Why does fancy indexing work like this?
Why does fancy indexing have this behavior?
a = np.empty((0, 1, 2)) b = np.empty((1, 1, 2)) a[np.array([10, 10])] Traceback (most recent call last): File "<stdin>", line 1, in <module> IndexError: index 10 is out of bounds for axis 0 with size 0 a[:, np.array([10, 10])] array([], shape=(0, 2, 2), dtype=float64) a[:, :, np.array([10, 10])] array([], shape=(0, 1, 2), dtype=float64) b[np.array([10, 10])] Traceback (most recent call last): File "<stdin>", line 1, in <module> IndexError: index 10 is out of bounds for axis 0 with size 1 b[:, np.array([10, 10])] Traceback (most recent call last): File "<stdin>", line 1, in <module> IndexError: index 10 is out of bounds for axis 1 with size 1 b[:, :, np.array([10, 10])] Traceback (most recent call last): File "<stdin>", line 1, in <module> IndexError: index 10 is out of bounds for axis 2 with size 2
As far as I can tell, the behavior is that if an array has a 0 dimension and an integer array index indexes an axis that isn't 0, there are no bounds checks. Why does it do this? It seems to be inconsistent with the behavior of shape () fancy indices (integer indices). I couldn't find any reference to this behavior in https://numpy.org/doc/stable/reference/arrays.indexing.html. Aaron Meurer
On Wed, 20200722 at 16:23 0600, Aaron Meurer wrote:
Why does fancy indexing have this behavior?
a = np.empty((0, 1, 2)) b = np.empty((1, 1, 2)) a[np.array([10, 10])] Traceback (most recent call last): File "<stdin>", line 1, in <module> IndexError: index 10 is out of bounds for axis 0 with size 0 a[:, np.array([10, 10])] array([], shape=(0, 2, 2), dtype=float64) a[:, :, np.array([10, 10])] array([], shape=(0, 1, 2), dtype=float64) b[np.array([10, 10])] Traceback (most recent call last): File "<stdin>", line 1, in <module> IndexError: index 10 is out of bounds for axis 0 with size 1 b[:, np.array([10, 10])] Traceback (most recent call last): File "<stdin>", line 1, in <module> IndexError: index 10 is out of bounds for axis 1 with size 1 b[:, :, np.array([10, 10])] Traceback (most recent call last): File "<stdin>", line 1, in <module> IndexError: index 10 is out of bounds for axis 2 with size 2
As far as I can tell, the behavior is that if an array has a 0 dimension and an integer array index indexes an axis that isn't 0, there are no bounds checks. Why does it do this? It seems to be inconsistent with the behavior of shape () fancy indices (integer indices). I couldn't find any reference to this behavior in https://numpy.org/doc/stable/reference/arrays.indexing.html.
The reason is because we used to not do this when there are *two* advanced indices: arr = np.ones((5, 6)) arr[[], [10, 10]] giving an empty result. If you check on master (and maybe on 1.19.x, I am not sure). You should see that all of your examples give a deprecation warning to be turned into an error (except the example I gave above, which can be argued to be correct).  Sebastian
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Ah, so I guess I caught this issue right as it got fixed. There are no warnings in 1.19.0, but I can confirm I get the warnings in numpy master. 1.19.1 isn't on conda yet, but I tried building it and didn't get the warning there. So I guess I need to wait for 0.19.2. How long do deprecation cycles like this tend to last (I'm also curious when the warnings for things like a[[[0, 1], [0, 1]]] will go away)? Aaron Meurer On Wed, Jul 22, 2020 at 4:32 PM Sebastian Berg <sebastian@sipsolutions.net> wrote:
On Wed, 20200722 at 16:23 0600, Aaron Meurer wrote:
Why does fancy indexing have this behavior?
a = np.empty((0, 1, 2)) b = np.empty((1, 1, 2)) a[np.array([10, 10])] Traceback (most recent call last): File "<stdin>", line 1, in <module> IndexError: index 10 is out of bounds for axis 0 with size 0 a[:, np.array([10, 10])] array([], shape=(0, 2, 2), dtype=float64) a[:, :, np.array([10, 10])] array([], shape=(0, 1, 2), dtype=float64) b[np.array([10, 10])] Traceback (most recent call last): File "<stdin>", line 1, in <module> IndexError: index 10 is out of bounds for axis 0 with size 1 b[:, np.array([10, 10])] Traceback (most recent call last): File "<stdin>", line 1, in <module> IndexError: index 10 is out of bounds for axis 1 with size 1 b[:, :, np.array([10, 10])] Traceback (most recent call last): File "<stdin>", line 1, in <module> IndexError: index 10 is out of bounds for axis 2 with size 2
As far as I can tell, the behavior is that if an array has a 0 dimension and an integer array index indexes an axis that isn't 0, there are no bounds checks. Why does it do this? It seems to be inconsistent with the behavior of shape () fancy indices (integer indices). I couldn't find any reference to this behavior in https://numpy.org/doc/stable/reference/arrays.indexing.html.
The reason is because we used to not do this when there are *two* advanced indices:
arr = np.ones((5, 6)) arr[[], [10, 10]]
giving an empty result. If you check on master (and maybe on 1.19.x, I am not sure). You should see that all of your examples give a deprecation warning to be turned into an error (except the example I gave above, which can be argued to be correct).
 Sebastian
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On Wed, Jul 22, 2020 at 4:55 PM Aaron Meurer <asmeurer@gmail.com> wrote:
Ah, so I guess I caught this issue right as it got fixed. There are no warnings in 1.19.0, but I can confirm I get the warnings in numpy master. 1.19.1 isn't on conda yet, but I tried building it and didn't get the warning there. So I guess I need to wait for 0.19.2.
Or rather 1.20 I guess https://github.com/numpy/numpy/pull/15900. By the way, it would be useful if deprecation warnings like this had a functionality to enable the actual postdeprecation behavior. Right now the warning says to run warnings.simplefilter('error'), but this causes the above indexing to raise DeprecationWarning, not IndexError. Aaron Meurer
On Wed, 20200722 at 16:55 0600, Aaron Meurer wrote:
Ah, so I guess I caught this issue right as it got fixed. There are no
Yes, on a general note. Advanced indexing grew over time in a maze of paths, and things like empty arrays were long not too well supported in many parts of NumPy. That this went through
warnings in 1.19.0, but I can confirm I get the warnings in numpy master. 1.19.1 isn't on conda yet, but I tried building it and didn't get the warning there. So I guess I need to wait for 0.19.2.
We don't add warnings in minor releases, so 1.19.2 will definitely never get it. I did not remember whether it was in there, because it was merged around the same time 1.19.x was branched. About your warnings, do you have a nice way to do that? The mechanism for warnings does not really give a good way to catch that a warning was raised and then turn it into an error. Unless someone contributes a slick way to do it, I am not sure the complexity pays off. IIRC, I added the note about raising the warning, because in this particular case the deprecation warning (turned into an error) happens to be chained due to implementation details. (so you do see the "original" error printed out).
How long do deprecation cycles like this tend to last (I'm also curious when the warnings for things like a[[[0, 1], [0, 1]]] will go away)?
Not sure, this is a corner case, and is bugging pandas a bit, so it may be a bit quicker, but likely still 2 releases? We are not always good about phasing out deprecations immediately when it is plausible. The one you mention strikes me as a bigger one though, so I think we should wait about 2 years. It is plausible that we are there already, even for a while. Cheers, Sebastian
Aaron Meurer
On Wed, Jul 22, 2020 at 4:32 PM Sebastian Berg <sebastian@sipsolutions.net> wrote:
On Wed, 20200722 at 16:23 0600, Aaron Meurer wrote:
Why does fancy indexing have this behavior?
a = np.empty((0, 1, 2)) b = np.empty((1, 1, 2)) a[np.array([10, 10])] Traceback (most recent call last): File "<stdin>", line 1, in <module> IndexError: index 10 is out of bounds for axis 0 with size 0 a[:, np.array([10, 10])] array([], shape=(0, 2, 2), dtype=float64) a[:, :, np.array([10, 10])] array([], shape=(0, 1, 2), dtype=float64) b[np.array([10, 10])] Traceback (most recent call last): File "<stdin>", line 1, in <module> IndexError: index 10 is out of bounds for axis 0 with size 1 b[:, np.array([10, 10])] Traceback (most recent call last): File "<stdin>", line 1, in <module> IndexError: index 10 is out of bounds for axis 1 with size 1 b[:, :, np.array([10, 10])] Traceback (most recent call last): File "<stdin>", line 1, in <module> IndexError: index 10 is out of bounds for axis 2 with size 2
As far as I can tell, the behavior is that if an array has a 0 dimension and an integer array index indexes an axis that isn't 0, there are no bounds checks. Why does it do this? It seems to be inconsistent with the behavior of shape () fancy indices (integer indices). I couldn't find any reference to this behavior in https://numpy.org/doc/stable/reference/arrays.indexing.html.
The reason is because we used to not do this when there are *two* advanced indices:
arr = np.ones((5, 6)) arr[[], [10, 10]]
giving an empty result. If you check on master (and maybe on 1.19.x, I am not sure). You should see that all of your examples give a deprecation warning to be turned into an error (except the example I gave above, which can be argued to be correct).
 Sebastian
Aaron Meurer _______________________________________________ NumPyDiscussion mailing list NumPyDiscussion@python.org https://mail.python.org/mailman/listinfo/numpydiscussion
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About your warnings, do you have a nice way to do that? The mechanism for warnings does not really give a good way to catch that a warning was raised and then turn it into an error. Unless someone contributes a slick way to do it, I am not sure the complexity pays off.
I don't really know how flags and options and such work in NumPy, but I would imagine something like if flags['postdeprecation'] = True: # Either a single flag for all deprecations or a perdeprecation flag raise IndexError(...) else: warnings.warn(...) I don't know if the fact that the code that does this is in C complicates things. In other words, something that works kind of like __future__ flags for upgrading the behavior to postdeprecation.
IIRC, I added the note about raising the warning, because in this particular case the deprecation warning (turned into an error) happens to be chained due to implementation details. (so you do see the "original" error printed out).
Yes, it's nice that you can see it. But for my use case, I want to be able to "except IndexError". Basically, for ndindex, I test against NumPy to make sure the semantics are identical, and that includes making sure identical exceptions are raised. I also want to make it so that the ndindex semantics always follow postdeprecation behavior for any NumPy deprecations, since that leads to a cleaner API. But that means that my test code has to do fancy shenanigans to catch these deprecation warnings and treat them like the right errors. But even as a general principle, I think for any deprecation warning, users should be able to update their code in such a way that the current version doesn't give the warning and also it will continue to work and be idiomatic for future versions. For simple deprecations where you remove a function x(), this is often as simple as telling people to replace x() with y(). But these deprecations aren't so simple, because the indexing itself is valid and will stay valid, it's just the behavior that will change. If there's no way to do this, then a deprecation warning serves little purpose because users who see the warning won't be able to do anything about it until things actually change. There would be little difference from just changing things outright. For the list as tuple indexing thing, you can already kind of do this by making sure your fancy indices are always arrays. For the out of bounds one, it's a little harder. I guess for most usecases, you aren't actually checking for IndexErrors, and the thing that will become an error usually indicates a bug in user code, so maybe it isn't a huge deal (I admit my usecases aren't typical). Aaron Meurer
On Wed, 20200722 at 17:35 0600, Aaron Meurer wrote:
About your warnings, do you have a nice way to do that? The mechanism for warnings does not really give a good way to catch that a warning was raised and then turn it into an error. Unless someone contributes a slick way to do it, I am not sure the complexity pays off.
I don't really know how flags and options and such work in NumPy, but I would imagine something like
if flags['postdeprecation'] = True: # Either a single flag for all deprecations or a perdeprecation flag raise IndexError(...) else: warnings.warn(...)
We have never done global flags for these things much in NumPy, I don't know of precedence in other packages, possibly aside future imports, but I am not even sure they have been used in this way.
I don't know if the fact that the code that does this is in C complicates things.
In other words, something that works kind of like __future__ flags for upgrading the behavior to postdeprecation.
IIRC, I added the note about raising the warning, because in this particular case the deprecation warning (turned into an error) happens to be chained due to implementation details. (so you do see the "original" error printed out).
Yes, it's nice that you can see it. But for my use case, I want to be able to "except IndexError". Basically, for ndindex, I test against NumPy to make sure the semantics are identical, and that includes making sure identical exceptions are raised. I also want to make it so that the ndindex semantics always follow postdeprecation behavior for any NumPy deprecations, since that leads to a cleaner API. But that means that my test code has to do fancy shenanigans to catch these deprecation warnings and treat them like the right errors.
But even as a general principle, I think for any deprecation warning, users should be able to update their code in such a way that the current version doesn't give the warning and also it will continue to
For FutureWarnings, I will always try very hard to give an option to optin to new behaviour or old behaviour – ideally with code compatible also with earlier NumPy versions. Here, for a DeprecationWarning that has obviously no "alternative", I cannot think of any precedence in any other package or Python itself doing such a dance. And it is extremely fringe (you only need it because you are testing another package against numpy behaviour!). So I am happy to merge it if its proposed (maybe its easier for you to add this to NumPy then work around it in your tests), but I am honestly concerned that proposing this as a general principle is far more churn then worth the trouble. At least unless there is some consensus (and probably precendence in the scientific python ecosystem or python itself). Cheers, Sebastian
work and be idiomatic for future versions. For simple deprecations where you remove a function x(), this is often as simple as telling people to replace x() with y(). But these deprecations aren't so simple, because the indexing itself is valid and will stay valid, it's just the behavior that will change. If there's no way to do this, then a deprecation warning serves little purpose because users who see the warning won't be able to do anything about it until things actually change. There would be little difference from just changing things outright. For the list as tuple indexing thing, you can already kind of do this by making sure your fancy indices are always arrays. For the out of bounds one, it's a little harder. I guess for most usecases, you aren't actually checking for IndexErrors, and the thing that will become an error usually indicates a bug in user code, so maybe it isn't a huge deal (I admit my usecases aren't typical).
Aaron Meurer _______________________________________________ NumPyDiscussion mailing list NumPyDiscussion@python.org https://mail.python.org/mailman/listinfo/numpydiscussion
On Thu, 20200723 at 10:18 0500, Sebastian Berg wrote:
On Wed, 20200722 at 17:35 0600, Aaron Meurer wrote:
About your warnings, do you have a nice way to do that? The mechanism for warnings does not really give a good way to catch that a warning was raised and then turn it into an error. Unless someone contributes a slick way to do it, I am not sure the complexity pays off.
I don't really know how flags and options and such work in NumPy, but I would imagine something like
if flags['postdeprecation'] = True: # Either a single flag for all deprecations or a perdeprecation flag raise IndexError(...) else: warnings.warn(...)
We have never done global flags for these things much in NumPy, I don't know of precedence in other packages, possibly aside future imports, but I am not even sure they have been used in this way.
I don't know if the fact that the code that does this is in C complicates things.
In other words, something that works kind of like __future__ flags for upgrading the behavior to postdeprecation.
IIRC, I added the note about raising the warning, because in this particular case the deprecation warning (turned into an error) happens to be chained due to implementation details. (so you do see the "original" error printed out).
Yes, it's nice that you can see it. But for my use case, I want to be able to "except IndexError". Basically, for ndindex, I test against NumPy to make sure the semantics are identical, and that includes making sure identical exceptions are raised. I also want to make it so that the ndindex semantics always follow postdeprecation behavior for any NumPy deprecations, since that leads to a cleaner API. But that means that my test code has to do fancy shenanigans to catch these deprecation warnings and treat them like the right errors.
But even as a general principle, I think for any deprecation warning, users should be able to update their code in such a way that the current version doesn't give the warning and also it will continue to
For FutureWarnings, I will always try very hard to give an option to optin to new behaviour or old behaviour – ideally with code compatible also with earlier NumPy versions.
Here, for a DeprecationWarning that has obviously no "alternative", I cannot think of any precedence in any other package or Python itself doing such a dance. And it is extremely fringe (you only need it because you are testing another package against numpy behaviour!).
So I am happy to merge it if its proposed (maybe its easier for you to add this to NumPy then work around it in your tests), but I am honestly concerned that proposing this as a general principle is far more churn then worth the trouble. At least unless there is some consensus (and probably precendence in the scientific python ecosystem or python itself).
After writing this, I realized that I actually remember the *opposite* discussion occurring before. I think in some of the equality deprecations, we actually raise the new error due to an internal try/except clause. And there was a complaint that its confusing that a nondeprecationwarning is raised when the error will only happen with DeprecationWarnings being set to error.  Sebastian
Cheers,
Sebastian
work and be idiomatic for future versions. For simple deprecations where you remove a function x(), this is often as simple as telling people to replace x() with y(). But these deprecations aren't so simple, because the indexing itself is valid and will stay valid, it's just the behavior that will change. If there's no way to do this, then a deprecation warning serves little purpose because users who see the warning won't be able to do anything about it until things actually change. There would be little difference from just changing things outright. For the list as tuple indexing thing, you can already kind of do this by making sure your fancy indices are always arrays. For the out of bounds one, it's a little harder. I guess for most usecases, you aren't actually checking for IndexErrors, and the thing that will become an error usually indicates a bug in user code, so maybe it isn't a huge deal (I admit my usecases aren't typical).
Aaron Meurer _______________________________________________ NumPyDiscussion mailing list NumPyDiscussion@python.org https://mail.python.org/mailman/listinfo/numpydiscussion
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After writing this, I realized that I actually remember the *opposite* discussion occurring before. I think in some of the equality deprecations, we actually raise the new error due to an internal try/except clause. And there was a complaint that its confusing that a nondeprecationwarning is raised when the error will only happen with DeprecationWarnings being set to error.
 Sebastian
I noticed that warnings.catch_warnings does the right thing with warnings that are raised alongside an exception (although it is a bit clunky to use). Aaron Meurer
These cases don't give any deprecation warnings in NumPy master:
np.arange(0)[np.array([0]), False] array([], dtype=int64) np.arange(0).reshape((0, 0))[np.array([0]), np.array([], dtype=int)] array([], dtype=int64)
Is that intentional? Aaron Meurer On Thu, Jul 23, 2020 at 12:18 PM Aaron Meurer <asmeurer@gmail.com> wrote:
After writing this, I realized that I actually remember the *opposite* discussion occurring before. I think in some of the equality deprecations, we actually raise the new error due to an internal try/except clause. And there was a complaint that its confusing that a nondeprecationwarning is raised when the error will only happen with DeprecationWarnings being set to error.
 Sebastian
I noticed that warnings.catch_warnings does the right thing with warnings that are raised alongside an exception (although it is a bit clunky to use).
Aaron Meurer
On Wed, 20200819 at 19:37 0600, Aaron Meurer wrote:
These cases don't give any deprecation warnings in NumPy master:
np.arange(0)[np.array([0]), False] array([], dtype=int64) np.arange(0).reshape((0, 0))[np.array([0]), np.array([], dtype=int)] array([], dtype=int64)
Is that intentional?
I guess it follows from `np.array([[1]])[[], [10]]` also not failing currently. And that was intentional not to deprecate when outofbound indices broadcast away. But I am not sure I actually think that was the better choice. My initial choice was that this would be an error as well, and I still slightly prefer it, but don't feel it matters much.  Sebastian
Aaron Meurer
On Thu, Jul 23, 2020 at 12:18 PM Aaron Meurer <asmeurer@gmail.com> wrote:
After writing this, I realized that I actually remember the *opposite* discussion occurring before. I think in some of the equality deprecations, we actually raise the new error due to an internal try/except clause. And there was a complaint that its confusing that a nondeprecationwarning is raised when the error will only happen with DeprecationWarnings being set to error.
 Sebastian
I noticed that warnings.catch_warnings does the right thing with warnings that are raised alongside an exception (although it is a bit clunky to use).
Aaron Meurer
NumPyDiscussion mailing list NumPyDiscussion@python.org https://mail.python.org/mailman/listinfo/numpydiscussion
On Wed, Aug 19, 2020 at 8:18 PM Sebastian Berg <sebastian@sipsolutions.net> wrote:
On Wed, 20200819 at 19:37 0600, Aaron Meurer wrote:
These cases don't give any deprecation warnings in NumPy master:
np.arange(0)[np.array([0]), False] array([], dtype=int64) np.arange(0).reshape((0, 0))[np.array([0]), np.array([], dtype=int)] array([], dtype=int64)
Is that intentional?
I guess it follows from `np.array([[1]])[[], [10]]` also not failing currently.
Sure, I think that's the same thing (sorry if my example is "too trivial". I was copypasting a hypothesis shrunk example).
And that was intentional not to deprecate when outofbound indices broadcast away. But I am not sure I actually think that was the better choice. My initial choice was that this would be an error as well, and I still slightly prefer it, but don't feel it matters much.
There's an inconsistency here, which is that outofbounds indices that are broadcast away are not bounds checked unless they are scalar indices, in which case they are.
a = np.empty((1, 1)) a[np.array([], dtype=int), np.array([10])] array([], dtype=float64) a[np.array([], dtype=int), 10] Traceback (most recent call last): File "<stdin>", line 1, in <module> IndexError: index 10 is out of bounds for axis 1 with size 1 np.broadcast_arrays(np.array([], dtype=int), np.array([10])) [array([], dtype=int64), array([], dtype=int64)] np.broadcast_arrays(np.array([], dtype=int), 10) [array([], dtype=int64), array([], dtype=int64)]
This breaks the rule that scalar integer indices have the same semantics as integer arrays with shape (). Aaron Meurer
 Sebastian
Aaron Meurer
On Thu, Jul 23, 2020 at 12:18 PM Aaron Meurer <asmeurer@gmail.com> wrote:
After writing this, I realized that I actually remember the *opposite* discussion occurring before. I think in some of the equality deprecations, we actually raise the new error due to an internal try/except clause. And there was a complaint that its confusing that a nondeprecationwarning is raised when the error will only happen with DeprecationWarnings being set to error.
 Sebastian
I noticed that warnings.catch_warnings does the right thing with warnings that are raised alongside an exception (although it is a bit clunky to use).
Aaron Meurer
NumPyDiscussion mailing list NumPyDiscussion@python.org https://mail.python.org/mailman/listinfo/numpydiscussion
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On Mon, 20200824 at 15:31 0600, Aaron Meurer wrote:
On Wed, Aug 19, 2020 at 8:18 PM Sebastian Berg <sebastian@sipsolutions.net> wrote:
On Wed, 20200819 at 19:37 0600, Aaron Meurer wrote:
These cases don't give any deprecation warnings in NumPy master:
np.arange(0)[np.array([0]), False] array([], dtype=int64) np.arange(0).reshape((0, 0))[np.array([0]), np.array([], dtype=int)] array([], dtype=int64)
Is that intentional?
I guess it follows from `np.array([[1]])[[], [10]]` also not failing currently.
Sure, I think that's the same thing (sorry if my example is "too trivial". I was copypasting a hypothesis shrunk example).
And that was intentional not to deprecate when outofbound indices broadcast away. But I am not sure I actually think that was the better choice. My initial choice was that this would be an error as well, and I still slightly prefer it, but don't feel it matters much.
There's an inconsistency here, which is that outofbounds indices that are broadcast away are not bounds checked unless they are scalar indices, in which case they are.
a = np.empty((1, 1)) a[np.array([], dtype=int), np.array([10])] array([], dtype=float64) a[np.array([], dtype=int), 10] Traceback (most recent call last): File "<stdin>", line 1, in <module> IndexError: index 10 is out of bounds for axis 1 with size 1 np.broadcast_arrays(np.array([], dtype=int), np.array([10])) [array([], dtype=int64), array([], dtype=int64)] np.broadcast_arrays(np.array([], dtype=int), 10) [array([], dtype=int64), array([], dtype=int64)]
This breaks the rule that scalar integer indices have the same semantics as integer arrays with shape ().
Good observation. I agree, that is a subtle inconsistency for 0D objects! (To be precise, I expect 0D arrays behave identically to integers, since they will be optimized out of the "advanced index" part of the indexing operation). I suppose this may be an argument for always checking indices even when they are broadcast away? I am not certain how straight forward, or even desirable, it is to fix it so that 0D integer arrays/integers can be "broadcast away".  Sebastian
Aaron Meurer
 Sebastian
Aaron Meurer
On Thu, Jul 23, 2020 at 12:18 PM Aaron Meurer <asmeurer@gmail.com
wrote:
After writing this, I realized that I actually remember the *opposite* discussion occurring before. I think in some of the equality deprecations, we actually raise the new error due to an internal try/except clause. And there was a complaint that its confusing that a nondeprecationwarning is raised when the error will only happen with DeprecationWarnings being set to error.
 Sebastian
I noticed that warnings.catch_warnings does the right thing with warnings that are raised alongside an exception (although it is a bit clunky to use).
Aaron Meurer
NumPyDiscussion mailing list NumPyDiscussion@python.org https://mail.python.org/mailman/listinfo/numpydiscussion
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