walk(top):
-        for fname in filenames:
-            path = os.path.join(dirpath, fname)
-            if not is_abinit_input(path): continue
-            nfiles += 1
-            try:
-                inp = abilab.AbinitInputFile.from_file(path)
-            except Exception as exc:
-                retcode += 1
-                if "udtset and jdtset are not supported" not in str(exc):
-                    print("[%s]: Exception:\n%s" % (path, exc))
-
-    print("failed: %d/%d [%.1f%%]" % (retcode, nfiles, 100 * retcode/nfiles))
-    return retcode
-
-
-if __name__ == "__main__":
-    import sys
-    try:
-        top = sys.argv[1]
-    except IndexError:
-        print("Usage: test_abinit_parser.py directory_with_input_files")
-        sys.exit(1)
-
-    # loglevel is bound to the string value obtained from the command line argument. 
-    # Convert to upper case to allow the user to specify --loglevel=DEBUG or --loglevel=debug
-    import logging
-    numeric_level = getattr(logging, "DEBUG", None)
-    #if not isinstance(numeric_level, int):
-    #    raise ValueError('Invalid log level: %s' % options.loglevel)
-    logging.basicConfig(level=numeric_level)
-
-    sys.exit(test_abinit_input_parser(top))

dev_scripts/pyclean.py

@@ -4,6 +4,8 @@ This script remove all pyc files and all __pycache__ directory.
 """
 from __future__ import print_function, division, unicode_literals
 
+
+import sys
 import os
 import shutil