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Cleanups and additional tests to improve test coverage (#2852)

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* disable builds of the StructChecker code by default

* operator"" _smarts() doesn't need to catch sanitization errors

* remove unused function

* turn back on some tests that shouldn't have been disabled

* Remove unused code from SMARTS parser and simplify a bit

SmilesParseOps::AddFragToMol is now used only from the SMARTS parser, so we can simplify the API

* Removes obsolete special case code for SMARTS

This was relevant when organic atoms in SMARTS queries were stored as two-part queries.

* improve SMARTS testing

make sure we can generate SMARTS from all the examples and then parse that again.

* Fixes #2814

* Fixes #2815

* some additional smarts tests to improve coverage

* test copy ctor and getPos

* remove obsolete test_list files

* include tests for the morgan invariant generators

* more cleanups and coverage improvements

* remove files that were mistakenly added
This commit is contained in:
Greg Landrum
2020-01-09 22:07:55 +01:00
committed by Brian Kelley
parent 22b86d0a94
commit a75018fe38
80 changed files with 172 additions and 930 deletions
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9
Code/Numerics/Alignment/Wrap/test_list.py
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@@ -1,9 +0,0 @@
tests = [("python", "testAlignment.py", {})]
longTests = []
if __name__ == '__main__':
import sys
from rdkit import TestRunner
failed, tests = TestRunner.RunScript('test_list.py', 0, 1)
sys.exit(len(failed))

14
Code/Numerics/Alignment/test_list.py
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@@ -1,14 +0,0 @@
import sys
tests = [
("testExecs/main.exe", "", {}),
("python", "test_list.py", {'dir': 'Wrap'}),
]
longTests = []
if __name__ == '__main__':
import sys
from rdkit import TestRunner
failed, tests = TestRunner.RunScript('test_list.py', 0, 1)
sys.exit(len(failed))

11
Code/Numerics/EigenSolvers/test_list.py
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@@ -1,11 +0,0 @@
import sys
tests = [("testExecs/main.exe", "", {}), ]
longTests = []
if __name__ == '__main__':
import sys
from rdkit import TestRunner
failed, tests = TestRunner.RunScript('test_list.py', 0, 1)
sys.exit(len(failed))

11
Code/Numerics/Optimizer/test_list.py
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@@ -1,11 +0,0 @@
import sys
tests = [("testExecs/testOptimizer.exe", "", {}), ]
longTests = []
if __name__ == '__main__':
import sys
from rdkit import TestRunner
failed, tests = TestRunner.RunScript('test_list.py', 0, 1)
sys.exit(len(failed))

39
Code/Numerics/testMatrices.cpp
View File

@@ -1,6 +1,5 @@
// $Id$
//
// Copyright (C) 2004-2006 Rational Discovery LLC
// Copyright (C) 2004-2019 Rational Discovery LLC
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
@@ -99,6 +98,42 @@ void test2Matrix() {
CHECK_INVARIANT(RDKit::feq(C.getVal(0, 1), 10), "");
CHECK_INVARIANT(RDKit::feq(C.getVal(1, 0), 10), "");
CHECK_INVARIANT(RDKit::feq(C.getVal(1, 1), 10.25), "");
auto Ccp(C);
Ccp += C;
CHECK_INVARIANT(RDKit::feq(Ccp.getVal(0, 0), 20.5), "");
CHECK_INVARIANT(RDKit::feq(Ccp.getVal(0, 1), 20), "");
CHECK_INVARIANT(RDKit::feq(Ccp.getVal(1, 0), 20), "");
CHECK_INVARIANT(RDKit::feq(Ccp.getVal(1, 1), 20.5), "");
Ccp -= C;
CHECK_INVARIANT(RDKit::feq(Ccp.getVal(0, 0), 10.25), "");
CHECK_INVARIANT(RDKit::feq(Ccp.getVal(0, 1), 10), "");
CHECK_INVARIANT(RDKit::feq(Ccp.getVal(1, 0), 10), "");
CHECK_INVARIANT(RDKit::feq(Ccp.getVal(1, 1), 10.25), "");
C *= 2.;
CHECK_INVARIANT(RDKit::feq(C.getVal(0, 0), 20.5), "");
CHECK_INVARIANT(RDKit::feq(C.getVal(0, 1), 20), "");
CHECK_INVARIANT(RDKit::feq(C.getVal(1, 0), 20), "");
CHECK_INVARIANT(RDKit::feq(C.getVal(1, 1), 20.5), "");
C /= 2.;
CHECK_INVARIANT(RDKit::feq(C.getVal(0, 0), 10.25), "");
CHECK_INVARIANT(RDKit::feq(C.getVal(0, 1), 10), "");
CHECK_INVARIANT(RDKit::feq(C.getVal(1, 0), 10), "");
CHECK_INVARIANT(RDKit::feq(C.getVal(1, 1), 10.25), "");
Vector<double> tRow(A.numCols());
A.getRow(1, tRow);
for (unsigned int i = 0; i < A.numCols(); ++i) {
TEST_ASSERT(RDKit::feq(A.getVal(1, i), tRow.getVal(i)));
}
Vector<double> tCol(A.numRows());
A.getCol(1, tCol);
for (unsigned int i = 0; i < A.numRows(); ++i) {
TEST_ASSERT(RDKit::feq(A.getVal(i, 1), tCol.getVal(i)));
}
}
void test3SquareMatrix() {

12
Code/Numerics/test_list.py
View File

@@ -1,12 +0,0 @@
tests = [
("python", "test_list.py", {'dir': 'Optimizer'}),
("python", "test_list.py", {'dir': 'EigenSolvers'}),
("python", "test_list.py", {'dir': 'Alignment'}),
("testExecs/main.exe", "", {}),
]
if __name__ == '__main__':
import sys
from rdkit import TestRunner
failed, tests = TestRunner.RunScript('test_list.py', 0, 1)
sys.exit(len(failed))