Deprecation warnings for features that will disappear (fixes #552) #580

stinebuu · 2016-12-07T15:43:13Z

Added deprecation warnings for features that will disappear in NEST 3, which includes all subnet functions, the subnet model, DataConnect() and the aeif_cond_alpha_RK5 model. This fixes #552.

The PR also includes partial work on #558, by making sure the examples do not display introduced deprecation warnings.

I suggest @heplesser and @jougs as reviewers.

deprecation warnings.

heplesser

@stinebuu Fine overall, but I have some suggestions on details.

heplesser · 2016-12-07T15:58:12Z

pynest/nest/lib/hl_api_models.py

@@ -186,6 +186,16 @@ def CopyModel(existing, new, params=None):
        Default parameters assigned to the copy. Not provided parameters are
        taken from the existing model.
    """
+    try:
+        deprecated_models = ['subnet', 'aeif_cond_alpha_RK5']


I would define a list of deprecated models at the module level. In that way, you can use the same list in all places that need it, avoiding code duplications. This will make things easier if we change the list of deprecated models in later versions. See also comment on Create() below, may turn this entire try into helper function.

Instead of a list, you could also turn this into a dictionary, mapping the name of the deprecated model to a text for what to do otherwise, e.g., suggest used of aeif_cond_alpha.

Why do you need the try-except here? Are there models without type_id? If that is the problem, could you make the try part more local?

heplesser · 2016-12-07T16:00:30Z

pynest/nest/lib/hl_api_nodes.py

+            text = get_wrapped_text(text)
+            warnings.warn('\n' + text)
+    except(KeyError, NESTError):
+        pass


This is almost the same code as in CopyModels() above. Maybe turn it into a helper function you can call from both places? And why do you also catch NESTError here, but not above?

heplesser · 2016-12-07T16:02:29Z

pynest/nest/lib/hl_api_nodes.py

@@ -72,6 +85,8 @@ def Create(model, n=1, params=None):


 @check_stack
+@deprecated("", "GetLID: LIDs disappear with subnets, use index into "
+            "GIDCollection")


Maybe better: "GetLID will be removed in NEST3. Use ..."

heplesser · 2016-12-07T16:07:04Z

topology/pynest/hl_api.py

@@ -1610,6 +1611,9 @@ def GetTargetNodes(sources, tgt_layer, tgt_model=None, syn_model=None):
    if len(tgt_layer) != 1:
        raise nest.NESTError("tgt_layer must be a one-element list")

+    # Turn of deprecation warning as users shouldn't change implementation of
+    # GetTargetNodes, it is done by the developers
+    hlh._deprecation_warning['GetLeaves'] = False


After GetLeaves() is done, you need to reset hlh._deprecation_warning to its old value. Applies also to the other functions below.

heplesser · 2016-12-07T21:16:45Z

topology/examples/ctx_2n.py


 nest.PrintNetwork(2, ctx)

+gids = range(ctx[0] + 1, col*row*len(el) + ctx[0] + 1)


I wonder if the cure here isn't worse than the problem ... The examples should show users how to do things, but we now will just confuse them with a work-around for a deprecation warning. A better way, I think would be to write these examples like this:

# Create Layer. ctx_subnet is a work-around until NEST3. ctx_subnet = topo.CreateLayer(...) ctx = nest.GetLeaves(ctx_subnet)[0] ... # use ctx in remaining example code

In this way, we isolate the problem in one place with a proper comment.

heplesser · 2016-12-08T04:50:29Z

topology/examples/ctx_2n.py


-nest.PrintNetwork(2)
+nest.PrintNetwork(2, (0,))

 nest.PrintNetwork(2, ctx)


I think we should use the opportunity here to improve the example. All these different PrintNetwork calls make very limited sense, and PrintNetwork will change anyways in NEST3. So I would reduce it to just one call to

nest.PrintNetwork(2)

I we then suppress the deprecation warning for CurrentSubnet() in PrintNetwork(), all should work nicely.

heplesser · 2016-12-08T04:51:48Z

pynest/nest/lib/hl_api_subnets.py

@@ -277,6 +287,8 @@ def EndSubnet():


 @check_stack
+@deprecated("", "LayoutNetwork: use Create(<model>, n=<number>) and get a "
+            "GIDCollection")


Better: "LayoutNetwork is deprecated and will be removed in NEST3. Use Create(, n=) instead."

@deprecated('LayoutNetwork', 'Create(<model>, n=<number>)')

heplesser · 2016-12-08T04:55:55Z

pynest/nest/lib/hl_api_subnets.py

@@ -236,6 +244,7 @@ def GetNetwork(gid, depth):


 @check_stack
+@deprecated("", "BeginSubnet: no longer needed, work with GIDCollections")


Better: "BeginSubnet is deprecated and will be removed in NEST3. See documentation for details."

heplesser · 2016-12-08T04:59:06Z

pynest/nest/lib/hl_api_connections.py

@@ -350,6 +350,7 @@ def Connect(pre, post, conn_spec=None, syn_spec=None, model=None):


 @check_stack
+@deprecated("", "DataConnect: use Connect() with one_to_one rule")


Better: @deprecated('DataConnect', 'Connect() with one_to_one rule'). In that way, the message will automatically have standard format.

jougs · 2016-12-08T09:07:00Z

I have a very general remark: shouldn't deprecation warnings be handled on the SLI level wherever possible? This way they'd automatically bubble up to PyNEST and would only have to be implemented once.

For models, we could for example add two flags in the Node base class (deprecated, deprecation_warning_issued) that are checked in all functions dealing with nodes. A similar mechanism could be thought of for SLIFunctions, where the interpreter could issue warnings whenever a function is used.

heplesser · 2016-12-08T13:05:45Z

@jougs Since we already had the nice @deprecated decorator in PyNEST and almost all end users use PyNEST today, I figured that doing it at the Python level would be easier and cover most cases.

are deprecated, made sure PrintNetwork does not display deprecation warning, re-did examples.

stinebuu · 2016-12-09T10:12:38Z

@heplesser I have made changes in accordance to your comments if you want to take a look.

…) call. Subnet and iaf_neuron marked as deprecated for NEST 3.0.

C++-level deprecations

heplesser · 2016-12-12T13:55:21Z

@jougs We have now added support for deprecation at the C++ level. I am wondering what to do about the SLI examples. We would have to write quite a bit of code programming around the lack of full support for GIDCollections, which will simplify significantly again in NEST 3. Therefore, I wonder if it isn't better to leave the SLI examples as they are, even though the user then will see some warnings. The problem does not (or to a much lesser degree) exist at the PyNEST level, since lists of GIDs there behave almost like GIDCollections will in NEST 3.

examples, made sure deprecation warnings are issued when CreateLayer is used.

some SLI-deprecations on Python level. Made sure SLI remember if deprecation warnings were issued for GetNetwork and LayoutNetwork. Made helper function to supress and reset deprecation warnings on Python level.

Conflicts: models/modelsmodule.cpp

stinebuu · 2016-12-15T16:14:21Z

There are now deprecation warnings on PyNEST and SLI level. Some PyNEST examples, like ctx_2n.py and hill_tononi_Vp.py still show deprecation warnings, but I have made comments saying it's a work-around. I have not done anything with the SLI-examples.

heplesser

Looks quite good, just a few language fixes needed.

heplesser · 2016-12-16T12:52:33Z

topology/examples/test_3d_exp.py

@@ -27,6 +27,10 @@
 3d layers are currently not supported, use at your own risk!

 Hans Ekkehard Plesser, UMB
+
+This example uses the function GetChildren, which is deprecated. A deprecation
+warning is therefore released. For details about deprecated functions, see


released -> issued (applies also in other places)

heplesser · 2016-12-16T12:53:32Z

pynest/nest/lib/hl_api_helper.py


    if model in deprecated_models:
        text = "The {0} model is deprecated and will be removed in a \
        future verstion of NEST, use {1} instead\
        ".format(model, deprecated_models[model])
        text = get_wrapped_text(text)
        warnings.warn('\n' + text)
+
+
+def turn_of_deprecation_warning(deprecated_func_name):


turn_of_... -> turn_off_...

in 2 comments.

heplesser · 2016-12-16T13:45:37Z

@apeyser Since @jougs is unavailable at the moment, could you be the second reviewer for this one?

jougs

Very nice work indeed. Many thanks for considering my concerns and making these extensive changes. I'll approve once my minor comments are addressed.

jougs · 2016-12-31T16:04:13Z

lib/sli/nest-init.sli

 /LayoutNetwork_l_a_dict
 {
  << >> begin
+  /LayoutNetwork /deprecation_warning GetOption true eq
+  {
+    (Sli function LayoutNetwork is deprecated in NEST 3.0.) M_DEPRECATED message


"Sli" -> "SLI"

There are some more changes like this that I won't comment on. Please search and replace all of them.

jougs · 2016-12-31T16:07:39Z

libnestutil/logging_event.cpp

@@ -63,6 +63,9 @@ std::ostream& operator<<( std::ostream& out, const LoggingEvent& e )
  case M_INFO:
    out << "[INFO] ";
    break;
+  case M_DEPRECATED:
+    out << "[INFO] ";


Wouldn't it be even more expressive if "[INFO]" was "[DEPRECATED]"? This would also allow to search the output log for such functions more easily.

jougs · 2016-12-31T16:08:36Z

models/modelsmodule.cpp

-    "aeif_cond_alpha_RK5" );
+    "aeif_cond_alpha_RK5",
+    /*private_model*/ false,
+    /*deprecation_model*/ "NEST 3.0" );


"deprecation_model" -> "deprecation_info"

jougs · 2016-12-31T16:13:36Z

pynest/nest/lib/hl_api_connections.py

@@ -350,6 +352,8 @@ def Connect(pre, post, conn_spec=None, syn_spec=None, model=None):


 @check_stack
+@deprecated('', 'DataConnect is deprecated and will be removed in NEST3. Use \


"NEST3" -> "NEST 3.0" to be consistent with the other messages

jougs · 2016-12-31T16:20:42Z

@heplesser: I agree regarding the SLI examples. We can't possibly re-formulate all of them now and they will be naturally adapted when the deprecated models/functions are removed. I'm happy to accept this PR with the current current scope once my comments are addressed.

heplesser · 2017-01-02T10:11:57Z

@apeyser @jougs has reviewed the PR now, so no need for action on your side.

jougs

Thanks for the changes.

stinebuu added 2 commits December 7, 2016 16:00

Fix 554, Added deprecation warnings, made sure examples avoid introduced

8bf610e

deprecation warnings.

Fix formatting

425aca4

heplesser requested changes Dec 8, 2016

View reviewed changes

stinebuu added 2 commits December 9, 2016 10:01

Changed the deprecation warnings, made a helper function for models that

c5ff0bc

are deprecated, made sure PrintNetwork does not display deprecation warning, re-did examples.

Fixed formatting

a779682

heplesser and others added 4 commits December 12, 2016 12:45

Neuron models can now be marked as deprecated in register_node_model(…

0cca6a1

…) call. Subnet and iaf_neuron marked as deprecated for NEST 3.0.

Added support for marking SLI functions as deprecated.

2b456e2

Fixed formatting.

e3ffe9b

Merge pull request #1 from heplesser/stine-fix552

9c18171

C++-level deprecations

heplesser added this to the NEST 2.12 milestone Dec 12, 2016

stinebuu added 2 commits December 13, 2016 16:13

Updated sli deprecation, changed iaf_neuron to iaf_cond_alpha in PyNEST

3c18a1a

examples, made sure deprecation warnings are issued when CreateLayer is used.

Fixed formatting.

7aabc1f

heplesser mentioned this pull request Dec 15, 2016

Ensure all examples work with 2.12 and avoid deprecated functions #558

Closed

stinebuu added 3 commits December 15, 2016 15:49

Added M_DEPRECATED to list of possible messages in order to suppress

0e98846

some SLI-deprecations on Python level. Made sure SLI remember if deprecation warnings were issued for GetNetwork and LayoutNetwork. Made helper function to supress and reset deprecation warnings on Python level.

Fixed formatting.

dcc2685

Merge remote-tracking branch 'nest_master/master' into fix552

ebdaf8c

Conflicts: models/modelsmodule.cpp

Fixed formatting and made sure tests go through

a8f5447

heplesser requested changes Dec 16, 2016

View reviewed changes

stinebuu added 2 commits December 16, 2016 14:19

A few language fixes.

e97933c

I was a bit quick with copy paste of comments. PrintNetwork -> PlotLayer

d053142

in 2 comments.

heplesser approved these changes Dec 16, 2016

View reviewed changes

heplesser requested a review from apeyser December 16, 2016 13:45

Small spelling error, verstion -> version.

f113398

jougs requested changes Dec 31, 2016

View reviewed changes

Made requested changes.

76f2b55

heplesser removed the request for review from apeyser January 2, 2017 10:09

jougs approved these changes Jan 4, 2017

View reviewed changes

jougs merged commit 090346c into nest:master Jan 4, 2017

This was referenced Jan 4, 2017

Converted NEST by example to Jupyter notebook and updated for 2.12. #602

Merged

Wrong import in hl_api from python 3 #617

Closed

stinebuu mentioned this pull request Jan 9, 2017

Removed iaf_neuron from docstring and documentation examples #626

Merged

stinebuu deleted the fix552 branch January 17, 2017 14:16

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		nest.PrintNetwork(2, ctx)

		gids = range(ctx[0] + 1, colrowlen(el) + ctx[0] + 1)

		@@ -236,6 +244,7 @@ def GetNetwork(gid, depth):


		@check_stack
		@deprecated("", "BeginSubnet: no longer needed, work with GIDCollections")

		@@ -350,6 +350,7 @@ def Connect(pre, post, conn_spec=None, syn_spec=None, model=None):


		@check_stack
		@deprecated("", "DataConnect: use Connect() with one_to_one rule")

		@@ -350,6 +352,8 @@ def Connect(pre, post, conn_spec=None, syn_spec=None, model=None):


		@check_stack
		@deprecated('', 'DataConnect is deprecated and will be removed in NEST3. Use \

Deprecation warnings for features that will disappear (fixes #552) #580

Deprecation warnings for features that will disappear (fixes #552) #580

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