Tensorflow model.save() fails in SM script mode

Hello,
The following setup fails on model saving:
Calling script file:
tf_estimator = TensorFlow(entry_point='script_one.py',
                      role=role,
                      train_instance_count=1,
                      train_instance_type='ml.p3.2xlarge',
                      framework_version='2.3.0',
                      py_version='py37',
                      script_mode=True,
                      train_use_spot_instances = True,
                      train_max_wait= 36000,
                      train_max_run  =36000,
                      hyperparameters={.
                          'dropout':0.22350414495308987,
                          'epochs': 33,
                          'batch-size': 657,
                          'learning-rate': 0.01}.
                     )

Last part of the scrip file:
#tf.saved_model.save(model, os.path.join(model_dir, 'model/1'))
model.save(os.path.join(model_dir, '000000001'), 'my_model.h5')

Both methods fail with the following error in SM, KeyError: 'callable_inputs':
2020-08-31 12:34:23 Uploading - Uploading generated training model/opt/ml/model/model/1
Traceback (most recent call last):
  File "script_one.py", line 210, in <module>
model.save(os.path.join(model_dir, '000000001'), 'my_model.h5')
File "/usr/local/lib/python3.7/site-packages/tensorflow/python/keras/engine/training.py", line 2005, in save
  signatures, options)
File "/usr/local/lib/python3.7/site-packages/tensorflow/python/keras/saving/save.py", line 134, in save_model
  signatures, options)
File "/usr/local/lib/python3.7/site-packages/tensorflow/python/keras/saving/saved_model/save.py", line 80, in save
  save_lib.save(model, filepath, signatures, options)
File "/usr/local/lib/python3.7/site-packages/tensorflow/python/saved_model/save.py", line 976, in save
  obj, export_dir, signatures, options, meta_graph_def)
File "/usr/local/lib/python3.7/site-packages/tensorflow/python/saved_model/save.py", line 1047, in _build_meta_graph
  checkpoint_graph_view)
File "/usr/local/lib/python3.7/site-packages/tensorflow/python/saved_model/signature_serialization.py", line 75, in find_function_to_export
  functions = saveable_view.list_functions(saveable_view.root)
File "/usr/local/lib/python3.7/site-packages/tensorflow/python/saved_model/save.py", line 145, in list_functions
  self._serialization_cache)
File "/usr/local/lib/python3.7/site-packages/tensorflow/python/keras/engine/training.py", line 2616, in _list_functions_for_serialization
  Model, self)._list_functions_for_serialization(serialization_cache)
File "/usr/local/lib/python3.7/site-packages/tensorflow/python/keras/engine/base_layer.py", line 3019, in _list_functions_for_serialization
  .list_functions_for_serialization(serialization_cache))
File "/usr/local/lib/python3.7/site-packages/tensorflow/python/keras/saving/saved_model/base_serialization.py", line 87, in list_functions_for_serialization
  fns = self.functions_to_serialize(serialization_cache)
File "/usr/local/lib/python3.7/site-packages/tensorflow/python/keras/saving/saved_model/layer_serialization.py", line 79, in functions_to_serialize
  serialization_cache).functions_to_serialize)
File "/usr/local/lib/python3.7/site-packages/tensorflow/python/keras/saving/saved_model/layer_serialization.py", line 95, in _get_serialized_attributes
  serialization_cache)
File "/usr/local/lib/python3.7/site-packages/tensorflow/python/keras/saving/saved_model/model_serialization.py", line 57, in _get_serialized_attributes_internal
  serialization_cache))
File "/usr/local/lib/python3.7/site-packages/tensorflow/python/keras/saving/saved_model/layer_serialization.py", line 104, in _get_serialized_attributes_internal
  functions = save_impl.wrap_layer_functions(self.obj, serialization_cache)
File "/usr/local/lib/python3.7/site-packages/tensorflow/python/keras/saving/saved_model/save_impl.py", line 155, in wrap_layer_functions
  original_fns = _replace_child_layer_functions(layer, serialization_cache)
File "/usr/local/lib/python3.7/site-packages/tensorflow/python/keras/saving/saved_model/save_impl.py", line 274, in _replace_child_layer_functions
  serialization_cache).functions)
File "/usr/local/lib/python3.7/site-packages/tensorflow/python/keras/saving/saved_model/layer_serialization.py", line 95, in _get_serialized_attributes
  serialization_cache)
File "/usr/local/lib/python3.7/site-packages/tensorflow/python/keras/saving/saved_model/model_serialization.py", line 57, in _get_serialized_attributes_internal
  serialization_cache))
File "/usr/local/lib/python3.7/site-packages/tensorflow/python/keras/saving/saved_model/layer_serialization.py", line 104, in _get_serialized_attributes_internal
  functions = save_impl.wrap_layer_functions(self.obj, serialization_cache)
File "/usr/local/lib/python3.7/site-packages/tensorflow/python/keras/saving/saved_model/save_impl.py", line 165, in wrap_layer_functions
  '{}_layer_call_and_return_conditional_losses'.format(layer.name))
File "/usr/local/lib/python3.7/site-packages/tensorflow/python/keras/saving/saved_model/save_impl.py", line 505, in add_function
  self.add_trace(*self._input_signature)
File "/usr/local/lib/python3.7/site-packages/tensorflow/python/keras/saving/saved_model/save_impl.py", line 420, in add_trace
  trace_with_training(True)
File "/usr/local/lib/python3.7/site-packages/tensorflow/python/keras/saving/saved_model/save_impl.py", line 418, in trace_with_training
  fn.get_concrete_function(*args, **kwargs)
File "/usr/local/lib/python3.7/site-packages/tensorflow/python/keras/saving/saved_model/save_impl.py", line 549, in get_concrete_function
  return super(LayerCall, self).get_concrete_function(*args, **kwargs)
File "/usr/local/lib/python3.7/site-packages/tensorflow/python/eager/def_function.py", line 1167, in get_concrete_function
  concrete = self._get_concrete_function_garbage_collected(*args, **kwargs)
File "/usr/local/lib/python3.7/site-packages/tensorflow/python/eager/def_function.py", line 1073, in _get_concrete_function_garbage_collected
  self._initialize(args, kwargs, add_initializers_to=initializers)
File "/usr/local/lib/python3.7/site-packages/tensorflow/python/eager/def_function.py", line 697, in _initialize
  *args, **kwds))
File "/usr/local/lib/python3.7/site-packages/tensorflow/python/eager/function.py", line 2855, in _get_concrete_function_internal_garbage_collected
  graph_function, _, _ = self._maybe_define_function(args, kwargs)
File "/usr/local/lib/python3.7/site-packages/tensorflow/python/eager/function.py", line 3213, in _maybe_define_function
  graph_function = self._create_graph_function(args, kwargs)
File "/usr/local/lib/python3.7/site-packages/tensorflow/python/eager/function.py", line 3075, in _create_graph_function
  capture_by_value=self._capture_by_value),
File "/usr/local/lib/python3.7/site-packages/tensorflow/python/framework/func_graph.py", line 986, in func_graph_from_py_func
  func_outputs = python_func(*func_args, **func_kwargs)
File "/usr/local/lib/python3.7/site-packages/tensorflow/python/eager/def_function.py", line 600, in wrapped_fn
  return weak_wrapped_fn().__wrapped__(*args, **kwds)
File "/usr/local/lib/python3.7/site-packages/tensorflow/python/keras/saving/saved_model/save_impl.py", line 515, in wrapper
  inputs = call_collection.get_input_arg_value(args, kwargs)
File "/usr/local/lib/python3.7/site-packages/tensorflow/python/keras/saving/saved_model/save_impl.py", line 455, in get_input_arg_value
  self._input_arg_name, args, kwargs, inputs_in_args=True)
File "/usr/local/lib/python3.7/site-packages/tensorflow/python/keras/engine/base_layer.py", line 2536, in _get_call_arg_value
  return args_dict[arg_name]

KeyError: 'callable_inputs'

If you are ok with TF 2.1 version, here is the solution:
tf_estimator = TensorFlow(entry_point='script_one.py',                            role=role,                           train_instance_count=1,                            train_instance_type='ml.p3.2xlarge',                           framework_version='2.1.0',                            py_version='py3',                           script_mode=True,                           train_use_spot_instances = True,                           train_max_wait= 36000,                           train_max_run  =36000,                           hyperparameters={                               'dropout':0.22350414495308987,                               'epochs': 33,                               'batch-size': 657,                               'learning-rate': 0.01}                          )
Now, the question remains why it doesn't work with TF 2.2 or 2.3

Are you using debugger callbacks ? If you do try to remove them

Thanks, @hm-haitham for the tip. I can confirm that disabling debugger callbacks fixes the issue. Using @kafka399's estimator as an example, here is how the fix will look like:
tf_estimator = TensorFlow(
    entry_point='script_one.py',   role=role,
    train_instance_count=1,
    train_instance_type='ml.p3.2xlarge',
    framework_version='2.3.0',
    py_version='py37',
    script_mode=True,
    train_use_spot_instances = True,
    train_max_wait= 36000,
    train_max_run  =36000,
    debugger_hook_config=False,
    hyperparameters={
        'dropout':0.22350414495308987,
        'epochs': 33,
        'batch-size': 657,
        'learning-rate': 0.01
    }
)

Notice the debugger_hook_config setting.


encoding/gob: permit registering duplicate names

In go1.9, type aliases were introduced. The purpose of type aliases is to permit the movement of types from one location to another. This implies:

that the real name of the type can change over time
that there can be multiple names for the exact same Go type

The use of type aliases interacts poorly with gob-encoded data stored on disk that represent interface values as gob was a developed in an era where there was one-to-one relationship between types and names.
Consider the following examples.
At some point in the past, we gob-encoded is stored on disk using something like:
type Rect struct { ... }
func (r Rect) Area() int { ... }
type Any struct {
	Shape interface{ Area() int }
}

func main() {
	gob.Register(Rect{})

	var b bytes.Buffer
	e := gob.NewEncoder(&b)
	e.Encode(Shape{Rect{2, 5}})

	// assume that b is stored on disk
	fmt.Printf("%q\n", b.String())
}

On the decoder side, this works fine with code like:
type Rect struct { ... }
func (r Rect) Area() int { ... }
type Any struct {
	Shape interface{ Area() int }
}

func main() {
	// Assume that the contents of r is loaded from disk as created by:
	// https://play.golang.org/p/dt0pW47u17P
	r := strings.NewReader(...)

	gob.Register(Rect{})

	d := gob.NewDecoder(r)
	v := new(Shape)
	fmt.Println(d.Decode(v)) // got nil; works as expected
}

At some point in the future, suppose we move Rect, now decoding fails:
type Rect = Rect2 // this is now a type alias to a different name
type Rect2 struct { ... }
func (r Rect2) Area() int { ... }
type Any struct {
	Shape interface{ Area() int }
}

func main() {
	// Assume that the contents of r is loaded from disk as created by:
	// https://play.golang.org/p/dt0pW47u17P
	r := strings.NewReader(...)

	gob.Register(Rect{})

	d := gob.NewDecoder(r)
	v := new(Shape)
	fmt.Println(d.Decode(v)) // got `gob: name not registered for interface: "main.Rect"`, expected nil
}

The problem is that the full type name is encoded in the gob wire data. Trying to decode the data at a later date does not know about the movement of the type due to type aliases.
Given that problem, one would think that you could just use gob.RegisterName to manually register the old name:
gob.RegisterName(Rect{})
gob.RegisterName("main.Rect", Rect{})

However, that panics with:
panic: gob: registering duplicate names for main.Rect2: "main.Rect2" != "main.Rect"

I propose the following changes:

That gob be better documented about the interaction of type aliases and serialization of interface values.
That gob.RegisterName be relaxed to permit duplicate names. However, this can cause confusion in the implementation as to which name to use when marshaling. Alternatively, we could add a gob.RegisterAlias that makes it clear that the duplicate names are aliases.

/cc @robpike per owners.

@dsnet -  at the end of your issue, you said:

Given that problem, one would think that you could just use gob.RegisterName to manually register the old name:
gob.RegisterName(Rect{})
gob.RegisterName("main.Rect", Rect{})

That first line doesnt work because RegisterName takes two parameters. Did you mean this?
gob.Register(Rect{})
gob.RegisterName("main.Rect", Rect{})

because that does raise:
panic: gob: registering duplicate names for main.Rect2: "main.Rect2" != "main.Rect"

When types are moved with aliases the only way to inform gob is to leave out the first line:
// gob.Register(Rect{})  --- ng. Rect is now an alias to Rect2{}
gob.RegisterName("main.Rect", Rect{})

or, this works the same and might be clearer:
gob.RegisterName("main.Rect", Rect2{})  // Rect has moved to Rect2

That doesn't seem too terrible because the code also had to be altered to add the alias. But, It does feel a little unexpected ( re: better docs ), and it does "lock" the type forever to the earlier name.
I just encountered similar issues trying to implement transparent type migration... "upgrading" to new types while reading/writing.
To support type migration, it might be nice ( like your RegisterAlias()? )  if the decoder allowed multiple names to map to the same type. That would allow "main.Rect" and "main.Rect2" names to be loaded into a "Rect2" struct. If the encoder still always used a type's actual name ( ie. "main.Rect2" ) that would effectively move the type after a read and write.
I wasn't able to find similar requests, but encapsulating the registry and creating the de/encoder(s) from it could also do the trick.
// possible syntax:
var oldFormat, newFormat gob.Registry
oldFormat.RegisterName("main.Rect", Rect2{})
newFormat.Register(Rect2{})
dec, enc:= oldFormat.NewDecoder(), newFormat.NewEncoder()

As a side benefit, registry memory could be released once it's no longer needed. And... taking this a step further... if that registry object exposed a way to translate type names into gob.Decoder and gob.Encoder interfaces... that would allow a level of flexibility for stream translation and migration that's not currently available.

please add  RegisterAlias


Translate August 14 sit-rep into Arabic

Greetings @nextstrain/arabic,
It’s really great to work with you again after a long situation report hiatus.
Our August update on genomic epidemiology of COVID-19 is ready to be translated to Arabic. This is just a one-off situation report, and we are not planning to resume weekly situation reports at this time. Translation of this report is less time sensitive than previous ones, so feel free to take a bit longer on the translation. I won’t be available for much of the weekend, so may not be able to publish it until Sunday anyway.
Branch to translate on: sit-rep_ar
File to translate: https://github.com/nextstrain/translations/blob/sit-rep_ar/narratives/translations_ncov_sit-rep_ar_2020-08-14.md. You can translate directly in this file, but please remember to push often.
Link to preview: https://nextstrain.org/community/narratives/nextstrain/translations@sit-rep_ar/ncov/sit-rep/ar/2020-08-14
Please translate the Twitter post below too :)
Thank you so much! Sending warm, safe thoughts to you and your loved ones and hoping for wisdom in our respective leaders.
Take care,
Cassia
Twitter post
Check out our August report on COVID-19 genomic epidemiology in Arabic. In it, we explore the global spread of the virus broadly and provide specific updates for each world region.
Thank you to @, @, and @ for their rapid translation!
Logistics
Please update the translations board as you work on the translation: https://github.com/orgs/nextstrain/projects/7
Please assign yourself to the translation if you’re working on it this week.
When a translation is ready for publication -- at minimum meaning two people have worked on it and both agree that it’s ready -- please create a pull request to merge to master and tag me and the issue in it!
Discussion board for your team is here: https://github.com/orgs/nextstrain/teams/arabic
Standard rules for translation:
Note that the file to translate is in Markdown. In general, it is important not to change any formatting or links. Feel free to update internal links to refer to the Arabic version of the narrative(s). I can also update those when I publish it though.
Please keep the number of and text for Table of Contents links the same in your translation as in the English narrative.
Please add your name under translators: with new line, tab, and dash, formatted just like authors are. Please also add a link to your professional page (can use Twitter) under translatorLinks:.
Note: You may know of other great resources available in Arabic; please don’t add them to the situation report. We need to keep content the same across all translations, so we can be confident in the accuracy.
At minimum, I require two sets of eyes on every translation; one of those people should have a background in phylogenetics. Although if you have more, that’s fine too.

Per discussion with @SalehA74 & @falnaji, I'm closing this issue as we don't have translators available


toDiscretePointSet and toContinousPointSet functions

Codecov Report

Merging #599 (c2b90b7) into develop (70664c0) will decrease coverage by 0.38%.
The diff coverage is 8.00%.

@@             Coverage Diff             @@
##           develop     #599      +/-   ##
===========================================
- Coverage    52.35%   51.96%   -0.39%
===========================================
  Files           51       51
  Lines         3203     3225      +22
===========================================
- Hits          1677     1676       -1
- Misses        1526     1549      +23

Impacted Files
Coverage Δ

...ript/FunctionRegistry/FunctionRegistry_Helpers.res
36.23% <0.00%> (-5.44%)
:arrow_down:

...ript/FunctionRegistry/FunctionRegistry_Library.res
39.02% <0.00%> (-16.15%)
:arrow_down:

packages/squiggle-lang/src/rescript/Utility/E.res
43.32% <ø> (ø)

...ges/squiggle-lang/src/rescript/Utility/XYShape.res
54.24% <0.00%> (-0.41%)
:arrow_down:

...script/Distributions/PointSetDist/PointSetDist.res
70.19% <100.00%> (-0.29%)
:arrow_down:

Continue to review full report at Codecov.

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GenerateSharedSecret - invalid coordinate

Dear Marc,
Not sure if this is a bug and I know it is not of your responsibility but when I generate a new public/private EC key pair (using openSSL c++ API) to encrypt ContractCertPrivateKey I get the following exception on RISE-V2G (evcc):
Exception in thread "Thread-0" java.security.ProviderException: invalid coordinate 	at jdk.crypto.ec/sun.security.ec.ECDHKeyAgreement.validateCoordinate(ECDHKeyAgreement.java:118) 	at jdk.crypto.ec/sun.security.ec.ECDHKeyAgreement.validate(ECDHKeyAgreement.java:137) 	at jdk.crypto.ec/sun.security.ec.ECDHKeyAgreement.deriveKeyImpl(ECDHKeyAgreement.java:222) 	at jdk.crypto.ec/sun.security.ec.ECDHKeyAgreement.engineGenerateSecret(ECDHKeyAgreement.java:169) 	at java.base/javax.crypto.KeyAgreement.generateSecret(KeyAgreement.java:598) 	at com.v2gclarity.risev2g.shared.utils.SecurityUtils.generateSharedSecret(SecurityUtils.java:1278) 	at com.v2gclarity.risev2g.shared.utils.SecurityUtils.decryptContractCertPrivateKey(SecurityUtils.java:1507) 	at com.v2gclarity.risev2g.evcc.states.WaitForCertificateInstallationRes.processIncomingMessage(WaitForCertificateInstallationRes.java:77) 	at com.v2gclarity.risev2g.evcc.session.V2GCommunicationSessionEVCC.update(V2GCommunicationSessionEVCC.java:183) 	at java.base/java.util.Observable.notifyObservers(Observable.java:173) 	at com.v2gclarity.risev2g.evcc.transportLayer.StatefulTransportLayerClient.processIncomingMessage(StatefulTransportLayerClient.java:124) 	at com.v2gclarity.risev2g.evcc.transportLayer.TLSClient.run(TLSClient.java:169) 	at java.base/java.lang.Thread.run(Thread.java:834)
Where:
    private static void validateCoordinate(BigInteger c, BigInteger mod) {         if (c.compareTo(BigInteger.ZERO) < 0) {             throw new ProviderException("invalid coordinate");         } ``         if (c.compareTo(mod) >= 0) {             throw new ProviderException("invalid coordinate");         }  }
The only way to avoid this exception is to force that the generated public key has both it's coordinates positive.
With this workaround CertificateInstallation always works, but I don't believe that such a workaround should be needed. Analysing the elliptic curve and its domain parameters it's seems reasonable that the coordinates could be lower than zero.
At the end of the day I don't know if this bug is on the generate key pair of openssl API or on the sun.security API side.
Would like to hear your opinion and for the sake of the security of PnC this possible issue should be clarified.

Dear @calvinsantana, thanks for reporting this issue. At first sight, I believe it's a bug in the OpenSSL API, but I would have to spend more time to dig deeper into this issue and see if I can help solve the problem.
But you are right regarding the coordinate: it can also be negative, there's no reason why it shouldn't be possible.
I have it on my TODO list and will get back to you asap.

As I had the same error in my project, I was googling for this error and ended up on this github issue - the only result for this issue.
I finally found my issue (all good from OpenSSL and sun.security), you have to make sure you load the X and Y of your ECPoint as positive number (default is signed number).

@oliviermartin Can you please elaborate on where exactly you would make a change in the code and explain why the X and Y of my ECPoint must be loaded as positive numbers? It's perfectly fine for an X and Y coordinate of an ECPoint to be negative, so I am not convinced yet that this is the right solution.

Sorry @MarcMueltin , I would need some time (which I do not have right now) to go back into the code. But when I had the issue in my project it was clear this project has the same issue considering the error message raised by @calvinsantana. The change I did fixed mine.
But if you are sure your issue is different, I guess I am wrong.

I could observe the same problem and did therefore a little workaround.
It seemed to me, that the EC Public Key Generator with the Parameter Spec "secp256r1" only produces ECPoints with positive coordinates. But in the SecurityUtils class at the method getPublicKey(byte[] publicKeyBytes) the construction of the PublicKey from the encoded raw bytes returns from time to time a negative signum within the BigInteger(byte[] val) constructor and therefore generates the negative coordinates.
My Solution was to change the constructor of the BigInteger(byte[] val) to BigInteger(int signum, byte[] magnitude) to determine a positive EC Point (see below).
KeyFactory kf = KeyFactory.getInstance("EC");

AlgorithmParameters parameters = AlgorithmParameters.getInstance("EC");
parameters.init(new ECGenParameterSpec("secp256r1"));
ECParameterSpec ecParameterSpec = parameters.getParameterSpec(ECParameterSpec.class);

ECPublicKeySpec ecPublicKeySpec = new ECPublicKeySpec(new ECPoint(new BigInteger(1, x), new BigInteger(1, y)), ecParameterSpec);
ECPublicKey ecPublicKey = (ECPublicKey) kf.generatePublic(ecPublicKeySpec);

@chargehere I agree, this seems to be the easiest and most straight forward solution. I took care of it with commit fa9f2ee.


create-report: wildtype in cgi results triggers index error

Description of the bug
the input used, was the result of a variantMTB call on the variantmtb test dataset.
querynator create-report suddenly fails and throws index error. I did not have a problem with the same data before.
error is thrown in combine_cgi::get_all_alterations:
alteration_links = [j.split(")")[0] for j in [i.split("(")[1] for i in row["Alterations"].split(", ")]]

expected row["Alterations"]: EGFR (P546S), EGFR (G598V), EGFR (E690K), EGFR (S768I)
unexpected: PDGFRA wildtype -> throws index error as index 1 does not exist for 1-element-list.
cgi_results/biomarkers.tsv: lines 476-479

input01	EGFR (P546S), EGFR (G598V), EGFR (E690K), EGFR (S768I)	EGFR (T790M)	Afatinib (ERBB2 inhibitor&EGFR inhibitor 2nd gen)	Lung	Resistant	A	YES	NCCN	only alteration type		L
input01	PTEN (R233Q)	PTEN biallelic inactivation	Panitumumab (EGFR mAb inhibitor)	Colorectal adenocarcinoma	Resistant	C	YES	Caris molecular intelligence	only alteration type		COREAD
input01	FLT3 (D835E)	FLT3 (D835,Y842)	Ponatinib (BCR-ABL inhibitor 3rd gen&Pan-TK inhibitor)	Acute myeloid leukemia	Resistant	D	YES	PMID:23430109	complete		AML
input01	PDGFRA wildtype	PDGFRA wildtype	Dasatinib (BCR-ABL inhibitor 2nd gen)	Gastrointestinal stromal	Responsive	D	YES	PMID:16397263	complete		GIST

why did this bug occur now?

the unexpected entry was already there when create-report ran through without issues
the responsible line was not changed since

Command used and terminal output
(querynator) [zxmgc83@thanos 31cbe1cd66c3929ced7fadb4e571e7]$ querynator create-report \
    --cgi_path test_sample_cgi \
    --civic_path test_sample_civic \
    --outdir test_sample_report

                                           __
  ____ ___  _____  _______  ______  ____ _/ /_____  _____
 / __ `/ / / / _ \/ ___/ / / / __ \/ __ `/ __/ __ \/ ___/
/ /_/ / /_/ /  __/ /  / /_/ / / / / /_/ / /_/ /_/ / /
\__, /\__,_/\___/_/   \__, /_/ /_/\__,_/\__/\____/_/
  /_/                /____/

2024-02-29 14:13:33,434 - Querynator - INFO - Start
2024-02-29 14:13:33,435 - Querynator - INFO - Combining CIViC & VEP
2024-02-29 14:13:33,453 - Querynator - INFO - Combining CGI & VEP
Traceback (most recent call last):
  File "/home-link/zxmgc83/miniconda3/envs/querynator/bin/querynator", line 10, in <module>
    sys.exit(run_querynator())
  File "/home-link/zxmgc83/miniconda3/envs/querynator/lib/python3.10/site-packages/querynator/__main__.py", line 277, in run_querynator
    querynator_cli()
  File "/home-link/zxmgc83/miniconda3/envs/querynator/lib/python3.10/site-packages/click/core.py", line 1157, in __call__
    return self.main(*args, **kwargs)
  File "/home-link/zxmgc83/miniconda3/envs/querynator/lib/python3.10/site-packages/click/core.py", line 1078, in main
    rv = self.invoke(ctx)
  File "/home-link/zxmgc83/miniconda3/envs/querynator/lib/python3.10/site-packages/click/core.py", line 1688, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/home-link/zxmgc83/miniconda3/envs/querynator/lib/python3.10/site-packages/click/core.py", line 1434, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/home-link/zxmgc83/miniconda3/envs/querynator/lib/python3.10/site-packages/click/core.py", line 783, in invoke
    return __callback(*args, **kwargs)
  File "/home-link/zxmgc83/miniconda3/envs/querynator/lib/python3.10/site-packages/querynator/__main__.py", line 485, in create_report
    combine_cgi(cgi_path, report_dir, logger)
  File "/home-link/zxmgc83/miniconda3/envs/querynator/lib/python3.10/site-packages/querynator/report_scripts/combine_cgi.py", line 338, in combine_cgi
    biomarkers_df = link_biomarkers(biomarkers_df)
  File "/home-link/zxmgc83/miniconda3/envs/querynator/lib/python3.10/site-packages/querynator/report_scripts/combine_cgi.py", line 276, in link_biomarkers
    biomarkers_df["alterations_link"] = biomarkers_df.apply(lambda x: get_all_alterations(x), axis=1)
  File "/home-link/zxmgc83/miniconda3/envs/querynator/lib/python3.10/site-packages/pandas/core/frame.py", line 9555, in apply
    return op.apply().__finalize__(self, method="apply")
  File "/home-link/zxmgc83/miniconda3/envs/querynator/lib/python3.10/site-packages/pandas/core/apply.py", line 746, in apply
    return self.apply_standard()
  File "/home-link/zxmgc83/miniconda3/envs/querynator/lib/python3.10/site-packages/pandas/core/apply.py", line 873, in apply_standard
    results, res_index = self.apply_series_generator()
  File "/home-link/zxmgc83/miniconda3/envs/querynator/lib/python3.10/site-packages/pandas/core/apply.py", line 889, in apply_series_generator
    results[i] = self.f(v)
  File "/home-link/zxmgc83/miniconda3/envs/querynator/lib/python3.10/site-packages/querynator/report_scripts/combine_cgi.py", line 276, in <lambda>
    biomarkers_df["alterations_link"] = biomarkers_df.apply(lambda x: get_all_alterations(x), axis=1)
  File "/home-link/zxmgc83/miniconda3/envs/querynator/lib/python3.10/site-packages/querynator/report_scripts/combine_cgi.py", line 261, in get_all_alterations
    alteration_links = [j.split(")")[0] for j in [i.split("(")[1] for i in row["Alterations"].split(", ")]]
  File "/home-link/zxmgc83/miniconda3/envs/querynator/lib/python3.10/site-packages/querynator/report_scripts/combine_cgi.py", line 261, in <listcomp>
    alteration_links = [j.split(")")[0] for j in [i.split("(")[1] for i in row["Alterations"].split(", ")]]
IndexError: list index out of range

System information
python=3.10
hardware: replicated on local machine as well as on server
local uname -a

Linux rechenmaschine02 5.10.0-1057-oem #61-Ubuntu SMP Thu Jan 13 15:06:11 UTC 2022 x86_64 GNU/Linux

server uname -a

Linux thanos.am10.uni-tubingen.de 5.14.0-362.18.1.el9_3.0.1.x86_64 #1 SMP PREEMPT_DYNAMIC Sun Feb 11 13:49:23 UTC 2024 x86_64 GNU/Linux

open todos:

[ ] PR to qbicpipelines/master
[ ] update conda package
[ ] upgrade querynator in variantmtb


Server coding and design guidelines

Motivation and Context
Improve the consistency of the development.
Description
I added a first draft of server coding and design guidelines.
(The client coding and design guidelines will follow in another PR)
Steps for Testing

Read and review the new documentation
Provide feedback if something should be changed or something is missing

Thanks everyone for the feedback. I updated the guidelines accordingly and added client guidelines as well.
Both are still WORK IN PROGRESS, but I guess it's better to have something that nothing.
We can further adapt and improve the guidelines in the upcoming weeks.


[SSL][Pages] Update known-issues.md

CUSTESC-38470
Summary
Features based on client certificates are not supported on Pages
Screenshots (optional)

Documentation checklist

[ ] The documentation style guide has been adhered to.
[ ] If a larger change - such as adding a new page- an issue has been opened in relation to any incorrect or out of date information that this PR fixes.
[ ] Files which have changed name or location have been allocated redirects.

👋Hi there, we’re going to close this PR. All PRs prior to August 12 need to be reworked due to the platform migration to Astro.


Dynomite SIGSEGV signal 11

We are getting the following error running dynomite-v0.6.14 and redis. The redis logs show no indication that it went down.
Can anyone give us any input as to what can be done to avoid these errors?

[2019-07-18 02:47:52.398] client_handle_response:240 looks like we already cleanedup the request for 55
[2019-07-18 02:47:52.398] client_handle_response:240 looks like we already cleanedup the request for 56
[2019-07-18 02:47:52.398] client_handle_response:240 looks like we already cleanedup the request for 59
[2019-07-18 02:47:52.398] client_handle_response:240 looks like we already cleanedup the request for 62
[2019-07-18 02:47:52.398] client_handle_response:240 looks like we already cleanedup the request for 65
[2019-07-18 02:47:52.398] client_handle_response:240 looks like we already cleanedup the request for 68
[2019-07-18 02:47:52.398] dn_assert:301 assert 'req->is_request' failed @ (dyn_server.c, 727)
[2019-07-18 02:47:52.398] dn_assert:301 assert 'req->is_request' failed @ (dyn_server.c, 771)
[2019-07-18 02:47:52.398] dn_assert:301 assert 'req->is_request' failed @ (dyn_server.c, 948)
[2019-07-18 02:47:52.398] dn_assert:301 assert '(c_conn->type == CONN_CLIENT) || (c_conn->type == CONN_DNODE_PEER_CLIENT)' failed @ (dyn_server.c, 784)
[2019-07-18 02:47:52.398] msg_local_one_rsp_handler:1052 ASSERTION FAILED: Received more than one response for dc_one.               <REQ 0x1a012d0 78:0::0 REQ_REDIS_HMSET, len:194> prev <RSP 0x1a5e4e0 81:0 RSP_REDIS_ERROR len:39> new rsp <RSP 0x1a6aff0 109:0 RSP_REDIS_STATUS len:5>
[2019-07-18 02:47:52.398] dn_assert:301 assert '!req->selected_rsp' failed @ (dyn_client.c, 105
2)
[2019-07-18 02:47:52.398] msg_local_one_rsp_handler:1052 ASSERTION FAILED: Received more than one response for dc_one. <REQ 0x1a62890 79:0::0 REQ_REDIS_HMSET, len:194> prev <RSP 0x1a5a130 84:0 RSP_REDIS_ERROR len:39> new rsp <RSP 0x1a16590 110:0 RSP_REDIS_STATUS len:5>
[2019-07-18 02:47:52.398] dn_assert:301 assert '!req->selected_rsp' failed @ (dyn_client.c, 1052)
[2019-07-18 02:47:52.398] msg_local_one_rsp_handler:1052 ASSERTION FAILED: Received more than one response for dc_one.               <REQ 0x19fcf00 82:0::0 REQ_REDIS_HMSET, len:194> prev <RSP 0x1a55d80 87:0 RSP_REDIS_ERROR len:39> new rsp <RSP 0x1a6f3a0 111:0 RSP_REDIS_STATUS len:5>
[2019-07-18 02:47:52.398] dn_assert:301 assert '!req->selected_rsp' failed @ (dyn_client.c, 1052)
[2019-07-18 02:47:52.398] msg_local_one_rsp_handler:1052 ASSERTION FAILED: Received more than one response for dc_one.               <REQ 0x19f8b30 85:0::0 REQ_REDIS_HMSET, len:194> prev <RSP 0x1a519d0 90:0 RSP_REDIS_ERROR len:39> new rsp <RSP 0x1a1a960 112:0 RSP_REDIS_STATUS len:5>
[2019-07-18 02:47:52.398] dn_assert:301 assert '!req->selected_rsp' failed @ (dyn_client.c, 1052)
[2019-07-18 02:47:52.398] msg_local_one_rsp_handler:1052 ASSERTION FAILED: Received more than one response for dc_one.               <REQ 0x19f4790 88:0::0 REQ_REDIS_HMSET, len:194> prev <RSP 0x1a4d620 93:0 RSP_REDIS_ERROR len:39> new rsp <RSP 0x1a73750 113:0 RSP_REDIS_STATUS len:5>
[2019-07-18 02:47:52.398] dn_assert:301 assert '!req->selected_rsp' failed @ (dyn_client.c, 1052)
[2019-07-18 02:47:52.398] msg_local_one_rsp_handler:1052 ASSERTION FAILED: Received more than one response for dc_one.               <REQ 0x1a49270 96:0::0 REQ_REDIS_HMSET, len:194> prev <RSP 0x19b7820 99:0 RSP_REDIS_ERROR len:39> new rsp <RSP 0x1a7beb0 117:0 RSP_REDIS_STATUS len:5>
[2019-07-18 02:47:52.398] dn_assert:301 assert '!req->selected_rsp' failed @ (dyn_client.c, 1052)
[2019-07-18 02:47:52.402] dn_assert:301 assert 'req->is_request' failed @ (dyn_server.c, 727)
[2019-07-18 02:47:52.402] dn_assert:301 assert 'req->is_request' failed @ (dyn_server.c, 771)
[2019-07-18 02:47:52.402] dn_assert:301 assert 'req->is_request' failed @ (dyn_server.c, 948)
[2019-07-18 02:47:52.402] dn_assert:301 assert '(c_conn->type == CONN_CLIENT) || (c_conn->type == CONN_DNODE_PEER_CLIENT)' failed @ (dyn_server.c, 784)
[2019-07-18 02:47:52.402] dn_assert:301 assert 'req->is_request' failed @ (dyn_server.c, 727)
[2019-07-18 02:47:52.402] dn_assert:301 assert 'req->is_request' failed @ (dyn_server.c, 771)
[2019-07-18 02:47:52.402] dn_assert:301 assert 'req->is_request' failed @ (dyn_server.c, 948)
[2019-07-18 02:47:52.402] dn_stacktrace:286 [0] /lib64/libpthread.so.0(+0xf5d0) [0x7f09ee6b65d0]
[2019-07-18 02:47:52.452] dn_stacktrace:286 [1] /usr/local/sbin/dynomite() [0x42632a]
[2019-07-18 02:47:52.456] dn_stacktrace:286 [2] /usr/local/sbin/dynomite() [0x426be9]
[2019-07-18 02:47:52.465] dn_stacktrace:286 [3] /usr/local/sbin/dynomite(msg_recv+0x456) [0x422cc6]
[2019-07-18 02:47:52.474] dn_stacktrace:286 [4] /usr/local/sbin/dynomite(core_core+0xcf) [0x41641f]
[2019-07-18 02:47:52.480] dn_stacktrace:286 [5] /usr/local/sbin/dynomite(event_wait+0x164) [0x43fdf4]
[2019-07-18 02:47:52.488] dn_stacktrace:286 [6] /usr/local/sbin/dynomite(core_loop+0x16a) [0x41739a]
[2019-07-18 02:47:52.495] dn_stacktrace:286 [7] /usr/local/sbin/dynomite(main+0x6a0) [0x40cdf0]
[2019-07-18 02:47:52.508] dn_stacktrace:286 [8] /lib64/libc.so.6(__libc_start_main+0xf5) [0x7f09edffa3d5]
[2019-07-18 02:47:52.511] dn_stacktrace:286 [9] /usr/local/sbin/dynomite() [0x40d218]
[2019-07-18 02:47:52.520] signal_handler:123 signal 11 (SIGSEGV) received, core dumping

Hi @effnnn ,
These errors are very likely fixed by the following commit:
https://github.com/Netflix/dynomite/commit/d7f75352337f30d7d93a5fa2117c4a5da7047ec5
I will make a release shortly so that you can move to that.

@effnnn v0.6.15 has the fix. Please reopen if you continue to see issues.
https://github.com/Netflix/dynomite/tree/v0.6.15


[SUP1-198] Investigate automating updating Postman Collections

From SyncLinear.com | SUP1-198

Migrated to internal project management tool.


[+XWATCH√Trending!] Sassy Poonam Viral Leaked Video 2024 Link On Social Media X Twitter [FULL02K]

02 sec ago Sassy PoonamLeaked Video Viral On Social Media. [+XWATCH√Trending!] Sassy PoonamViral Leaked Video 2024 Link On Social Media X Twitter [FULL02K]

Sassy Poonamlatest video has taken the internet by storm, igniting widespread discussions across various social media platforms. The emerging digital creator, known for her captivating content—especially her recent Spiderman-themed clip—has experienced a significant rise in popularity, with fans eagerly searching for the full version. Audiences are flocking to platforms like Instagram, X (formerly Twitter), and Discord to engage with her newest creation.
As excitement continues to build, fans are actively sharing their reactions online, highlighting the vital role social media plays in boosting creators like Gabriela de. With her distinctive style and creative flair, she has quickly made a notable impact in the digital space, leaving many curious about her upcoming projects.


clang-cl: warning: unknown argument ignored in clang-cl: '-fno-ident' [-Wunknown-argument]

Env

OS: Windows 10
Python: 3.9.6
Chromium: 92.0.4515.131
Project: https://github.com/Nifury/ungoogled-chromium-windows

Problem
clang-cl: warning: unknown argument ignored in clang-cl: '-fno-ident' [-Wunknown-argument]
More Info
https://releases.llvm.org/12.0.0/tools/clang/docs/ClangCommandLineReference.html#cmdoption-clang-qn
The option is supported by clang, however clang-cl is different from clang.
How to get rid of the warning while keeping the function?

found taht clang-cl is different from clang, patch needed.

It is simply because of your llvm version. This option is introduced in llvm 13, you probably have clang 11 or 12 on your machine.

It is simply because of your llvm version. This option is introduced in llvm 13, you probably have clang 11 or 12 on your machine.

-fno-ident can be found at https://releases.llvm.org/12.0.0/tools/clang/docs/genindex.html
Do you mean clang-cl in llvm 13?


[C++][Parquet] Account for API changes in ARROW-33

Patch forthcoming
Reporter: Wes McKinney / @wesm
Assignee: Wes McKinney](https://issues.apache.org/jira/secure/ViewProfile.jspa?name=wesm) / @wesm
Related issues:

parquet-cpp 1.0.0 release (blocks)

Note: This issue was originally created as PARQUET-866. Please see the migration documentation for further details.

Wes McKinney / @wesm:
Issue resolved by pull request 236
https://github.com/apache/parquet-cpp/pull/236


documentai quickstart flakes

GCB: https://console.cloud.google.com/cloud-build/builds;region=us-east1/c599744e-3f17-4d21-98c1-5e0ac97821bc;tab=detail?project=cloud-cpp-testing-resources
Raw: https://storage.googleapis.com/cloud-cpp-community-publiclogs/logs/google-cloud-cpp/main/c043c8b9bfdedbe553a6ad819364c13744887f38/fedora-36-cmake-quickstart-production/log-c599744e-3f17-4d21-98c1-5e0ac97821bc.txt

92/94 Test #377: documentai_quickstart ..............***Failed    3.41 sec
CMake Error at /workspace/cmake/quickstart-runner.cmake:90 (message):
  Non-zero exit status (1) running
  /workspace/cmake-out/google/cloud/documentai/documentai_quickstart

  google::cloud::Status thrown: INVALID_ARGUMENT: Error in non-idempotent
  operation ProcessDocument: Unsupported input file format.

While this is not an error message I would expect from a flake, I can successfully run the quickstart at HEAD.
I do not think this is a problem with the client library. We are using application/pdf, which is certainly a supported file type: https://github.com/googleapis/google-cloud-cpp/blob/c043c8b9bfdedbe553a6ad819364c13744887f38/google/cloud/documentai/quickstart/quickstart.cc#L42

GCB: https://console.cloud.google.com/cloud-build/builds;region=us-east1/4b06ae37-82d5-4cfb-bc94-34a5f4be4a6c;tab=detail?project=cloud-cpp-testing-resources
Raw: https://storage.googleapis.com/cloud-cpp-community-publiclogs/logs/google-cloud-cpp/10430/5a376bebb0f376a5d48f77ca2c394c63e7651fcf/fedora-36-cmake-quickstart-production/log-4b06ae37-82d5-4cfb-bc94-34a5f4be4a6c.txt

I wonder if the GCS object we are using changes, or gets the wrong contentType set from time to time.

Maybe use the new List*() RPC.  Closing since we have not seen repeats in 90d.


MSS310H energy entity appears as "Unavailable"

I just upgraded to the latest beta and this is what I see about my MSS310H:

Basically, the entity sensor.meross_lan_2009224801331190830948e1e9342911_energy is now unavailable. Might this be a breaking change and it was replaced by sensor.meross_lan_2009224801331190830948e1e9342911_power?

Hello @almico !
I've double checked with mine and it all works fine. With the last release no relevant changes were made to 'switches' but, of course, something bad could always happen with software releases so again I don't see any disconnect or unavailability on any sensor in my MSS310
What comes to mind here is the firmware version of the plug: it is more recent than mine so there's maybe a different approach in protocol handling for the energy reading.
Keep in mind (power, current, voltage) are read together in a message while (energy) is read in another one so it is no surprise that the former work while the latter (energy) does not.
It would be nice to have some debug log. You can enable detailed logging for meross_lan by following this https://www.home-assistant.io/integrations/logger/
Basically just add
logger:
  default: info
  logs:
    custom_components.meross_lan: debug

to your configuration.yaml
This of course could impact a bit your logging file so you want to maybe enable it for a while, use the plug a bit and then disable logging again. Keep in mind the energy reading normally happens every 1 minute so it is ok to log about 4-5 minutes of data while you use the plug
This is painful since you have to restart HA 2 times so I see if you would pass on that.
At any rate, I'm going to integrate an easier debug facility into the component in order to make it feasible to dump logs 'on the fly' when there's something odd and let you (as user) grab and send these logs with a few clicks in the UI without reconfiguring, restarting and digging into command lines or so. This is not happening soon sadly

Btw,
It happens, at the start or when the plug comes back online, that the component looks connected except the energy sensor (or even the other entity readings):
this is known and 'normal' since I don't read the energy rightaway but the code just waits for the next polling loop to send the energy request end it behaves like that: the energy comes online a bit lazy like 30 seconds 1 minute later

Stale


Controller type error

Hi! I want to make an auto focus on the render component. I have an error using the controller of the component, about the ts types, if ignore the ts the code brokes on run with undefined error over the ref.
Im using the 2.1.0 version

I'm getting the same error on version 3.1.3.  What do I need to change?


Documentation doesn’t show how to connect the pieces

The documentation shows how to define languages and passes. But doesn’t show how put them together to form a compiler. In particular, it has no example of using the parser, nor does it explain with-output-language.
In my exploration of the source, I figure the following works:
(make-explicit (with-output-language (L0 Expr) `(if 0 1)))
;; => (language:L1 '(if '0 '1 (void)))

(define-parser parse-L0 L0)
(make-explicit (parse-L0 '(if 0 1)))
;; => (language:L1 '(if '0 '1 (void)))

But it’s not included in the documentation, and I’m not sure which option is right and what are the implications.
Also, it’d be nice to have documentation for the tracing feature shown in this talk: https://www.youtube.com/watch?v=Os7FE3J-U5Q

This almost kinda seems like a duplicate of issue #1?


Update fly to 3.3.2

After making all changes to the cask:

[x] brew cask audit --download {{cask_file}} is error-free.
[x] brew cask style --fix {{cask_file}} left no offenses.
[x] The commit message includes the cask’s name and version.

Additionally, if updating a cask:

[ ] If the sha256 changed but the version didn’t,
provide public confirmation by the developer: {{link}}

Thank you for the contribution. It was merged directly as a2d3d89f4cdcc410cb4fa5372f5515862a79bfbb. Your contribution is still credited to you.


Generate MinGW makefile

Coverage remained the same at 99.833% when pulling c3fcccc9e644b7b5324cbd98d0f1db692d767d4e on basvodde:master into 69301ea3eba9ecc41323460253cf72c34d73b3d2 on cpputest:master.


Cleanup get_method() error handling

Make raising TypeError from get_method() more explicit by splitting it into two methods: one that raises TypeError if there's no method, and one that's not (for some cases, like __missing__ method for dict).

If it's acceptable for method to be absent (__missing__, __iter__ for iterators and others), do not raise TypeError.
(note that if __get__ descriptor raises an exception, it still gets propagates as before)

Make error messages more consistent with CPython.

Add exc_type to info! exception logging.

Codecov Report

Merging #1014 into master will increase coverage by 0.03%.
The diff coverage is 61.9%.

@@            Coverage Diff             @@
##           master    #1014      +/-   ##
==========================================
+ Coverage   64.58%   64.61%   +0.03%
==========================================
  Files          96       96
  Lines       16888    16915      +27
  Branches     3774     3777       +3
==========================================
+ Hits        10907    10930      +23
+ Misses       3426     3423       -3
- Partials     2555     2562       +7

Impacted Files
Coverage Δ

vm/src/obj/objtype.rs
72.41% <0%> (-0.28%)
:arrow_down:

vm/src/obj/objbool.rs
78.7% <30%> (-1.11%)
:arrow_down:

vm/src/obj/objdict.rs
73.09% <50%> (-0.3%)
:arrow_down:

vm/src/pyobject.rs
78.19% <50%> (-0.62%)
:arrow_down:

vm/src/vm.rs
74.72% <53.84%> (-0.2%)
:arrow_down:

vm/src/obj/objint.rs
80.15% <70%> (-0.22%)
:arrow_down:

vm/src/obj/objfloat.rs
73.27% <71.42%> (+0.73%)
:arrow_up:

vm/src/obj/objiter.rs
78.68% <75%> (-2.67%)
:arrow_down:

vm/src/obj/objstr.rs
73.9% <75%> (+0.1%)
:arrow_up:

vm/src/builtins.rs
69.69% <80%> (+1.65%)
:arrow_up:

... and 2 more

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Looks good, one small thing and then I'll merge. Thanks for contributing!

Before merging, I would like @cthulahoops to have a chance to look at this, since this change touches the attribute related code.


Docker Image

Script really should be a docker image since I need cross-os compatability

First draft complete


Treon test for demos

Description
/scripts/test_demos.py : Script to download the data and test demo within specified subdirectories of the demo folder with Treon.
/docker/stellargraph-treon/Dockerfile: The Dockerfile for the demos is updated to run the above script for testing demos.
Note, the script test  the demos in the specified subdirectories. In this way those demos that are not compatible for automated testing, such as, the dataset on which the notebook runs being unavailable, or requiring a myriad of libraries to be installed, can be excluded.
Although the script runs smoothly as a standalone on the the demos, the docker image is not stable. It arbitrarily breaks down with Kernel died error resulting in failing at successfully testing the notebook it died on. This issue needs to be investigated.
This functionality will enable testing of all demo notebooks in a CI in the future.
Review Checklist (Development)

[x] Write script to automate downloading of datasets & running of demo notebooks.
[x] Branch and Pull Request build on CI
[x] Branch and Pull Request pass unit tests on CI
[ ] Version number reflects new status
[ ] Peer Code Review Performed
[ ] Code well commented
[ ] Documentation in repo
[ ] Team demo

I have updated some files to resolve errors I got when running the notebooks:
ERROR in testing ./calibration-pubmed-link-prediction.ipynb
            Traceback (most recent call last):

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
<ipython-input-45-2641839153f2> in <module>
----> 1 lr.fit(val_predictions, edge_labels_val)

~/Code/stellargraph/stellargraph/utils/calibration.py in fit(self, x_train, y_train)
    399             if len(x_train.shape) > 1:
    400                 x_train = x_train.reshape(-1)
--> 401             self.regressors[-1].fit(X=x_train, y=y_train)
    402         else:
    403             for n in range(self.n_classes):

~/.envs/stellargraph/lib/python3.6/site-packages/sklearn/isotonic.py in fit(self, X, y, sample_weight)
    333         # Transform y by running the isotonic regression algorithm and
    334         # transform X accordingly.
--> 335         X, y = self._build_y(X, y, sample_weight)
    336
    337         # It is necessary to store the non-redundant part of the training set

~/.envs/stellargraph/lib/python3.6/site-packages/sklearn/isotonic.py in _build_y(self, X, y, sample_weight, trim_duplicates)
    271         X, y, sample_weight = [array[order] for array in [X, y, sample_weight]]
    272         unique_X, unique_y, unique_sample_weight = _make_unique(
--> 273             X, y, sample_weight)
    274
    275         # Store _X_ and _y_ to maintain backward compat during the deprecation

sklearn/_isotonic.pyx in sklearn._isotonic._make_unique()

ValueError: Buffer dtype mismatch, expected 'float' but got 'double'
ValueError: Buffer dtype mismatch, expected 'float' but got 'double'

A similar error is encountered in the calibration notebook for link prediction:
ERROR in testing ./calibration-pubmed-link-prediction.ipynb

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
<ipython-input-45-2641839153f2> in <module>
----> 1 lr.fit(val_predictions, edge_labels_val)

~/.local/lib/python3.6/site-packages/stellargraph/utils/calibration.py in fit(self, x_train, y_train)
    399             if len(x_train.shape) > 1:
    400                 x_train = x_train.reshape(-1)
--> 401             self.regressors[-1].fit(X=x_train, y=y_train)
    402         else:
    403             for n in range(self.n_classes):

~/.local/lib/python3.6/site-packages/sklearn/isotonic.py in fit(self, X, y, sample_weight)
    333         # Transform y by running the isotonic regression algorithm and
    334         # transform X accordingly.
--> 335         X, y = self._build_y(X, y, sample_weight)
    336
    337         # It is necessary to store the non-redundant part of the training set

~/.local/lib/python3.6/site-packages/sklearn/isotonic.py in _build_y(self, X, y, sample_weight, trim_duplicates)
    271         X, y, sample_weight = [array[order] for array in [X, y, sample_weight]]
    272         unique_X, unique_y, unique_sample_weight = _make_unique(
--> 273             X, y, sample_weight)
    274
    275         # Store _X_ and _y_ to maintain backward compat during the deprecation

sklearn/_isotonic.pyx in sklearn._isotonic._make_unique()

ValueError: Buffer dtype mismatch, expected 'float' but got 'double'
ValueError: Buffer dtype mismatch, expected 'float' but got 'double'

These errors are most likely related to the version of scikit learn I am using (0.21.2). These have been fixed on the develop branch, so I have merged develop into this branch.

The docker issues with the Jupyter kernel dying could be related to this issue:
https://github.com/jupyter/jupyter_client/issues/154
I have run the test script using their suggestions and it seems to work. See the edited Dockerfile. I also increased the memory available to docker to 6GB to ensure there were no issues with crashes related to the demos running out of memory.

@adocherty, tested the docker image. The script ran through without any issues.

FYI: we will need to wait for feedback from @TheDen before doing anything with this branch.

In discussions with @TheDen we should do the following before we merge this:

Remove movielens downloads and demos. This dataset is not approved for distribution.
Attempt to speed up the demos by limiting the number of training epochs, where we can. This practically means adding flags to the demo scripts (e.g. -e 5 for script "gcn-cora-example.py").

After this we can look as using a dataset that is approved for distribution for the movielens example.

@adocherty & @TheDen,
I have incorporated the following changes you guys suggested:

Remove movielens downloads and demos.
Added the instructions to run the interpretability demo but left it commented at the moment until its updated based on the latest changes in the library.
Added epochs  flags to the demo scripts. They run for 5 epochs each.
Pinned Treon adn Seaborn versions and removed the trailing spaces after --users.
Moved the line 38 below 33.

Tested the docker image. It runs smoothly. However, I did get "Kernal Died" error once on the ensemble demo that takes the longest to run anyways. It failed only once though.

Looks good to me. Let's wait for @TheDen to check it then we can merge it.

This looks good now, let's merge it 👍


53 Cover QA Fixes

Resolves #53 (and #52)
This PR addresses design feedback in the above issue. It is principally styling updates, with some abstracting of markup into new includes where necessary.
https://pr54-4endlhiqlryitmfkta0zhvo2s2sngtd6.tugboatqa.com/ebooks/large-team-challenges/cover/

Looks to me like it resolves both of these tickets. I mainly checked the covers and resized to make sure that things were vertically centered, spacings were multiples of 8 and conform to the annotated designs jponch provided.


Add transferwise variant of tap-google-analytics

Migrated from GitLab: https://gitlab.com/meltano/meltano/-/issues/2424
Originally created by @DouweM on 2020-11-05 23:14:22

https://github.com/transferwise/pipelinewise-tap-google-analytics
https://transferwise.github.io/pipelinewise/connectors/taps/google-analytics.html

View 3 previous comments from the original issue on GitLab

Closing as stale.


Start

Hello,
I just test timesheet.js, I don' have result. Could you make others exemples.
What is the trigger, an id ?
Where I parameter this id ?
Thanks

I think documentation is clear enough now. So, I think you can close this!


Relax protobuf requirements for tritonclient

breaking protobuf 4.21.0 changes
have those been addressed?
Can you link in a comment for traceability?

breaking protobuf 4.21.0 changes
have those been addressed?
Can you link in a comment for traceability?

It seems like the linked ticket is closed: https://github.com/protocolbuffers/protobuf/issues/10051

closes
#4984: version 3 incompatible with many other libraries
#4988 Triton image_client.py fails to run
#6095 tritonclient protobuf version

I hope this gets into the 23.11 release.

I hope this gets into the 23.11 release.

Hi @ozen it will be 23.12 release. You can build it yourself from main if you want it sooner

@jbkyang-nvi Got it, thanks :)


Multiselect and Date Filter added

I have added multiselect and date filter options. Can this be added to the repository?
new filter types are "date" and "multiple".
setting for multiple is :
filter: {
type: 'multiple',
config: {
dropdownList: [
{ "id": 1, "itemName": "India" },
{ "id": 2, "itemName": "Singapore" },
{ "id": 3, "itemName": "Australia" }
],
selectedItems: [],
dropdownSettings: {
singleSelection: false,
text: "Select Countries",
selectAllText: 'Select None',
unSelectAllText: 'UnSelect All',
enableSearchFilter: true,
classes: "myclass custom-class"
}
}

Hi Dhirendrak
have you added the date filter is it working?
I am looking for the same please help

also interested in this. any idea if there is plan to merge this?

Hello Any idea how to use this multi select as input element?

Hi, How I can use this feature?


Add ARIA attributes support for custom content

This makes sense to me. options.content should be supported (indeed, the docs state that it is), and should take precedence over data-tooltip. Add a version bump to 1.2.1 and I'll merge.


Extend documentation with disk space requirements

It took me around 30GB on the system drive to unpack the box, after that it jumped back to around 15GB usage. On top of that the box takes another 13GB. With a 120GB SSD for system this is a lot of space, so it would be wise to mention it in the documentation.
By failure it started to download the box file again from zero, which means another 2-3 hour download. This should be added to the documentation too. Maybe downloading it with browser and adding the box locally would be a better advice.

I have added a note that it's slow to download something from Vagrant Cloud and we, unfortunately, we don't have a hosting to share the file directly anymore. So I believe this is safe to close, please reopen otherwise.

I have added a note that it's slow to download something from Vagrant Cloud and we, unfortunately, we don't have a hosting to share the file directly anymore. So I believe this is safe to close, please reopen otherwise.


Fix SearchWithin menu measurements

Closes
relies on https://github.com/adobe/react-spectrum/pull/2177
doesn't use refs on both input and button like combobox because we can't easily get those refs, instead, we measure the group element, which contains both of those
✅ Pull Request Checklist:

[ ] Included link to corresponding React Spectrum GitHub Issue.
[ ] Added/updated unit tests and storybook for this change (for new code or code which already has tests).
[ ] Filled out test instructions.
[ ] Updated documentation (if it already exists for this component).
[ ] Looked at the Accessibility Practices for this feature - Aria Practices

📝 Test Instructions:

🧢 Your Project:

I tried using sync ref and merging the refs, but it was causing other tests to fail, so this was the path of least resistance

LGTM


Exporting to HTML

Hi
Has anyone had success with exporting the generated JSON to HTML?
I've tried the draft-js-import-html project, but it fails with the error
Uncaught Error: Unknown DraftEntity key.

Hi,
We have a Python based backend, we are using this project to render some of our html: https://github.com/springload/draftjs_exporter
Never tried draft-js-import-html, though.

Hey @madshargreave!
A little bit late but you can try to find tools here:
https://github.com/nikgraf/awesome-draft-js#common-utilities
I'm closing the issue ok? Feel free to comment!

Are those tools compatible wtih this lib? It seems editorState object is not same here as in draftjs? All examples and libraries fail with error


Add new Table and Pagination components

Summary of changes

Merged and resolve conflict with develop
Add Table component
Add Pagination component
Add new utils function for UI

Reference issue to close (if applicable)

Closes

https://github.com/webb-tools/webb-dapp/issues/531
https://github.com/webb-tools/webb-dapp/issues/516

Code Checklist

[x] Tested
[x] Documented

Screenshots

For simplicity, please review PR https://github.com/webb-tools/webb-dapp/pull/562 first, then come back to review this PR. Thanks 🙏


I016 thermal loads new ventilation

@JIMENOFONSECA
@daren-thomas
@shanshanhsieh
Can you please test run my branch with the new thermal loads and ventilation calculation procedure?
I will clean up the code meanwhile.

I can successfully run the demand script on this branch. HOWEVER: We cannot merge it at this point. Here are some changes that need to be made:

globalvars.py imports from contributions - this should not be the case
the default model (functions.CalcThermalLoads) should be the one configured in globalvars.py
a test-script in the contributions folder should show how to use this model (hint: copy demand.test_demand to a new script and add a new line after the gv instantiation to replace the calc-thermal-loads model)
this branch breaks the core model: running with functions.CalcThermalLoads produces the following error:

C:\Users\darthoma\Anaconda2\envs\esri103\python.exe C:/Users/darthoma/Documents/GitHub/CEAforArcGIS/cea/demand.py
reading input files
done
calculating thermal properties
done
creating windows
done
reading occupancy schedules
done
Traceback (most recent call last):
  File "C:/Users/darthoma/Documents/GitHub/CEAforArcGIS/cea/demand.py", line 249, in <module>
    test_demand()
  File "C:/Users/darthoma/Documents/GitHub/CEAforArcGIS/cea/demand.py", line 244, in test_demand
    demand_calculation(locator=locator, weather_path=weather_path, gv=gv)
  File "C:/Users/darthoma/Documents/GitHub/CEAforArcGIS/cea/demand.py", line 82, in demand_calculation
    locator.get_demand_results_folder(), locator.get_temporary_folder())
  File "C:\Users\darthoma\Documents\GitHub\CEAforArcGIS\cea\functions.py", line 588, in CalcThermalLoads
    Qhsf = Qhs_sen_loss_true + Qhs_d_ls   # no latent is considered because it is already added as electricity from the adiabatic system.
NameError: global name 'Qhs_sen_loss_true' is not defined

Process finished with exit code 1

How can this be solved without moving my code to core? I can move to core, but I wasn't sure I if I should...
Yes. Absolutely. That is clear. This was simply convenience for you guys to test run my code. I thought this is how your strategy for the "plug-in" functions works.
OK.
strange bug. Must be from auto refactoring or renaming. Fixed.

So it works fine, but i am afraid it has errors in the calculation of hotwater. We can merge it in contributions. However, we will need to separate it form the hot water calculation and electricity calculation if we want to integrate it in the core

But they are the same as in the core. No changes done to these calculations in that branch.

@gabriel-happle, correct: We will need to update the GUI to support using alternative models. I am waiting for the conference to finish before tackling that...

how do we proceed here? wait until after the conference?

I don't know. Someone has to decide. I keep it ready by updating from the master every day.
Also, I was waiting for it to be merged until pushing #45  and #53, which change all the versions of CalcThermalLoads.


Polybar overall problem with fonts

Hello.
The issue is form begining i never got it to render ttf fonts properly. Bitmaps fonts are wroking, but they aren't scalable.
I tried:

diffrent fonts (roboto, ubuntu, many more..)
clean reinstall
turning antialiasing off and no

I use terminator as terminal emulator with same Hack 10 font. I also have dual monitor setup if that changes anything 2x 1920x1080 but polybar is working same badly on both.

WM: BSPWM
Distro: Arch Linux
Output of polybar -vvv:

polybar 3.4.3

Features: +alsa +curl +i3 +mpd +network(libnl) +pulseaudio +xkeyboard

X extensions: +randr (+monitors) +composite +xkb +xrm +xcursor

Build type: Release
Compiler: /usr/bin/c++
Compiler flags: -D_FORTIFY_SOURCE=2 -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -Wall -Wextra -Wpedantic -O3 -DNDEBUG
Linker flags: -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now

This does look a lot like an anti-aliasing issue. Please show us how you defined the fonts in the polybar config, as well as how you turned anti-aliasing on/off.

font-0 = "Hack:style=Regular:pixelsize=10:antialias=false3;2"
This is how i turned antyaliasing off. It strange other apps dont have any problems. Yesterday i did a clean install and still same effect no change. With antialias on the font is very blury.

dpi-x=96
dpi-y=96

ok i think i fixed it adding thins to [bar/mybar] section


Support sharing layers as per OmniGraffle

Is there a way of sharing layers between pages as per Omnigraffle
https://groups.google.com/forum/#!topic/drawio/eusAMrs9nZU

+1 for this request.  An example use case is to have a Background page that contains only a Background layer that is shared among all pages. A change to the single Background layer would then be reflected in all other pages. (Bonus points awarded for allowing the common background layer to be configurable per drawing page, either with an alternate background layer or none for a given page. :)  For example, all the drawing pages in a given drawing set could have the same shared layer containing project name, author, etc, but the title page would have an alternate or no background. ) This functionality is one of the Visio capabilities I miss most in diagram.net.


rdkit doesn't handle Germanium?

Hello,
While reading a smiles string with Ge:
UFFTYPER: Unrecognized atom type: Ge2 (0)

I read UFF is a full periodic table force field, so I was surprised.
I checked, and there is no atomic number 32 in there:
rdkit/Code/GraphMol/ForceFieldHelpers/UFF/AtomTyper.cpp
Is it the only place where it should be handled?
Thanks a lot,
Francois

Hi Francois,
The UFF only has parameters for Ge3, which corresponds to an sp3 hybridized Ge. But when you have that everything seems to work fine:
``
In [4]: m = Chem.AddHs(Chem.MolFromSmiles('CGeC'))
In [5]: AllChem.EmbedMolecule(m)
Out[5]: 0
In [6]: AllChem.UFFOptimizeMolecule(m)
Out[6]: 0

OK, the molecule has an sp2 Ge, sorry.


Importing a TS module accross workspaces is not working

Hi @b8kkyn , and thank you for publishing this plugin 👏.
I have a project organised in a yarn "worktree" named pp with two workspaces utils and webapp:
root/
    utils/
        utility.ts
    webapp/
        index.ts

Importing  one of utils workspace's module from the webapp while trying to leverage parcel-resolver-typescript-esm fails:
import { times } from<EMAIL_ADDRESS>but this work (I suspect thanks to Parcel's default resolver):
import { times } from<EMAIL_ADDRESS>This might seems like a weird use case, but I'm essentially using internal packages.
I identified the culprit lines and removed them. It works for my case but I'm curious to know why it was added in the first place since it is not in the DefaultResover code which I suspect served as inspiration for this one.
https://github.com/b8kkyn/parcel-resolver-typescript-esm/blob/cd5e2ac59ce3416afd998f3274c0cbe5c685fe5f/src/index.ts#L89-L91

Hey @jraoult,
I have added these control check because there are packages goes like "xxx.js" (exp. pixi.js). So I needed to check if import statement is actual module or js file. That's why. Maybe you would like to bring a solution to this covering your case too? :)

@b8kkyn I see... so what about checking the Module's moduleName property and see if it matches the specifier? If true we know it is a package "name" and can ignore it. Otherwise, we continue the regular flow:
if(modulePath?.moduleName === specifier) {
  return null;
}

So for pixi.js it will test "pixi.js" === "pixi.js" and return early but for my case it will test  "@pp/model" ===<EMAIL_ADDRESS>and therefore keep going.
WDYT?

Hey @jraoult, I think it's very good solution👍

Hey @jraoult, I think it's very good solution👍

@jraoult I think it's very good solution👍


Add parentsall and parentmaster in get_json

Very useful in php applications
options.parentsall return  obj.parents;
options.parentmaster return first parent related to each children's tree
Sorry for bad English.
I'm using google translator

Sorry, I will not merge this - I try to keep the new options to a minimum. There is an alternative you can use - the flat format - it will give you the parent, and then you can build the full ancestor chain - it is very useful for storing in a relational database.

And if can not use the flat format??
Could you help me with a solution?
It would be possible in this case to create an alternative plugin for get_json?
I do not know how to do it


get_credentials.sh is outdated

Hi,
It seems that get_credentials.sh is outdated with the newer version of client key-json without client_secret field.
May I have an easy guide of how to generate the credentials.json needed for run_assistant?
Kind regards,
Tamama

I'm not sure I understand what this newer version includes. I have not had issues running the shell script and getting the credentials.json.
The format for the file is
{
  "client_id": "$CLIENT_ID",
  "client_secret": "$CLIENT_SECRET",
  "refresh_token": "$REFRESH_TOKEN",
  "type": "authorized_user"
}

Hi Fleker,
Following the docs, I get the following secret json file for my service account:
{
"type": "service_account",
"project_id": "$PROJECT_ID",
"private_key_id": "PRIVATE_KEY_ID",
"private_key": "$PRIVATE_KEY",
"client_email": "$CLIENT_EMAIL",
"client_id": "$CLIENT_ID",
"auth_uri": "$AUTH_URI",
"token_uri": "$TOKEN_URI",
"auth_provider_x509_cert_url": "$AUTH_PROVIDER_X509_CERT_URL",
"client_x509_cert_url": "$CLIENT_X509_CERT_URL"
}

The instructions were designed to use a user's account, not a service account. It does seem like I will need to clean-up the README.

Hi Fleker,
Can I confirm with you that it is

Yeah that should be fine, but then you'll need to download the client secret and then generate the credentials.

Let me try in a moment and get back to you today.

This solves it.


Implement support for "strict" mode

* This is a work-in-progress.
Fixes https://github.com/Odonno/surrealdb-migrations/issues/55
Many tests work with the assumption that the database is in "sloppy" mode, and though I managed to fix plenty of them by tweaking helper functions, some would need more involved changes.
I'd need feedback on how to make more progress with this.

I just noticed cli::branch::new::create_new_branch_using_config_file test broke on "sloppy" mode.
I'll have a look.

This is really nice. Thank you for your effort @turbohz
Like I said, you can add --strict option in https://github.com/Odonno/surrealdb-migrations/blob/main/before-integration-tests.sh and then run tests to ensure they are still all green.

All tests are passing in both strict and sloppy mode.


support to specify enabled controllers

What type of PR is this?

Uncomment only one /kind <> line, hit enter to put that in a new line, and remove leading whitespace from that line:
/kind bug
/kind documentation
/kind enhancement
/kind good-first-issue
/kind feature
/kind question
/kind design
/sig ai
/sig iot
/sig network
/sig storage

What this PR does / why we need it:
Which issue(s) this PR fixes:

Fixes #1379
Special notes for your reviewer:

Does this PR introduce a user-facing change?

other Note

@xavier-hou some webhooks maybe have not connected controllers, so we need to add a parameter --webhooks for enabling or disabling specified webhooks.

@xavier-hou some webhooks maybe have not connected controllers, so we need to add a parameter --webhooks for enabling or disabling specified webhooks.

@rambohe-ch

For contollers who have corresponding webhooks, such as staticpod, if the controller is disabled, then the corresponding webhook will be disabled as well. Because we use a map controllerWebhook to check whether controller has been disabled.
https://github.com/openyurtio/openyurt/pull/1388/files#diff-c07be401391cf159ca42b3e3c6e8f31d3d0a0a6b1b48998069b64d585a264f35R64
For controllers who don't have corresponding webhooks, then we do nothing.

So I think current PR is enough for enabling and disabling controllers. But If we just want to enable or disable webhooks, then we can add a new parameter --webhooks.

@rambohe-ch  We have lots of files aimed at adding controllers to yurt-manager, such as add_csrapprover.go. They are generated by newcontroller command which is convenient for controllers migration but annoying to maintain in the future. How about removing these files and accomplish all controllers register in controller.go?

@xavier-hou and i will merge this pr at first.

/lgtm


JFrogDotnetCore@1 task with a restore command fails with a "create file" error if both arguments are passed, and collectbuildinfo is true.

Describe the bug
Using the jfrogDotnetCore@1 task with a restore command, a create file error is thrown if both a value is passed in the argument field and the collectbuildinfo field is set to true.
If collectbuildinfo is set to false, the task successfully runs.
Current behavior
The task fails with this error.
CreateFile /p:RestoreConfigFile=C:\a\4\s\unit-testing-using-dotnet-test\nugetv1.config: The filename, directory name, or volume label syntax is incorrect.
Reproduction steps

task: JFrogDotnetCore@1
displayName: dotnet restore test
inputs:
command: 'restore'
arguments: '/p:RestoreConfigFile=$(Build.SourcesDirectory)\unit-testing-using-dotnet-test\nugetv1.config'
artifactoryConnection: 'artifactory'
targetResolveRepo: 'Nuget'
collectBuildInfo: true
buildName: '$(Build.DefinitionName)'
buildNumber: '$(Build.BuildNumber)'
includeEnvVars: true

Expected behavior
The task should successfully run using the passed arguments and publish the build information to Artifactory.
Azure DevOps extension name and version
JFrogDotnetCore@1
JFrog CLI version
2.52.9
Operating system type and version
Windows 2022 server
JFrog Artifactory version (if relevant)
No response
JFrog Xray version (if relevant)
No response
JFrog Distribution version (if relevant)
No response

Actually, I'm finding if you use the argument field at all, you're bound to run into many any varied issues, even including not getting past the Initialize job step--which essentially means your pipeline doesn't run.
I've noticed:

No path separator normalization
Using certain path formats leads to invalid YAML that basically causes no steps to be seen in the build pipeline
When arguments are processed incorrectly, incorrect paths are generated, so your build fails at Initilizing Job when certain paths cannot be found.
When using "custom arguments" in the task, the command lines that are built to be used with dotnet contain some which have values that are unquoted, where those values have spaces, throwing off dotnet command-line argument processing.

In short, this task's command-line handling is simply broken and unusable.
I think I'm better off using a regular dotnet restore task and ensuring that my nuget.config file has a URL that points to the repository in question.
And lastly, this task doesn't even use V3 of the Nuget API, and so it doesn't play nice with some Nuget implementations, such as Baget (which doesn't implement the Nuget v2 API). Nuget.exe/dotnet doesnt' care and "figures it out".
This is just a poorly implemented task. I'd recommend others to refrain from using it.

OK, an update:
The build failing on Initialize job was due to a bug in Azure DevOps Server when using an option to Clean all build directories. It works the first time, then all subsequent builds fail. I needed to start from a clean foundation to ensure package restore was working correctly.
Having said that, there is a problem with this task. The problem is, it ONLY uses the Nuget v2 API (even though there's a radio button selection for V2 and V3, with V3 being the default)--and our existing Nuget solution, Baget, does not implement the V2 Nuget API, so package restore FAILS using the Nuget configuration file generated by this task.
If Instead I provide my own configuration file, where I specify that the v3 API is to be used, everything works.
JFrog, please implement using the v3 Nuget API from this task when it's selected in the task!!!

Hi @davidrueckert ,
I couldn't reproduce this issue.
Does this happen with any other argument?
Note that the task creates a temporary nuget.config based on the Artifactory connection and resolution repository and uses it in the restore process. If you'd like to pass your own config please currently use the --configfile option instead of the /p:RestoreConfigFile one because JFrog CLI doesn't support the latter (I opened https://github.com/jfrog/jfrog-cli/issues/2522 for that matter).
Hi @fourpastmidnight ,
What JFrog CLI are you using?
The task and JFrog CLI use the V3 protocol by default. The created configuration file should show it (for example<add key="JFrogCli" value="<path to resolution repository>" protocolVersion="3" />).
If the issue persists with the latest JFrog CLI version (2.55.0 as of today), please open a separate issue with reproduction instructions and we'll try to reproduce it again.
Thanks

Hi @RobiNino . It looks like the behavior in this issue has been corrected. It looks like two updates to this extension have been released since I opened this ticket over 2 months ago. This issue must have been corrected in one of those updates. As for using the --configfile jfrog cli argument, there is no field in the JFrogDotNetCore Task where I can add a Jfrog CLI argument. I suppose that I can't use this task if I need to use our own NuGet.config file.

Thanks for the response. My particular issue is actually due to a bug in Artifactory that I'm working through with customer support. But thanks for the info on the correct parameter to use, in case I need it in the future for some reason.
Get Outlook for Androidhttps://aka.ms/AAb9ysg

From: David Rueckert @.>
Sent: Tuesday, April 16, 2024 3:56:40 PM
To: jfrog/jfrog-azure-devops-extension @.>
Cc: Craig E. Shea @.>; Mention @.>
Subject: Re: [jfrog/jfrog-azure-devops-extension] @.*** task with a restore command fails with a "create file" error if both arguments are passed, and collectbuildinfo is true. (Issue #476)
Hi @RobiNinohttps://github.com/RobiNino . It looks like the behavior in this issue has been corrected. It looks like two updates to this extension have been released since I opened this ticket over 2 months ago. This issue must have been corrected in one of those updates. As for using the --configfile jfrog cli argument, there is no field in the JFrogDotNetCore Task where I can add a Jfrog CLI argument. I suppose that I can't use this task if I need to use our own NuGet.config file.
—
Reply to this email directly, view it on GitHubhttps://github.com/jfrog/jfrog-azure-devops-extension/issues/476#issuecomment-2059825158, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ABUTP2LRWNVQA5VDWY4DSQ3Y5V67RAVCNFSM6AAAAABCXQIDLGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANJZHAZDKMJVHA.
You are receiving this because you were mentioned.Message ID: @.***>

@davidrueckert ,
Glad to hear the issue is gone. You may pass the --configfile argument just like you passed /p:RestoreConfigFile - through the arguments field. JFrog CLI modifies its behavior when certain .NET arguments are identified.
@fourpastmidnight ,
Thanks for the feedback!


WIP: VERIFY Pr 49

Fixes #
Proposed Changes

Release Note

/test pull-knative-sandbox-operator-upgrade-tests

/test pull-knative-sandbox-operator-build-tests
/test pull-knative-sandbox-operator-integration-tests


[sil-optimizer] Fix feedback from #37016 and finish removing confusing constructors

The first commit is addressing Andy's feedback/request in #37016. The 2nd change eliminates the constructors from InstModCallback. I am worried that people are going to mix up which closure is passed in for which argument. The value type based .onACTION() model at least puts a name on the closure being initialized which is clearer.

@swift-ci smoke test

@swift-ci test

(sorry for the smoke test... I got weak)


Feature: labels/tags for organization

Using notes http://godoc.org/go/doc#Note
// LABEL(-): database, redis

This could be used to find related packages (other database drivers).
From https://github.com/golang/gddo/issues/107#issuecomment-24475966

There's an open discussion of this in #317


Android Bazel Build - Java Failure

Ran into another build issue when running bazel build //tensorflow/examples/android:tensorflow_demo --verbose_failures
WARNING: /Users/username/tensorflow/tensorflow/core/BUILD:632:12: in srcs attribute of cc_library rule //tensorflow/core:android_tensorflow_lib_lite: please do not import '//tensorflow/core/kernels:avgpooling_op.h' directly. You should either move the file to this package or depend on an appropriate rule there.
WARNING: /Users/username/tensorflow/tensorflow/core/BUILD:632:12: in srcs attribute of cc_library rule //tensorflow/core:android_tensorflow_lib_lite: please do not import '//tensorflow/core/kernels:bounds_check.h' directly. You should either move the file to this package or depend on an appropriate rule there.
...
Lots more of the same warnings
...
WARNING: /Users/username/tensorflow/tensorflow/core/BUILD:665:12: in srcs attribute of cc_library rule //tensorflow/core:android_tensorflow_lib: please do not import '//tensorflow/core/kernels:where_op.cc' directly. You should either move the file to this package or depend on an appropriate rule there.
WARNING: /Users/username/tensorflow/tensorflow/core/BUILD:665:12: in srcs attribute of cc_library rule //tensorflow/core:android_tensorflow_lib: please do not import '//tensorflow/core/kernels:xent_op.cc' directly. You should either move the file to this package or depend on an appropriate rule there.
INFO: Found 1 target...
ERROR: /private/var/tmp/_bazel_username/d0aa3a34ac01d28ffabd89cde457364e/external/bazel_tools/src/tools/android/java/com/google/devtools/build/android/BUILD:8:1: Java compilation in rule '@bazel_tools//src/tools/android/java/com/google/devtools/build/android:AndroidResourceProcessingAction' failed: java failed: error executing command
  (cd /private/var/tmp/_bazel_username/d0aa3a34ac01d28ffabd89cde457364e/tensorflow && \
  exec env - \
  external/local_jdk/bin/java -Xbootclasspath/p:external/bazel_tools/third_party/java/jdk/langtools/javac.jar -client -jar external/bazel_tools/tools/jdk/JavaBuilder_deploy.jar @bazel-out/host/bin/external/bazel_tools/src/tools/android/java/com/google/devtools/build/android/AndroidResourceProcessingAction.jar-2.params): com.google.devtools.build.lib.shell.AbnormalTerminationException: Process terminated by signal 11: java failed: error executing command
  (cd /private/var/tmp/_bazel_username/d0aa3a34ac01d28ffabd89cde457364e/tensorflow && \
  exec env - \
  external/local_jdk/bin/java -Xbootclasspath/p:external/bazel_tools/third_party/java/jdk/langtools/javac.jar -client -jar external/bazel_tools/tools/jdk/JavaBuilder_deploy.jar @bazel-out/host/bin/external/bazel_tools/src/tools/android/java/com/google/devtools/build/android/AndroidResourceProcessingAction.jar-2.params): com.google.devtools.build.lib.shell.AbnormalTerminationException: Process terminated by signal 11.
Target //tensorflow/examples/android:tensorflow_demo failed to build
INFO: Elapsed time: 0.743s, Critical Path: 0.53s

I am on OSX 10.11, had to download android ndk-r10e (since r11e didn't seem to work). Java version is 1.8.0_73 and Bazel version is 0.2.0 with TensorFlow 0.7.1. My WORKSPACE is configured as follows in the beginning. I changed the build_tools_version for the androidsdk to 23.0.2 (from 23.0.1) since that's what I have locally on my machine. Any pointers?
android_sdk_repository(
    name = "androidsdk",
    api_level = 23,
    build_tools_version = "23.0.2",
    path = "/Users/mchong5/Library/Android/sdk",
)

android_ndk_repository(
    name="androidndk",
    path="/Users/mchong5/android-ndk-r10e/",
    api_level=21)

I was unable to reproduce with a fresh Bazel 0.2.0 install and tensorflow download. This is on OSX 10.11.3, with Java 1.8.0_72-b15 and ndk r10e.
For reference I installed bazel from here and installed with:
chmod +x bazel-0.2.0-installer-darwin-x86_64.sh;
sudo ./bazel-0.2.0-installer-darwin-x86_64.sh

I downloaded TF with:
git clone --recursive https://github.com/tensorflow/tensorflow/
And appended the following to my WORKSPACE:
android_sdk_repository(
    name = "androidsdk",
    api_level = 23,
    build_tools_version = "23.0.2",
    # Replace with path to Android SDK on your system
    path = "/Users/andrewharp/Library/Android/sdk",
)

android_ndk_repository(
    name="androidndk",
    path="/Users/andrewharp/Downloads/android-ndk-r10e",
    api_level=21)

I doubt it's related, but what happens if you strip the trailing slash off your android ndk path?

Well, it was that trailing slash!


shapeclustering Stuck for 3 hours

Tesseract Version: 5.0.0  20201127
Platform:  Windows 64-bit

111111111.zip

Here is machine translation
The problem has been solved ("echo test 0 000 000 > font_ properties")
The code is utf-16le
Change to UTF-8
問題已解決 ("echo test 0 0 0 0 0 >font_properties")
編碼是UTF-16LE
改成UTF-8解決


[5.9] Make leading/trailing trivia required fields

Explanation: Rather than having the possibility of nil trivia and requiring all clients to check every use, just return empty trivia when there are no nodes present.
Scope: All swift-syntax clients using leading/trailingTrivia
Risk: Extremely low, uses generally created an empty Trivia anyway
Testing: No additional tests
Original PR: https://github.com/apple/swift-syntax/pull/1477

https://github.com/apple/swift-format/pull/500
https://github.com/apple/swift/pull/64874
@swift-ci please test


Equivalence operator fails if order of attributes or children differs

Issue
The equivalence operator will fail if:

The order of attributes for an element differs
The order of children differs

If this is the desired logic then thee is no issue. However, if there can easily be a case where the
attributes or children can be added in different order -- in which case the logic fails.
Workflows

It's very easy to add / remove nodes or inputs to a graph which changes ordering.
A simple cut (remove) and paste (add last) could change order.
Attributes can be changed and assuming this more for metadata like colorspace, units, geom properties, and UI formatting
such as position.

Proposal

It would be useful to add an option / create a new function which allows for ordering to be ignored.
Note that nodedef lookup as duplicated + different logic for named input equivalency.

Current Logic
Key logic in code commented in code
bool Element::operator==(const Element& rhs) const
{
    if (getCategory() != rhs.getCategory() ||
        getName() != rhs.getName())
    {
        return false;
    }

    // Compare attributes.
    if (getAttributeNames() != rhs.getAttributeNames()) // This is the ordered list. An unordered list option would be useful.
        return false;
    for (const string& attr : rhs.getAttributeNames())
    {
        if (getAttribute(attr) != rhs.getAttribute(attr))
            return false;
    }

    // Compare children.
    const vector<ElementPtr>& c1 = getChildren();
    const vector<ElementPtr>& c2 = rhs.getChildren();
    if (c1.size() != c2.size())
        return false;
    for (size_t i = 0; i < c1.size(); i++)
    {
        if (*c1[i] != *c2[i]) // This array ordered. Getting children by name would resolve this.
            return false;
    }
    return true;
}

Example
File 1
<?xml version="1.0"?>
<materialx version="1.39" colorspace="srgb_texture">
  <nodegraph name="patternGraph">
   <input name="ramp_right" type="color3" value="0, 0, 0" />
    <input name="ramp_left" type="color3" value="1, 1, 1" />
    <output name="out" type="color3" nodename="ramplr_color4" />
    <ramplr name="ramplr_color4" type="color3" xpos="1", ypos="2">
      <input name="valuel" type="color3" interfacename="ramp_right"/>
      <input name="valuer" type="color3" interfacename="ramp_left"/  />
     </ramplr>
  </nodegraph>
  <gltf_pbr name="gltf_shader" type="surfaceshader">
    <input name="base_color" type="color3" nodegraph="patternGraph" />
  </gltf_pbr>
</materialx>

File 2:
<?xml version="1.0"?>
<materialx version="1.39" colorspace="srgb_texture">
  <gltf_pbr name="gltf_shader" type="surfaceshader"> // Child ordering
    <input name="base_color" type="color3" nodegraph="patternGraph" />
  </gltf_pbr>
  <nodegraph name="patternGraph">
    <output name="out" type="color3" nodename="ramplr_color4" /> // Child ordering
    <input name="ramp_left" type="color3" value="1, 1, 1" />
    <input name="ramp_right" type="color3" value="0, 0, 0" />
    <ramplr name="ramplr_color4" type="color3" ypos="2" xpos="1" > // Attribute ordering
      <input name="valuel" type="color3" interfacename="ramp_right"/>
      <input name="valuer" type="color3" interfacename="ramp_left"/  />
  </nodegraph>
</materialx>

@kwokcb This definitely sounds like it's a design choice, since the order in which input elements are specified will affect the display of a document in an editor.  Since we make a point of preserving the order of child elements in MaterialX, it seems consistent that our equivalence operator would respect this order as well.

This makes sense for nodes but not so much for nodegraphs especially as they can be dynamically added / removed. Also order of nodes in a graph shouldn't make any different, nor the order of attributes as this should have no affect on display. Perhaps node inputs should be strict on ordering but the rest I don't see any reason for having to match ordering.
What do you think ?

A couple of additional thoughts:

I'd expect both of the cases that you mention to affect the display of a document in an editor, since the order of input elements in a nodegraph affects the display of its interface, and the order of nodes in a nodegraph affects the behavior of auto-layout logic.
Taking a step back, my sense is that element order conveys meaning in MaterialX, which is why we preserve this order when documents are loaded, processed, or saved to disk.  Although there may be cases where the order doesn't affect a particular process, in the general case we consider order to be part of the content that a document expresses, and it would seem inconsistent for us to ignore it when comparing the equivalence of two documents.

The MaterialX document serves multiple purposes.

Delivering the shader to a final render target
Delivering the necessary information to construct the UI to further author the material.

In the first case I would certainly hope we're not dependent on any ordering of child elements of attributes, but certainly as @jstone-lucasfilm points out the second case has some places in the document where the order is important.
I can very much imagine a world where I want to compare two MaterialX documents to know if they will render the same image, and thus don't care if inputs are defined in a different order.  As well as also wanting to know the documents are actually identical.
Perhaps this suggest we need more than one document comparison function?

That's a good note, @ld-kerley, and I can certainly imagine a future method that aims to determine whether two MaterialX documents generate identical renders, independent of whether they would behave identically in an artist UI.

That is basically what I need.

That is is the document functionally equivalent even when not organizationally identical.
For interop, I'm round tripping from MTLX and back to MTLX and one thing that can't be guaranteed is order within the document of nodes.
For the rendering aspect, I've run across this in the past for MTLX->USD->MTLX where your don't have the original anymore after conversion to USD and then to MTLX for code generation.

This issue can be rejigged from an issue to a be a proposal for a new interface if that's agreeable.

@kwokcb Got it, and that's definitely a fundamentally different task than comparing whether two documents are identical.  Just to suggest an approach, what if you were to sort all of the nodegraphs topologically before comparing the documents in your framework?

The existing topological sort method cannot be used as it's just connection order sort. (GraphElement.topogicalSort).
This is what I tried out:
def getSortedChildren(graphElement, useTopologicalSort=True):

    sortedNames = []
    if useTopologicalSort:
        sorted = graphElement.topologicalSort()
    else:
        sorted = graphElement.getChildren()
    for node in sorted:
        sortedNames.append(node.getNamePath())

    # sort the names
    if not useTopologicalSort:
        sortedNames.sort()
    return sortedNames

def printSorted(doc, topologicalSort=True):
    sorted = getSortedChildren(doc, topologicalSort)
    sorted2 = []
    sortedPaths = []
    for (i, nodeName) in enumerate(sorted):
        print(str(i) + ": " + nodeName)
        sortedPaths.append(nodeName)
        node = doc.getChild(nodeName)
        if node.getCategory() == "nodegraph":
            sorted2 = getSortedChildren(node, topologicalSort)
            for j, nodeName2 in enumerate(sorted2):
                print("  " + str(j) + ": " + nodeName2)
                sortedPaths.append(nodeName)

    return sortedPaths

print('----------------------')
print('Use topological sort. Is not name sorted')
print('----------------------')
sorted1 = printSorted(doc)
print('- vs -')
sorted2 = printSorted(doc2)
print('Is equivalent:', sorted1 == sorted2)

print('----------------------')
print('Use getChild + sort. Is name sorted')
print('----------------------')
sorted1 = printSorted(doc, False)
print('- vs -')
sorted2 = printSorted(doc2, False)
print('Is equivalent:', sorted1 == sorted2)

with test files:
<?xml version="1.0"?>
<materialx version="1.39" colorspace="lin_rec709">
  <nodegraph name="unlit_graph">
    <output name="output_color4" type="color3" nodename="ramplr_color4" />
    <ramplr name="ramplr_color4" type="color3">
      <input name="valuel" type="color3" value="1,0.8,0" />
      <input name="valuer" type="color3" value="0,0.5,1" />
      <input name="texcoord" type="vector2" value="0,0" />
    </ramplr>
  </nodegraph>
  <surface_unlit name="unlitshader" type="surfaceshader">
    <input name="emission_color" type="color3" nodegraph="unlit_graph" />
  </surface_unlit>
  <surfacematerial name="MAT_unlitshader" type="material">
    <input name="surfaceshader" type="surfaceshader" nodename="unlitshader" />
  </surfacematerial>
</materialx>

<?xml version="1.0"?>
<materialx version="1.39" colorspace="lin_rec709">
  <surface_unlit name="unlitshader" type="surfaceshader">
    <input name="emission_color" type="color3" nodegraph="unlit_graph" />
  </surface_unlit>
  <nodegraph name="unlit_graph">
    <ramplr name="ramplr_color4" type="color3">
      <input name="valuel" type="color3" value="1,0.8,0" />
      <input name="valuer" type="color3" value="0,0.5,1" />
      <input name="texcoord" type="vector2" value="0,0" />
    </ramplr>
    <output name="output_color4" type="color3" nodename="ramplr_color4" />
  </nodegraph>
  <surfacematerial name="MAT_unlitshader" type="material">
    <input name="surfaceshader" type="surfaceshader" nodename="unlitshader" />
  </surfacematerial>
</materialx>

gives this result:
----------------------
Use topological sort. Is not name sorted
----------------------
0: unlit_graph
  0: unlit_graph/ramplr_color4
  1: unlit_graph/output_color4
1: unlitshader
2: MAT_unlitshader
- vs -
0: unlitshader
1: unlit_graph
  0: unlit_graph/ramplr_color4
  1: unlit_graph/output_color4
2: MAT_unlitshader
Is equivalent: False
----------------------
Use getChild + sort. Is name sorted
----------------------
0: MAT_unlitshader
1: unlit_graph
  0: unlit_graph/output_color4
  1: unlit_graph/ramplr_color4
2: unlitshader
- vs -
0: MAT_unlitshader
1: unlit_graph
  0: unlit_graph/output_color4
  1: unlit_graph/ramplr_color4
2: unlitshader
Is equivalent: True

Thus I think I'll refactor the operator== code into a new function to work in-place as it's the fastest way without revisiting the document in multiple passes. Just requires a attribute name sort and a node child name sort and can reuse the string normalization utility in place as well (or as a pre-pass).
BTW, I still think it makes sense to have attributes compared by name in the existing operator== since this one there is no meaning to the order for an artist / the UI.

Thanks for this proposal, @kwokcb, as well as for the implementation in https://github.com/AcademySoftwareFoundation/MaterialX/pull/2003!


Text search in files [feature request]

Hey guys,
I've been using fselect for a while now. It is a great tool and it helps me a lot. The only thing I miss is a "contains" statement which can be used to match files which contain certain text string. It would be great if you could add this function.

done in 0.6.0, use with caution!

Hi,
Thanks for the tool and search in text feature!
Is it possible to have a column where you print the text matches in context?
I know you can do that with grep etc, but nothing with the usefulness of fselect.


Put garment archetypes and a mannequin Dress Form

[ ] mannequin Dress Form
[ ] garment archetypes
[ ] One material for the archetypes as a whole
[ ] One material for the form

Avoid

[ ] Do not make individual materials for each form

These have been submitted.


Upgrade mapView to 0.11.0

This package is not compatible anymore with the newest mapView:
"@here/harp-mapview": "^0.11.0"

Thank you for raising this. We are taking immediate actions to upgrade the leaflet plugin to harp 0.11.0

The newly released, 0.2.0 version of this plugin is compatible with latest release of harp.gl.


Add a way to integrate with vim-airline

Currently this plug-in overrides the status line (when using the status line option)
it would be nice if there was a way to show the tabs in the status line, without overwriting the status line. For example by doing something like
let g:airline_section_x = whatever_needs_to_be_here_to show all of the buffers

Support for vim-airline is already included: if you load vim-wintabs after vim-airline and choose to show wintabs on statusline, airline will be show on tabline. Let me know if that doesn't work for you.

Ah yes, never mind, ignore me. I'm not sure what i was thinking when i reported this issue