"histone demethylase activity" revisions/additions/obsoletions

I've just been reviewing the branch shown below (with current EC/RHEA xrefs):
histone demethylase activity
|__histone demethylase activity (H3-R2 specific)
|__histone demethylase activity (H4-R3 specific)
|__histone demethylase activity (H3-K4 specific)
|   |__histone demethylase activity (H3-monomethyl-K4 specific)
|   |__histone demethylase activity (H3-dimethyl-K4 specific)
|   |__histone demethylase activity (H3-trimethyl-K4 specific) (EC:<IP_ADDRESS>)
|__histone demethylase activity (H3-K9 specific) (EC:<IP_ADDRESS>, EC:<IP_ADDRESS>)
|__histone demethylase activity (H4-K20 specific)
|__histone demethylase activity (H3-K27 specific) (EC:<IP_ADDRESS>)
|__histone demethylase activity (H3-K36 specific) (EC:<IP_ADDRESS>, RHEA:42032)

Looks like several improvements should be made to:

[x] add consistent parentage under "2-oxoglutarate-dependent dioxygenase activity (GO:0016706)" (= EC:1.14.11.-)
add/split out subtypes for all cases (as already done for "histone demethylase activity (H3-K4 specific)" above)
add additional RHEA xrefs
change term names where necessary to distinguish between similar reactions (e.g. trimethyl-K4 -> diimethyl-K4 (RHEA:60212) vs trimethyl-K4 -> unmethylated-K4 (RHEA:60208)
[x]  give definitions a consistent format

Some specific suggestions below (indicated by '=>') - note I've omitted the synonyms/Reactome xrefs for brevity:
[Term]
id: GO:0032452
name: histone demethylase activity
namespace: molecular_function
def: "Catalysis of the removal of a methyl group from a histone." [GOC:mah]
is_a: GO:0140457 ! protein demethylase activity

[x]  => Add additional is_a "2-oxoglutarate-dependent dioxygenase activity (GO:0016706)" parent

[Term]
id: GO:0033746
name: histone demethylase activity (H3-R2 specific)
namespace: molecular_function
def: "Catalysis of the removal of a methyl group from arginine at position 2 of the histone H3 protein." [GOC:mah]
is_a: GO:0032452 ! histone demethylase activity
=> (can't find EC/RHEA for this)
[Term]
id: GO:0033749
name: histone demethylase activity (H4-R3 specific)
namespace: molecular_function
def: "Catalysis of the removal of a methyl group from arginine at position 3 of the histone H4 protein." [GOC:mah]
is_a: GO:0032452 ! histone demethylase activity
=> (can't find EC/RHEA for this)
[Term]
id: GO:0032453
name: histone demethylase activity (H3-K4 specific)
namespace: molecular_function
def: "Catalysis of the removal of a methyl group from lysine at position 4 of the histone H3 protein." [GOC:mah]
is_a: GO:0032452 ! histone demethylase activity
=> add additional child term for RHEA:60212 (2-oxoglutarate + N6,N6,N6-trimethyl-L-lysyl4-[histone H3] + O2 = CO2 + formaldehyde + N6,N6-dimethyl-L-lysyl4-[histone H3] + succinate)
[Term]
id: GO:0034649
name: histone demethylase activity (H3-monomethyl-K4 specific)
namespace: molecular_function
def: "Catalysis of the reaction: histone H3 N6-methyl-L-lysine (position 4) + O2 + FAD + H2O = histone H3 L-lysine (position 4) + H2O2 + formaldehyde + FADH2. This reaction is the removal of a methyl group from monomethylated lysine at position 4 of the histone H3 protein." [GOC:mah, PMID:16223729]
is_a: GO:0016705 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
is_a: GO:0032453 ! histone demethylase activity (H3-K4 specific)
=> add RHEA:60220 (2-oxoglutarate + N6-methyl-L-lysyl4-[histone H3] + O2 = CO2 + formaldehyde + L-lysyl4-[histone H3] + succinate)

[x]  => remove "is_a: GO:0016705" parent

[Term]
id: GO:0034648
name: histone demethylase activity (H3-dimethyl-K4 specific)
namespace: molecular_function
def: "Catalysis of the removal of a methyl group from dimethylated lysine at position 4 of the histone H3 protein." [GOC:mah, PMID:17550896]
is_a: GO:0032453 ! histone demethylase activity (H3-K4 specific)

[x]=> add RHEA:60216 (2-oxoglutarate + N6,N6-dimethyl-L-lysyl4-[histone H3] + O2 = CO2 + formaldehyde + N6-methyl-L-lysyl4-[histone H3] + succinate)

[Term]
id: GO:0034647
name: histone demethylase activity (H3-trimethyl-K4 specific)
namespace: molecular_function
def: "Catalysis of the removal of a methyl group from trimethylated lysine at position 4 of the histone H3 protein." [GOC:mah, PMID:17550896]
xref: EC:<IP_ADDRESS>
is_a: GO:0032453 ! histone demethylase activity (H3-K4 specific)
=> add RHEA:60208 (3 2-oxoglutarate + N6,N6,N6-trimethyl-L-lysyl4-[histone H3] + 3 O2 = 3 CO2 + 3 formaldehyde + L-lysyl4-[histone H3] + 3 succinate)
[Term]
id: GO:0032454
name: histone demethylase activity (H3-K9 specific)
namespace: molecular_function
def: "Catalysis of the reaction: histone H3 N6-methyl-L-lysine (position 9) + alpha-ketoglutarate + O2 = succinate + CO2 + formaldehyde + lysine. This reaction is the removal of a methyl group from lysine at position 9 of the histone H3 protein." [PMID:16362057]
xref: EC:<IP_ADDRESS>
xref: EC:<IP_ADDRESS>
is_a: GO:0032452 ! histone demethylase activity
=> make 5 child terms and move EC numbers to first two:

RHEA:60188	2 2-oxoglutarate + N6,N6-dimethyl-L-lysyl9-[histone H3] + 2 O2 = 2 CO2 + 2 formaldehyde + L-lysyl9-[histone H3] + 2 succinate (EC:<IP_ADDRESS>)
RHEA:60200	2 2-oxoglutarate + N6,N6,N6-trimethyl-L-lysyl9-[histone H3] + 2 O2 = 2 CO2 + 2 formaldehyde + N6-methyl-L-lysyl9-[histone H3] + 2 succinate (EC:<IP_ADDRESS>)
RHEA:60192	2-oxoglutarate + N6,N6-dimethyl-L-lysyl9-[histone H3] + O2 = CO2 + formaldehyde + N6-methyl-L-lysyl9-[histone H3] + succinate
RHEA:60196	2-oxoglutarate + N6-methyl-L-lysyl9-[histone H3] + O2 = CO2 + formaldehyde + L-lysyl9-[histone H3] + succinate
RHEA:60204	2-oxoglutarate + N6,N6,N6-trimethyl-L-lysyl9-[histone H3] + O2 = CO2 + formaldehyde + N6,N6-dimethyl-L-lysyl9-[histone H3] + succinate

[Term]
id: GO:0035575
name: histone demethylase activity (H4-K20 specific)
namespace: molecular_function
def: "Catalysis of the reaction: histone H4 N6-methyl-L-lysine (position 20) + 2-oxoglutarate + O2 = histone H4 L-lysine (position 20) + succinate + formaldehyde + CO2. This reaction is the removal of a methyl group from lysine at position 20 of the histone H4 protein." [PMID:20622853]
is_a: GO:0032452 ! histone demethylase activity
=> (can't find EC/RHEA for this)
[Term]
id: GO:0071558
name: histone demethylase activity (H3-K27 specific)
namespace: molecular_function
def: "Catalysis of the removal of a methyl group from lysine at position 27 of the histone H3 protein." [GOC:sp, PMID:20622853]
xref: EC:<IP_ADDRESS>
is_a: GO:0032452 ! histone demethylase activity
=> make 3 child terms corresponding to these RHEAs and move EC xref to first one

RHEA:60224	2 2-oxoglutarate + N6,N6,N6-trimethyl-L-lysyl27-[histone H3] + 2 O2 = 2 CO2 + 2 formaldehyde + N6-methyl-L-lysyl27-[histone H3] + 2 succinate (EC:<IP_ADDRESS>)
RHEA:60228	2-oxoglutarate + N6,N6,N6-trimethyl-L-lysyl27-[histone H3] + O2 = CO2 + formaldehyde + N6,N6-dimethyl-L-lysyl27-[histone H3] + succinate
RHEA:60232	2-oxoglutarate + N6,N6-dimethyl-L-lysyl27-[histone H3] + O2 = CO2 + formaldehyde + N6-methyl-L-lysyl27-[histone H3] + succinate

[Term]
id: GO:0051864
name: histone demethylase activity (H3-K36 specific)
namespace: molecular_function
def: "Catalysis of the reaction: histone H3 N6-methyl-L-lysine (position 36) + alpha-ketoglutarate + O2 = succinate + CO2 + formaldehyde + lysine. This reaction is the removal of a methyl group from lysine at position 36 of the histone H3 protein." [PMID:16362057]
xref: EC:<IP_ADDRESS>
xref: MetaCyc:RXN-8660
xref: MetaCyc:RXN-8661
xref: RHEA:42032
is_a: GO:0016706 ! 2-oxoglutarate-dependent dioxygenase activity
is_a: GO:0032452 ! histone demethylase activity

[x] => remove "is_a: GO:0016706" parent
=> make 5 child terms corresponding to these RHEAs and move EC/RHEA xrefs to first one:

RHEA:42032	2 2-oxoglutarate + N6,N6-dimethyl-L-lysyl36-[histone H3] + 2 O2 = 2 CO2 + 2 formaldehyde + L-lysyl36-[histone H3] + 2 succinate (EC:<IP_ADDRESS>)
RHEA:60236	2 2-oxoglutarate + N6,N6,N6-trimethyl-L-lysyl36-[histone H3] + 2 O2 = 2 CO2 + 2 formaldehyde + N6-methyl-L-lysyl36-[histone H3] + 2 succinate (EC:<IP_ADDRESS>)
RHEA:60240	2-oxoglutarate + N6,N6,N6-trimethyl-L-lysyl36-[histone H3] + O2 = CO2 + formaldehyde + N6,N6-dimethyl-L-lysyl36-[histone H3] + succinate
RHEA:10784	2-oxoglutarate + N6-methyl-L-lysyl36-[histone H3] + O2 = CO2 + formaldehyde + L-lysyl36-[histone H3] + succinate
RHEA:21788	2-oxoglutarate + N6,N6-dimethyl-L-lysyl36-[histone H3] + O2 = CO2 + formaldehyde + N6-methyl-L-lysyl36-[histone H3] + succinate

Also note that "protein demethylase activity (GO:0140457)" has "histone demethylase activity (GO:0032452)" as its single child term, and all annotations appear to be on the latter.  So maybe they should be merged?

Hi @hdrabkin Would you have any thoughts on this one?

I'll take this as part of the transcription project.

[x] Added '2-oxoglutarate-dependent dioxygenase activity' as a parent to the general term 'protein demethylase activity', as this is also a dioxygenase (see PMID:28360925)

Also note that "protein demethylase activity (GO:0140457)" has "histone demethylase activity (GO:0032452)" as its single child term, and all annotations appear to be on the latter. So maybe they should be merged?

I will not do that, as there are other substrates such as the ER receptor (see PMID:24498420 cited in GO:0140457).
The histone code has an important biological significance, for now we have decided to capture it in GO.

[x] give definitions a consistent format, "Catalysis of the removal of a X group from monomethylated lysine at position N of the histone H# protein."

Hi @sjm41
I made a number of changes, except for the specific tri/di/mono methyl reactions, since in Rhea at least some of them are represented as multistep reactions: for eg RHEA:60208 trimethyl-K4 -> unmethylated-K4 states: multi step reaction: (1) tri -> dimethy;  (2) di -> monomethyl ; -> (3) mono -> unmethylated
From looking quickly it seems that indeed the same enzyme catalyzes the step-wise demethylation, so I may merge |__histone demethylase activity (H3-K4 specific)
|   |__histone demethylase activity (H3-monomethyl-K4 specific)
|   |__histone demethylase activity (H3-dimethyl-K4 specific)
|   |__histone demethylase activity (H3-trimethyl-K4 specific) (EC:<IP_ADDRESS>)
which would anyway correspond to EC:<IP_ADDRESS>, as this also states that the enzyme can act on tri, di, and momomethylated lysines.
I just want to check the annotations to make sure there is no enzyme specific for any one of the modifications.
Let me know if you are aware that these take place as individual reactions.
@colinlog may be able to help on this.
Thanks, Pascale

Thanks for working on this.
You've made all the key changes - I'd missed that the tri/di methylations were multistep reactions (which of course makes sense). I'd just noticed the apparent inconsistency that some GO terms had children for these steps and some didn't. Merging the histone demethylase activity (H3-K4 specific) children into the parent would also fix that issue. I don't know of enzymes specific for each modification myself, but the existence of EC:<IP_ADDRESS> and EC:<IP_ADDRESS> suggests there might be?

Hi,
Sorry to be late commenting here. I had a distant memory that not all histone demethylases are
2-oxoglutarate-dependent dioxygenase dependent, (i.e these is a difference between SWIRM and Lsd) but I could not easily find the papers describing the different mechanisms, so it fell off my radar.
Anway Wikipedia seems to confirm this:
https://en.wikipedia.org/wiki/Demethylase
Cofactors include: alpha-keto glutarate (JmjC-domain containing demethylases), CoREST (LSD), FAD, Fe (II) or NOG (N-oxalylglycine).[4] Domains include:
SWIRM1 (Swi3, Rsc, and Moira domain): Proposed anchor site for histone molecules; found in several chromatin modifying complexes; facilitates demethylase protein and co-factor CoREST (nucleosomal substrate binding)[5]
Jumonji (N/C terminal domains): Binding domain of key cofactors such as alpha-keto glutarate; connected by a beta-hairpin/mixed domain[4][6]
PHD-finger: hydrophobic cage of residues that acts to bind methylated peptides; plays key role in recognition and selectivity for methylated histone residues[4]
Zinc-finger: DNA binding domain[4]
Amine oxidase domain: catalytic active site of LSD proteins; larger than related proteins to help fit size of the histone tail [4]

Thanks Val!
So that wikipedia page says:
Defined by their mechanisms, two main classes of histone demethylases exist:
(i) a flavin adenine dinucleotide (FAD)-dependent amine oxidase, and
(ii) an Fe(II) and α-ketoglutarate-dependent hydroxylase.
Far as I can tell from that page and looking up domains of the human proteins, the FAD-dependent mechanism is only used by:
KDM1 family

FAD-dependent amine oxidase
KDM1A acts on mono- and dimethylated H3K4 and H3K9
KDM1B acts only on mono- and dimethylated H3K4

All other family members are α-ketoglutarate-dependent:
KDM2

JHDM-type => α-ketoglutarate-dependent hydroxylase
KDM2A acts on mono- and dimethylated H3K36 and trimethylated H3K4
KDM2B acts only on mono- and dimethylated H3K36.

KDM3

JHDM-type => α-ketoglutarate-dependent
KDM3A acts on mono- and dimethylated H3K9

KDM4

JHDM-type => α-ketoglutarate-dependent
acts on di- and trimethylated H3K9, H3K36, H1K26

KDM5

JHDM-type => α-ketoglutarate-dependent
act on di- and trimethylated H3K4

KDM6

JHDM-type => α-ketoglutarate-dependent
KDM6A and KDM6B act on di- and trimethylated H3K27

So, we'll need to check if the GO terms corresponding to KDM2-6 activities do have the "2-oxoglutarate-dependent dioxygenase activity (GO:0016706)" parent, whereas the GO terms corresponding to KDM1 does not.  I can do this later on today.

FYI - I edited my previous comment to include the mappings to the existing GO terms.

Couple of useful reviews:

Molecular mechanisms and potential functions of histone demethylases (PMID: 22473470)
Histone lysine methylation dynamics: establishment, regulation, and biological impact (PMID: 23200123)

From PMID: 22473470, Figure 1:
"The two different reaction mechanisms used by Lys-specific demethylase 1 (LSD1) and LSD2 [i.e. KDM1 family] (a) and the Jumonji C (JMJC) family (b) of demethylases are depicted. a | The flavin adenine dinucleotide (FAD)-dependent amine oxidation reaction is used by LSD1 and LSD2 to demethylate mono- and dimethylated substrates. b | The JMJC family uses a dioxygenase reaction that is dependent on Fe(II) and α-ketoglutarate for demethylating mono-, di- and trimethylated residues."
So, it seems both types use an oxidation mechanism to catalyse the demethylation, so I think all the GO terms should have an oxidoreductase parent (at some level). If we're convinced that some GO terms apply ONLY to JMJC family Demethylases (KDM2-8), then those GO terms could have a "2-oxoglutarate-dependent dioxygenase activity" parent, whereas GO terms that apply ONLY to LSD family demethylases (KDM1) or apply to both types, could have a higher-level oxidoreductase parent (maybe top-level "oxidoreductase activity").

As far as I can tell, there is no demethlyase with specificity for either tri, di- or mono methlyated histone lysine, so I will merge
|   |__histone demethylase activity (H3-monomethyl-K4 specific)
|   |__histone demethylase activity (H3-dimethyl-K4 specific)
|   |__histone demethylase activity (H3-trimethyl-K4 specific) (EC:<IP_ADDRESS>)
into |__histone demethylase activity (H3-K4 specific)

There was a commnet that thee specificity will be deleted here, so I opened this for PomBase:
https://github.com/pombase/curation/issues/3042
however, the comment
"As far as I can tell, there is no demethlyase with specificity for either tri, di- or mono methlyated histone lysine, so I will merge"
is gone. So not sure if I need to priorities this...?

"As far as I can tell, there is no demethlyase with specificity for either tri, di- or mono methlyated histone lysine, so I will merge"

I deleted this because as @sjm41 pointed out, there is at least one enzyme that doesn't act on the tri-methylated histone (LSD1) and LSD2 [i.e. KDM1 family)

I am not sure how to handle this one. We are missing at least some substrates (for example monomethylated and dimethylated lysine 20 in histone H4 are mentioned in PMID:33318631), and the specificity of the enzymes do not align with the current MF structure, for example in the same paper, LSD1 has substrates H3K4me1/2 and H3K9me1/2, as well as  H4K20me1/2.
We dont typically capture mechanisms, so I would prefer not to create FAD-dependent and  α-ketoglutarate-dependent versions of the different enzymes.
Also about the H3-K4: I dont know why we have the specific mono, di, tri methyl versions, and not for others, like K20.

Maybe we are following EC:

<IP_ADDRESS>   [Histone H3]-dimethyl-L-lysine(36) demethylase.
(AN: [Histone-H3]-lysine-36 demethylase.
H3-K36-specific demethylase.
Histone demethylase.
Histone-lysine (H3-K36) demethylase.
JHDM1A.
JmjC domain-containing histone demethylase 1A.)

<IP_ADDRESS>   [Histone H3]-dimethyl-L-lysine(9) demethylase.

<IP_ADDRESS>   [Histone H3]-trimethyl-L-lysine(9) demethylase.

<IP_ADDRESS>   [Histone H3]-trimethyl-L-lysine(4) demethylase.

<IP_ADDRESS>   [Histone H3]-trimethyl-L-lysine(27) demethylase.

<IP_ADDRESS>   [Histone H3]-trimethyl-L-lysine(36) demethylase.

There is one FAD-dependent EC, which we dont have a cross reference - <IP_ADDRESS>   [Histone-H3]-N(6),N(6)-dimethyl-L-lysine(4) FAD-dependent demethylase

Well, no, since they only have a single H3K4 reaction and we have 3; and they have 2 H3K9 reactions and we have one.
I'll see if we can align on RHEA.

Also about the H3-K4: I dont know why we have the specific mono, di, tri methyl versions, and not for others, like K20.

At PomBase we have only requested terms where we have data, and we have no data for K20 specific demethylases.  The demethylases have been identified relatively recently (i.e last decade) and it is possible that this is not yet known for all  methylated histone residues.

We dont typically capture mechanisms,

Really? To the extent that MF distinctions follow EC, they do capture mechanisms, and anyway this kind of mechanistic distinction is important biologically - that difference in co-factor almost certsinly points to a difference in protein family / subfamily and to different physiological conditions in which the r4eaction is happening. @ukemi

This is right. I should probably have written, we dont systematically capture mechanisms.

... and I should have phrased my comment as a request for an exception. I suspect that this is a general (and annoying) problem: It's very hard to find uniform algorithms to define granularity boundaries that also reliably capture biologically important distinctions - even the best general formulas I know need individual tweaking.

Hello,
I checked EC and RHEA, and they are aligned for all the activities, so I propose we do the same. This involves the following changes:
*** H3-K36**

[ ] GO:0051864	histone demethylase activity (H3-K36 specific)
Mapped to EC:<IP_ADDRESS> [Histone H3]-dimethyl-L-lysine-36 demethylase.
Mapped to RHEA:42032	dimethylated to unmethylated (multistep reaction)
EXP annotations: 28
Actions:

Fix term label: histone H3-dimethyl-L-lysine-36 demethylase activity
Add EXACT synonym: histone H3-K36me2 demethylase activity
Add RELATED synonym: histone H3-K36me demethylase activity
Fix definition:
Current: Catalysis of the reaction: histone H3 N6-methyl-L-lysine (position 36) + alpha-ketoglutarate + O2 = succinate + CO2 + formaldehyde + lysine. This reaction is the removal of a methyl group from lysine at position 36 of the histone H3 protein.
Proposed: Catalysis of the reaction: histone H3-dimethyl-L-lysine-36 + 2 2-oxoglutarate + 2 O(2) = histone H3-L-lysine-36 + 2 succinate + 2 formaldehyde + 2 CO(2). Note that this enzyme can act on histone H3 mono- and di-methylated at lysine-36.

[ ] NTR: histone H3-trimethyl-L-lysine-36 demethylase activity

Add EXACT synonym: histone H3-K36me3 demethylase activity
Add RELATED synonym: histone H3-K36me2 demethylase activity
Add EC: <IP_ADDRESS> [Histone H3]-trimethyl-L-lysine(36) demethylase.	(Missing from GO)
Add RHEA:60236	trimethylated to monomethylated (multistep reaction) (Missing from GO)
Add def: Catalysis of the reaction: histone H3-dimethyl-L-lysine-36 + 2 2-oxoglutarate + 2 O(2) = histone H3-methyl-L-lysine-36 + 2 succinate + 2 formaldehyde + 2 CO(2). Note that this enzyme can act on histone H3 tri- and di-methylated at lysine-36.

*** H3-K27**
- [ ] GO:0071558	histone demethylase activity (H3-K27 specific)
- Mapped to <IP_ADDRESS> [Histone H3]-trimethyl-L-lysine(27) demethylase.
- Add RHEA:60224 trimethylated to monomethylated (multistep reaction) (Missing from GO)
- Add EXACT synonym: histone H3-K27me3 demethylase activity
- Add RELATED synonym: histone H3-K27me2 demethylase activity
- EXP: 26
- Fix def:
Current: Catalysis of the removal of a methyl group from lysine at position 27 of the histone H3 protein.
Proposed: Catalysis of the reaction: histone H3-trimethyl-L-lysine-27 + 2 2-oxoglutarate + 2 O(2) <=> histone H3-methyl-L-lysine-27 + 2 succinate + 2 formaldehyde + 2 CO(2). Note that this enzyme can act on histone H3 tri- and di-methylated at lysine-27.
*** H3-K9**
- [ ] GO:0032454	histone H3-K9 demethylase activity
Mapped to EC:<IP_ADDRESS> [Histone H3]-dimethyl-L-lysine-9 demethylase.
Mapped to RHEA:60188	dimethylated to unmethylated (multistep reaction) (Missing from GO)	EXP annotations:43
Obsolete and replace by 2 terms:
- [ ] NTR: histone H3-diimethyl-L-lysine-9 demethylase activity
- Definition: Catalysis of the reaction: histone H3-dimethyl-L-lysine-9 + 2 2-oxoglutarate + 2 O(2) <=> histone H3-L-lysine-9 + 2 succinate + 2 formaldehyde + 2 CO(2). Note that this enzyme can act on histone H3 di- and mono-methylated at lysine-9.
- Add RHEA:60188
- Add EC:<IP_ADDRESS>
- Add BROAD synonym: histone H3-K9me2 demethylase activity
- Add RELATED synonym: histone H3-K9me demethylase activity

- [ ] NTR: histone H3-trimethyl-L-lysine-9 demethylase activity
- Definition: Catalysis of the reaction: histone H3-trimethyl-L-lysine-9 + 2 2-oxoglutarate + 2 O(2) <=> histone H3-methyl-L-lysine-9 + 2 succinate + 2 formaldehyde + 2 CO(2). Note that this enzyme can act on histone H3 tri- and di-methylated at lysine-9.
- Add RHEA:60200  trimethylated to monomethylated (multistep reaction) (missing from GO)
- Add EC:<IP_ADDRESS>
- Add BROAD synonym: histone H3-K9me2 demethylase activity
- Add RELATED synonym: histone H3-K9me demethylase activity

EXP Annotations to GO:0032454
https://docs.google.com/spreadsheets/d/1x3WOUqg63QLg-Lz5CZFieDG32Yb3qP_GVVj2-2Pxlso/edit#gid=0
*** H3K4**

[ ] GO:0034647	histone demethylase activity (H3-trimethyl-K4 specific)	-> 13 EXP

Mapped to <IP_ADDRESS> [Histone H3]-trimethyl-L-lysine(4) demethylase.
Add RHEA:60208	trimethylated to unmethylated (multistep reaction) (Missing from GO)
Fix definition
Old: Catalysis of the removal of a methyl group from trimethylated lysine at position 4 of the histone H3 protein.
Proposed: Catalysis of the reaction: histone H3-trimethyl-L-lysine-4 + 2 2-oxoglutarate + 2 O(2) <=> histone H3-L-lysine-4 + 2 succinate + 2 formaldehyde + 2 CO(2). Note that this enzyme can act on histone H3 tri-, di- and mono-methylated at lysine-9.

NTR: histone H3-dimethyl-L-lysine-4 FAD-dependent demethylase activity

ADD EC:	<IP_ADDRESS> [Histone-H3]-N(6),N(6)-dimethyl-L-lysine(4) FAD-dependent demethylase

ADD RHEA:60244	dimethylated to unmethylated (multistep reaction)

Add def: Catalysis of the reaction: histone H3-dimethyl-L-lysine-4 + 2 2-oxoglutarate + 2 O(2) = histone H3-methyl-L-lysine-4 + 2 succinate + 2 formaldehyde + 2 CO(2). Note that this enzyme can act on histone H3 di- and mono-methylated at lysine-4.

[ ] GO:0032453	histone demethylase activity (H3-K4 specific) -> 20 EXP

[ ] GO:0034648	histone demethylase activity (H3-dimethyl-K4 specific) -> 13 EXP

[ ] GO:0034649	histone demethylase activity (H3-monomethyl-K4 specific) -> 5 EXP
Obsolete and replace as suggested in https://docs.google.com/spreadsheets/d/1Te65Plm-bTVVkJL0CDZT1Dhwf-HYfR1gCR8-QaPdx2o/edit#gid=0

*** Others**
No EC, No RHEA correspond to the following reactions:
- GO:0033746	histone demethylase activity (H3-R2 specific) 2	EXP
- GO:0033749	histone demethylase activity (H4-R3 specific)	4 EXP
- GO:0035575	histone demethylase activity (H4-K20 specific)	3 EXP
Additional references: PMID:32209475, PMID:26214369
- [Histone-H3]-dimethyl-L-lysine(9) FAD-dependent demethylase (also missing from GO)
- parent class histone demethylase activity	 15 EXP	-> add DO NOT ANNOTATE FLAG?

@sjm41 @deustp01 Is that OK for you?

[x] added DO NOT annotate to GO:0032452 histone demethylase activity
[ ] annotation to be reviewed: https://docs.google.com/spreadsheets/d/10Dw_iiPW10B3jWRgfCu08w_QOy9YV0r7a_f78ql_LU4/edit#gid=0

Are you sure? I have 2 predicted histone demethylases for which I don't know the specificity (jmj2 and 4)

Also,I have been meaning to ask, should the word "specific" be removed from these terms?
histone demethylase activity (H3-trimethyl-K4 specific)
specific could be confused to mean this is the only residue demethylated?

Really? jmj2 is annotated to
histone demethylase activity (H3-trimethyl-K4 specific) Source: PomBase
histone demethylase activity (H3-dimethyl-K4 specific) Source: PomBase
histone demethylase activity (H3-K36 specific) Source: PomBase
histone demethylase activity (H3-K4 specific) Source: PomBase
not sure about the Pfam evidence for
http://pfam.xfam.org/family/PF02373 "The JmjC domain belongs to the Cupin superfamily [3]. JmjC-domain proteins may be protein hydroxylases that catalyse a novel histone modification [4]."

Sorry I mean jmj1 & 4

GO:0071558 histone demethylase activity (H3-K27 specific)

EXP: 26
Mapped to <IP_ADDRESS> [Histone H3]-trimethyl-L-lysine(27) demethylase.
[ ]  fix term label to "histone H3-tri/di-methyl-L-lysine-27 demethylase activity" (protein serine/threonine kinase activity, ie can act on either substrate)
[ ] Add RHEA:60224 trimethylated to monomethylated (multistep reaction) (Missing from GO)
[ ] Add RELATED synonym: histone H3-K27me3 demethylase activity
[ ] Add RELATED synonym: histone H3-K27me2 demethylase activity
[ ]  Fix def:
Current: Catalysis of the removal of a methyl group from lysine at position 27 of the histone H3 protein.
Proposed: Catalysis of the removal of a methyl group from a tri-methyl-lysine or a di-methyl-lysine at position 27 of the histone H3 protein.

jmj1 & 4

Are you sure your mapping from PF02373 is correct?

GO:0051864 histone demethylase activity (H3-K36 specific)
GO:0051864	histone demethylase activity (H3-K36 specific)

[ ] Remove cross refs
Mapped to EC:<IP_ADDRESS> [Histone H3]-dimethyl-L-lysine-36 demethylase.
Mapped to RHEA:42032	dimethylated to unmethylated (multistep reaction)

EXP annotations: 28
Actions:

[ ] Fix term label: histone H3-dimethyl-L-lysine-36 demethylase activity

[ ] Fix definition:
Current: Catalysis of the reaction: histone H3 N6-methyl-L-lysine (position 36) + alpha-ketoglutarate + O2 = succinate + CO2 + formaldehyde + lysine. This reaction is the removal of a methyl group from lysine at position 36 of the histone H3 protein.
Proposed: Catalysis of the reaction: histone H3-dimethyl-L-lysine-36 + 2 2-oxoglutarate + 2 O(2) = histone H3-L-lysine-36 + 2 succinate + 2 formaldehyde + 2 CO(2). Note that this enzyme can act on histone H3 mono- and di-methylated at lysine-36.

[ ] NTR: histone H3-tri/dimethyl-L-lysine-36 demethylase activity

Add EXACT synonym: histone H3-K36me3 demethylase activity
Add RELATED synonym: histone H3-K36me2 demethylase activity
Add EC: <IP_ADDRESS> [Histone H3]-trimethyl-L-lysine(36) demethylase.	(Missing from GO)
Add RHEA:60236	trimethylated to monomethylated (multistep reaction) (Missing from GO)
Add def: Catalysis of the reaction: histone H3-dimethyl-L-lysine-36 + 2 2-oxoglutarate + 2 O(2) = histone H3-methyl-L-lysine-36 + 2 succinate + 2 formaldehyde + 2 CO(2). Note that this enzyme can act on histone H3 tri- and di-methylated at lysine-36.

[ ] NTR: histone H3-di/mono-methyl-L-lysine-36 demethylase activity

[ ] Add  EC:<IP_ADDRESS> [Histone H3]-dimethyl-L-lysine-36 demethylase.

[ ] Add RHEA:42032	dimethylated to unmethylated (multistep reaction)

It may be possible to annotate to a more specific term:
Annotations: https://docs.google.com/spreadsheets/d/1GbU-e8i95rsA0qaMNZmhp7l3-noUYHL9oeFVbgsJkHE/edit#gid=0

+[Term]
+id: GO:0140680
+name: histone H3-di/mono-methyl-lysine-36 demethylase activity
+namespace: molecular_function
+def: "Catalysis of the removal of a methyl group from a di-methyl-lysine or a mono-methyl-lysine residue at position 27 of the histone H3 protein." [PMID:20531378]
+is_a: GO:0051864 ! histone H3-methyl-lysine-36 demethylase activity
+property_value: term_tracker_item https://github.com/geneontology/go-ontology/issues/21089 xsd:anyURI
+created_by: pg
+creation_date: 2021-07-08T14:12:22Z
+
+[Term]
+id: GO:0140681
+name: histone H3-tri/dimethyl-lysine-36 demethylase activity
+namespace: molecular_function
+def: "Catalysis of the removal of a methyl group from a tri-methyl-lysine or a di-methyl-lysine residue at position 36 of the histone H3 protein." [PMID:21914792]
+synonym: "histone H3-K36me2 demethylase activity" BROAD []
+synonym: "histone H3-K36me3 demethylase activity" RELATED []
+xref: EC:<IP_ADDRESS> {source="skos:exactMatch"}
+xref: MetaCyc: RXN-8660
+xref: RHEA:60236
+is_a: GO:0051864 ! histone H3-methyl-lysine-36 demethylase activity
+property_value: term_tracker_item https://github.com/geneontology/go-ontology/issues/21089 xsd:anyURI
+created_by: pg
+creation_date: 2021-07-08T14:12:31Z
+

GO:0032453 histone demethylase activity (H3-K4 specific)
GO:0034647 histone demethylase activity (H3-trimethyl-K4 specific)
-> 13 EXP

Mapped to <IP_ADDRESS> [Histone H3]-trimethyl-L-lysine(4) demethylase.

[x] Fix term label to 'histone H3-tri/di/monomethyl-lysine-4 demethylase activity'

[ ] Add RHEA:60208 trimethylated to unmethylated (multistep reaction) (Missing from GO)

[ ]  Fix definition
Old: Catalysis of the removal of a methyl group from trimethylated lysine at position 4 of the histone H3 protein.
NEW: Catalysis of the removal of a methyl group from a tri, a di or a mono-methyl-lysine residue at position 4 of the histone H3 protein. This is a dioxygenase reaction that is dependent on Fe(II) and 2-oxoglutarate.

[ ]   Add subclass ' 2-oxoglutarate-dependent dioxygenase activity'
NTR: histone H3-dimethyl-L-lysine-4 FAD-dependent demethylase activity
ADD EC: <IP_ADDRESS> [Histone-H3]-N(6),N(6)-dimethyl-L-lysine(4) FAD-dependent demethylase
ADD RHEA:60244 dimethylated to unmethylated (multistep reaction)
Add def: Catalysis of the reaction: histone H3-dimethyl-L-lysine-4 + 2 2-oxoglutarate + 2 O(2) = histone H3-methyl-L-lysine-4 + 2 succinate + 2 formaldehyde + 2 CO(2). Note that this enzyme can act on histone H3 di- and mono-methylated at lysine-4.
GO:0032453 histone demethylase activity (H3-K4 specific) -> 20 EXP
GO:0034648 histone demethylase activity (H3-dimethyl-K4 specific) -> 13 EXP
GO:0034649 histone demethylase activity (H3-monomethyl-K4 specific) -> 5 EXP
Obsolete and replace as suggested in https://docs.google.com/spreadsheets/d/1Te65Plm-bTVVkJL0CDZT1Dhwf-HYfR1gCR8-QaPdx2o/edit#gid=0

[ ]  GO:0033746 histone demethylase activity (H3-R2 specific) 2 EXP
GO:0033749 histone demethylase activity (H4-R3 specific) 4 EXP
GO:0035575 histone demethylase activity (H4-K20 specific) 3 EXP
See if we can add subclass ' 2-oxoglutarate-dependent dioxygenase activity'

GO:0032454 histone H3-K9 demethylase activity
create 2 children

jmj1 & 4

Are you sure your mapping from PF02373 is correct?

Maybe it is too specific. I'm not sure these are histone demethylases?
Jmj4 appears to be a histone demethylase (human ortholog JMJD7)
but jmj1, (human ortholog JMJD4) possibly not?
I expected the jumonjo specificities to be different (analogous to the set family of methyltransferases see https://www.pombase.org/term/GO:0042054)
and currently we don't know the proteins that reverse all of the known histone methylation marks (or do we ? @colinlog ). I don't even know if they are all reversible....

and currently we don't know the proteins that reverse all of the known histone methylation marks (or do we ? @colinlog ). I don't even know if they are all reversible....

For sure. But other than K36 (see https://github.com/geneontology/go-ontology/issues/21089#issuecomment-876457093), the data I looked at in papers matched pretty well the EC/Rhea families. We can remove the do not annotate if needed.

I would like to be able to annotate to
"histone demethylase activity" for family members with no experimental data. If these are like set domain we can't assume that all members have the same specificity.
The methyltransferase specificities:
Systematic ID | Gene name | Product description
SPAC29B12.02c | set2 | histone lysine H3-K36 methyltransferase Set2
SPCC297.04c | set7 | histone lysine H3-K37 methyltransferase Set7
SPCC306.04c | set1 | histone lysine H3-K4 methyltransferase Set1
SPBC428.08c | clr4 | histone lysine H3-K9 methyltransferase Clr4
SPCC4B3.12 | set9 | histone lysine H4-K20 methyltransferase Set9
SPAC22E12.11c | set3 | histone lysine methyltransferase Set3
SPCC1739.05 | set5 | histone lysine methyltransferase Set5 (predicted)
SPBP8B7.07c | set6 | histone lysine methyltransferase Set6 (predicted)

GO:0032454 histone H3-K9 demethylase activity

GO:0032454 histone H3-K9 demethylase activity: keep as grouping term, and add specific children

[x] remove mappings EC:<IP_ADDRESS> [Histone H3]-dimethyl-L-lysine-9 demethylase. and to EC:<IP_ADDRESS> [Histone H3]-trimethyl-L-lysine(9) demethylase.

[x] Change term label to 'histone H3-methyl-lysine-9 demethylase activity'

[x] Change definition
Current: Catalysis of the removal of a methyl group from lysine at position 9 of the histone H3 protein.
NEW: Catalysis of the removal of a methyl group from a modified lysine residue at position 9 of the histone H3 protein.

[ ] NTR: histone H3-di/monomethyl-lysine-9 demethylase activity

[x]  Definition: Catalysis of the removal of a methyl group from a tri or a dimethyl-lysine residue at position 9 of the histone H3 protein. This is a dioxygenase reaction that is dependent on Fe(II) and 2-oxoglutarate.

[x] Add RHEA:60188

[x]  Add EC:<IP_ADDRESS>

[x] Add BROAD synonym: histone H3-K9me2 demethylase activity

[x]  Add RELATED synonym: histone H3-K9me demethylase activity

[x]  Add subclass ' 2-oxoglutarate-dependent dioxygenase activity'

[ ] NTR: histone H3-tri/dimethyl-lysine-9 demethylase activity

[ ] Definition: Catalysis of the removal of a methyl group from a tri or a dimethyl-lysine residue at position 9 of the histone H3 protein. This is a dioxygenase reaction that is dependent on Fe(II) and 2-oxoglutarate.

[ ] Add RHEA:60200 trimethylated to monomethylated (multistep reaction) (missing from GO)

[ ]  Add EC:<IP_ADDRESS>

[ ] Add BROAD synonym: histone H3-K9me2 demethylase activity

[ ]  Add RELATED synonym: histone H3-K9me3 demethylase activity

[ ]  Add subclass ' 2-oxoglutarate-dependent dioxygenase activity'

EXP Annotations to GO:0032454
https://docs.google.com/spreadsheets/d/1x3WOUqg63QLg-Lz5CZFieDG32Yb3qP_GVVj2-2Pxlso/edit#gid=0

+[Term]
+id: GO:0140683
+name: histone H3-di/monomethyl-lysine-9 demethylase activity
+namespace: molecular_function
+def: "Catalysis of the removal of a methyl group from a di or a monomethyl-lysine residue at position 9 of the histone H3 protein. This is a dioxygenase reaction that is dependent on Fe(II) and 2-oxoglutarate." []
+synonym: "histone H3-K9me2 demethylase activity" BROAD []
+synonym: "histone H3-K9me3 demethylase activity" RELATED []
+xref: EC:<IP_ADDRESS>
+xref: RHEA:60200
+is_a: GO:0016706 ! 2-oxoglutarate-dependent dioxygenase activity
+is_a: GO:0032454 ! histone H3-methyl-lysine-9 demethylase activity
+property_value: term_tracker_item https://github.com/geneontology/go-ontology/issues/21089 xsd:anyURI
+created_by: pg
+creation_date: 2021-07-09T06:03:06Z
+
+[Term]
+id: GO:0140684
+name: histone H3-tri/dimethyl-lysine-9 demethylase activity
+namespace: molecular_function
+def: "Catalysis of the removal of a methyl group from a tri or a dimethyl-lysine residue at position 9 of the histone H3 protein. This is a dioxygenase reaction that is dependent on Fe(II) and 2-oxoglutarate." []
+synonym: "histone H3-K9me demethylase activity" RELATED []
+synonym: "histone H3-K9me2 demethylase activity" BROAD []
+xref: EC:<IP_ADDRESS>
+xref: RHEA:60188
+is_a: GO:0016706 ! 2-oxoglutarate-dependent dioxygenase activity
+is_a: GO:0032454 ! histone H3-methyl-lysine-9 demethylase activity
+property_value: term_tracker_item https://github.com/geneontology/go-ontology/issues/21089 xsd:anyURI
+created_by: pg
+creation_date: 2021-07-09T06:03:55Z

@ValWood I removed the DO NOT ANNOTATE from the parent class histone demethylase activity.

Dear all,
The proposal has been made to obsolete
GO:0034649 histone demethylase activity (H3-monomethyl-K4 specific)
and
GO:0034648 histone demethylase activity (H3-dimethyl-K4 specific)
The reason for obsoletion is to align with RHEA and EC: these reactions are sub-reactions of both RHEA and EC.
These terms have 5 and 13 EXP annotations, respectively.
GO:0034648 is mapped to RHEA:60216, but this is part of  RHEA:60208, which corresponds to GO:0034647.
Suggestions to move existing annotations are here: https://docs.google.com/spreadsheets/d/1mlEpZji59zgeTQaxan0Ky6hE8B7rEjrrGRg9RpfcatE/edit#gid=0
(note that this requires a GO term created

NTR  'histone H3-di/monomethyl-lysine-9 FAD-dependent demethylase activity'
+[Term]
+id: GO:0140685
+name: histone H3-di/monomethyl-lysine-9 FAD-dependent demethylase activity
+namespace: molecular_function
+def: "Catalysis of the removal of a methyl group from a di- or a monomethyl-lysine residue at position 9 of the histone H3 protein. This is a flavin adenine dinucleotide (FAD)-dependent amine oxidation reaction." [PMID:22473470]
+synonym: "histone H3K9me demethylase activity" BROAD []
+synonym: "histone H3K9me2 demethylase activity" BROAD []
+is_a: GO:0032454 ! histone H3-methyl-lysine-9 demethylase activity
+property_value: term_tracker_item https://github.com/geneontology/go-ontology/issues/21089 xsd:anyURI
+created_by: pg
+creation_date: 2021-07-09T07:18:00Z

Hi @pgaudet
Looks like the EC & Rhea xrefs and the synonyms need to be swapped on these two:
+id: GO:0140683
+name: histone H3-di/monomethyl-lysine-9 demethylase activity
+def: "Catalysis of the removal of a methyl group from a di or a monomethyl-lysine residue at position 9 of the histone H3 protein. This is a dioxygenase reaction that is dependent on Fe(II) and 2-oxoglutarate." [PMID:16603238]
+synonym: "histone H3-K9me2 demethylase activity" BROAD []
+synonym: "histone H3-K9me3 demethylase activity" RELATED []
+xref: EC:<IP_ADDRESS>
+xref: RHEA:60200
+id: GO:0140684
+name: histone H3-tri/dimethyl-lysine-9 demethylase activity
+def: "Catalysis of the removal of a methyl group from a tri or a dimethyl-lysine residue at position 9 of the histone H3 protein. This is a dioxygenase reaction that is dependent on Fe(II) and 2-oxoglutarate." [PMID:20208542, PMID:20531378]
+synonym: "histone H3K9me demethylase activity" RELATED []
+synonym: "histone H3K9me2 demethylase activity" BROAD []
+xref: EC:<IP_ADDRESS>
+xref: RHEA:60188

Thanks for spotting this!

@pgaudet I was just about to mention that we also need a FAD-dependent H3-di/monomethyl-lysine-9 demethylase, but I notice you added this as GO:0140685 this morning - thanks!  I think that needs the "is_a: GO:0016705 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen" parent adding?

Annotation review ticket: https://github.com/geneontology/go-annotation/issues/3871

Will the same heirarchy be added for example:
histone H3-tri/dimethyl-lysine-36methylase activity?

@ValWood    I believe most of the histone methylase activity terms are there and I guess it will be the same hierarchy, eccept that we are talking about different EC numbers and a different hierarchy of eactivities, aren't we?
Furthermore, how to express that one enzyme is only able to monomethylate but not di- or trimethylate a particular lysine?
In a GO-CAM the relation between the activities would be 'provides substrate for'. In protein to GO it is an extension with the same relation.
Example 1: the human H3K4 monomethylase MLL4
https://www.uniprot.org/uniprotkb/Q9UMN6/entry
Example 2: the human H3K4me2/3 methylase MLL1
https://www.uniprot.org/uniprotkb/Q03164/entry
with a figure from PMID: 34440566 here ( https://pubmed.ncbi.nlm.nih.gov/34440566/#&gid=article-figures&pid=figure-2-uid-1 ) to explain the concept visually.
Note that in Uniprot only the monomethylation activity is displayed, also for MLL1 which is a H3K4 di- and trimethylase.

No worries, I had a note to update set2 to
histone H3-tri/dimethyl-lysine-36methylase activity
and then I realize this was  about demethylases.
So I was just curious if there would be an. equivalent
histone H3-tri/dimethyl-lysine-36methylase activity.
It was just a question, but it isn't a big deal.  I'm sure it will  exist eventually. I wondered if it was on @sjm41  s future radar.

yes we'll harmonize both branches.


Features not following proper casing

It seems https://github.com/web-platform-dx/web-features/tree/main/features uses dash for each word (even if a word is a method composed of many words). So for example canvas-createconicgradient.yml. This translates to incorrectly named enums as in https://chromium-review.googlesource.com/c/chromium/src/+/5734512.

For the most part feature IDs separate each word, as in request-video-frame-callback. But you're right that we have some exceptions:

abortsignal-any
array-copywithin
array-findlast
array-fromasync
array-isarray
canvas-createconicgradient
canvas-roundrect
document-caretpositionfrompoint
growable-sharedarraybuffer
promise-allsettled
promise-withresolvers
resizable-arraybuffer
transferable-arraybuffer
url-canparse
urlpattern

How do we avoid doing this again (linting?) and should we change the existing identifiers?
cc @ddbeck @Elchi3 @captainbrosset


Add Meixian Information Technology School

@billmxitaccn I am sorry, this request has signs of fraud. I have to close it without merging. If you are a student of this school, please apply with official document ("OFFICIAL DOCUMENT" tab at https://www.jetbrains.com/shop/eform/students).


fix(bag_time_manager_rviz_plugin): update create_client API to use rc…

Description

rclcpp::create_client in rolling deprecated rmw_qos_profile_t in favor of the rclcpp::QoS API
Fixes https://github.com/autowarefoundation/autoware.universe/issues/2782
Pre-review checklist for the PR author
The PR author must check the checkboxes below when creating the PR.

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thanks for pr, is this also tested by humble version？

@esteve
thanks for pr, is this also tested by humble version？

This PR should work with Humble, but I'm building it right now to check, I'll report with the results, don't approve it yet. Thanks.

@taikitanaka3 I fixed the latest commit because the changes were not building for Humble and lower.

@esteve
can you take a look at this comment https://github.com/autowarefoundation/autoware.universe/issues/2782 ?

@esteve I've made some changes to make maintenance costs minimum for this PR on following commit: https://github.com/autowarefoundation/autoware.universe/commit/c79c2b103c63adf684de037bc5521cd2deb49888

@xmfcx looks good, can you push it here? Thanks.


Fixing the policy in the docstring for AutoTagUser

The policy listed in the docstring for AutoTagUser is invalid, so I fixed that along with a few other small wording changes.

Not sure what is up with coveralls... I only changed a docstring.


Example code does not work when no IPv6 address is available

I tried to run greeter_server / greeter_client example code on Ubuntu 15.10 x64 on GCE. It crashes:
I1203 16:57:05.100617195   15582 socket_utils_common_posix.c:148] Disabling AF_INET6 sockets because ::1 is not available.

Program received signal SIGSEGV, Segmentation fault.
0x00007ffff78d8e71 in grpc_tcp_server_add_port (s=0x62aec0, addr=0x7fffffffe190, addr_len=28) at src/core/iomgr/tcp_server_posix.c:467
467         allocated_port = sp->port;
(gdb) bt
#0  0x00007ffff78d8e71 in grpc_tcp_server_add_port (s=0x62aec0, addr=0x7fffffffe190, addr_len=28) at src/core/iomgr/tcp_server_posix.c:467
#1  0x00007ffff78e9ddd in grpc_server_add_insecure_http2_port (server=0x6329a0, addr=0x62b890 "<IP_ADDRESS>:50051") at src/core/surface/server_chttp2.c:110
#2  0x00007ffff7bac20e in grpc::(anonymous namespace)::InsecureServerCredentialsImpl::AddPortToServer (this=0x6328c0, addr="<IP_ADDRESS>:50051", server=0x6329a0)
at src/cpp/server/insecure_server_credentials.cc:45
#3  0x00007ffff7bacf3e in grpc::Server::AddListeningPort (this=0x632340, addr="<IP_ADDRESS>:50051", creds=0x6328c0) at src/cpp/server/server.cc:376
#4  0x00007ffff7bb2b5e in grpc::ServerBuilder::BuildAndStart (this=0x7fffffffe3d0) at src/cpp/server/server_builder.cc:128
#5  0x000000000040d73c in RunServer () at greeter_server.cc:71
#6  0x000000000040d87d in main (argc=1, argv=0x7fffffffe5a8) at greeter_server.cc:80

GCE has no IPv6 support. No network interface has an IPv6 address ; not even ::1. Apparently this results in 'sp' being NULL within src/core/iomgr/tcp_server_posix.c!grpc_tcp_server_add_port().

seems very similar to fixed issue https://github.com/grpc/grpc/issues/4340. Please reopen if still an issue.


the size in "dataset/words" is not working

from
http://ves-ebi-4d.ebi.ac.uk:8100/Tools/ddi/ws/dataset/words?q=liver%20c&size=10

I get 42 suggestion words.

Done


One more level of error unwrapping in s3_table_reader.go

My mistake was assuming that, when a network read error happens, the
Err field of the resulting net.OpError would directly contain a
unix.Errno. What actually happens is that there's an *os.SyscallError
in there, which is the thing that's actually wrapped around the
unix.Errno. Hence, my IsConnReset() function was always returning
false.
This patch has been tested in the field, so I'm confident it will
work to mitigate #3255 in practice.

PTAL

Codecov Report

Merging #3292 into master will increase coverage by 0.01%.
The diff coverage is 100%.

Impacted Files
Coverage Δ

go/nbs/s3_table_reader.go
82.25% <100%> (+0.9%)
:arrow_up:

go/datas/http_batch_store.go
85.53% <0%> (+0.62%)
:arrow_up:

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Remove createJSModules @override - RN 0.47 compatibility

createJSModules is now not required on Android from RN 0.47. This is backwards compatible according to my tests.

Is this going to be merged in soon? It is causing me to not be able to upgrade my project to 0.47 which has some vital bug fixes that I need.

Is this going to be merged sometime soon?

Is this going to be published soon?

@RyanMitchellWilson 2.2.0 has been published!


Added pytest dependency required for launch_test ( Windows )

As seen in osrf/ros2_test_cases#1330, windows installation misses pytest depencency required for launch_test launch testing examples

I'm okey adding this, @clalancette what do you think, is it fine to add here a testing dependency ?

I'm honestly not sure.  I'm kind of thinking that we should move this to https://github.com/ros2/ros2_documentation/blob/70dd69a58a825b208f050fda21fd54d6dd816cba/source/Installation/Alternatives/Windows-Development-Setup.rst#L44 , as that is where we install our other testing dependencies.

https://github.com/ros2/ros2_documentation/blame/70dd69a58a825b208f050fda21fd54d6dd816cba/source/Installation/Alternatives/Windows-Development-Setup.rst#L44
In this line the pytest module is already included. But, the user would download pytest only when it is build from source code. The binary installation step does not install the pytest module even though windows release binary comes with launch_test script. So, anyone who installs though binary method will get launch_test script but without it's dependency ( pytest ) installed.


forcing short cask names makes it impossible to resolve ambiguous names

When closing https://github.com/Homebrew/homebrew-bundle/issues/598 with https://github.com/Homebrew/homebrew-bundle/pull/600 we introduced logic which will always shorten fully-qualified cask names (tap + cask) into the short name (just cask).
Both of these taps contain a adoptopenjdk8 cask:

adoptopenjdk/openjdk
homebrew/cask-versions

When using brew cask directly with just the short name, I initially get this error:
% brew cask install adoptopenjdk8
Error: Cask adoptopenjdk8 exists in multiple taps:
  homebrew/cask-versions/adoptopenjdk8
  adoptopenjdk/openjdk/adoptopenjdk8

But when I provide the full name and it will install the desired cask:
% brew cask install homebrew/cask-versions/adoptopenjdk8
# works

The problem is that when specifying in a Brewfile, the new logic will force use of the ambiguous short name and fail:
tap "adoptopenjdk/openjdk"
tap "homebrew/cask-versions"
cask "homebrew/cask-versions/adoptopenjdk8"

% brew bundle
Warning: treating 'homebrew/cask-versions/adoptopenjdk8' cask as 'adoptopenjdk8'!
Please change `cask "homebrew/cask-versions/adoptopenjdk8"` to `cask "adoptopenjdk8"` in your `Brewfile`.
...
Error: Cask adoptopenjdk8 exists in multiple taps:
  homebrew/cask-versions/adoptopenjdk8
  adoptopenjdk/openjdk/adoptopenjdk8

I propose the logic should not force short names unless a special flag is given. The default should be to take the name as given by the user, like brew cask does.
Related to https://github.com/Homebrew/homebrew-cask/issues/73730
Related to https://github.com/AdoptOpenJDK/homebrew-openjdk/issues/106

That was fast! Nice one @MikeMcQuaid - looks like that's working now, thank you.

You're welcome @estraph!


Own - have.own.property

This code is valid:
expect(element.attributes).to.have.own.property('data-a');
However, I get this type error:
test/t1.ts(42,44): error TS2339: Property 'own' does not exist on type 'Assertion'.
I'll suggest to add "own" to interface LanguageChains.

PR welcome.
Also, chai is trying to add the typings to the library directly: https://github.com/chaijs/chai/pull/822
When that happens, this and the DT version will be deprecated.


Refacto solution

Hello,
Some refacto.
What kind of code style to you want to use? Can you add a setting in the repo?
Thank you !

My style is fairly straightforward. Always use explicit typing (var is the devil), and in any code blocks, use squiggly brackets. This especially applies for one line if and else blocks.
I believe both of these significantly increase readability and reduce the possibility for confusion.

var is the devil

To quote  Ilya Ryzhenkov:

Using var keyword can significantly improve your code, not just save you some typing. However, it may require discipline to apply good practices when using implicitly typed variables. Here is my list:

It is required to express variables of anonymous type. This is pretty obvious - you cannot declare local variable of anonymous type without using var.
It induces better naming for local variables. When you read local variable declaration with explicit type, you have more information at that moment and something like "IUnitTestElement current" makes sense. However, when this local variable is used later, you read "current" which takes some time to figure out the meaning. Using "var currentElement" makes it easier to read at any place.
It induces better API. When you let compiler deduce type from method return type or property type, you have to have good types in the first place. When you don't have explicit type in the initialization expression, you have to have best names for members.
It induces variable initialization. It is generally a good practice to initialize variable in the declaration, and compiler needs initializer to infer type for local variable declared with "var" keyword.
It removes code noise. There are a lot of cases, when implicitly typed local will reduce amount of text developer needs to read, or rather skip. Declaring local variable from new object expression or cast expression requires specifying type twice, if we don't use "var". With generics it can lead to a lot of otherwise redundant code. Another example would be iteration variable in foreach over Dictionary<TKey,TValue>.
It doesn't require using directive. With var, you don't have explicit reference to type, as compiler infers type for you, so you don't need to import namespace when you need a temporary variable.

source
But If you don't like it I can change it.

any code blocks, use squiggly brackets. This especially applies for one line if and else blocks.

Less cluttered code is easiest to read. Less cognitive load. Once again it is your code, your rules.
Can you add a stylecop or a R# settings for the repo?


[Feature request] Python 3.12 support

Add support for Python 3.12 (release Oct 2023).
Several upstream dependencies will need 3.12 support before this can land, e.g., single-cell-data/TileDB-SOMA#1849

I was investigating the support for Python 3.12 today. Some notes:

TileDB-SOMA supports Python 3.12 (https://github.com/single-cell-data/TileDB-SOMA/issues/1849, https://github.com/single-cell-data/TileDB-SOMA/pull/2108)
It appears that cellxgene-census supports Python 3.12 on Linux but not macOS (https://github.com/chanzuckerberg/cellxgene-census/pull/1189)

https://github.com/chanzuckerberg/cellxgene-census/blob/f32c2748e9664cc196bb1758acb22f5a460fe188/.github/workflows/py-dependency-check.yml#L26-L31


Also fetch EM data from the designated test crops

Done in https://github.com/janelia-cellmap/cellmap-segmentation-challenge/pull/56/commits/949b831dc39c828cfef311f1245069bddc4e12ca


Ability to add extensions to compiler

Ability to add extensions to compiler through extend() method

@riadloukili Thanks :+1:

This is available in release 3.1.0

Any documentation on how to create new extension? Thanks

It's as simple as 1-2-3, just checkout this question http://stackoverflow.com/questions/13002626/laravels-blade-how-can-i-set-variables-in-a-template and you'll figure it out.. Basically, call extend method on blade instance. 😅

@ptraceur It's often better to use the directive() approach to add extra functionality

Thanks to both 😄


More robust MPI handling/finding

Untested, but this should behave better than the previous
implementation and should try really hard to "do what you mean" ™
I'll also try to address #246 as best we can... just do it through checking the .mod file compatibility... readelf is not something I want to deal with, and strings -a doesn't work because everyone uses strip before shipping binaries.
@jerryd mentioned that you might be able to unzip .mod files and get the GFortran version, but I haven't been able to do this, despite a few tries.

Current coverage is 48.18% (diff: 100%)

Merging #258 into master will not change coverage

@@             master       #258   diff @@
==========================================
  Files             2          2
  Lines           907        907
  Methods          42         42
  Messages          0          0
  Branches        195        195
==========================================
  Hits            437        437
  Misses          392        392
  Partials         78         78

Powered by Codecov. Last update 75a1aa4...0298b49

I cancelled a bunch of CI tests for individual commits since Travis-CI has a huge OS X backlog
I have also tested this on Debian 24 in every conceivable way, and everything looks kosher.
@jerryd:  Please try test driving this branch on your Debian machine to ensure that I haven't missed something. I'll wait the usually 24 hours before self-approving unless I hear back sooner.

LGTM

@jerryd confirmed over Gchat that this fixed the issues he's experienced on Fedora.


Disabling INFO / NOTE logs and JavaScript

I was wondering if there is a way to disable the terminal logging statements that begin with
[07-29:01:09:32] Torbutton INFO: ...
[07-29:01:09:32] Torbutton NOTE: ...

I was also wondering how you can disable JavaScript. Here is what I have tried:
pref_dict = {"noscript.global": False, "extensions.torbutton.security_custom": True}
driver = TorBrowserDriver("/path/to/my/tor-browser_en-US/", tor_cfg=pref_dict)

I was wondering if there is a way to disable the terminal logging statements that begin with

The pref that controls the Torbutton log level is: extensions.torbutton.loglevel
You may want to try different levels to find the one that suits your needs.

I was also wondering how you can disable JavaScript. Here is what I have tried:

You can set the security level to "High" ( "Safest") to disable JavaScript. See the test here:
https://github.com/webfp/tor-browser-selenium/blob/main/tbselenium/test/test_set_security_level.py#L84
Sorry for the delayed response.

The pref that controls the Torbutton log level is: extensions.torbutton.loglevel

Can you get code of this? I don't understand how to change extersions value

Would be something like this:
with TorBrowserDriver(TBB_PATH, pref_dict={'extensions.torbutton.loglevel': LOG_LEVEL}) as driver:
    driver.load_url(...)


Use the /api/users endpoint to get flags

At the moment the flag mechanism calls the /mini endpoint for all players, which is fine for a game, but not fine for a list of 10000 games, for example.
The /api/users endpoint can handle up to 300 user ids, for which it returns a json with a lot of their characteristics, like the profile country. Unfortunately, the name of the country is not sent, just the abbreviation. Lichess devs refused to add it to the API, so several ideas might work here:

maintain a list of abbreviations and their country names

this would require to always sync with the list lichess provides, and they have some custom flags as well

automatically maintain a local cache of abbreviations and the country names that also expire in like a month

this would call /mini for any player that does not have the flag in cache, but then it wouldn't need to for a month

assume that country names don't change, so never expire country abbreviation/name cache

Will get closed with the publication of V2.01


Query timeout

Hello!  I have a question about query timeout, when I search using "http://localhost:8080/search/?timeout=200", the query results  can be returned in less than 200s, from the results, I found that only part of the whole documents had been scanned when executing searching, and the "timeout" is true, I wonder why the query can not be executed until the timeout I set to scan as many docs as possible. Firstly, it seems that the arg"timeout" does not work. Secondly, I want to find a way to scan all documents  when doing search.
I'm eager to get your help! Thank you very much!

Hello, so timeout=200 means 200 seconds and is the upper bound and if soft timeout is enabled (default true) the search core will return whatever it has ranked.  How long does it take? And what are you doing that takes 200 seconds? :) Could you include the time it takes and the actual coverage element in the json response.
See https://docs.vespa.ai/documentation/graceful-degradation.html for documentation on timeout and soft timeout behaviour.

Thanks for your guide, I tested and found that when some content nodes were unhealthy, timeout didn't take effect, coverage was less than 100% and when the cluster was OK, timeout took effect, coverage could reach 100%, So I guess nodes problem lead to my query issue.
I found proton process on the bad node was down, when I tried to start it, an exception "Failed creating domain 'im' on TLS 'tcp/vespa7:19113'" was thrown out, I checked network and other cluster envs and found nothing bad, can u give me any ideas? thank u very much again!

Thanks for the feedback on the timeout/coverage guide.
On the node could you check 'vespa-proton-cmd --local getProtonStatus'. See https://docs.vespa.ai/documentation/reference/vespa-cmdline-tools.html#vespa-proton-cmd
The TLS component is the transaction log service which proton talks to.

Thanks for your reply. I'll check next time when the error occurs again.


good first issue

This is the good first issue in repository

GitHub Pages has deployed to my site.


Ruby 3.2.2 alpine3.18, Jekyll v4.3.2

Hello @envygeeks 👋
This PR updates:

base_image from ruby:3.1.1-alpine3.15 to ruby:3.2.2-alpine3.18.
jekyll version from 4.2.2 to 4.3.2.
GitHub Actions CI with ruby/setup-ruby@v1 and docker/login-action@v2.

This PR attempts to fix:

https://github.com/envygeeks/jekyll-docker/issues/364
https://github.com/envygeeks/jekyll-docker/issues/363
https://github.com/envygeeks/jekyll-docker/issues/353
https://github.com/envygeeks/jekyll-docker/issues/351
https://github.com/envygeeks/jekyll-docker/issues/346

As a workaround I've pushed to Docker Hub an updated version for jekyll/builder image:
https://hub.docker.com/r/jvconseil/jekyll-docker
Best,
@JV-conseil

I'm not sure this is picking up Jekyll 4.3.2, I just tried the image from dockerhub and still see 4.2.2.
$ docker run --rm --volume="$PWD:/srv/jekyll:Z" --publish 4000:4000 jvconseil/jekyll-docker jekyll serve
Unable to find image 'jvconseil/jekyll-docker:latest' locally
latest: Pulling from jvconseil/jekyll-docker
96526aa774ef: Already exists
dbd63fce5754: Pull complete
e76a10241e06: Pull complete
40fe5969d3cc: Pull complete
11d2b779d185: Pull complete
55199802b6c4: Pull complete
Digest: sha256:9a5b600d8b6612d789106436db92cc06c57cd2f707df8fc27c9adccf5ef73812
Status: Downloaded newer image for jvconseil/jekyll-docker:latest
Bundler 2.4.20 is running, but your lockfile was generated with 2.3.25. Installing Bundler 2.3.25 and restarting using that version.
Fetching gem metadata from https://rubygems.org/.
Fetching bundler 2.3.25
Installing bundler 2.3.25
Fetching gem metadata from https://rubygems.org/...........
Using bundler 2.3.25
Using public_suffix 5.0.3
Using colorator 1.1.0
Using concurrent-ruby 1.2.2
Using eventmachine 1.2.7
Using http_parser.rb 0.8.0
Using forwardable-extended 2.6.0
Using rb-fsevent 0.11.2
Fetching rexml 3.2.6
Fetching ffi 1.16.3
Installing rexml 3.2.6
Using liquid 4.0.4
Using mercenary 0.4.0
Using rouge 3.30.0
Using safe_yaml 1.0.5
Using unicode-display_width 1.8.0
Using addressable 2.8.5
Using em-websocket 0.5.3
Using i18n 1.14.1
Using pathutil 0.16.2
Using kramdown 2.4.0
Fetching terminal-table 2.0.0
Installing ffi 1.16.3 with native extensions
Installing terminal-table 2.0.0
Using kramdown-parser-gfm 1.1.0
Using sassc 2.4.0
Using rb-inotify 0.10.1
Using jekyll-sass-converter 2.2.0
Using listen 3.8.0
Using jekyll-watch 2.2.1
Fetching jekyll 4.2.2
Installing jekyll 4.2.2
Using jekyll-seo-tag 2.8.0
Using jekyll-feed 0.17.0
Using minima 2.5.1
Bundle complete! 7 Gemfile dependencies, 31 gems now installed.
Use `bundle info [gemname]` to see where a bundled gem is installed.
ruby 3.2.2 (2023-03-30 revision e51014f9c0) [x86_64-linux-musl]
Configuration file: /srv/jekyll/_config.yml
            Source: /srv/jekyll
       Destination: /srv/jekyll/_site
 Incremental build: disabled. Enable with --incremental
      Generating...
       Jekyll Feed: Generating feed for posts
                    done in 0.201 seconds.
 Auto-regeneration: enabled for '/srv/jekyll'
                    ------------------------------------------------
      Jekyll 4.2.2   Please append `--trace` to the `serve` command
                     for any additional information or backtrace.
                    ------------------------------------------------
/usr/gem/gems/jekyll-4.2.2/lib/jekyll/commands/serve/servlet.rb:3:in `require': cannot load such file -- webrick (LoadError)
        from /usr/gem/gems/jekyll-4.2.2/lib/jekyll/commands/serve/servlet.rb:3:in `<top (required)>'
        from /usr/gem/gems/jekyll-4.2.2/lib/jekyll/commands/serve.rb:179:in `require_relative'
        from /usr/gem/gems/jekyll-4.2.2/lib/jekyll/commands/serve.rb:179:in `setup'
        from /usr/gem/gems/jekyll-4.2.2/lib/jekyll/commands/serve.rb:100:in `process'
        from /usr/gem/gems/jekyll-4.2.2/lib/jekyll/command.rb:91:in `block in process_with_graceful_fail'
        from /usr/gem/gems/jekyll-4.2.2/lib/jekyll/command.rb:91:in `each'
        from /usr/gem/gems/jekyll-4.2.2/lib/jekyll/command.rb:91:in `process_with_graceful_fail'
        from /usr/gem/gems/jekyll-4.2.2/lib/jekyll/commands/serve.rb:86:in `block (2 levels) in init_with_program'
        from /usr/gem/gems/mercenary-0.4.0/lib/mercenary/command.rb:221:in `block in execute'
        from /usr/gem/gems/mercenary-0.4.0/lib/mercenary/command.rb:221:in `each'
        from /usr/gem/gems/mercenary-0.4.0/lib/mercenary/command.rb:221:in `execute'
        from /usr/gem/gems/mercenary-0.4.0/lib/mercenary/program.rb:44:in `go'
        from /usr/gem/gems/mercenary-0.4.0/lib/mercenary.rb:21:in `program'
        from /usr/gem/gems/jekyll-4.2.2/exe/jekyll:15:in `<top (required)>'
        from /usr/local/bundle/bin/jekyll:27:in `load'
        from /usr/local/bundle/bin/jekyll:27:in `<main>'

This is a life saver!


Add .Net 4.5 version of Analytics library for Xamarin compatible

Analytics.Xamarin library is based on .Net framework 4.5.1.
We can use Analytics.Net library with .Net 4.5.1 instead of Analytics.Xamarin.Pcl.

@kevingilliard awesome!


A redundant proof section appears when the appendix is not inline

Hello, I seemed to bump into a bug. Here is a minimal working example:
\documentclass{article}
\usepackage{apxproof}
\newtheoremrep{theorem}{Theorem}
\newtheoremrep{proposition}{Proposition}
\author{Author}
\begin{document}
\title{Title}
\maketitle
\section{A Section}
\begin{propositionrep}
This is a proposition
\end{propositionrep}
\begin{proof}
This is a proof
\end{proof}
\section{Another Section}
This is a section without proofs
\begin{toappendix}
\section{Appendix Section}
\end{toappendix}
\end{document}

The above code works fine. But if I change \section{Appendix Section} to \include{appendix}, an empty section "B Proofs for Section 2 (Another Section)" will be created in the appendix even though Section 2 has no proofs. Cheers!

Thanks for your bug report. I am aware of the issue, but this is something that is not easily fixable: the current behavior is as follows:

if \nosectionappendix is used, no section is created in the appendix;
if there is no appendix material at all within a \section, no section is created in the appendix;
if there is a toappendix environment within a \section, apxproof first checks whether the very first command within the toappendix is a \section command; or whether it is an \input of a file whose very first command is a \section command; if such a \section command is found, no section is created in the appendix;
otherwise, a section is created in the appendix.

The special \input check already does kind of what you want, but for \input and not \include; I cannot do the exact same thing for \include, as \include has other side effects than simply reading the file (in particular, setting up a new .aux file) that are not easy to simulate. I would have to think whether there is a better way to handle this.
That being said, the following two workarounds should work for you:

If you actually don't need the extra features of \include, use \input (which is usually more versatile anyway).
Otherwise, just put \nosectionappendix after the \section for which no section in appendix should be produced.

Please let me know whether these workarounds are ok for you.

@PierreSenellart Thanks a lot for the explanations and workarounds! Using \input instead of \include works for me. By the way, I just noticed that newlines before the first \section or \input in the toappendix environment also lead to a redundant section:
\begin{toappendix}

\section{Appendix Section}
\end{toappendix}

Perhaps you can skip newlines when you check the first command? Anyway, thank you again for creating this convenient package :-)


Fix breakage on Python 3.10

We have some imports from collections that should be imports from collections.abc; these break on Python 3.10 and Python 3.11.

Hi we are also seeing this issue:
File "/usr/local/lib/python3.10/dist-packages/refcycle/key_transform_dict.py", line 27, in
class KeyTransformDict(collections.MutableMapping):
AttributeError: module 'collections' has no attribute 'MutableMapping'
Do you have a plan to fix this? Thanks.

@coyotelll It's fixed in the latest release, which I've just pushed to PyPI: https://pypi.org/project/refcycle/0.3.0/


Upgrade to Django 3.2

Fixes https://github.com/sandiegopython/pythonsd-django/issues/112

I saw some errors in the CI log around not finding the Meetup and Youtube data. Is that anything to be concerned about? That's the only thing I have a question about, the rest of the PR is good to go.

That is normal. I'm going to do a separate PR around silencing logging during tests.


Logic Alternatives

(NOTE: This issue is a migrated issue from the old git instance)
As an alternative to having a bunch of named ID buttons and elements, store a counter in page, and use a general button to call a master function to do things.
Could abstract functions out to a single scripts page, and, either include specific items using jinja, or perhaps just the naming of the socketio.emits/.ons

(NOTE: This issue is a migrated issue from the old git instance)
Can also set the counter to specific values for things that are cyclical. For instance, update score can return the counter to 0, Daily Double can set the counter to 100, then return to 0 after the round is complete.

(NOTE: This issue is a migrated issue from the old git instance)
Can also set the counter to specific values for things that are cyclical. For instance, update score can return the counter to 0, Daily Double can set the counter to 100, then return to 0 after the round is complete.


Update README to reflect our changes

We have forked cargo-mobile and maintain this for a while. But we never update the README so users might get confuse on where to start.
We should add this note to README. The note itself is also outdated a bit.
Besides, we should also update wry's README to redirect mobile instructions to here.

I agree, README should be updated.

Hmm the info on that hackmd link is definitely a lot different than the readme on this repo ha 😅
I will try to run this again on Win 10, if it works I'll volunteer to do update the readme if it's literally just copy paste from hackmd into this repo.


add parenthesis around delta_log check to short circuit

Looks like I forgot the parenthesis around the new check for parquet checkpoint files to shortcircuit if its a delta_log file.

build

build

build


Column purposes should have Sampling Key

Is your feature request related to a problem? Please describe.
At the moment, Advanced Data Options dialog box only supports 3 column purposes: Feature / Label / Ignore.
Some datasets overfit easily when validation/test data is chosen randomly. These might include datasets which include items about the same entity (for example, blood results of the same patient at different times or credit card fraud transactions dataset where one person has commited multiple fraud) or time based series for related items (for example, will it rain tomorrow in a specific location and dataset only include one country). Running this kinds of experiments with Model Builder will often lead to overfitted models, which blocks usage of Model builder for these purposes.
Describe the solution you'd like
Add "Sampling Key" purpose to Advanced Data Options.
Additional context
This has been been suggested earlier by justinormont in 2019 https://github.com/dotnet/machinelearning-modelbuilder/issues/75#issuecomment-506642972 but I did not notice discussion about it not being suitable for ML Builder, so maybe it could be now reconsidered?

@LittleLittleCloud before this is implemented do you know if there is a possibility to "hack" and replace test.bin in the temp folder with my own data or will it get overwritten when starting a new run? Although if new tuner should have same performance as modelbuildee I might not need it.


Commutativity problems

Right now, using types for commutativity is a bit awkward. There are a few problems:

It's easy to forget to provide types like CRing in addition to Ring
In cases where both types could be provided with different evidence, you have to use the "low-priority" implicit pattern to avoid ambiguity.
In cases where you can accept Ring or CRing but would prefer the latter for optimization reasons, it's hard to do this. There has been some talk about using some kind of Fallback type class to help fix this.

I'm not sure what the best approach is. One option is to stop differentiation CRing and Ring, but instead use a type witness like CommutativeMult[A] or something. Another approach is to leave things alone but just make sure commutativity is being supported everywhere it might be needed (e.g. add CSemiring and CRng). A third option is to figure out a more radical plan.

We added the CSemiring and CRng types, so going with the second option.


GiphyMediaView Not Rendering Background Alpha Correctly

🐛 Bug Report
On a fresh app (npx react-native init test --template react-native-template-typescript) I Followed the installation and basic usage instructions using all the default values for configuration. After selecting a sticker/text from the GiphyDialog and presenting it in a GiphyMediaView, it isn't rendering the alpha of stickers/text correctly, resulting in a checkerboard pattern behind the content. As of now I'm only able to verify this behaviour on android. Note that using a FastImage to present the content results in the correct behaviour.
To Reproduce

Select a sticker or text from a GiphyDialog and set it to a state variable, as per the documentation

const [media, setMedia] = useState<GiphyMedia | null>(null);
useEffect(() => {
    const handler: GiphyDialogMediaSelectEventHandler = e => {
      setMedia(e.media);
      GiphyDialog.hide();
    };
    const listener = GiphyDialog.addListener(
      GiphyDialogEvent.MediaSelected,
      handler,
    );
    return () => {
      listener.remove();
    };
  }, []);

Present the media in a GiphyMediaView, again like in the documentation

{media && (
      <GiphyMediaView
          media={media}
          style={{ aspectRatio: media.aspectRatio }}
      />
)}

Expected behavior
The background of stickers/text would be correctly rendered as transparent without the checkerboard pattern.
Actual Behavior
The background of stickers/text is a checkerboard pattern with no transparency.

Your Environment

Giphy React Native SDK version: 1.3.0
React Native version: 0.66.4
Platform(s) (iOS, Android, or both?): Android
Device info (Simulator/Device? OS version? Debug/Release?): Android simulator and real device, both debug and release variants on Android 12 (API 31)

Reproducible Demo
Create a new project with npx react-native init test --template react-native-template-typescript and yarn add @giphy/react-native-sdk  as a dependency. Then simply use the code block listed under "basic usage" of the GiphyMediaView in the documentation. Note that I've also tried explicitly setting the "showCheckeredBackground" config to false on android, but this does not affect it.

Hu @Kesmek, thanks for the report. We will add a new property to GiphyMediaView to control the checkered background in the next release.

We recently released Giphy RN SDK v1.4.0 with the showCheckeredBackground property. This property will allow enabling/disabling the checkered background in GiphyMediaView.


Add support for cancellation_date field

It would be great if the receipt object would expose the cancellation_date field for auto-renewable subscriptions!
From the receipt fields docs:

For a transaction that was canceled by Apple customer support, the time and date of the cancellation.  Treat a canceled receipt the same as if no purchase had ever been made.

Thanks for adding it, seems like the original author of this gem has gone AWOL..


Omit Exec Code if Empty

Do not send or display the exec.code if it is empty for Docker actions

Closes https://github.com/openwhisk/openwhisk/issues/1465

PG1 800

PG2 552

@rabbah, ready for review.

Can we use this pr to make exec a JSON interface? This is just going to be an endless race.
> touch x.zip
> wsk action create z x.zip --kind nodejs
> wsk action get z -v
Response body received:
{
  "name": "z",
  "publish": false,
  "annotations": [],
  "version": "0.0.1",
  "exec": {
    "kind": "nodejs",
    "code": "",
    "binary": true
  },
  "parameters": [],
  "limits": {
    "timeout": 60000,
    "memory": 256,
    "logs": 10
  },
  "namespace": "guest"
}
ok: got action z
{
    "namespace": "guest",
    "name": "z",
    "version": "0.0.1",
    "publish": false,
    "exec": {
        "kind": "nodejs",
        "code": ""
    },
    "limits": {
        "timeout": 60000,
        "memory": 256,
        "logs": 10
    }
}

The binary property is defined for some but not all action types (docker and node being two of them).

@dubeejw can you rebase?

PG2 733

PG2 773.

@rabbah, anything else on this one?

Merged as https://github.com/openwhisk/openwhisk/commit/c4064ae0e93dd156682c36632924ae63cf719410.


im getting an error donno why

Enter blog address:  https://lokisenpai.blogspot.com/2022/09/sasaki-and-miyano-my-first-bl-anime.html
How many views you want: 4
Traceback (most recent call last):
File "/home/loki/.local/lib/python3.10/site-packages/socks.py", line 787, in connect
super(socksocket, self).connect(proxy_addr)
ConnectionRefusedError: [Errno 111] Connection refused
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/python3/dist-packages/urllib3/contrib/socks.py", line 96, in _new_conn
conn = socks.create_connection(
File "/home/loki/.local/lib/python3.10/site-packages/socks.py", line 209, in create_connection
raise err
File "/home/loki/.local/lib/python3.10/site-packages/socks.py", line 199, in create_connection
sock.connect((remote_host, remote_port))
File "/home/loki/.local/lib/python3.10/site-packages/socks.py", line 47, in wrapper
return function(*args, **kwargs)
File "/home/loki/.local/lib/python3.10/site-packages/socks.py", line 800, in connect
raise ProxyConnectionError(msg, error)
socks.ProxyConnectionError: Error connecting to SOCKS5 proxy localhost:9050: [Errno 111] Connection refused
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 699, in urlopen
httplib_response = self._make_request(
File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 382, in _make_request
self._validate_conn(conn)
File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 1012, in _validate_conn
conn.connect()
File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 353, in connect
conn = self._new_conn()
File "/usr/lib/python3/dist-packages/urllib3/contrib/socks.py", line 127, in _new_conn
raise NewConnectionError(
urllib3.exceptions.NewConnectionError: <urllib3.contrib.socks.SOCKSHTTPSConnection object at 0x7f9e8732eda0>: Failed to establish a new connection: [Errno 111] Connection refused
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/python3/dist-packages/requests/adapters.py", line 439, in send
resp = conn.urlopen(
File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 755, in urlopen
retries = retries.increment(
File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 574, in increment
raise MaxRetryError(_pool, url, error or ResponseError(cause))
urllib3.exceptions.MaxRetryError: SOCKSHTTPSConnectionPool(host='lokisenpai.blogspot.com', port=443): Max retries exceeded with url: /2022/09/sasaki-and-miyano-my-first-bl-anime.html (Caused by NewConnectionError('<urllib3.contrib.socks.SOCKSHTTPSConnection object at 0x7f9e8732eda0>: Failed to establish a new connection: [Errno 111] Connection refused'))
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/loki/Documents/TOOLS/breakfold/breakfold.py", line 113, in
visit()
File "/home/loki/Documents/TOOLS/breakfold/breakfold.py", line 95, in visit
session.get(address, headers=header)	#visiting the URL given by the user
File "/usr/lib/python3/dist-packages/requests/sessions.py", line 555, in get
return self.request('GET', url, **kwargs)
File "/usr/lib/python3/dist-packages/requests/sessions.py", line 542, in request
resp = self.send(prep, **send_kwargs)
File "/usr/lib/python3/dist-packages/requests/sessions.py", line 655, in send
r = adapter.send(request, **kwargs)
File "/usr/lib/python3/dist-packages/requests/adapters.py", line 516, in send
raise ConnectionError(e, request=request)
requests.exceptions.ConnectionError: SOCKSHTTPSConnectionPool(host='lokisenpai.blogspot.com', port=443): Max retries exceeded with url: /2022/09/sasaki-and-miyano-my-first-bl-anime.html (Caused by NewConnectionError('<urllib3.contrib.socks.SOCKSHTTPSConnection object at 0x7f9e8732eda0>: Failed to establish a new connection: [Errno 111] Connection refused'))

I'm having the exact same problem. Is the ISP blocking TOR traffic?

me too, after the password error now this


inversed voting mechanism

👎  => positive vote
👍 => negative vote
... chaos :)

@larsnolden Even better: automatic acceptance

👍

@EtherTyper We tried that in #48 (which got in on a technicality). It didn't seem like a terribly popular idea, but it was only reverted because it was buggy.

👍

So does that mean this has 27 downvotes or 27 upvotes?


add sysguard_cpu direcitve for sysguard module

add sysguard_cpu direcitve for sysguard module, described as follows:
sysguard_cpu usage=num [period=time] [action=/url]
Default: period=3s
Context: http, server, location
This directive tells the module to protect the system by monitoring the CPU usage. When the system in the period (units: s) within the CPU reach to num (note: the num is a integer. such as protection CPU is 50% and could be set the usage = 50), the incoming request will be redirected to the url specified by 'action' parameter. If the action is not configured, tengine will return 503 directly.
cpu usage formula
    cpu_usage = [(cur.usr + cur.nice + cur.sys) - (pre.usr + pre.nice + pre.sys)]/
                [(cur.usr + cur.nice + cur.sys + cur.iowait + cur.irq
                 + cur.softirq + cur.idle)
                 - (pre.usr + pre.nice + pre.sys + pre.iowait + pre.irq
                 + pre.softirq + pre.idle)] * 100

https://github.com/alibaba/tengine/blob/master/tests/nginx-tests/cases/sysguard.t
Could you please add test case for sysguard_cpu?  thx


Spatial 'look_at' strange behaviour

Godot version: 3.2.1
OS/device including version: Windows 10
Issue description: See example project
Steps to reproduce: See example project
Minimal reproduction project: https://github.com/Albatros53113/Turn-Zylinder/tree/master
The issue is best described by looking at the example project 'readme'. Sorry if this is not an issue and I missunderstood some concepts, but seems like 'look_at' changes the axis it looks with.

Is it maybe related to #35880?

Sorry, but it's mandatory you try to explain what your problem is. Not everyone has the time to open, test you project, and try to understand what you felt was wrong.

Yes I know. Tried really hard to cut it down to a simple, reproducable example, but wasn't able to do so. Found an functional error on my side, but that didn't help with the 'look_at' problem. As I print out a (local) 'look_at' vector and the 'basis.z' vector straight before the 'look_at' function and they are perfectly aligned, all I can say is that in my example project there never should be a turn on a mouseclick.
I have another solution that works now, so this is for someone who is interested in a possible problem. It's really simple code.
From this other solution I raised into another problem, that gives me some headache. Don't want to open another issue here, as I don't want to jangle s.o. nerves with minor problems that perhaps are only mine: The Vector3.dot() function sometimes gives values that are >1. Would be nice if this cases were captured, as this leads to poor errors that costs time.
Reproducable with:
func _ready():
var vec1 = Vector3(0.061474, 0, 0.998109)
var vec2 = Vector3(0.061474, 0, 0.998109)
var scal = vec1.dot(vec2)
print(str(scal))
var angle = acos(scal)
print(str(angle))


Move deprecations along.

This includes deprecating std.c.*, which apparently was marked as
scheduled for deprecation in 2.068 but never actually deprecated (though
it looks like it was previously removed from the documentation build,
since it doesn't show up on dlang.org).

:white_check_mark:

Auto-merge toggled on

Wow I just traced this back over #2841 and #2337.
It seems like it was planned to be removed in December 2015, but that plan go busted by @CyberShadow #2841.
Imho it was removed from the documentation in 2014 and we are already over the initial deprecation plan - isn't June 2017 a bit far in the future? Is anyone still using this?
@jmdavis you explained at #2337 that the current deprecation policy is 12 months - what did change? Did someone complain?

The current policy is 12 months as deprecated and documented followed by 6 months as deprecated and undocumented. Ideally, that would be 12 months from a release and 6 months from a release respectively, but it's kind of hard to hit it exactly, so I tend to pick a month or two farther out in an attempt to make those dates be about 12 or 6 months from the release.


Documentation references a "Users" tab, but I do not see this in Settings.

Is this documentation out of date? I recently installed WAC 2110 on a Windows Server 2019 which is domain integrated. I am logged-in as a domain admin but I do not see a "Users" tab (as referenced in the "Active Directory or local machine groups" section). There is no where to "manage gateway user and administrator access from within the Windows Admin Center interface". As it is right now any user in my domain can log into the the web interface for WAC, and there appears to be no way to control access to WAC when looking at the Settings section of the web interface!

Document Details
⚠ Do not edit this section. It is required for docs.microsoft.com ➟ GitHub issue linking.

ID: bb766b65-907c-1c8e-4af2-fc312a8572ad
Version Independent ID: a07c9822-76ae-d3cf-5e82-0b56e180d91d
Content: Configuring user access control and permissions
Content Source: WindowsServerDocs/manage/windows-admin-center/configure/user-access-control.md
Product: windows-server
Technology: windows-admin-center
GitHub Login: @IngridAtMicrosoft
Microsoft Alias: wscontent

We hugely appreciate your contribution, feedback, and support to our technical documentation.
We’ve phased out GitHub Issues on this repository as the feedback mechanism for content and have replaced it with a new feedback system. For more information see, Content User Feedback. As part of this rollout, we are migrating your issue where our team will use your comments to improve the documentation experience. Unfortunately, this does mean you won't be able to access this issue after the migration is complete.
All issues will be migrated by Thursday 29th August 2024.
Once again, thank you for your valuable feedback, we hope you’ll continue to contribute using our new feedback system.


Update last check timestamp in monitorHealth

Hi,
I'm seeing the following pattern of modification times in an agent container:
-rw-r--r-- 1 root root    0 2015-06-10 23:01:26.125525713 +0000 .healthcheck
-rw-r--r-- 1 root root    0 2015-06-10 23:01:34.127525840 +0000 .healthcheck
-rw-r--r-- 1 root root    0 2015-06-10 23:01:36.126525872 +0000 .healthcheck

The logs show that the state watcher process has to restart constantly (only one cycle is shown below):
time="2015-06-10T23:01:26Z" level="info" msg="Starting event router."
time="2015-06-10T23:01:26Z" level="info" msg="Watching state directory: /var/lib/rancher/state/containers"
time="2015-06-10T23:01:26Z" level="info" msg="Processing event: &docker.APIEvents{Status:\"start\", ID:\"c467f40211d7b84438eef729a9108e12ff9f5652b2151a880c92db6e74a6c68e\", From:\"-simulated-\", Time:0}"
time="2015-06-10T23:01:26Z" level="info" msg="Processing event: &docker.APIEvents{Status:\"start\", ID:\"94a93af165f867f7694aacb0c6ee0a15009c708814c224fa5f938473a909a065\", From:\"-simulated-\", Time:0}"
time="2015-06-10T23:01:26Z" level="info" msg="Processing event: &docker.APIEvents{Status:\"start\", ID:\"ac8409e03067f67903f75a05065068fc97537faa2c36d37155af48b00e70240c\", From:\"-simulated-\", Time:0}"
time="2015-06-10T23:01:26Z" level="info" msg="Assigning IP [<IP_ADDRESS>/16], ContainerId [c467f40211d7b84438eef729a9108e12ff9f5652b2151a880c92db6e74a6c68e], Pid [6479]"
time="2015-06-10T23:01:26Z" level="info" msg="Assigning IP [<IP_ADDRESS>/16], ContainerId [94a93af165f867f7694aacb0c6ee0a15009c708814c224fa5f938473a909a065], Pid [4854]"
time="2015-06-10T23:01:36Z" level="warning" msg="Rancher state watcher returned with error. Waiting 0 and then restarting. Error that caused exit: Failed health check."
time="2015-06-10T23:01:46Z" level="warning" msg="Rancher state watcher returned with error. Waiting 2 and then restarting. Error that caused exit: Failed health check."
time="2015-06-10T23:01:58Z" level="warning" msg="Rancher state watcher returned with error. Waiting 4 and then restarting. Error that caused exit: Failed health check."
time="2015-06-10T23:02:12Z" level="warning" msg="Rancher state watcher returned with error. Waiting 8 and then restarting. Error that caused exit: Failed health check."
time="2015-06-10T23:02:30Z" level="warning" msg="Rancher state watcher returned with error. Waiting 16 and then restarting. Error that caused exit: Failed health check."

It seems that even though .healthcheck gets written at the start and every 8 seconds as expected, the 10 seconds timer still fires and reports an error condition.

@cjellick

On further inspection, I must have skipped a method when reading code and mistook the timer for a ticker. :blush: The proposed one-liner doesn't make too much sense that way.

I updated to RancherOS version 0.3.3 in the meantime, and this no longer happens.


Move all threading to use ActiveJob instead

It appears that the old weird CI issues were caused by us calling Thread.new in various places. Really, everywhere we do that, we should either not be doing that or be using ActiveJob. This issue is to eliminate all uses of Thread.new in MS and replace them with calls to ActiveJob.

There are 4 remaining instances of Thread.new:

AuthenticationController#send_invalidations: This should probably not be in a thread, we want to be able to forward the status of the invalidations to the user instead of just saying they were "queued". Maybe the token store needs to be able to do bulk invalidations.
StackExchangeUsersController#update_data: This should become a job, I just have weird feelings about it because it does HTTP requests.
PostConcerns#spam_wave_autoflag: This should almost certainly just be a job, the problem is that the logs would get eaten up by workers, and I think we want those logs.
Feedback, after_save callback: Again, should prolly be a job, just gives me weird feelings. Maybe because of actioncable stuff.

Ready for review or do you want to work on those last 4?


Set metadata when webview is created

Task/Issue URL: https://app.asana.com/0/488551667048375/1206405649234091/f
Description
Set metadata only when webview is created
Steps to test this PR

[ ]
[ ]

UI changes

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After

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develop

#4105   👈

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\dfrac in superscript is larger than elsewhere

\ddot{x} = -v_0 \dfrac{k}{m} e^{-\dfrac{kt}{m}}

also, \tfrac and \frac have different size in superscript (not sure if it is intended).

da31c21
\tfrac and \frac being different sizes wasn't really intended, but that's what Mathjax does too.


Sampling inside tetrahedral mesh

fixes #299

I agree, "while loop" should be avoided. I have tested the proposed one and it works.

Checks failed due to mal formatted test sources. Commit follows in an instant. Missed to execute both:

scalariformFormat
test:scalariformFormat


Updating documentation and updating to new Unity version

Closed in favor of https://github.com/dagguh/data-hunt/pull/2026

Closed in favor of https://github.com/dagguh/data-hunt/pull/2026


Fix Cross-compilation.rst header hierarchy

Cross-compilation.rst was using the page header format for sections headers. This caused the tutorial's list to display the sections instead of the full tutorial, what could be confusing. For example an 'Overview' tutorial would be expected to be a ROS2 overview, instead of a Cross-Compilation overview.
This change adds a page header and lowers the others headers one step in the hierarchy, based on Colcon-Tutorial.rst. It also adds a Table of Contents and the redirect-from info to keep it similar to the rest of the tutorials.

LGTM! And thank you for your contribution.

No problem! I'll try to make it a habit 😄


Skyline/work/20190320 transition level explicit values

Several explicit overrides that were formerly on the precursor level have been moved to the transition level where they more properly belong, so that individual fragments of a precursor can have individual overrides:
    CollisionEnergy  // For import formats with explicit values for CE
    DeclusteringPotential // For import formats with explicit values for DP
    SLens  // For Thermo
    ConeVoltage  // For Waters
    IonMobilityHighEnergyOffset// For import formats with explicit values for ion mobility

Looks like it has a code inspection issue.

Skyline-Daily (left) vs revision


Turn off output on idle

Awesome job mill1000!
It works flawlessly on my setup :)
I ran into some small problem in my setup:
I'm using active speakers for a multi room setup.
SnapCast-Server -> SnapCast Client on Raspberry Pi Zero -> raspdif -> LED -> Toslink to my speakers.
My speakers are able to automatically activate on Toslink signal and deactivate themselves after 10s without signal.
BUT no signal means Toslink being turned off completely.
I realized in standard configuration, even with "no-keep-alive" the output never turns off, so my speakers are never going to sleep.
I've added a few lines to turn of PCM completely during buffer underrun, this solves my issue and my speakers are going to sleep.
Maybe this might help somebody else with a similar setup.
Thanks again for your amazing work, I really appreciate it!
Regards
Jens

Thanks for the contribution! Glad it's working well for you.
If you can fix the minor formatting issues reported by the checks I'll get this merged.


Reactions drawer

Closes #938 - Reactions detail drawer

Summary by CodeRabbit
Release Notes

New Features

Introduced a bottom sheet for displaying detailed reaction information in chat messages.
Added a new "subtle" variant for the IconButton, enhancing visual representation options.
Added a new component, ChatMessageReactions, for displaying message reactions in the chat interface.
Integrated MessageReactionsDrawer to manage the display of reactions in a modal.

Bug Fixes

Improved layout management for the bottom sheet based on device safe areas.

Style

Updated styles for the IconButton and bottom sheet header for better aesthetics.
Enhanced color definitions in both light and dark themes, including a new "danger" color and updated scrim opacity.
Introduced a new scrim background property in both light and dark themes.

Chores

Removed the ChatMessageReactions component, which previously displayed user reactions in chat messages.
Updated the Chat component to incorporate new message reactions functionality.

Thanks @thierryskoda for the review! I create separate issues below:

https://github.com/ephemeraHQ/converse-app/issues/1144
https://github.com/ephemeraHQ/converse-app/issues/1143


Bump markdown to latest alpha and fix fn name

I agree that when the request is merged I assign the copyright of the request to the repository owner.
Latest release renames BlockQuote -> Blockquote.

Oh thanks! I'll try it out and merge it in a bit.
Is there a useful change in the latest alpha?

@andrewbaxter  Thanks, and sorry should have been more clear in the description. There is nothing specific im looking for in the newest alpha. However, the markdown dependency is specified as markdown = { version = "1.0.0-alpha.12" } which means trying to build the latest pulls in 1.0.0-alpha.21 and fails to build because fn rename BlockQuote -> Blockquote. Alternatively, we can just pin to exact version.

Ah no, that makes perfect sense, sorry. I'm just surprised since I was working on it last week or two ago, updating deps I think, I guess that just changed.

Hmm, yeah.  TBH I don't have all of the dependency versioning conventions down yet, but I think pinning the exact version might be best for now (alpha21 is fine).  Otherwise if there's already a locked version it'll happily try to use that, and I guess there are no guarantees about backwards compatibility for alpha releases.
Also (unrelated to this MR) I think after merging this I'll need to bump the versions (here + aargvark) and release, otherwise the binary keeps trying to use the crate version and hits the blockquote issue.  I feel like I'm doing something wrong.

Sorry, I didn't mean to confuse things here.  I think if you make it an exact selection I'd be happy to merge and complete the follow-on changes.  Otherwise I can do everything together if that would be easier.

IIUC this was impacting new installations, so I went ahead and pinned the version and released it.  Thanks for the MR though and letting me know of the issue!


PR was opened but not automatically merged

A PR was opened but not automatically merged and I had to manually merge it
 errors: [
    {
      resource: 'PullRequest',
      code: 'custom',
      message: 'A pull request already exists for antirez:unstable.'
    }

Should be fixed in 1.1.3