L-beta-ethynylserine pathway

Hi GO,
we would need a bunch of new terms for a new pathway
Thanks
Sylvain
Term:
L-beta-ethynylserine biosynthetic process
Definition:
The chemical reactions and pathways resulting in the formation of L-beta-ethynylserine, an antibiotic produced by Streptomyces bacteria.
Category: Process
child of:
GO:0017000 antibiotic metabolic process
GO:0008652 cellular amino acid biosynthetic process
GO:0043453 alkyne biosynthetic process
Xref
PMID:30867596
PMID:3082841
Term:
L-propargylglycine biosynthetic process
Definition:
The chemical reactions and pathways resulting in the formation of L-propargylglycine (Pra), an antibiotic produced by Streptomyces bacteria.
Category: Process
child of:
GO:0017000 antibiotic metabolic process
GO:0008652 cellular amino acid biosynthetic process
GO:0043453 alkyne biosynthetic process
Xref
PMID:30867596
Term:
L-propargylglycine synthase activity
Definition:
Catalysis of the reaction: L-2-amino-4-chloropent-4-enoate = chloride + H(+) + L-propargylglycine.
Category: Function
child of:
carbon-halide lyase activity ; GO:0016848
Xref
PMID:30867596
Rhea:59892
Term:
L-propargylglycine--L-glutamate ligase activity
Definition:
Catalysis of the reaction: ATP + L-glutamate + L-propargylglycine = ADP + H(+) + L-gamma-glutamyl-L-propargylglycine + phosphate.
Category: Function
child of:
acid-amino acid ligase activity ; GO:0016881
PMID:30867596
Rhea:59896
Term:
4-chloro-allylglycine synthase activity
Definition:
Catalysis of the reaction: 4-chloro-L-lysine + AH2 + O2 = A + formaldehyde + H2O + L-2-amino-4-chloropent-4-enoate + NH4(+).
Category: Function
child of:
oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen ; GO:0016705
Xref
PMID:30867596
Rhea:59888
Term:
L-lysine 4-chlorinase activity
Definition:
Catalysis of the reaction: 2-oxoglutarate + chloride + H(+) + L-lysine + O2 = 4-chloro-L-lysine + CO2 + H2O + succinate.
Category: Function
child of:
oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, with 2-oxoglutarate as one donor, and the other dehydrogenated ; GO:0050498
Xref
PMID:30867596
Rhea:59884
Term:
L-gamma-glutamyl-L-propargylglycine hydroxylase activity
Definition:
Catalysis of the reaction: 2-oxoglutarate + L-gamma-glutamyl-L-propargylglycine + O2 = CO2 + L-gamma-glutamyl-(3R)-L-beta-ethynylserine + succinate.
Category: Function
child of:
2-oxoglutarate-dependent dioxygenase activity ; GO:0016706
Xref
PMID:30867596
Rhea:59900

Looks like this might require some new ChEBI terms, so handing off to @hdrabkin.

Hi David,
Rhea reactions are public and all ChEBI accessions are described in the reactions:
https://www.rhea-db.org/reaction?id=59884
https://www.rhea-db.org/reaction?id=59888
https://www.rhea-db.org/reaction?id=59896
https://www.rhea-db.org/reaction?id=59892
Thanks
Sylvain

Thanks Sylvain. I'll try to get these in today.

I don't see the final L-beta-ethynylserine (compound 7,figure 2, PMID:30867596), but will add the term so you can annotate.

Adding terms in #17788.

@hdrabkin can you investigate adding L-beta-ethynylserine to ChEBI? You might get to draw a structure. Once that is in, can you add it and L-propargylglycine (CHEBI:43797) to the import files and create logical defs for L-beta-ethynylserine biosynthetic process and L-propargylglycine biosynthetic process after we are able to rebuild the ChEBI import files?

Also note that I did not add the antibiotic parent you requested. We will only add these if the role is universal/rigid.  If you think this to be the case and these compound ever only have the role of an antibiotic, I will add them. pinging @krchristie

CHEBI:144729,  L-beta-ethynylserine, has been submitted to CHEBI

Looking at the two papers that @sylvainpoux cited, the 1986 paper discovering beta-ethynylserine calls it an antibiotic:
from Sanada M, et al. 1986. beta-Ethynylserine, an antimetabolite of L-threonine, from Streptomyces cattleya. J Antibiot (Tokyo). 39(2):304-5. PMID:3082841.

This antibiotic was also an antimetabolite of L-threonine and was identified as beta-ethynylserine from its physicochemical properties.

However, the 2019 paper describing discovery of the pathway refers to antibiotics only in the context of selecting for E. coli that have the appropriate plasmids in the process of putting this biosynthetic pathway into E. coli.
Marchand JA, et al. 2019. Discovery of a pathway for terminal-alkyne amino acid biosynthesis. Nature. 567(7748):420-424. PMID:30867596.
To make sure I don't forget about this, I'm going to add this to the ChEBI roles project so that I remember to take a look at this once we've come up with a plan for how we want to handle these types of roles that may be context/organism specific, but not universal.

@hdrabkin - Once you're done with your part of this ticket, please leave it open and reassign it to me.

It's a chicken and egg situation. @hdrabkin can't finish his part until we can update the ChEBI import, which currently has lots of inferences we don't want based on roles. I think the general roles need to be addressed first.

@krchristie will do. @ukemi , did you just add the process term only?

No. I added them all.

I've added myself to the assignment list then, and left @hdrabkin. He can unassign himself if/when he feels that his part is complete.

CHEBI:144729 is now public. Not clear if I can do a CHEBI import

@hdrabkin you can just add it to https://github.com/geneontology/go-ontology/blob/master/src/ontology/imports/chebi_terms.txt and the import will be regenerated soon.

@balhoff told me we use a special pre-roles copy to merge new stuff into, so I'll add to the txt file

Term:
L-beta-ethynylserine biosynthetic process
child of:
GO:0008652 cellular amino acid biosynthetic process
GO:0043453 alkyne biosynthetic process
had to leave this parentage directly asserted because ChEBI has NOT asserted that L-beta-ethynylserine is an alkyne.

Term:
L-propargylglycine biosynthetic process
Definition:
The chemical reactions and pathways resulting in the formation of L-propargylglycine (Pra), an antibiotic produced by Streptomyces bacteria.
Category: Process
child of:
GO:0017000 antibiotic metabolic process
GO:0008652 cellular amino acid biosynthetic process
GO:0043453 alkyne biosynthetic process
Xref
PMID:30867596
Term:
L-propargylglycine synthase activity
Definition:
Catalysis of the reaction: L-2-amino-4-chloropent-4-enoate = chloride + H(+) + L-propargylglycine.
Category: Function
child of:
carbon-halide lyase activity ; GO:0016848
Xref
PMID:30867596
Rhea:59892
Term:
L-propargylglycine--L-glutamate ligase activity
Definition:
Catalysis of the reaction: ATP + L-glutamate + L-propargylglycine = ADP + H(+) + L-gamma-glutamyl-L-propargylglycine + phosphate.
Category: Function
child of:
acid-amino acid ligase activity ; GO:0016881
PMID:30867596
Rhea:59896
Term:
4-chloro-allylglycine synthase activity
Definition:
Catalysis of the reaction: 4-chloro-L-lysine + AH2 + O2 = A + formaldehyde + H2O + L-2-amino-4-chloropent-4-enoate + NH4(+).
Category: Function
child of:
oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen ; GO:0016705
Xref
PMID:30867596
Rhea:59888
Term:
L-lysine 4-chlorinase activity
Definition:
Catalysis of the reaction: 2-oxoglutarate + chloride + H(+) + L-lysine + O2 = 4-chloro-L-lysine + CO2 + H2O + succinate.
Category: Function
child of:
oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, with 2-oxoglutarate as one donor, and the other dehydrogenated ; GO:0050498
Xref
PMID:30867596
Rhea:59884
Term:
L-gamma-glutamyl-L-propargylglycine hydroxylase activity
Definition:
Catalysis of the reaction: 2-oxoglutarate + L-gamma-glutamyl-L-propargylglycine + O2 = CO2 + L-gamma-glutamyl-(3R)-L-beta-ethynylserine + succinate.
Category: Function
child of:
2-oxoglutarate-dependent dioxygenase activity ; GO:0016706
Xref
PMID:30867596
Rhea:59900

Are all of these RHEAs public?

Never mind just checked; yes they are so can use immediately.

While the source paper does talk about production of a terminal alkyne:
Marchand JA, Neugebauer ME, Ing MC, Lin CI, Pelton JG, Chang MCY. Discovery of a pathway for terminal-alkyne amino acid biosynthesis. Nature. 2019;567(7748):420-424. doi:10.1038/s41586-019-1020-y
PMID: 30867596

Here we report the discovery and characterization of a unique pathway to produce a terminal alkyne-containing amino acid in the bacterium Streptomyces cattleya.

ChEBI does not use the phrase terminal alkyne. In ChEBI, both L-beta-ethynylserine & L-propargylglycine classify under terminal acetylenic compound. If I create a term in GO for cellular terminal acetylenic compound biosynthetic process and remove direct SubClass assertions, I get this classification where neither L-beta-ethynylserine & L-propargylglycine classify under alkyne biosynthetic process

It seems best to go with ChEBI's classification, so I'm going to proceed with this.
I also seem to recall that we should be using the species prevalent at pH 7.3, which would be the zwitterions for both L-beta-ethynylserine & L-propargylglycine. Let me know if I've misunderstood this, or if it doesn't apply to a pathway only known to occur in bacterium as opposed to vertebrates.
@cmungall @pgaudet - let me know if you think is OK or not.

I was going to just do this, but the build has failed for a non-content reason, so I'm going to tag this to talk about it on Monday's call if I haven't figured out how to restart the checks by then.

7/27/2020 - Discussion at Ontology Editors cal

We had decided that I was going to do what I wrote above.

However, in the call, you guys reinforced my initial thought that alkyne is "anything with a triple bond", and I checked some more stuff. I have some questions about what ChEBI is doing, so I am submitting a ticket to them.
Then, in rechecking my branch, it isn't working like I thought it was, and I also checked the classification of L-beta-ethynylserine versus L-beta-ethynylserine zwitterion on ChEBI's website. Basically, I think we may want to discuss the implications switching to the 7.3 terms may have for automatic classification of compounds since it doesn't look to me like the zwitterions of these two compounds classify chemically where the non-zwitterion terms do. @balhoff @cmungall
Here are pics of the graphs from ChEBI. The compound of interest is the very bottom one in each graph. Automatic classification using the zwitterion terms looks like it will classify terms to organic compound, but not to any kind of acetylenic compound (what ChEBI is using for anything containing a carbon carbon triple bond).

Hi Karen
the problem of inconsistent hierarchies in ChEBI between charge states is a common one. But could you incorporate the ChEBI charge state mapping that Rhea provides into the reasoning process to deal with this?
This file - chebi_pH7_3_mapping.tsv - at https://www.rhea-db.org/download maps "other" charge states to that used in Rhea.
So for
CHEBI:144729 - L-β-ethynylserine zwitterion (used in Rhea)
CHEBI:144833 - L-β-ethynylserine (the one with a better developed hierarchy)
the file gives
CHEBI	CHEBI_PH7_3	ORIGIN
144833	144729	computation
i.e. a computed relation between the two.
For reasoning you could infer relations using the hierarchy of both, but this could have some issues (like where one of the parents is also a specific charge form too).
Would another alternative be to add all charge states from ChEBI as xrefs in the GO? So you would add ChEBI:144833 and ChEBI:144729 as xrefs for this pathway. Again for this one could use the  chebi_pH7_3_mapping.tsv might help.
An alternative

Hi Karen, all
I share with you our working document on  how to index  ChEBI "is a" relationships.
https://docs.google.com/presentation/d/1xLa1Z3EVFGuncWN4BUllymY6rVdpfYJbtEumyNABhkU/edit#slide=id.p
Do not hesitate to contact us if something is not clear or if you need additional information.
All the best, Anne

Thanks @alanbridge and @amorgat - that's really helpful!!

For now, I'm going to commit a version

using the ChEBI zwitterion forms of L-beta-ethynylserine and L-propargylglycine in the equivalence axioms of the biosynthetic terms
including a new grouping term for cellular terminal acetylenic compund biosynthesis as a parent for these two biosynthetic terms
manually asserting that parentage since it is not inferred from the zwitterion forms in ChEBI

I will also open a ticket about alkyne biosynthetic process since GO is using a general definition of alkyne but referencing the ChEBI term for alkyne which is restricted to simple unsubstituted straight chain alkynes.

Issue to discuss: Using some 7.3 terms affects automatic classification of compounds
I also checked the classification of L-beta-ethynylserine versus L-beta-ethynylserine zwitterion on ChEBI's website. Basically, I think we may want to discuss the implications switching to the 7.3 terms may have for automatic classification of compounds within GO since it doesn't look to me like the zwitterions of these two compounds classify chemically where the non-zwitterion terms do.

Two things about thse ChEBI entries confuse me.
First, ChEBI relates (incoming / outgoing) these two compounds by saying that each is the tautomer of the other, but does not have an incoming / outgoing conjugate acid - conjugate base relationship. I would have expected the opposite - conjugate acid / base but not tautomer. What am I missing in the chemistry here? And related to this, Karen's question: why should the zwitterion form lack the non-proteinogenic amino acid parent that the non-zwitterion form has? (Looking a bit more, I see the same difference for L-leucine: it has all sorts of chemical parents that its zwitterion lacks. @hdrabkin ?
Second, I've noticed that ChEBI sometimes does not identify the form of an ionizable compound that is predominant at pH 7.3, so an issue may be whether GO ontology developers and curators may sometimes need to figure this our for an individual compound and if so, can that figuring be confirmed by Rhea and passed on to ChEBI so they can fill in the missing bit in their annotation for the chemical.

Hi Peter, let me try to answer to your questions.
Concerning the case of L-β-ethynylserine
CHEBI:144729	L-β-ethynylserine zwitterion
InChiKey: RBWXRFBKVDBXEG-DMTCNVIQSA-N
CHEBI:144833	L-β-ethynylserine
InChiKey: RBWXRFBKVDBXEG-DMTCNVIQSA-N
You will notice that both ChEBI entries have the same InChiKey. The 2 structures are tautomers as they only differ by the position of one proton (the proton of the carboxylic acid is on the amino group in the zwitterionic form). CHEBI:144729, as a zwitterion, is both a conjugated acid and a conjugated base of CHEBI:144833, so it makes no sense using "is conjugate acid/base of" relationships, that's why ChEBI curators use the "is tautomer of" relationship instead.
As discussed during the last ChEBI workshop @EBI in May 2019, Adnan (the ChEBI curator) informed us that their guideline is to annotate most of the relationships on the fully hydrogenated form only.
ChEBI entries describing the different protonation states of a molecule are linked by  "is conjugate base of", "is conjugate acid of" and "is tautomer of" relationships. The reality is that some relationships may be missing and retrieving all species maybe tricky when they have several ionizable groups (need of a recursive procedure). That's why instead of these 3 relationships, the SIB developers use an additional relationship "has_major_microspecies_at_pH_7_3" which is available in the chebi.owl file (published by Rhea) but not used/displayed in the ChEBI public web site. This relationship is computed using the Marvin plugin provided by Chemaxon (https://docs.chemaxon.com/display/docs/Major+Microspecies+Plugin)
For your second point:
"Second, I've noticed that ChEBI sometimes does not identify the form of an ionizable compound that is predominant at pH 7.3, so an issue may be whether GO ontology developers and curators may sometimes need to figure this our for an individual compound and if so, can that figuring be confirmed by Rhea and passed on to ChEBI so they can fill in the missing bit in their annotation for the chemical"
It's true that sometimes the major species at pH 7.3 is missing. CHEBI is aware of the issue and one of the outcomes of the ChEBI workshop was Project 1: Unify alternative forms of chemical entities with collaborative effort.
At the moment, we (SIB curators) submit the missing entries when needed for Rhea or UniProt. I'm not sure I understand in which cases you would need a ChEBI compound that is not used in Rhea? Is it in the definition of GO:BP term (biosynthesis of XX / degradation of YY) where the reactions are not yet clearly defined?

@balhoff - I was thinking I would split off the 7.3 vs full protonated parentage issue issue into a separate ticket since it goes beyond the scope of the original ticket that only asked for creation of a couple terms. Is there an existing ticket where it would be good to add these 7.3 related issues, or should I just create a new ticket?

I'm not sure I understand in which cases you would need a ChEBI compound that is not used in Rhea? Is it in the definition of GO:BP term (biosynthesis of XX / degradation of YY) where the reactions are not yet clearly defined?

I wasn't clear - I don't see any cases here where this is needed.
For the rest, I was missing some history as well as a good understanding of the acid-base / tautomer relationship. Apologies for going over old ground.

Summary of Discussion - Ontology editors call 8/17/2020

Karen brought to the attention of the GO ontology editors group that @alanbridge has found that "the problem of inconsistent hierarchies in ChEBI between charge states is a common one" and pointed out the Rhea working document on how to index ChEBI "is a" relationships shared by @amorgat
@balhoff asked if the zwitterion terms that I had used had been newly requested when I used them and I said they had been available without my needing to request them
Action Item - @balhoff is going to look into whether the logic needs to be adjusted to accomodate this situation. @krchristie is available for taking a look at results if requested

the SIB developers use an additional relationship "has_major_microspecies_at_pH_7_3" which is available in the chebi.owl file (published by Rhea) but not used/displayed in the ChEBI public web site.

@amorgat are those relations in that chebi file identical to the information provided in chebi_pH7_3_mapping.tsv from the Rhea download page?

@balhoff, chebi_pH7_3_mapping.tsv tells you if a ChEBI entity is the major species at pH 7.3 (CHEBI == CHEBI_PH7_3) or what is the corresponding CHEBI_PH7_3 if it's not the case`
CHEBI   CHEBI_PH7_3  ORIGIN
3           3                      computation
...
15361   15361	 computation
32816   15361  computation
...
In the chebi.owl, the relationships "has_major_microspecies_at_pH_7_3" are only provided between a ChEBI entry and its major species at pH 7.3.
In the previous example, only CHEBI_32816 has this relationship whereas CHEBI_3 and CHEBI_15361 haven't any "has_major_microspecies_at_pH_7_3" relationships.
To be discussed with Jerven Bolleman if you would need it.

@amorgat thank you, I think I understand. From my perspective I think I have everything I need in the TSV file, i.e., there isn't additional information in the OWL file.

@krchristie in the branch for #20093 (bio-chebi based on pH 7.3 mappings), these are inferable:

'L-beta-ethynylserine biosynthetic process' SubClassOf 'terminal acetylenic compound biosynthetic process'
'L-propargylglycine biosynthetic process' SubClassOf 'terminal acetylenic compound biosynthetic process'


pycolmap.Image constructor fails in 0.2.0

Hi,
I observed an error that occurs for me when constructing an Image object manually:
import pycolmap

points = [pycolmap.Point2D((100, 200))]
pts = pycolmap.ListPoint2D(points)
image = pycolmap.Image("image.png", pts)

In 0.1.0 this used to work fine, while in 0.2.0 it raises the following error:
Traceback (most recent call last):
  File "image_construct.py", line 5, in <module>
    image = pycolmap.Image("image.png", pts)
RecursionError: maximum recursion depth exceeded while calling a Python object

Note that when default-constructing the object without point list it also works fine.
Environment: Python 3.8 on Ubuntu 20.04, pycolmap 0.2.0 installed from PyPi

Hi, the problem is that pybind fails to resolve the constructor here. You can either serve the points via the keyword argument:
image = pycolmap.Image("image.png", points2D=pts)

or use the much simpler auto conversion:
import pycolmap
image = pycolmap.Image("image.png", keypoints=[(100,200)])
# or
image = pycolmap.Image("image.png", [(100,200)])

On branch fix-image-constructor I pushed a fix which should also resolve your issue.


Rerunnable -> Arrow/Task

As discussed in #926, we want to try replacing Rerrunable with Arrow/Task (https://github.com/traneio/arrows).
This is an internal API change and should not affect users.

This is implemented in #964. We'll release both Finch with Rerunnable and Finch with Arrows in 0.23 (under different artifacts but same version).


Incorrect warning shown

Bug Description
The following warning is shown when using steal mode and not specifying a target:
"Steal mode is not compatible with a targetless agent, please either disable this option or specify a target."
It shouldn't be shown since the user can still select a target in the dropdown.
Steps to Reproduce
Use steal mode in the IDE.
Backtrace
No response
Relevant Logs
No response
Your operating system and version
N/A
Local process
N/A
Local process version
No response
Additional Info
No response

Wait, how is this even possible? We don't have this warning anymore:
https://github.com/metalbear-co/mirrord/blob/a5488d593c7f2c7573aba155c196c564746f925d/mirrord/config/src/lib.rs#L392C9-L420


Unit Tests Using Mocking Layer

As a lightwalletd developer, I would like a comprehensive testing suite to reliably test interactions with the zcashd RPC without having to run a zcashd node to keep the testing suite self contained.
Acceptance Criteria:

[x] Lightwalletd library test coverage to 80% (coverage is 53.2% at start of ticket)

Merged https://github.com/zcash/lightwalletd/pull/164


KAFKA-4937: Batch offset fetches in the Consumer

change consumer.position so that it always updates any partitions that need an update. Keep track of partitions that seekToBeginning in StoreChangeLogReader and do the consumer.position call after all seekToBeginning calls.

@guozhangwang WDYT?

While reviewing the code I feel there are some code cleanup / refactoring that we can do in Fetcher (not in the scope of this PR).
For example, updateFetchPositions() is only triggered in KafkaConsumer#updateFetchPositions(), in which resetOffsetsIfNeeded() is always triggered beforehand, so inside that function these two conditions subscriptions.committed(tp) == null and subscriptions.isOffsetResetNeeded(tp) should never be true unless it is used in unit tests; maybe we can tighten the logic a bit for such cases in a separate PR?

One minor comment: can we change the title to emphasize that the batching is done in the consumer?

Updated. Thanks @hachikuji @guozhangwang

The newly added unit test hangs (cc @bbejeck ):

org.apache.kafka.streams.integration.RegexSourceIntegrationTest > shouldAddStateStoreToRegexDefinedSource STARTED
Build timed out (after 180 minutes). Marking the build as aborted.
Build was aborted
Recording test results
Setting GRADLE_2_4_RC_2_HOME=/home/jenkins/jenkins-slave/tools/hudson.plugins.gradle.GradleInstallation/Gradle_2.4-rc-2

retest this please.

@guozhangwang i think we have a general build hanging issue with some integration tests. But we should at least wait to see the builds go green

@guozhangwang https://github.com/guozhangwang if this continues to be a
problem can we disable this test? I won't be able to dig into it until later
On Fri, Mar 31, 2017 at 1:22 PM, Guozhang Wang<EMAIL_ADDRESS>wrote:

The newly added unit test hangs (cc @bbejeck https://github.com/bbejeck
):
org.apache.kafka.streams.integration.RegexSourceIntegrationTest > shouldAddStateStoreToRegexDefinedSource STARTED
Build timed out (after 180 minutes). Marking the build as aborted.
Build was aborted
Recording test results
Setting GRADLE_2_4_RC_2_HOME=/home/jenkins/jenkins-slave/tools/hudson.plugins.gradle.GradleInstallation/Gradle_2.4-rc-2
—
You are receiving this because you were mentioned.
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retest this please

retest this please

retest this please

retest this please

@ijuma can you have a look at this one too, please?

@ijuma hopefully this is good to go now. thanks

Would it make sense to also include https://github.com/apache/kafka/pull/2637?

@guozhangwang @hachikuji is this ok to merge yet?

LGTM! Thanks.

Merged to trunk.


Sound corresp

Here is a big PR on the sound correspondence code. These are all the changes and improvements made since start of November, while working with @erichround (does he have the rights to view this repository ? If not it would be good if he did) and which led to the presentation right before the holidays.
I cleaned up the code and added some more features while preparing the PR, such as the export of a few examples with the counts.
Among important changes:

We use a custom coarsening to ignore some of the noise in the data.
ASJP is now usable only with the ASJP dataset, for comparison purposes.
Forbids the alignment of tones with other types of sounds
The similarity threshold for cognacy is a proportion of the number of syllables in words
The similarity threshold for cognacy is computed on SCA strings (but the actual alignment isn't)
Addition of contexts
The cutoff is proportional to the size of the list (with a minimum of 2)
We export metadata in order to track the parameters which lead to results, including an account of the coarsening classes, with  the coarse features.
Refactoring and docstrings for documentation and legibility.

This can be run on a single dataset as:
 cldfbench lexitools.correspondences --clts-version v1.4.1 --model Coarse --cutoff 0.05 --threshold 1 --dataset lexibank/kraftchadic

Or on the hard-coded lexicore list as:
 cldfbench lexitools.correspondences --clts-version v1.4.1 --model Coarse --cutoff 0.05 --threshold 1 --dataset lexibank/kraftchadic

(just sent an invite to Erich)

(just sent an invite to Erich)

Thanks for the reviews ! I did my best to document things enough so that a few weeks (or more) without touching the code wouldn't hurt later progress.

As to the feature reduction system: This is essentially some kind of a sound class system, and I'd love to include it on the longer run in CLTS. I wonder only if it can be done in a slightly more transparent manner, but this is something that one can easily test later. Having reduction systems inside the pyclts code is generally important to make sure they are in line with the most recent pyclts version, I think, although we hope that the most recent changes were the last changes we did so far.

I agree that it would be better somewhere in CLTS. The compatibility issue is already pertinent: right now it depends on v1.4.1, and I have not investigated yet how to update it for the new version. Erich and I are not completely done refining the coarsening scheme itself, so maybe it should all better wait until this is done.
I am aware that the coarsening might be a bit hacky, as I don't know the inner workings of CLTS well enough to formulate something that would mesh seamlessly with existing systems. If I understand properly, current sound class systems are given as direct mappings of sounds, but I think there is value (and a form of transparency) in being able to specify reductions or transformations on the features instead -- this makes it easier not to forget some specific diacritic combination.
That said, I unfortunately doubt I will have much dev time for this project in my new job, and when I do, the priority will be towards steps that take us  closer to a written paper.

One point to discuss and test is: if the argument is that the SCA-cognate detection can be used by the alignments are done with edit distance, one could also use another cognate detection method and see what this changes.

I'm not sure I follow your summary of the argument, but:

I agree that we could add a mechanism to swap out cognate detection methods.

I saw that lexstat in lingpy is intended for this, but I think I understand that you have several possible algorithms to do cognate detection. Do you have a suggestion of what we should try ? A pointer to some class in lingpy, some code which uses it, or examples, would help me.

Moreover, we have some gold cognacy data in Lexibank, and I think we probably should use it.

that is... unless we are afraid it again would introduce too much bias ?
We could use the COGID when the dataset has it
For ST languages, we sometimes have COGIDS and segmented words, and what we are currently doing is probably catastrophic, we should instead be comparing parts of words. I know @MacyL has been trying to figure out the best way to decide how to match partial words, but I am not sure what exactly I should do for this.
Note that we would still need detection for when comparing across datasets, and when the datasets does not have gold cognate sets.

For now, I'll add a few "TODO" indications in the code for these questions, but we should discuss them further.

I'd furthermore also argue to disallow vowel-consonant matches, since the whole discussion in phonology about glides becoming vowels and the like is barely met in real-world alignments, but rather in morphology, and we explicitly want to deal with sound change. But this is for later discussion.

While this may be true, the issue is that the fact that we do find neat C/V clusters with transitions via glides is currently one of the results of our work (and while the hypothesis is trivial, it is cool to have it quantified). If we specify it in input, then we can not claim anymore that it is a result. If we don't mind that, then we surely can do this C/V restriction.
I'll re-run everything on the full lexibank today, try to spot any leftover problems, and merge after fixing them.

Thanks for the reviews ! I did my best to document things enough so that a few weeks (or more) without touching the code wouldn't hurt later progress.

As to the feature reduction system: This is essentially some kind of a sound class system, and I'd love to include it on the longer run in CLTS. I wonder only if it can be done in a slightly more transparent manner, but this is something that one can easily test later. Having reduction systems inside the pyclts code is generally important to make sure they are in line with the most recent pyclts version, I think, although we hope that the most recent changes were the last changes we did so far.

I agree that it would be better somewhere in CLTS. The compatibility issue is already pertinent: right now it depends on v1.4.1, and I have not investigated yet how to update it for the new version. Erich and I are not completely done refining the coarsening scheme itself, so maybe it should all better wait until this is done.
I am aware that the coarsening might be a bit hacky, as I don't know the inner workings of CLTS well enough to formulate something that would mesh seamlessly with existing systems. If I understand properly, current sound class systems are given as direct mappings of sounds, but I think there is value (and a form of transparency) in being able to specify reductions or transformations on the features instead -- this makes it easier not to forget some specific diacritic combination.
That said, I unfortunately doubt I will have much dev time for this project in my new job, and when I do, the priority will be towards steps that take us  closer to a written paper.

One point to discuss and test is: if the argument is that the SCA-cognate detection can be used by the alignments are done with edit distance, one could also use another cognate detection method and see what this changes.

I'm not sure I follow your summary of the argument, but:

I agree that we could add a mechanism to swap out cognate detection methods.

I saw that lexstat in lingpy is intended for this, but I think I understand that you have several possible algorithms to do cognate detection. Do you have a suggestion of what we should try ? A pointer to some class in lingpy, some code which uses it, or examples, would help me.

Moreover, we have some gold cognacy data in Lexibank, and I think we probably should use it.

that is... unless we are afraid it again would introduce too much bias ?
We could use the COGID when the dataset has it
For ST languages, we sometimes have COGIDS and segmented words, and what we are currently doing is probably catastrophic, we should instead be comparing parts of words. I know @MacyL has been trying to figure out the best way to decide how to match partial words, but I am not sure what exactly I should do for this.
Note that we would still need detection for when comparing across datasets, and when the datasets does not have gold cognate sets.

For now, I'll add a few "TODO" indications in the code for these questions, but we should discuss them further.

I'd furthermore also argue to disallow vowel-consonant matches, since the whole discussion in phonology about glides becoming vowels and the like is barely met in real-world alignments, but rather in morphology, and we explicitly want to deal with sound change. But this is for later discussion.

While this may be true, the issue is that the fact that we do find neat C/V clusters with transitions via glides is currently one of the results of our work (and while the hypothesis is trivial, it is cool to have it quantified). If we specify it in input, then we can not claim anymore that it is a result. If we don't mind that, then we surely can do this C/V restriction.
I'll re-run everything on the full lexibank today, try to spot any leftover problems, and merge after fixing them.

It turns out that my refactors while improving readability made the code much slower and more memory hungry, to the point that it quickly fills my 15G of RAM. I will spend a little while trying to optimize both.

It turns out that my refactors while improving readability made the code much slower and more memory hungry, to the point that it quickly fills my 15G of RAM. I will spend a little while trying to optimize both.


Problem with emphasis (emphasis) regex

this_is_a test returns thisisa test
Expected: this_is_a test

Escape them if you don't want the markdown equivalent


Phoenix 6166 - Make Tephra support optional for phoenix 5 connectors

I've tested the last version, and it doesn't exclude tephra.
However, I plan to switch over to using the shade plugin, it's probably going to be easier to solve this with that.

Alright we can deal with this problem later.


PHP Fatal error during platform check

Since v1.0.5 I encountered this error on MacOs and Docker (Linux alpine image)
PHP Fatal error:  Composer detected issues in your platform: Your Composer dependencies require a PHP version ">= 8.1.0". You are running 8.0.30. in phar:///..../.composer/vendor/dbrekelmans/bdi/bdi/vendor/composer/platform_check.php on line 24

Here is the detailed output :
# composer global exec bdi -vvv

> __exec_command: bdi
Executing command (CWD): bdi

Box Requirements Checker
========================

> Using PHP 8.0.30
> PHP is using the following php.ini file:
  /usr/local/etc/php/8.0/php.ini

> Checking Box requirements:
  ✔ The application requires a version matching "^7.2|^8.0".
  ✔ The application requires the extension "json".
  ✔ The package "myclabs/php-enum" requires the extension "json".
  ✔ The application requires the extension "zip".
  ✔ The application requires the extension "zlib".
  ✔ The package "symfony/service-contracts" conflicts with the extension "psr".

  You are running 8.0.30. in phar:///Users/prometee/.composer/vendor/dbrekelmans/bdi/bdi/vendor/composer/platform_check.php on line 24

Fatal error: Composer detected issues in your platform: Your Composer dependencies require a PHP version ">= 8.1.0". You are running 8.0.30. in phar:///Users/prometee/.composer/vendor/dbrekelmans/bdi/bdi/vendor/composer/platform_check.php on line 24
Script bdi handling the __exec_command event returned with error code 255

Using the v1.0.4 no issue encountered.

It is due to this commit : https://github.com/dbrekelmans/browser-driver-installer/commit/6ac390c7cddaacc82118b2dac0cc3787a936a850
By building on PHP8.2 instead of PHP7.2, it increase the minimal allowed version of php in the platform_check.php file of the phar.
@dbrekelmans Because you test all on accept PHP7.2 on https://github.com/dbrekelmans/browser-driver-installer/blob/acf0efa4a79785a670a34af7433fdce3b3bf0f34/.github/workflows/qa.yml you must build also on php7.2 and not php8.2

Yes, same as us https://github.com/dbrekelmans/browser-driver-installer/pull/78#issuecomment-1727597625

This should now be fixed in 1.0.7

I can confirm it's fixed, thank you guys


Mock data fixed for contextual work item add

@sanbornsen snapshot fabric8-ui is deployed and available for testing at https://fabric8-ui-fabric8-ui-pr-2058-fabric8-planner.badger.fabric8.io

@sanbornsen snapshot fabric8-ui is deployed and available for testing at https://fabric8-ui-fabric8-ui-pr-2058-fabric8-planner.badger.fabric8.io


Add Wizard Component

As you see here, footer button can be different for services, we need to provide a mechanism to change button names.
It's a good also to check locators for every part, as some of them can be a bit different for Compliance and Remediation wizards. Maybe in some cases is better to use .//[contains(@*, "")]

Replaced by https://github.com/RedHatQE/widgetastic.patternfly4/pull/121


Problem with too many open files

Hello,
My current setup looks like follows:

Manage GKE cluster 1.29.3-gke.1282001
Cloud Storage Fuse CSI driver enabled in latest version
Bucket in the same region as k8s cluster
Pods running with root privileges

What is working
I am able to create PV, PVC and mount my Bucket as a storage in pod.
I can write to it, delete update files and so on.
What is not working
My whole configuration with FUSE is created to have RWX type of storage since I would like to run some nextflow pipeline which required sharing storage between pods. Everything is working until worker pod is started and try to run my workload. Soon after that I receive following error message from FUSE pod:
I0515 12:44:53.622504       1 main.go:48] Running Google Cloud Storage FUSE CSI driver sidecar mounter version v1.2.0-gke.0
I0515 12:44:55.123322       1 sidecar_mounter_config.go:101] connecting to socket "/gcsfuse-tmp/.volumes/gcs-fuse-csi-pv/socket"
I0515 12:44:55.123454       1 fdchannel.go:48] get the underlying socket
I0515 12:44:55.123473       1 fdchannel.go:60] calling recvmsg...
I0515 12:44:55.123690       1 fdchannel.go:69] parsing SCM...
I0515 12:44:55.123713       1 fdchannel.go:76] parsing SCM_RIGHTS...
I0515 12:44:55.123930       1 sidecar_mounter_config.go:269] gcsfuse config file content: map[cache-dir: logging:map[file-path:/dev/fd/1 format:json severity:warning]]
I0515 12:44:55.124012       1 sidecar_mounter.go:49] start to mount bucket "bucket-to-test-fuse" for volume "gcs-fuse-csi-pv"
I0515 12:44:55.124105       1 sidecar_mounter.go:68] gcsfuse mounting with args [--app-name gke-gcs-fuse-csi --foreground --uid 0 --gid 0 --temp-dir /gcsfuse-buffer/.volumes/gcs-fuse-csi-pv/temp-dir --config-file /gcsfuse-tmp/.volumes/gcs-fuse-csi-pv/config.yaml --implicit-dirs bucket-to-test-fuse /dev/fd/3]...
I0515 12:44:55.124275       1 main.go:73] waiting for SIGTERM signal...
I0515 12:44:55.125416       1 sidecar_mounter.go:103] gcsfuse for bucket "bucket-to-test-fuse", volume "gcs-fuse-csi-pv" started with process id 21
{"timestamp":{"seconds":1715777124,"nanos":810077094},"severity":"ERROR","message":"Rename: too many open files, too many objects to be renamed: too many open files"}
{"timestamp":{"seconds":1715777124,"nanos":810207701},"severity":"ERROR","message":"fuse: *fuseops.RenameOp error: too many open files"}
I0515 12:45:31.875930       1 main.go:110] received SIGTERM signal, waiting for all the gcsfuse processes exit...
I0515 12:45:31.876018       1 sidecar_mounter.go:75] sending SIGTERM to gcsfuse process: /gcsfuse --app-name gke-gcs-fuse-csi --foreground --uid 0 --gid 0 --temp-dir /gcsfuse-buffer/.volumes/gcs-fuse-csi-pv/temp-dir --config-file /gcsfuse-tmp/.volumes/gcs-fuse-csi-pv/config.yaml --implicit-dirs bucket-to-test-fuse /dev/fd/3
I0515 12:45:31.882649       1 sidecar_mounter.go:111] [gcs-fuse-csi-pv] gcsfuse was terminated.
I0515 12:45:31.882676       1 main.go:118] exiting sidecar mounter...

How I was trying to fix my problem
I was trying to add more ephemeral storage, CPU and memory to FUSE pod but without any luck.
I also was trying to change sysctl max files open but I am receiving following error forbidden sysctl: "fs.file-max" not allowlisted (please note that I am new to GPC).
Could you advise me how can I handle this issue?

This error
"fuse: *fuseops.RenameOp error: too many open files"
--rename-dir-limit is the flag that needs to be set ,as your application seems to be doing rename dir operation.
is discussed here as well:
https://github.com/GoogleCloudPlatform/gcsfuse/issues/644

Thank you for help. This indeed resolved issue with too many open files.


Feature: when a space is minted, it is first encrypted using the Lit protocol before uploading to ipfs

Next owner of the space can unencrypt the space when they own it.

Git it Lit 🔥


Feedback

The tweet restricted length changes if I am happy or sad about my experience.
Happy face = 257 chars
Sad face = 270 chars

/duplicate of #73307


BlockImpTest failures with Clang 8 on RHEL8

On latest master:
`98% tests passed, 4 tests failed out of 178
Total Test time (real) =  29.15 sec
The following tests FAILED:
25 - BlockImpTest (SEGFAULT)
26 - BlockImpTest_optimised (SEGFAULT)
27 - BlockImpTest_legacy (SEGFAULT)
28 - BlockImpTest_legacy_optimised (SEGFAULT)`
`$ lldb Test/BlockImpTest
(lldb) target create "Test/BlockImpTest"
Current executable set to 'Test/BlockImpTest' (x86_64).
(lldb) run
Process 4784 launched: '/home/ares/labs2/libobjc2/Build/Test/BlockImpTest' (x86_64)
Process 4784 stopped

thread #1, name = 'BlockImpTest', stop reason = signal SIGSEGV: address access protected (fault address: 0x652000)
frame #0: 0x0000000000652000
->  0x652000: movq   -0x1007(%rip), %rsi
0x652007: xchgq  %rsi, %rdi
0x65200a: jmpq   *-0x1008(%rip)
0x652010: movq   -0x1007(%rip), %rsi
(lldb) bt
thread #1, name = 'BlockImpTest', stop reason = signal SIGSEGV: address access protected (fault address: 0x652000)

frame #0: 0x0000000000652000
frame #1: 0x00000000004016fa BlockImpTestmain at BlockImpTest.m:38:2 frame #2: 0x00007ffff75d9873 libc.so.6.annobin_libc_start.c + 243
frame #3: 0x000000000040140e BlockImpTest.annobin_init.c.hot + 46

Do you have any unusual SELinux settings enabled?  The block-to-imp code has been tested (in CI) on x86-64 Linux, but it may be that you have a setting that prevents changing permission of pages from read-write to read-execute.

Hello,
I use the default SELinux policy for CentOS 8. I can however confirm that all the tests pass with SELinux off. (tested it on another machine using the same OS)
For reference, Clang version is:
$ clang -v
clang version 8.0.1 (Red Hat 8.0.1-1.module_el8.1.0+215+a01033fb)
Target: x86_64-unknown-linux-gnu
Thread model: posix
InstalledDir: /usr/bin
Found candidate GCC installation: /usr/bin/../lib/gcc/x86_64-redhat-linux/8
Found candidate GCC installation: /usr/lib/gcc/x86_64-redhat-linux/8
Selected GCC installation: /usr/bin/../lib/gcc/x86_64-redhat-linux/8
Candidate multilib: .;@m64
Candidate multilib: 32;@m32
Selected multilib: .;@m64
Thanks,

A quick check reveals that using mmap() with MAP_ANONYMOUS makes things work under CentOS 8's SELinux policy. As far as I'm ware, MAP_ANONYMOUS is not portable, though.
diff --git a/block_to_imp.c b/block_to_imp.c
index 655489a..8377623 100644
--- a/block_to_imp.c
+++ b/block_to_imp.c
@@ -163,7 +163,7 @@ static struct trampoline_set *alloc_trampolines(char *start, char *end)
 #if _WIN32
        metadata->buffers = VirtualAlloc(NULL, sizeof(struct trampoline_buffers), MEM_COMMIT | MEM_RESERVE, PAGE_READWRITE);
 #else
-       posix_memalign((void **)&metadata->buffers, getpagesize(), sizeof(struct trampoline_buffers));
+       metadata->buffers = mmap(NULL, sizeof(struct trampoline_buffers), PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0);
 #endif
        for (int i=0 ; i<HEADERS_PER_PAGE ; i++)
        {

Interesting.  I'm not sure why we're using posix_memalign here.  Please can you send a PR that replaces it with mmap?  There's no reason why it can't use mmap, the Windows code path uses the Windows equivalent.


[HWKAGENT-161] Add option to installer to make config changes without…

… module install

Not sure if this is the best way to implement this, just submitting for discussion.
And this PR does not currently include tests.

This looks fine to me the way it is implemented. We have several installer tests in itests and since those all pass, at least nothing was broken.
One way you could test this is add something to https://github.com/hawkular/hawkular-agent/blob/master/hawkular-wildfly-agent-itest-parent/hawkular-wildfly-agent-all-itests/hawkular-wildfly-agent-installer-itest/src/test/java/org/hawkular/wildfly/agent/installer/AgentInstallerStandalonePrepare.java (or create a new test class that does something similar) - your new test would ensure it runs after this one (this AgentInstallerStandalonePrepare installs the agent - both config and add-ons). So you would install after that code runs.
The problem is, installing on top of WildFly that already had an agent <subsystem> would cause problems (I've seen it where it adds a second <subsystem>). Perhaps this is the time to get the agent installer to fix that issue and let it install config over one where the agent config already exists.

@pgier most of my requested changes are minor and should be trivial. The only substantial change I asked for is the change to the DeployerConfiguration so as to keep the wildfly-module-installer artifact code hawkular-agnostic. But that too should be fairly easy to change.
Other than that, this code should be good and can be merged when those changes are made. Travis shows "red" but I looked at the raw log and the tests did fully pass - its just the underlying cassandra server/h-metrics failed to shutdown timely and that causes travis to think it failed. Once you submit the changes, we'll see if travis goes green which I suspect it will.

I was told that @pgier is away so rather than wait, I made the requested changes on top of this PR in my own PR #301. If all goes green, I'll merge that PR and close this one. If I run into problems, I'll wait to hear back from @pgier.

Since Paul is out for a bit, rather than submit a PR on his PR, I simply took this PR and put my changes on top and squash merged it. See PR #301. That passed all tests, travis was green. So this PR can be closed since it has been superceded by PR #301.


Package ApexRecipes Install Failed

Summary
Package ApexRecipes Install Failed
Steps To Reproduce:
1)Log in to your org
2)f you are setting up a Developer Edition: go to Setup, under My Domain, register a My Domain.
3)Please be sure that the domain is both registered and deployed and that your user has logged into the new domain.
4)Go to Setup, under Platform Cache, and click the "Request Trial Capacity" button. Request a Platform Cache Trial
5)Click this link to install the Apex Recipes unlocked package in your org.
6)Select Install for All Users
Expected result
Package installed
Actual result
Your request to install package "ApexRecipes Winter '21 release" was unsuccessful. None of the data or setup information in your salesforce.com organization was affected.
If your install continues to fail, contact Salesforce CRM Support through your normal channels and provide the following information.
Organization: HarpiaCloud (00Df4000002cmIj)
User: Jose Costa (005f4000000cRaq)
Package: ApexRecipes (04t3g000000ki8s)
Error Number:<PHONE_NUMBER>-198382<PHONE_NUMBER>)
Problem:

Permission Read Account depends on permission(s): Read Contact
Provides_Edit_Access_to_Accounts_Except_ShippingStreet: Permission Read Account depends on permission(s): Read Contact

Permission Read Account depends on permission(s): Read Contact
Provides_Read_Only_Access_to_Account_and_All_Fields: Permission Read Account depends on permission(s): Read Contact

Permission Read Account depends on permission(s): Read Contact
Proving_With_Security_Enforced_Works: Permission Read Account depends on permission(s): Read Contact

Additional information
Feel free to attach a screenshot or code snippets.

@Josecjr - Can you try the latest package version please?

Same error. I've used this one: https://login.salesforce.com/packaging/installPackage.apexp?p0=04t3g000000ki9CAAQ

Your request to install package "ApexRecipes Winter '21 release" was
unsuccessful. None of the data or setup information in your
salesforce.com organization
was affected.
If your install continues to fail, contact Salesforce CRM Support through
your normal channels and provide the following information.
Organization: HarpiaCloud (00Df4000002cmIj)
User: Jose Costa (005f4000000cRaq)
Package: ApexRecipes (04t3g000000ki9C)
Error Number: 300611045-38708<PHONE_NUMBER>)
Ocultar texto das mensagens anteriores
Problem:

Permission Read Account depends on permission(s): Read Contact
Provides_Edit_Access_to_Accounts_Except_ShippingStreet: Permission Read
Account depends on permission(s): Read Contact

Permission Read Account depends on permission(s): Read Contact
Provides_Read_Only_Access_to_Account_and_All_Fields: Permission Read
Account depends on permission(s): Read Contact

Permission Read Account depends on permission(s): Read Contact
Proving_With_Security_Enforced_Works: Permission Read Account depends on
permission(s): Read Contact

Em seg., 19 de out. de 2020 10:15 PM, Kevin Poorman <
<EMAIL_ADDRESS>escreveu:

@Josecjr https://github.com/Josecjr - Can you try the latest package
version please?
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
https://github.com/trailheadapps/apex-recipes/issues/22#issuecomment-712544238,
or unsubscribe
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.

@Josecjr - I just spun up a new de org and installed the package just fine. I used this installation link: https://login.salesforce.com/packaging/installPackage.apexp?p0=04t3g000000ki9CAAQ
Is it possible you're installing it in an org that has pre-existing modifications?

The same.. that is weird... My org is a Partner Dev Org (the one with more
limits) with some low level customizations.
Organization: HarpiaCloud (00Df4000002cmIj)
User: Jose Costa (005f4000000cRaq)
Package: ApexRecipes (04t3g000000ki9C)
Error Number: 348708159-32495<PHONE_NUMBER>)
Problem:

Permission Read Account depends on permission(s): Read Contact
Provides_Edit_Access_to_Accounts_Except_ShippingStreet: Permission Read
Account depends on permission(s): Read Contact

Permission Read Account depends on permission(s): Read Contact
Provides_Read_Only_Access_to_Account_and_All_Fields: Permission Read
Account depends on permission(s): Read Contact

Permission Read Account depends on permission(s): Read Contact
Proving_With_Security_Enforced_Works: Permission Read Account depends on
permission(s): Read Contact
José Costa Junior

Em qua., 21 de out. de 2020 às 09:29, Kevin Poorman <
<EMAIL_ADDRESS>escreveu:

@Josecjr https://github.com/Josecjr - I just spun up a new de org and
installed the package just fine. I used this installation link:
https://login.salesforce.com/packaging/installPackage.apexp?p0=04t3g000000ki9CAAQ
Is it possible you're installing it in an org that has pre-existing
modifications?
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
https://github.com/trailheadapps/apex-recipes/issues/22#issuecomment-713574565,
or unsubscribe
https://github.com/notifications/unsubscribe-auth/AEF5NO6R2RP4YX2INGXHUWLSL3O33ANCNFSM4SWJLOMA
.

Mind trying in a standard DE org, or Partner org with no modifications?
On Oct 21, 2020, 10:39 AM -0400, Josecjr<EMAIL_ADDRESS>wrote:

The same.. that is weird... My org is a Partner Dev Org (the one with more
limits) with some low level customizations.
Organization: HarpiaCloud (00Df4000002cmIj)
User: Jose Costa (005f4000000cRaq)
Package: ApexRecipes (04t3g000000ki9C)
Error Number: 348708159-32495<PHONE_NUMBER>)
Problem:

Permission Read Account depends on permission(s): Read Contact
Provides_Edit_Access_to_Accounts_Except_ShippingStreet: Permission Read
Account depends on permission(s): Read Contact

Permission Read Account depends on permission(s): Read Contact
Provides_Read_Only_Access_to_Account_and_All_Fields: Permission Read
Account depends on permission(s): Read Contact

Permission Read Account depends on permission(s): Read Contact
Proving_With_Security_Enforced_Works: Permission Read Account depends on
permission(s): Read Contact
José Costa Junior

Em qua., 21 de out. de 2020 às 09:29, Kevin Poorman <
<EMAIL_ADDRESS>escreveu:

@Josecjr https://github.com/Josecjr - I just spun up a new de org and
installed the package just fine. I used this installation link:
https://login.salesforce.com/packaging/installPackage.apexp?p0=04t3g000000ki9CAAQ
Is it possible you're installing it in an org that has pre-existing
modifications?
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
https://github.com/trailheadapps/apex-recipes/issues/22#issuecomment-713574565,
or unsubscribe
https://github.com/notifications/unsubscribe-auth/AEF5NO6R2RP4YX2INGXHUWLSL3O33ANCNFSM4SWJLOMA
.

—
You are receiving this because you were assigned.
Reply to this email directly, view it on GitHub, or unsubscribe.

In a new sandbox it worked.
José Costa Junior
Em qua., 21 de out. de 2020 às 10:49, Kevin Poorman <
<EMAIL_ADDRESS>escreveu:

Mind trying in a standard DE org, or Partner org with no modifications?
On Oct 21, 2020, 10:39 AM -0400, Josecjr<EMAIL_ADDRESS>wrote:

The same.. that is weird... My org is a Partner Dev Org (the one with
more
limits) with some low level customizations.
Organization: HarpiaCloud (00Df4000002cmIj)
User: Jose Costa (005f4000000cRaq)
Package: ApexRecipes (04t3g000000ki9C)
Error Number: 348708159-32495<PHONE_NUMBER>)
Problem:

Permission Read Account depends on permission(s): Read Contact
Provides_Edit_Access_to_Accounts_Except_ShippingStreet: Permission Read
Account depends on permission(s): Read Contact

Permission Read Account depends on permission(s): Read Contact
Provides_Read_Only_Access_to_Account_and_All_Fields: Permission Read
Account depends on permission(s): Read Contact

Permission Read Account depends on permission(s): Read Contact
Proving_With_Security_Enforced_Works: Permission Read Account depends on
permission(s): Read Contact
José Costa Junior

Em qua., 21 de out. de 2020 às 09:29, Kevin Poorman <
<EMAIL_ADDRESS>escreveu:

@Josecjr https://github.com/Josecjr - I just spun up a new de org
and
installed the package just fine. I used this installation link:

https://login.salesforce.com/packaging/installPackage.apexp?p0=04t3g000000ki9CAAQ

Is it possible you're installing it in an org that has pre-existing
modifications?
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You are receiving this because you were mentioned.
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https://github.com/trailheadapps/apex-recipes/issues/22#issuecomment-713574565
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I've got the same problem on an existing Sandbox:
Your request to install package "ApexRecipes Winter '21 release" was successful.

Did you find out the reason?

I've tried to install the unlocked package 'Apex Recipes' with this link 'https://test.salesforce.com/packaging/installPackage.apexp?p0=04t3g000000kiDJAAY' on one of our sandboxes and get the following error:
Organization: Colliers International Deutschland GmbH (00D0E0000002LcN)
User: Christian Schwabe (0050O000009pHg3)
Package: ApexRecipes (04t3g000000kiDJ)
Error Number: 752431791-1832068<PHONE_NUMBER>)
Problem:

Permission Read Account depends on permission(s): Read Contact
Provides_Edit_Access_to_Accounts_Except_ShippingStreet: Permission Read Account depends on permission(s): Read Contact

Permission Read Account depends on permission(s): Read Contact
Provides_Read_Only_Access_to_Account_and_All_Fields: Permission Read Account depends on permission(s): Read Contact

Permission Read Account depends on permission(s): Read Contact
Proving_With_Security_Enforced_Works: Permission Read Account depends on permission(s): Read Contact


Simplify subscript expressions of aliased tables as strings

Summary of the changes / Why this improves CrateDB
Fixes part of https://github.com/crate/crate/issues/13504
cr> select a[1]['b']['s'] from (select a[1]['b']['s'] from test) q;
ColumnUnknownException[Column a['b']['s'] unknown]

Checklist

[x] Added an entry in CHANGES.txt for user facing changes
[x] Updated documentation & sql_features table for user facing changes
[x] Touched code is covered by tests
[x] CLA is signed
[x] This does not contain breaking changes, or if it does:

It is released within a major release
It is recorded in CHANGES.txt
It was marked as deprecated in an earlier release if possible
You've thought about the consequences and other components are adapted
(E.g. AdminUI)

It makes something that looks like a subscript expression more ambiguous.

Do you mean that exposing subscripted column from alias tables are already ambiguous? I think I see the issue here but
we already allowed simpler cases like
cr> select a['b'] from (select a['b'] from r) as alias;
+--------+
| a['b'] |
+--------+
+--------+
SELECT 0 rows in set (0.097 sec)

but we already allowed simpler cases like

That's not ideal, but also not a compelling reason to extend support further.
The subscript-resolving logic is already quite complex. Unless there's a good use-case I don't think we need to extend it to more variants

Thanks for reviewing and clarifying @mfussenegger, @matriv closing this.


Change space to underscore in normalizeFullDisplayName

A job name formatter was added In #77 that removed spaces from job name tags. The job name tags were previously sent with the space, and then converted in the Datadog backend to underscores.
This PR changes the space to an underscore on the plugin side so tags do not change for jobs with spaces.

Our blacklist feature already removes spaces from the name, closing this PR for consistency and noting changes from #77 in the Changelog.


Need help to read sqlite database

Hi
In my app i use large size of sqlite database, so i directly copy the files to Documents folder of internal memory.
i am trying to use this library and i use the storageHelper.openFolderPicker(2, new FileFullPath(this, "/storage/emulated/0/Documents")); to select the folder, now how to open the database and to use it
This is my code for reading the db which i used before sdk 30
mypath = Environment.getExternalStoragePublicDirectory(Environment.DIRECTORY_DOCUMENTS).toString() + "/mydb.sqlite"; database = SQLiteDatabase.openDatabase(myPath, Utils.getpw(), null, SQLiteDatabase.OPEN_READONLY);
also i need to read the content of a dat file from the Documents folder, which code i need to use after i got the folder permisssion?
Anybody help me please.

SQLiteDatabase.openDatabase() only accepts String path or java.io.File:

There's no option to read database from InputStream, thus it is not possible to read the database file from path storage/emulated/0/Documents. The only accessible path is your own app private directory, i.e. storage/emulated/0/Android/data/<your-package-name>. You can use this path like this:
val privateDir = context.getExternalFilesDir(null)
val database = SQLiteDatabase.openDatabase(privateDir, ...)


Selector does not recognize nested nodes after pressing Cancel run > Progress (...)

"Unknown error" is displayed, the console says:
got prompt
ERROR:aiohttp.server:Error handling request
Traceback (most recent call last):
  File "P:\cui\python_embeded\lib\site-packages\aiohttp\web_protocol.py", line 433, in _handle_request
    resp = await request_handler(request)
  File "P:\cui\python_embeded\lib\site-packages\aiohttp\web_app.py", line 504, in _handle
    resp = await handler(request)
  File "P:\cui\python_embeded\lib\site-packages\aiohttp\web_middlewares.py", line 117, in impl
    return await handler(request)
  File "P:\cui\ComfyUI\server.py", line 46, in cache_control
    response: web.Response = await handler(request)
  File "P:\cui\ComfyUI\server.py", line 472, in post_prompt
    valid = execution.validate_prompt(prompt)
  File "P:\cui\ComfyUI\execution.py", line 598, in validate_prompt
    class_ = nodes.NODE_CLASS_MAPPINGS[prompt[x]['class_type']]
KeyError: 'MyNode'

The MyNode isnt the first one after / before the selector, it is an unrelated one to the part where I press the buttons
Otherwise it works fine and it is a really great addition to workflows

Didn't find "MyNode" in the code so I have no idea where this error come from.
Could you make a minimum workflow that can reproduce this error?

I see I made a mistake here. Posted it in the wrong extension, sorry for the confusion (it was about the comfyui image picker not selector)


package type function can not reimplement for low memory using purpose

Go version
go 1.23.1 windows amd64
Output of go env in your module/workspace:
not need

What did you do?
func Test8(t *testing.T) {
	wm := New[[]byte, int]()
	wm.KeyFromBytes = func(b []byte) (k []byte) {
		return nil
	}
	wm.Put([]byte("ab"), 33)
	wm.Put([]byte("zb"), 34)
	wm.Put([]byte("cb"), 35)
	fmt.Println("Put end")
	fmt.Println(wm.Get([]byte("ab")))
	fmt.Println("Get end")
	fmt.Println(wm.Del([]byte("zb")))
	fmt.Println("Del end")
	fmt.Println(wm.Get([]byte("cb")))
	fmt.Println("Get 2 end")
}

What did you see happen?
wmap [wmap.test]
.\wmap_test.go:415:2: cannot assign to wm.KeyFromBytes (neither addressable nor a map index expression)
FAIL	wmap [build failed]
What did you expect to see?
make golang suport reimplement for large items purpose.

This looks like a misunderstanding of the language.  Show us a complete standalone test case.
Note that we do not use the issue tracker for questions.  You will get better and faster answers on a forum.  See https://go.dev/wiki/Questions.  Thanks.


Issues when searching for windows...

When you search for a window the list is actually filtered, and any window not matching the search text is removed.

When searching, any parent window of those matched should be shown in the list (recursive).

When you have searched and have a window selected and active in the search list, and you cancel the search, then when the complete list of ll windows is shown again the selection should be preserved and scrolled into the visible part of the list.

There should be a way to do what's traditionally called a search, that is, you should highlight the matches and be able to move back and forth between the found matches. Perhaps a radio-button next to the "search field": Filter | Search ?

Ends up showing too many unrelated entries to the search.
The selection is already preserved but the view doesnt get scrolled because searching often changes the position of entries.
The support for this there but its already being used for showing details about the entries.


INotifyPropertyChanged support

It would be nice that when the Object implements the INotifyPropertyChanged interface, that it subscribes to the interface and updates the Json text when the property has changed.

Any update on this? It would be a great feature to have since it would mean that a quick wrap of collections like Dictionry<TKey, TValue> or List<TType> to call the PropertyChanged event, and in return solve the awkward issue of updating collections....
Unless there is an alternative to taking the collection, modifying it, and setting the object itself as the collection again...


PLAT-5742: Fix to use the information (visible, install and enable) for the POD

Build triggered. sha1 is merged.

Build started sha1 is merged.

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Codecov Report

Merging #184 into dev will decrease coverage by 0.8%.
The diff coverage is 73.07%.

@@            Coverage Diff             @@
##              dev     #184      +/-   ##
==========================================
- Coverage   89.65%   88.84%   -0.81%
==========================================
  Files         144      175      +31
  Lines        2755     3577     +822
  Branches      265      353      +88
==========================================
+ Hits         2470     3178     +708
- Misses        220      290      +70
- Partials       65      109      +44

Impacted Files
Coverage Δ

...ation/provisioning/client/AppRepositoryClient.java
89.09% <100%> (ø)

...ation/provisioning/service/ApplicationService.java
84.12% <70.83%> (ø)

...ion/provisioning/properties/KeyPairProperties.java
0% <0%> (ø)

...on/provisioning/exception/UserSearchException.java
100% <0%> (ø)

...roperties/ConfigurationProvisioningProperties.java
0% <0%> (ø)

...ration/provisioning/service/AppKeyPairService.java
100% <0%> (ø)

...oning/properties/CompanyCertificateProperties.java
0% <0%> (ø)

...rovisioning/service/CompanyCertificateService.java
81.33% <0%> (ø)

...ration/provisioning/properties/UserProperties.java
0% <0%> (ø)

...ng/exception/ApplicationProvisioningException.java
100% <0%> (ø)

... and 23 more

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update 53ad7c1...e0eb835. Read the comment docs.

Build triggered. sha1 is merged.

Build started sha1 is merged.

Build finished.

Build triggered. sha1 is merged.

Build started sha1 is merged.

Build finished.

Build triggered. sha1 is merged.

Build started sha1 is merged.

Build finished.

Build triggered. sha1 is merged.

Build started sha1 is merged.

Build finished.


Add compliance pipeline for running APIScan.

This mostly copies Roslyn's approach here: https://github.com/dotnet/roslyn/pull/61905

Fixes https://devdiv.visualstudio.com/DevDiv/_workitems/edit/1531320

I'm trying to figure out how to create a pipeline with this bit like @JoeRobich did. Looks like I don't have access or I'm doing it wrong.

I'm trying to figure out how to create a pipeline with this bit like @JoeRobich did. Looks like I don't have access or I'm doing it wrong.

I tried as well but I don't have permissions for the razor-tooling repo.


Client meeting: 2/9

Required

[x] CI System demo
[x] One user story per person
[x] List of what is needed to finish: #104

Other

[x] Mention that locks are on hold right now because we have higher priorities

Scrum Quicksheet, if anyone needs to easily reference

"You definitely need some linting"

Complete


Firestore State Store: Add option to skip indexing

Firestore has a limit to the data it can index. There should be an option (new metadata property) to skip the indexing.
This can be done like so:
https://cloud.google.com/datastore/docs/concepts/indexes#datastore-datastore-properties-go

cc @yaron2


v0.3.1

Checklist

[ ] Used a personal fork of the feedstock to propose changes
[ ] Bumped the build number (if the version is unchanged)
[ ] Reset the build number to 0 (if the version changed)
[ ] Re-rendered with the latest conda-smithy (Use the phrase @conda-forge-admin, please rerender in a comment in this PR for automated rerendering)
[ ] Ensured the license file is being packaged.

Hi! This is the friendly automated conda-forge-linting service.
I just wanted to let you know that I linted all conda-recipes in your PR (recipe) and found it was in an excellent condition.

@conda-forge-admin, please rerender

@agoose77 @bollwyvl Requesting review and merge. Thanks!

@conda-forge-admin please rerender


Switch frontend handlers to use internal types

What changed?
Switch frontend handlers to use internal types. At this point thrift conversions are moved to the final position - thriftHandler.

Why?
To propagate internal types throughout Cadence codebase.

How did you test it?

Potential risks

Coverage increased (+0.3%) to 60.172% when pulling 28f8d3a0e1594f1a7b2073989bbf42cd54ece568 on vytautas-karpavicius:frontend-internal-types into 49b64fc4407024e775f7ae7d6afaa0bf34496e42 on uber:master.


pull request for e2e test at 12/21/2016 17:56:22

:white_check_mark: Validation status: passed
For more details, please refer to the build report.
Note: If you changed an existing file name or deleted a file, broken links in other files to the deleted or renamed file are listed only in the full build report.


Import not working

Hi Luigi,
I'm try to import the lib with desktop and web version of draw.io, but isn't work.
Can you try it?
Regards,

Hi.
I've just reimported the library and it seems to work fine.
Can you please tell me what kind of error you get?
Luigi

Of course.
In desktop (OS X version), there Is no objects in the palette:

In web version (safari browser):

the same behavior.
Do you want another test in my set? Try to import it again?

What version draw.io version do you have?
I've just installed the 12.9.9 (OS X) and I was able to correctly import the library.
It is slightly different from the online version so I've updated the installation instructions.

So, the desktop version is the same (latest 12.9.9).
I'm try the new installation instructions and with git clone, works.

Thanks for your attention,
Regards,


[Live server] Live server is stopped

When I install Atom-Live-Server, after the installation
I try to launch Live Server I get a message that the server has stopped

Same issue does anyone have the fix?


[docs] Remove duplicate link to migration helper

[X] I have followed (at least) the PR section of the contributing guide.

Why?

It's duplicated :)

@charlax Thanks for taking the time! Ok, it's a coordination issue between Me, Matt and Josh, it happens, let's merge :).

Sure no worries and thanks again for material-ui!


TypeError: Cannot read properties of undefined (reading 'push') [ethOnline-hackathon-urgent]

Describe the bug
Cannot run local-tableland in my OSX machine
To Reproduce
Steps to reproduce the behavior:
npm install @tableland/local2^2.0.2"
or
npm install @tableland/local@latest
Expected behavior
Local Tableland to launch
Screenshots
[Registry] An unexpected error occurred:
[Registry] TypeError: Cannot read properties of undefined (reading 'push')
[Registry] at extendEnvironment (/Users/myname/Desktop/Dev/oneclickdapp-ethonline/node_modules/hardhat/src/internal/core/config/config-env.ts:141:28)
[Registry] at Object.<anonymous> (/Users/myname/Desktop/Dev/oneclickdapp-ethonline/node_modules/@nomiclabs/hardhat-ethers/src/internal/index.ts:27:18)
[Registry] at Module._compile (node:internal/modules/cjs/loader:1256:14)
[Registry] at Module._extensions..js (node:internal/modules/cjs/loader:1310:10)
[Registry] at Object.require.extensions.<computed> [as .js] (/Users/myname/Desktop/Dev/oneclickdapp-ethonline/node_modules/ts-node/src/index.ts:1608:43)
[Registry] at Module.load (node:internal/modules/cjs/loader:1119:32)
[Registry] at Function.Module._load (node:internal/modules/cjs/loader:960:12)
[Registry] at Module.require (node:internal/modules/cjs/loader:1143:19)
[Registry] at require (node:internal/modules/cjs/helpers:119:18)
[Registry] at Object.<anonymous> (/Users/myname/Desktop/Dev/oneclickdapp-ethonline/node_modules/@nomicfoundation/hardhat-chai-matchers/src/index.ts:1:1)

Desktop (please complete the following information):

OS: MacOS Ventura

"devDependencies": {
    "@nomicfoundation/hardhat-toolbox": "2.0.0",
    "@nomiclabs/hardhat-ethers": "2.2.1",
    "@openzeppelin/contracts-upgradeable": "4.8.0",
    "@openzeppelin/hardhat-upgrades": "1.21.0",
    "@tableland/evm": "^4.3.0",
    "@tableland/local": "^2.0.2",
    "@typechain/hardhat": "6.1.5",
    "dotenv": "16.0.3",
    "erc721a-upgradeable": "4.2.3",
    "hardhat": "^2.18.2",
    "hardhat-gas-reporter": "1.0.9",
    "prettier": "2.8.1",
    "prettier-plugin-solidity": "1.1.0",
    "solidity-coverage": "0.8.2"
  }

Hey @bitsandtea
sorry to hear you're having trouble.  I'm not sure if its a typo in your issue, but @tableland/local2 is not a project.
If you try npm install @tableland/local then npx local-tableland does that work?
Side note: this repository is no longer being used, I'm going to transfer this issue to our new repo.


Math formula not properly displayed in PDF

Most of the times, it works. Sometimes, it doesn't. I think I should let wkhtmltopdf wait for everything to render properly before doing its processes.

The problem is because of loading time of katex.


finetuning a language model: Unexpected keyword argument 'lm_corpus_path'

I am using https://github.com/speechbrain/speechbrain/tree/develop/recipes/LibriSpeech/LM to fine-tune a transformer based lm model.
I am having problems defining the LM corpus path, and getting the error:
TypeError: init() got an unexpected keyword argument 'lm_corpus_path'
Our goal is to finetune the Transformer language model on our dataset. I have some confusion around which folder location should point to our custom dataset. In our setting we set data_folder == our_data/ and lm_corpus_path = our_data. Is that correct?
The our_data folder contains custom train.trans.txt, dev.trans.txt and test.trans.txt
I have tried using huggingface datasets version 1.6.2 as suggested here https://github.com/speechbrain/speechbrain/pull/1223  however the same error is still arising.

@mravanelli we should add the fact of getting rid of HuggingFace Dataset in our LM training, it's terrible to have an external dependency in such an important point.
@mjhewitt1 could you please post the entire stack trace as well as your environment?

@mjhewitt1 Did you figure out how to finetune the Transformer LM with your dataset ?
@TParcollet It's not clear to me why we would still need the HuggingFace Dataset dependency for the LM finetuning ?

I did manage to finetune the Transformer LM with my dataset. I changed the transformer.yaml file so it looked like this where the datasets are defined (see image)

data_folder was commented out
the train, dev and test files were explicitly defined, instead of using lm_corpus_path

Hope this is helpful & makes sense

Thanks a lot for your answer. With this config yaml, I still got an error.
I guess you did modify the dataio_prepare function in train.py  as well in order to make it work ?
Because it seems to expect data in the LibriSpeech format as it is.

Apologies, I forgot to include that part.
For completeness, I changed the datio_prepare function in train.py to look like:


add bitbucket issues

This is currently out of scope. I would suggest creating a separate extension for BitBucket.


Command interface

Accept user commands, act on the game world, display results.

A Command might have a "keyword" that uniquely identifies it. It might also accept any number of arguments. I'd picture something like this:
interface Command {
     public String getKeyword();
     public void execute(String[] args, Game game);
}

So maybe a "Research" command could be executed by typing "Research WarpDrive" - where "Research" is the keyword that identifies the command, and "WarpDrive" is passed in the args.

Yeah, that's spot on. I like the functional style of passing the game in.


Change BackLink  to  to allow href links and fix mouse hov…

Change BackLink  to  to allow href links and fix mouse hover behaviour
Checklist:

[x] Documentation
[x] Tests
[x] Ready to be merged

Codecov Report

Merging #351 into master will not change coverage.
The diff coverage is 100%.

@@          Coverage Diff          @@
##           master   #351   +/-   ##
=====================================
  Coverage     100%   100%
=====================================
  Files          76     76
  Lines         400    400
  Branches       14     14
=====================================
  Hits          400    400

Impacted Files
Coverage Δ

components/back-link/src/index.js
100% <100%> (ø)
:arrow_up:

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@Loque- @taranchauhan is there anything further we need to do on this one before it's merged?

No this looks great @Joe-Brady, apologies for the delay getting this merged - just had another look to confirm and it looks ace. Thanks for the PR!


Simplifies template scripts and reduces duplications

Moved HTML elements for layout to the layout script and reduces many duplications in the view scripts.

ping @ezimuel

Thanks, @froschdesign!


Updating wording own tenant vs B2C tenant

Addresses comments made in #73667 @erickuhn19, @barclayn  please review

@jcruiz : Thanks for your contribution! The author(s) have been notified to review your proposed change.

#sign-off


Unknown model knn_implicit

After running the test
gorse test knn_implicit --load-csv games.csv --csv-sep ',' --eval-precision --eval-recall --eval-ndcg --eval-map --eval-mrr
I am getting an error like this:
Unknown model knn_implicit
I tried both, with -tags='avx2' and without
gorse version
0.1.3

knn_implicit has been elimited. This issues has to been closed.


CodeQL workflow breaks

fixed in https://github.com/nils-org/Topshelf.LightCore/commit/4d6659792407586d5fe2841037d466d9a6cfa430


Headless setup appears may not work with this version

Raspberry Pi Deep PanTilt version: Pi4, 4GB, 64SD
Python version: 3.7
Operating System: Debian

Description
Describe what you were trying to get done.:
Trying to setup as headless upon boot, so I can use it as a freestanding tracking application.
Tell us what happened, what went wrong, and what you expected to happen.:
In headless setup & running autostart (no monitor & keyboard attached), Ran few second & servo moves random with jitter, does not detect and freezes at the end (even when VNC viewer connected, it doesn't show video feed in anyway to begin with)--no detection window can be seen in VNC viewer but Terminal showing only Run-time is running txt.
What I Did
1: Enabled & edited /etc/xdg/lxsession/LXDE-pi/autostart to run --lxterminal -e "/home/pi/rpi-deep-pantilt/detection_start.sh"-- which include script to run "rpi-deep-pantilt track"
2: Ran Raspi-config & set resolution to 1024*768 (note; other setting including default will not even start detect session)
3: Upon "rpi-deep-pantilt track", pan tracks ok but tilt stays still & does not move and stop eventually.
This is terminal output from VNC viewer.
INFO: Initialized TensorFlow Lite runtime.
Exception in thread Thread-1:
Traceback (most recent call last):
File "/home/pi/rpi-deep-pantilt/.venv/lib/python3.7/site-packages/picamera/camera.py", line 1704, in capture_continuous
'Timed out waiting for capture to end')
picamera.exc.PiCameraRuntimeError: Timed out waiting for capture to end
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/python3.7/threading.py", line 917, in _bootstrap_inner
self.run()
File "/usr/lib/python3.7/threading.py", line 865, in run
self._target(*self._args, **self._kwargs)
File "/home/pi/rpi-deep-pantilt/.venv/lib/python3.7/site-packages/rpi_deep_pantilt/detect/camera.py", line 99, in flush
for f in self.stream:
File "/home/pi/rpi-deep-pantilt/.venv/lib/python3.7/site-packages/picamera/camera.py", line 1710, in capture_continuous
encoder.close()
File "/home/pi/rpi-deep-pantilt/.venv/lib/python3.7/site-packages/picamera/encoders.py", line 431, in close
self.stop()
File "/home/pi/rpi-deep-pantilt/.venv/lib/python3.7/site-packages/picamera/encoders.py", line 419, in stop
self._close_output()
File "/home/pi/rpi-deep-pantilt/.venv/lib/python3.7/site-packages/picamera/encoders.py", line 349, in _close_output
mo.close_stream(output, opened)
File "/home/pi/rpi-deep-pantilt/.venv/lib/python3.7/site-packages/picamera/mmalobj.py", line 371, in close_stream
stream.flush()
File "/home/pi/rpi-deep-pantilt/.venv/lib/python3.7/site-packages/picamera/array.py", line 238, in flush
self.array = bytes_to_rgb(self.getvalue(), self.size or self.camera.resolution)
File "/home/pi/rpi-deep-pantilt/.venv/lib/python3.7/site-packages/picamera/array.py", line 127, in bytes_to_rgb
'Incorrect buffer length for resolution %dx%d' % (width, height))
picamera.exc.PiCameraValueError: Incorrect buffer length for resolution 320x320
Solved!
sudo rasps-config
advanced--resolution--set to DMT Mode 82 1920*1080--save--restart
sudo nano /boot/config.txt
set frame buffer width 1920 & frame buffer height to 1024--save--restart
this appear new Pi4's HW (HDMI driver) related issue

Solved!
sudo rasps-config
advanced--resolution--set to DMT Mode 82 1920*1080--save--restart
sudo nano /boot/config.txt
set frame buffer width 1920 & frame buffer height to 1024--save--restart
this appear new Pi4's HW (HDMI driver) related issue


The ribbon is blurry on HiDPI devices

The Problem
The current version of this plugin performed poorly on high DPI devices, such as MacBook Pro with Retina Display. As shown below:

Notice those edges and angles, they are obviously less sharp than they should be.
The Cause
As a result of my investigation, the source canvas-ribbon of this plugin has some adaption problems on high DPI devices.
A Solution
Although I'm not able to fix the source code directly, I found another solution for this. Use this hustcc/ribbon.js as the source of the plugin, instead of the buggy original one. By applying the new source, it fixes the problem effectively as shown below:

As you can see, this is way sharper than the original one.

Fixed in https://github.com/theme-next/theme-next-canvas-ribbon/commit/2b41ae14433eb4a13cd99ac9736635723e813c32


operators [N] [CI] project-quay (3.6.2)

Adds Quay, direct copy of recent PR in community operatorhub: https://github.com/k8s-operatorhub/community-operators/pull/781
Signed-off-by: Dave O'Connor<EMAIL_ADDRESS>Thanks submitting your Operator. Please check below list before you create your Pull Request.
New Submissions

[ ] Are you familiar with our contribution guidelines?
[ ] Have you packaged and deployed your Operator for Operator Framework?

[ ] Have you tested your Operator in all supported installation modes?
[ ] Have you considered whether you want use semantic versioning order?
[ ] Is your submission signed?
[ ] Is operator icon set?

Updates to existing Operators

[ ] Did you create a ci.yaml file according to the update instructions?
[ ] Is your new CSV pointing to the previous version with the replaces property if you chose replaces-mode via the updateGraph property in ci.yaml?
[ ] Is your new CSV referenced in the appropriate channel defined in the package.yaml or annotations.yaml ?
[ ] Have you tested an update to your Operator when deployed via OLM?
[ ] Is your submission signed?

Your submission should not

[ ] Modify more than one operator
[ ] Modify an Operator you don't own
[ ] Rename an operator - please remove and add with a different name instead
[ ] Modify any files outside the above mentioned folders
[ ] Contain more than one commit. Please squash your commits.

Operator Description must contain (in order)

[ ] Description about the managed Application and where to find more information
[ ] Features and capabilities of your Operator and how to use it
[ ] Any manual steps about potential pre-requisites for using your Operator

Operator Metadata should contain

[ ] Human readable name and 1-liner description about your Operator
[ ] Valid category name1
[ ] One of the pre-defined capability levels2
[ ] Links to the maintainer, source code and documentation
[ ] Example templates for all Custom Resource Definitions intended to be used
[ ] A quadratic logo

Remember that you can preview your CSV here.
--
1 If you feel your Operator does not fit any of the pre-defined categories, file an issue against this repo and explain your need
2 For more information see here

/merge possible

/merge possible

/retest

/merge possible

@J0zi @mvalarh All tests have passed...is there anything else I need to do to get this merged?

/merge possible


Is there a way to set an option programmatically?

I need my modal selector to change value conditionally depending on an incoming prop value. I could not find any way to do it in the docs.
Is there any method that I can use?
Thanks

Refer to #52 for a possible solution


Exclude more failing tests on z/OS tck 11 + Clean up dups in previous excludes

Additional excludes for /backlog/issues/669 for failures observed in the latest extended tck 11 run on z/OS + cleanup of duplications in excludes introduced in https://github.com/adoptium/aqa-tests/pull/3160.
Custom target updated to only run api/java_math/BigInteger.

Signed-off-by: Mesbah-Alam<EMAIL_ADDRESS>

Just for the record, jck_custom is a special target for triaging or debugging purposes. The testing for api/java_math is covered in  jck-runtime-api-java_math


Running with MPS as device (for apple M1 chips)

Hi!
I've been trying to set this up on a MacBook with an M1 chip. However, simply changing  ".cuda()" -> .to(device) with device being set to "mps" does not work.
As far as I can understand, the issue boils down to the use of torch.cuda.amp (the gradient scaler and autocaster) in trainer.py. I tried setting enabled=false by hand, but that does not work either. My current knowledge is not enough to figure out how to modify the code to get around that. It does work if I set the device to "CPU" though.
Any pointers on how to do it?
Thanks for the hard work in this implementation, looking forward to making it work on my M1 MacBook.

Since this was somehow connected to 8105 maybe it will work now.


Making desactivation of soft deletable working

This patch make sure that the filter is enabled in the onFlush event before applying the behavior.
I experienced malfunction of this behavior, when I did something like that :
    $em->getFilters()->disable('softdeleteable');
    $product = $em->getRepository('AppBundle:Product')->findOneBy(['idWorldwide' => 'XSWQAZ']);
    $em->remove($product);
    $em->flush();

It doesn't work the soft deletable behavior is still applied, this patch correct this.

I think it would be easier to detach listener from event manager. it would be compatible with both, orm and odm

Hi @l3pp4rd thanks for your work, I don't understand what you mean in your comment can you give me some hint on what you are expecting so I can try to do it ?
The patch seems to work : https://travis-ci.org/Atlantic18/DoctrineExtensions/jobs/95424505
The failed one are likely due to misconfiguration, see https://travis-ci.org/Atlantic18/DoctrineExtensions/jobs/95424506 for example.

I meant that to disable softdeleatable, you can create a method like this to switch it on or off based on your needs.

Hello, and thank you for your contribution.
In the interest of spring cleaning and package modernization, I'm going through and closing old issues and pull requests that have had no recent activity, do not have associated tests, or have failing tests.
If you are still experiencing this issue or wish to contribute an up-to-date pull request, please create a new issue.
Thank you!


Video Autoplay

Is there a way to autoplay the video without starting it in full screen? I would like to set it up like this but with AutoPlay enabled.
jcVideoPlayerStandard.setUp("http://streaming.hearstdigitalstudios.com/hearst_magazines/573b974ed55930587ca86f44_1463523182.m3u8"
, JCVideoPlayerStandard.SCREEN_LAYOUT_NORMAL, "");

jcVideoPlayerStandard.looping=true;

Thank you!

Doesn't work for me.
jcVideoPlayerStandard.looping = true; jcVideoPlayerStandard.setUp(getSource(),JCVideoPlayerStandard.SCREEN_LAYOUT_NORMAL, "");
What am I doing wrong?

@pmpandit04 Is you mother lauguage English, could you help me to improve readme.md, make it in native English.

use new version


fix the failing golang-ci lint test

Notes for Reviewers
This PR fixes the failing golang-ci lint tests
Signed commits

[x] Yes, I signed my commits.

yay! 🎈

This is a draft pr ,so many tests are failing. I will commit more changes here


docs: add OSS Insight to showcase

Motivation
We want to add https://ossinsight.io into showcases.
Have you read the Contributing Guidelines on pull requests?
Yes
Test Plan

Related PRs

Great to see PingCAP using it—been following TiDB for a long time.
Just remember to upload the image and sign the CLA so we can review & merge

Off-topic: half a year ago, Docusaurus was 29k stars and TiDB was 30k; now Docusaurus is 32k and TiDB is 31k :DDD

Cool oss features 👍