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better insty tests #1944

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better insty tests #1944

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jamesmkrieger
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Now each InSty calculation is run in its own test rather than having them all in the setup function and only some of them are saved and loaded

karolamik13
karolamik13 reviewed Aug 23, 2024
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@karolamik13 karolamik13 left a comment •
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This is what I've got when running test on proteins only:

nosetests prody.tests.proteins

...............S...EEEEEEEE.....................................EEEE....

ERROR: Test for all types of interactions.

Traceback (most recent call last):
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/tests/proteins/test_insty.py", line 34, in setUp
self.data_all = self.INTERACTIONS_ALL.calcProteinInteractionsTrajectory(self.ATOMS)
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/proteins/interactions.py", line 3529, in calcProteinInteractionsTrajectory
hydrogen_bonds = calcHydrogenBonds(atoms.protein, **kwargs)
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/proteins/interactions.py", line 434, in calcHydrogenBonds
contacts = findNeighbors(atoms.heavy, distA)
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/measure/contacts.py", line 306, in findNeighbors
return list(iterNeighbors(atoms, radius, atoms2, unitcell, seqsep))
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/measure/contacts.py", line 217, in iterNeighbors
for (i, j), r in zip(*kdtree(radius)):
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/kdtree/kdtree.py", line 179, in call
return self.getIndices(), self.getDistances()
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/kdtree/kdtree.py", line 259, in getIndices
if self.getCount():
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/kdtree/kdtree.py", line 291, in getCount
return self._kdtree.neighbor_get_count()
AttributeError: 'C KDTree' object has no attribute 'neighbor_get_count'
-------------------- >> begin captured logging << --------------------
.prody: DEBUG: 1231 atoms and 15 coordinate set(s) were parsed in 0.04s.
.prody: INFO: Model: 0
--------------------- >> end captured logging << ---------------------

======================================================================
ERROR: Test for disulfide bonds interactions.

Traceback (most recent call last):
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/tests/proteins/test_insty.py", line 34, in setUp
self.data_all = self.INTERACTIONS_ALL.calcProteinInteractionsTrajectory(self.ATOMS)
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/proteins/interactions.py", line 3529, in calcProteinInteractionsTrajectory
hydrogen_bonds = calcHydrogenBonds(atoms.protein, **kwargs)
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/proteins/interactions.py", line 434, in calcHydrogenBonds
contacts = findNeighbors(atoms.heavy, distA)
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/measure/contacts.py", line 306, in findNeighbors
return list(iterNeighbors(atoms, radius, atoms2, unitcell, seqsep))
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/measure/contacts.py", line 217, in iterNeighbors
for (i, j), r in zip(*kdtree(radius)):
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/kdtree/kdtree.py", line 179, in call
return self.getIndices(), self.getDistances()
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/kdtree/kdtree.py", line 259, in getIndices
if self.getCount():
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/kdtree/kdtree.py", line 291, in getCount
return self._kdtree.neighbor_get_count()
AttributeError: 'C KDTree' object has no attribute 'neighbor_get_count'
-------------------- >> begin captured logging << --------------------
.prody: DEBUG: 1231 atoms and 15 coordinate set(s) were parsed in 0.04s.
.prody: INFO: Model: 0
--------------------- >> end captured logging << ---------------------

======================================================================
ERROR: Test for hydrogen bonds.

Traceback (most recent call last):
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/tests/proteins/test_insty.py", line 34, in setUp
self.data_all = self.INTERACTIONS_ALL.calcProteinInteractionsTrajectory(self.ATOMS)
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/proteins/interactions.py", line 3529, in calcProteinInteractionsTrajectory
hydrogen_bonds = calcHydrogenBonds(atoms.protein, **kwargs)
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/proteins/interactions.py", line 434, in calcHydrogenBonds
contacts = findNeighbors(atoms.heavy, distA)
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/measure/contacts.py", line 306, in findNeighbors
return list(iterNeighbors(atoms, radius, atoms2, unitcell, seqsep))
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/measure/contacts.py", line 217, in iterNeighbors
for (i, j), r in zip(*kdtree(radius)):
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/kdtree/kdtree.py", line 179, in call
return self.getIndices(), self.getDistances()
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/kdtree/kdtree.py", line 259, in getIndices
if self.getCount():
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/kdtree/kdtree.py", line 291, in getCount
return self._kdtree.neighbor_get_count()
AttributeError: 'C KDTree' object has no attribute 'neighbor_get_count'
-------------------- >> begin captured logging << --------------------
.prody: DEBUG: 1231 atoms and 15 coordinate set(s) were parsed in 0.04s.
.prody: INFO: Model: 0
--------------------- >> end captured logging << ---------------------

======================================================================
ERROR: Test for hydrophobic interactions.

Traceback (most recent call last):
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/tests/proteins/test_insty.py", line 34, in setUp
self.data_all = self.INTERACTIONS_ALL.calcProteinInteractionsTrajectory(self.ATOMS)
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/proteins/interactions.py", line 3529, in calcProteinInteractionsTrajectory
hydrogen_bonds = calcHydrogenBonds(atoms.protein, **kwargs)
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/proteins/interactions.py", line 434, in calcHydrogenBonds
contacts = findNeighbors(atoms.heavy, distA)
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/measure/contacts.py", line 306, in findNeighbors
return list(iterNeighbors(atoms, radius, atoms2, unitcell, seqsep))
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/measure/contacts.py", line 217, in iterNeighbors
for (i, j), r in zip(*kdtree(radius)):
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/kdtree/kdtree.py", line 179, in call
return self.getIndices(), self.getDistances()
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/kdtree/kdtree.py", line 259, in getIndices
if self.getCount():
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/kdtree/kdtree.py", line 291, in getCount
return self._kdtree.neighbor_get_count()
AttributeError: 'C KDTree' object has no attribute 'neighbor_get_count'
-------------------- >> begin captured logging << --------------------
.prody: DEBUG: 1231 atoms and 15 coordinate set(s) were parsed in 0.04s.
.prody: INFO: Model: 0
--------------------- >> end captured logging << ---------------------

======================================================================
ERROR: Test for pi-stacking interactions.

Traceback (most recent call last):
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/tests/proteins/test_insty.py", line 34, in setUp
self.data_all = self.INTERACTIONS_ALL.calcProteinInteractionsTrajectory(self.ATOMS)
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/proteins/interactions.py", line 3529, in calcProteinInteractionsTrajectory
hydrogen_bonds = calcHydrogenBonds(atoms.protein, **kwargs)
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/proteins/interactions.py", line 434, in calcHydrogenBonds
contacts = findNeighbors(atoms.heavy, distA)
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/measure/contacts.py", line 306, in findNeighbors
return list(iterNeighbors(atoms, radius, atoms2, unitcell, seqsep))
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/measure/contacts.py", line 217, in iterNeighbors
for (i, j), r in zip(*kdtree(radius)):
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/kdtree/kdtree.py", line 179, in call
return self.getIndices(), self.getDistances()
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/kdtree/kdtree.py", line 259, in getIndices
if self.getCount():
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/kdtree/kdtree.py", line 291, in getCount
return self._kdtree.neighbor_get_count()
AttributeError: 'C KDTree' object has no attribute 'neighbor_get_count'
-------------------- >> begin captured logging << --------------------
.prody: DEBUG: 1231 atoms and 15 coordinate set(s) were parsed in 0.04s.
.prody: INFO: Model: 0
--------------------- >> end captured logging << ---------------------

======================================================================
ERROR: Test for pi-stacking interactions.

Traceback (most recent call last):
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/tests/proteins/test_insty.py", line 34, in setUp
self.data_all = self.INTERACTIONS_ALL.calcProteinInteractionsTrajectory(self.ATOMS)
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/proteins/interactions.py", line 3529, in calcProteinInteractionsTrajectory
hydrogen_bonds = calcHydrogenBonds(atoms.protein, **kwargs)
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/proteins/interactions.py", line 434, in calcHydrogenBonds
contacts = findNeighbors(atoms.heavy, distA)
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/measure/contacts.py", line 306, in findNeighbors
return list(iterNeighbors(atoms, radius, atoms2, unitcell, seqsep))
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/measure/contacts.py", line 217, in iterNeighbors
for (i, j), r in zip(*kdtree(radius)):
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/kdtree/kdtree.py", line 179, in call
return self.getIndices(), self.getDistances()
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/kdtree/kdtree.py", line 259, in getIndices
if self.getCount():
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/kdtree/kdtree.py", line 291, in getCount
return self._kdtree.neighbor_get_count()
AttributeError: 'C KDTree' object has no attribute 'neighbor_get_count'
-------------------- >> begin captured logging << --------------------
.prody: DEBUG: 1231 atoms and 15 coordinate set(s) were parsed in 0.05s.
.prody: INFO: Model: 0
--------------------- >> end captured logging << ---------------------

======================================================================
ERROR: Test for repulsive ionic bonding.

Traceback (most recent call last):
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/tests/proteins/test_insty.py", line 34, in setUp
self.data_all = self.INTERACTIONS_ALL.calcProteinInteractionsTrajectory(self.ATOMS)
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/proteins/interactions.py", line 3529, in calcProteinInteractionsTrajectory
hydrogen_bonds = calcHydrogenBonds(atoms.protein, **kwargs)
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/proteins/interactions.py", line 434, in calcHydrogenBonds
contacts = findNeighbors(atoms.heavy, distA)
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/measure/contacts.py", line 306, in findNeighbors
return list(iterNeighbors(atoms, radius, atoms2, unitcell, seqsep))
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/measure/contacts.py", line 217, in iterNeighbors
for (i, j), r in zip(*kdtree(radius)):
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/kdtree/kdtree.py", line 179, in call
return self.getIndices(), self.getDistances()
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/kdtree/kdtree.py", line 259, in getIndices
if self.getCount():
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/kdtree/kdtree.py", line 291, in getCount
return self._kdtree.neighbor_get_count()
AttributeError: 'C KDTree' object has no attribute 'neighbor_get_count'
-------------------- >> begin captured logging << --------------------
.prody: DEBUG: 1231 atoms and 15 coordinate set(s) were parsed in 0.05s.
.prody: INFO: Model: 0
--------------------- >> end captured logging << ---------------------

======================================================================
ERROR: Test for salt bridges.

Traceback (most recent call last):
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/tests/proteins/test_insty.py", line 34, in setUp
self.data_all = self.INTERACTIONS_ALL.calcProteinInteractionsTrajectory(self.ATOMS)
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/proteins/interactions.py", line 3529, in calcProteinInteractionsTrajectory
hydrogen_bonds = calcHydrogenBonds(atoms.protein, **kwargs)
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/proteins/interactions.py", line 434, in calcHydrogenBonds
contacts = findNeighbors(atoms.heavy, distA)
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/measure/contacts.py", line 306, in findNeighbors
return list(iterNeighbors(atoms, radius, atoms2, unitcell, seqsep))
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/measure/contacts.py", line 217, in iterNeighbors
for (i, j), r in zip(*kdtree(radius)):
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/kdtree/kdtree.py", line 179, in call
return self.getIndices(), self.getDistances()
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/kdtree/kdtree.py", line 259, in getIndices
if self.getCount():
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/kdtree/kdtree.py", line 291, in getCount
return self._kdtree.neighbor_get_count()
AttributeError: 'C KDTree' object has no attribute 'neighbor_get_count'
-------------------- >> begin captured logging << --------------------
.prody: DEBUG: 1231 atoms and 15 coordinate set(s) were parsed in 0.04s.
.prody: INFO: Model: 0
--------------------- >> end captured logging << ---------------------

======================================================================
ERROR: testSaveWaterBridges (prody.tests.proteins.test_waterbridges.TestWaterBridges)

Traceback (most recent call last):
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/tests/proteins/test_waterbridges.py", line 30, in setUp
self.waterBridgesChain = calcWaterBridges(self.atoms)
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/proteins/waterbridges.py", line 419, in calcWaterBridges
tooFarAtoms = atoms.select(
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/atomic/atomic.py", line 234, in select
return SELECT.select(self, selstr, **kwargs)
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/atomic/select.py", line 895, in select
indices = self.getIndices(atoms, selstr, **kwargs)
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/atomic/select.py", line 953, in getIndices
torf = self.getBoolArray(atoms, selstr, **kwargs)
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/atomic/select.py", line 1005, in getBoolArray
tokens = parser(selstr, parseAll=True)
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/atomic/select.py", line 1110, in _noParser
return [self._default(selstr, 0, selstr.split())]
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/atomic/select.py", line 1128, in _default
torf, err = self._and2(sel, loc, tokens)
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/atomic/select.py", line 1495, in _and2
arr, err = self._unary(sel, loc, unary.pop(0))
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/atomic/select.py", line 1560, in _unary
which, err = self._and2(sel, loc, which)
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/atomic/select.py", line 1489, in _and2
torf, err = self._unary(sel, loc, unary.pop(0))
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/atomic/select.py", line 1571, in _unary
return self._within(sel, loc, tokens)
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/atomic/select.py", line 1671, in _within
search(within, xyz)
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/kdtree/kdtree.py", line 205, in search
self._kdtree.search_center_radius(center, radius)
AttributeError: 'C KDTree' object has no attribute 'search_center_radius'
-------------------- >> begin captured logging << --------------------
.prody: DEBUG: 7641 atoms and 1 coordinate set(s) were parsed in 0.07s.
--------------------- >> end captured logging << ---------------------

======================================================================
ERROR: testSingleWaterBridgesChain (prody.tests.proteins.test_waterbridges.TestWaterBridges)

Traceback (most recent call last):
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/tests/proteins/test_waterbridges.py", line 30, in setUp
self.waterBridgesChain = calcWaterBridges(self.atoms)
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/proteins/waterbridges.py", line 419, in calcWaterBridges
tooFarAtoms = atoms.select(
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/atomic/atomic.py", line 234, in select
return SELECT.select(self, selstr, **kwargs)
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/atomic/select.py", line 895, in select
indices = self.getIndices(atoms, selstr, **kwargs)
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/atomic/select.py", line 953, in getIndices
torf = self.getBoolArray(atoms, selstr, **kwargs)
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/atomic/select.py", line 1005, in getBoolArray
tokens = parser(selstr, parseAll=True)
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/atomic/select.py", line 1110, in _noParser
return [self._default(selstr, 0, selstr.split())]
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/atomic/select.py", line 1128, in _default
torf, err = self._and2(sel, loc, tokens)
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/atomic/select.py", line 1495, in _and2
arr, err = self._unary(sel, loc, unary.pop(0))
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/atomic/select.py", line 1560, in _unary
which, err = self._and2(sel, loc, which)
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/atomic/select.py", line 1489, in _and2
torf, err = self._unary(sel, loc, unary.pop(0))
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/atomic/select.py", line 1571, in _unary
return self._within(sel, loc, tokens)
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/atomic/select.py", line 1671, in _within
search(within, xyz)
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/kdtree/kdtree.py", line 205, in search
self._kdtree.search_center_radius(center, radius)
AttributeError: 'C KDTree' object has no attribute 'search_center_radius'
-------------------- >> begin captured logging << --------------------
.prody: DEBUG: 7641 atoms and 1 coordinate set(s) were parsed in 0.06s.
--------------------- >> end captured logging << ---------------------

======================================================================
ERROR: testSingleWaterBridgesCluster (prody.tests.proteins.test_waterbridges.TestWaterBridges)

Traceback (most recent call last):
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/tests/proteins/test_waterbridges.py", line 30, in setUp
self.waterBridgesChain = calcWaterBridges(self.atoms)
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/proteins/waterbridges.py", line 419, in calcWaterBridges
tooFarAtoms = atoms.select(
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/atomic/atomic.py", line 234, in select
return SELECT.select(self, selstr, **kwargs)
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/atomic/select.py", line 895, in select
indices = self.getIndices(atoms, selstr, **kwargs)
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/atomic/select.py", line 953, in getIndices
torf = self.getBoolArray(atoms, selstr, **kwargs)
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/atomic/select.py", line 1005, in getBoolArray
tokens = parser(selstr, parseAll=True)
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/atomic/select.py", line 1110, in _noParser
return [self._default(selstr, 0, selstr.split())]
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/atomic/select.py", line 1128, in _default
torf, err = self._and2(sel, loc, tokens)
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/atomic/select.py", line 1495, in _and2
arr, err = self._unary(sel, loc, unary.pop(0))
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/atomic/select.py", line 1560, in _unary
which, err = self._and2(sel, loc, which)
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/atomic/select.py", line 1489, in _and2
torf, err = self._unary(sel, loc, unary.pop(0))
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/atomic/select.py", line 1571, in _unary
return self._within(sel, loc, tokens)
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/atomic/select.py", line 1671, in _within
search(within, xyz)
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/kdtree/kdtree.py", line 205, in search
self._kdtree.search_center_radius(center, radius)
AttributeError: 'C KDTree' object has no attribute 'search_center_radius'
-------------------- >> begin captured logging << --------------------
.prody: DEBUG: 7641 atoms and 1 coordinate set(s) were parsed in 0.07s.
--------------------- >> end captured logging << ---------------------

======================================================================
ERROR: testSingleWaterBridgesOutputInfo (prody.tests.proteins.test_waterbridges.TestWaterBridges)

Traceback (most recent call last):
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/tests/proteins/test_waterbridges.py", line 30, in setUp
self.waterBridgesChain = calcWaterBridges(self.atoms)
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/proteins/waterbridges.py", line 419, in calcWaterBridges
tooFarAtoms = atoms.select(
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/atomic/atomic.py", line 234, in select
return SELECT.select(self, selstr, **kwargs)
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/atomic/select.py", line 895, in select
indices = self.getIndices(atoms, selstr, **kwargs)
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/atomic/select.py", line 953, in getIndices
torf = self.getBoolArray(atoms, selstr, **kwargs)
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/atomic/select.py", line 1005, in getBoolArray
tokens = parser(selstr, parseAll=True)
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/atomic/select.py", line 1110, in _noParser
return [self._default(selstr, 0, selstr.split())]
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/atomic/select.py", line 1128, in _default
torf, err = self._and2(sel, loc, tokens)
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/atomic/select.py", line 1495, in _and2
arr, err = self._unary(sel, loc, unary.pop(0))
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/atomic/select.py", line 1560, in _unary
which, err = self._and2(sel, loc, which)
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/atomic/select.py", line 1489, in _and2
torf, err = self._unary(sel, loc, unary.pop(0))
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/atomic/select.py", line 1571, in _unary
return self._within(sel, loc, tokens)
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/atomic/select.py", line 1671, in _within
search(within, xyz)
File "/home/karolamik/test_ProDy/ProDy_2.5_beforeRelease/ProDy/prody/kdtree/kdtree.py", line 205, in search
self._kdtree.search_center_radius(center, radius)
AttributeError: 'C KDTree' object has no attribute 'search_center_radius'
-------------------- >> begin captured logging << --------------------
.prody: DEBUG: 7641 atoms and 1 coordinate set(s) were parsed in 0.07s.
--------------------- >> end captured logging << ---------------------

Ran 72 tests in 120.559s

FAILED (SKIP=1, errors=12)

@jamesmkrieger
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I think there's a problem with nosetests seeing the extensions. I also saw something similar

@jamesmkrieger
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Try using pytest instead

pip install pytest
pip install pytest-skip-slow
pytest -v --slow prody/tests/proteins/test_insty.py

@jamesmkrieger
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Building with --inplace may help the tests find the extensions. See #1915

karolamik13
karolamik13 reviewed Sep 30, 2024
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I installed pytest. This is the outcome:

====== short test summary info =========
FAILED ../ProDy/prody/tests/proteins/test_insty.py::TestInteractions::testAllInteractionsCalc - AttributeError: 'C KDTree' object has no attribute 'neighbor_get_count'
FAILED ../ProDy/prody/tests/proteins/test_insty.py::TestInteractions::testAllInteractionsSave - AttributeError: 'C KDTree' object has no attribute 'neighbor_get_count'
FAILED ../ProDy/prody/tests/proteins/test_insty.py::TestInteractions::testHydrogenBonds - AttributeError: 'C KDTree' object has no attribute 'neighbor_get_count'
FAILED ../ProDy/prody/tests/proteins/test_insty.py::TestInteractions::testHydrophobicInteractions - IndexError: list index out of range
FAILED ../ProDy/prody/tests/proteins/test_insty.py::TestInteractions::testPiCation - ValueError: Missing atoms from the side chains of the structure. Use addMissingAtoms.
FAILED ../ProDy/prody/tests/proteins/test_insty.py::TestInteractions::testRepulsiveIonicBonding - AttributeError: 'C KDTree' object has no attribute 'search_center_radius'
FAILED ../ProDy/prody/tests/proteins/test_insty.py::TestInteractions::testSaltBridgesCalc - AttributeError: 'C KDTree' object has no attribute 'search_center_radius'
FAILED ../ProDy/prody/tests/proteins/test_insty.py::TestInteractions::testSaltBridgesSave - AttributeError: 'C KDTree' object has no attribute 'search_center_radius'
ERROR ../ProDy/prody/tests/proteins/test_insty.py::TestInteractions::testSaltBridgesSave - FileNotFoundError: [Errno 2] No such file or directory: 'test_2k39_all.npy'
========= 8 failed, 4 passed, 372 warnings, 1 error in 39.19s ==========

@jamesmkrieger
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That’s still a problem with the c extensions. Did you try installing prody with build_ext and --inplace?

karolamik13
karolamik13 approved these changes Sep 30, 2024
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Installation with build_ext and --inplace helped.

collected 12 items

../ProDy/prody/tests/proteins/test_insty.py::TestInteractions::testAllInteractionsCalc PASSED [ 8%]
../ProDy/prody/tests/proteins/test_insty.py::TestInteractions::testAllInteractionsSave PASSED [ 16%]
../ProDy/prody/tests/proteins/test_insty.py::TestInteractions::testDisulfideBondsCalc PASSED [ 25%]
../ProDy/prody/tests/proteins/test_insty.py::TestInteractions::testDisulfideBondsSave PASSED [ 33%]
../ProDy/prody/tests/proteins/test_insty.py::TestInteractions::testHydrogenBonds PASSED [ 41%]
../ProDy/prody/tests/proteins/test_insty.py::TestInteractions::testHydrophobicInteractions PASSED [ 50%]
../ProDy/prody/tests/proteins/test_insty.py::TestInteractions::testImportHpb PASSED [ 58%]
../ProDy/prody/tests/proteins/test_insty.py::TestInteractions::testPiCation PASSED [ 66%]
../ProDy/prody/tests/proteins/test_insty.py::TestInteractions::testPiStacking PASSED [ 75%]
../ProDy/prody/tests/proteins/test_insty.py::TestInteractions::testRepulsiveIonicBonding PASSED [ 83%]
../ProDy/prody/tests/proteins/test_insty.py::TestInteractions::testSaltBridgesCalc PASSED [ 91%]
../ProDy/prody/tests/proteins/test_insty.py::TestInteractions::testSaltBridgesSave PASSED [100%]

=========================================== warnings summary ============================================
../ProDy/prody/utilities/misctools.py:425
/home/karolamik/test_ProDy/ProDy_JK__/ProDy/prody/utilities/misctools.py:425: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
import pkg_resources

../../../anaconda3/envs/prody_tests/lib/python3.10/site-packages/pkg_resources/init.py:3154
/home/karolamik/anaconda3/envs/prody_tests/lib/python3.10/site-packages/pkg_resources/init.py:3154: DeprecationWarning: Deprecated call to pkg_resources.declare_namespace('mpl_toolkits').
Implementing implicit namespace packages (as specified in PEP 420) is preferred to pkg_resources.declare_namespace. See https://setuptools.pypa.io/en/latest/references/keywords.html#keyword-namespace-packages
declare_namespace(pkg)

prody/tests/proteins/test_insty.py: 115 warnings
/home/karolamik/test_ProDy/ProDy_JK__/ProDy/prody/tests/proteins/test_insty.py:140: DeprecationWarning: The truth value of an empty array is ambiguous. Returning False, but in future this will result in an error. Use array.size > 0 to check that an array is not empty.
assert_equal(sorted([i[-1][-1] for i in data_test if i]), sorted([i[-1][-1] for i in self.DISU_INTERACTIONS if i]),

prody/tests/proteins/test_insty.py: 115 warnings
/home/karolamik/test_ProDy/ProDy_JK__/ProDy/prody/tests/proteins/test_insty.py:147: DeprecationWarning: The truth value of an empty array is ambiguous. Returning False, but in future this will result in an error. Use array.size > 0 to check that an array is not empty.
assert_equal(sorted([i[-1][-1] for i in data_test if i]), sorted([i[-1][-1] for i in self.DISU_INTERACTIONS if i]),

prody/tests/proteins/test_insty.py: 129 warnings
/home/karolamik/test_ProDy/ProDy_JK__/ProDy/prody/tests/proteins/test_insty.py:153: DeprecationWarning: The truth value of an empty array is ambiguous. Returning False, but in future this will result in an error. Use array.size > 0 to check that an array is not empty.
assert_equal(sorted([i[-1][-1] for i in data_test if i]), sorted([i[-1][-1] for i in self.DISU_INTERACTIONS if i]),

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
============ 12 passed, 361 warnings in 188.56s (0:03:08) ============

@jamesmkrieger
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I'm not sure why it's complaining about arrays being empty, but I've fixed the utilities misctools warning about pkg_resources

@jamesmkrieger
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oh, because we're testing disulphides on a system without any disulphides

I'm not sure why it's complaining about arrays being empty, but I've fixed the utilities misctools warning about pkg_resources

@jamesmkrieger
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We should probably have a test where there are disulphides too e.g. 3o21, which is also in our datafiles already. I'll try adding that

@jamesmkrieger
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It also looks like we don't have tests without trajectory anyway, so that would anyway be good to have

karolamik13
karolamik13 approved these changes Sep 30, 2024
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Looks good.

====================== test session starts =======================
platform linux -- Python 3.10.15, pytest-8.3.3, pluggy-1.5.0 -- /home/karolamik/anaconda3/envs/prody_tests/bin/python3.10
cachedir: .pytest_cache
configfile: pyproject.toml
plugins: skip-slow-0.0.5
collected 14 items

../ProDy/prody/tests/proteins/test_insty.py::TestInteractions::testAllInteractionsCalc PASSED [ 7%]
../ProDy/prody/tests/proteins/test_insty.py::TestInteractions::testAllInteractionsSave PASSED [ 14%]
../ProDy/prody/tests/proteins/test_insty.py::TestInteractions::testDisulfideBondsCalcNone PASSED [ 21%]
../ProDy/prody/tests/proteins/test_insty.py::TestInteractions::testDisulfideBondsCalcSomeNotTraj PASSED [ 28%]
../ProDy/prody/tests/proteins/test_insty.py::TestInteractions::testDisulfideBondsSaveNone PASSED [ 35%]
../ProDy/prody/tests/proteins/test_insty.py::TestInteractions::testDisulfideBondsSaveSomeNotTraj PASSED [ 42%]
../ProDy/prody/tests/proteins/test_insty.py::TestInteractions::testHydrogenBonds PASSED [ 50%]
../ProDy/prody/tests/proteins/test_insty.py::TestInteractions::testHydrophobicInteractions PASSED [ 57%]
../ProDy/prody/tests/proteins/test_insty.py::TestInteractions::testImportHpb PASSED [ 64%]
../ProDy/prody/tests/proteins/test_insty.py::TestInteractions::testPiCation PASSED [ 71%]
../ProDy/prody/tests/proteins/test_insty.py::TestInteractions::testPiStacking PASSED [ 78%]
../ProDy/prody/tests/proteins/test_insty.py::TestInteractions::testRepulsiveIonicBonding PASSED [ 85%]
../ProDy/prody/tests/proteins/test_insty.py::TestInteractions::testSaltBridgesCalc PASSED [ 92%]
../ProDy/prody/tests/proteins/test_insty.py::TestInteractions::testSaltBridgesSave PASSED [100%]
============== 14 passed in 189.43s (0:03:09) =======

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@jamesmkrieger @karolamik13