text:
NTR: regulation terms for GO:0005319 lipid transporter activity

Could I please have all the regulation terms for GO:0005319 lipid transporter activity
For PMID:27365390
Please add references:
GOC:rph
GOC:BHF
GOC:BHF_miRNA

I'm not sure it would. It's for annotating a miRNA that the authors show reduces MTP (lipid transport) activity. The miRNA is also shown to reduce the mRNA expression of the lipid transporter MTP, but it was not shown to directly bind the MTP transcript, so we can't say that it silences the gene.
As we don't know if it's direct, I'd prefer to use a regulation term. Even if it was shown to directly silence MTP, I'm not sure I would want to annotate the miRNA with an activity term like this.

In this case why not use 'regulation of lipid transport'?

The authors do show an effect on lipid secretion in a separate experiment, so I can annotate to reg. of lipid transport as well, but the figure I want to annotate is showing that the miRNA reduces MTP activity, so this seems a more specific annotation. The miRNA is acting on the transporter rather than anything else that might be involved in the transport.

I'm not sure I understand you. Here is the paper https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4479415/
Extract:
"miR-34a also reduced MTP and ApoB protein levels (Fig. 3b, c and Supplementary Fig. 6a) and MTP activity (Supplementary Fig. 6b). In contrast, loss of miR-34a increased MTP activity (Supplementary Fig. 6c). Consistent with the latter data, miR-34a inhibited VLDL secretion (Fig. 3d)."
Proposed annotations:
From Fig 3b, c and Supp Fig. 6a we can annotate miR-34a to neg. reg. of gene expression of MTP and ApoB
From Supp. Fig. 6b/c we want to annotate miR-34a to neg. reg. of lipid transporter activity (has_regulation_target MTP)
From Fig. 3d we can annotate miR-34a to neg. reg. of lipid transport (but instead I've opted for cholesterol homeostasis, as I wasn't sure that the secretion was transport).
So although they have shown reduced MTP activity with miR-34a and reduced VLDL secretion, they haven't shown that the latter is caused by the former, they are two independent experiments.

@rachhuntley
To be consistent with previous annotation, I will add the requested regulation terms.
It would be good to discuss this example wrt a GO-CAM model and use of the expanded set of gene product-to-term relations as it's a common theme, i.e. an upstream molecule regulating expression of a downstream molecule with activity 'x', and going forward we want to make sure we're all annotating these types of experiments similarly.

Thanks Kimberly @vanaukenk, I agree it would be good to get a consensus on this.

authors: pgaudet rachhuntley vanaukenk


text:
Term merge dATP/ATP triphosphate pyrophosphatase

Hello,
Working on the annotation ticket https://github.com/geneontology/go-annotation/issues/3581 NUDT1 (P36639)
I think we need to edit the ontology as follows:

GO:0044714  2-hydroxy-(deoxy)adenosine-triphosphate pyrophosphatase activity (no annotations, mapped to Reactome R-HSA-2395818 "NUDT1 hydrolyses 2-OH-dATP to 2-OH-dAMP ") should merge into  "GO:0008828
dATP pyrophosphohydrolase activity" : RHEA:31583; EC:3.6.1.56 (label is 2-hydroxy-dATP diphosphatase  in EC)

GO:0044713 2-hydroxy-adenosine triphosphate pyrophosphatase activity (no annotations, mapped to Reactome R-HSA-2395872 NUDT1 hydrolyses 2-OH-ATP to 2-OH-AMP ) should merge into GO:0008828 dATP pyrophosphohydrolase activity (RHEA:31583; EC:3.6.1.56)

GO:0035539 8-oxo-7,8-dihydrodeoxyguanosine triphosphate pyrophosphatase activity: Add EC:3.6.1.55

@ukemi
@deustp01
Do you agree ?
Thanks, Pascale

@ukemi
@deustp01
@kaxelsen
If there are no objections I will go ahead and implement this.
Thanks, Pascale

@ukemi
@deustp01
@kaxelsen
If there are no objections I will go ahead and implement this.
Thanks, Pascale

I have no objections

I have no objections

no objections here either

no objections here either

source: gharchive/issue

authors: deustp01 kaxelsen pgaudet

repo: geneontology/go-ontology

license_type: permissive

license_source: github-api


text:
NTR: negative (and positive regulation) of aldehyde dehydrogenase (NAD+) activity

Dear GO editors,
could you please consider creating the regulation terms for GO:0004029 aldehyde dehydrogenase (NAD+) activity
PubMed=33495566 shows that PRMT3 UniProtKB/O60678 interacts and inhibits the  aldehyde dehydrogenase (NAD+) activity ALDH1A1.
Thanks.

Hi @lbreuza
We are not creating BP terms for regulation of activity anymore. I can create 'aldehyde dehydrogenase (NAD+) inhibitor activity'; I'd rather not create the other terms until we find evidence that the functions exist.
Does that work for you?
Thanks, Pascale

+[Term]
+id: GO:0140631
+name: aldehyde dehydrogenase (NAD+) inhibitor activity
+namespace: molecular_function
+def: "Binds to and stops, prevents or reduces the activity of aldehyde dehydrogenase (NAD+)." [PMID:33495566]
+is_a: GO:0004857 ! enzyme inhibitor activity
+relationship: negatively_regulates GO:0004029 ! aldehyde dehydrogenase (NAD+) activity
+property_value: term_tracker_item https://github.com/geneontology/go-ontology/issues/21265 xsd:anyURI
+created_by: pg
+creation_date: 2021-04-09T09:40:21Z

authors: lbreuza pgaudet


text:
endopolyphosphatase activity (possible merge or obsolete)

Is
endopolyphosphatase activity
A useful grouping term?
And if so, should it be a parent of
GO:0034431	bis(5'-adenosyl)-hexaphosphatase activity
GO:0034432	bis(5'-adenosyl)-pentaphosphatase activity
GO:0008486	diphosphoinositol-polyphosphate diphosphatase activity
GO:0050072	m7G(5')pppN diphosphatase activity
GO:0047710	bis(5'-adenosyl)-triphosphatase activity

but I think it could be obsoleted and things would either be reannotated to
pyrophosphatase of one of the descendants. It is a bit orthogonal and most thing are annotated to  two terms.
It could probably be a synonym of  pyrophosphatase ?
Note the definition is
Catalysis of the reaction: polyphosphate + n H2O = (n+1) oligophosphate. The product contains 4 or 5 phosphate residues.
(I',m not even sure that the second part is true but it isn't part of the necessary and sufficient bit of the def which matches the parent?)

I think the chemistry disagrees
GO:0000298 endopolyphosphatase activity
EC 3.6.1.10
phosphate + n H2O <=> n H(+) + (n+1) phosphate         <<<<< a polyphosphate
RHEA:22452
phosphate](n+1) + n H2O = n H+ + (n+1) phosphate
Example:
GO:0034431
EC 3.6.1.60 diadenosine hexaphosphate hydrolase (AMP-forming)
RHEA:32047;
Note the substrates; 3.6.1.10 works on a polyphosphate; that is not the substrate of EC:36.1.60 (CHEBI:63740)
These are all sibs with an EC class 3.6.1.-
None of the other term's substrates are classified as 'polyphosphates' in CHEBI.
@kaxelsen , what do you think?

I thought
bis(5'-adenosyl)-hexaphosphatase/ bis(5'-adenosyl)-pentaphosphatase activity
are dinucleotide polyphosphate/bis(5'-adenosyl)-triphosphatase
are dinucleoside polyphosphates
GO:0008486	diphosphoinositol-polyphosphate diphosphatase activity
has polyphosphate in the term name
pppN diphosphatase looks 'polyphosphate -ish

I think the use of 'polyphosphate' in the term names is a bit misleading; the CHEBI term for polyphosphate has only phosphate to phosphate esters;
I would want to hear from CHEBI also (I put ticket in https://github.com/ebi-chebi/ChEBI/issues/4303)
GO:0008486 diphosphoinositol-polyphosphate diphosphatase activity,
has polyphosphate in the term name
EC:3.6.1.52:   again, a sib of EC:3.6.1.10;
The RHEAS associated with 3.6.1.52 (three, GO:0008486 diphosphoinositol-polyphosphate diphosphatase activity
has polyphosphate in the term name) uses the exact substrate name in the reaction.

Note also that the gene product for arg82 is described as a "polyphosphate kinase"
https://www.yeastgenome.org/locus/YDR173C
and UniProt, eg human
https://www.uniprot.org/uniprotkb/Q8NFU5/entry
but here the specificity doe not seem to be phosphate-phosphate esters:

If CHEBI is correct, these will also need fixing.

@hdrabkin I agree. The definition fits EC 3.6.1.10 for which the substrate is a polymer of phosphate units.
In all the terms @ValWood suggests could be child terms, the 'poly' refers to a number of phosphate groups attached to a nucleoside or inositol. The same is true for arg82.

Right so this is all OK? Close?

authors: ValWood hdrabkin kaxelsen


text:
astral spindle assembly (possible obsoletion)

Astral spindle assembly appears to be the same as 'normal spindle assembly'
as opposed to "anastral spindle asssembly'
It has only 3 EXP annotations (drosophila). @hattrill  can you comment on this term, and if it would be appropriate to migrate your annotations to the corresponding canonical spindle terms?

Some context:
The spindle assembly organization in GO is independent of the type of MTOC:

but then we have children:
GO:0090307    mitotic spindle assembly | is_a
GO:0051255    spindle midzone assembly | part_of
GO:0055048    anastral spindle assembly | is_a
GO:0055049    astral spindle assembly | is_a
GO:0090306    meiotic spindle assembly
so we have 2 axis of classification, anastral and astral are not much used. What do anastral spindles do? are they still:
The aggregation, arrangement and bonding together of a set of components to form the spindle, the array of microtubules and associated molecules that serves to move duplicated chromosomes apart.

I will have a look. Probably some phenotypic thing.

Of the 3 annotations, 1 is FB, the other 2 are UniProt.
FBgn0021761	Nup154 (UniProt)
FBgn0037301	Mms19 (UniProt)
FBgn0262598	mtsh (FlyBase)
Looking at them, I am happy for you to obsolete this term as there seems nothing special about this - for mtsh and Nup154, they are indirect/phenotypic. Mms19 is probably worth UniProt having another look at PMID:33211700 again to see what the best BPs are to describe it's action.

@Antonialock  could you have a look at these 2 uniprot annotations?

I think the term can go?
I think the term might mean to distinguish between "inner spindle microtubules" and "astral microtubules"?
this paper mentions it (referenced in the mms19 paper):
https://www.sciencedirect.com/science/article/pii/S0960982219309418?via%3Dihub
this wikipedia graphic also shows the various MTs associating with spindles

I moved the mms19 annotation to "astral microtubule organization"
based on
" It thus appears that Mms19 might bind along the surface of MTs, facilitating their assembly or stabilizing MTs, and possibly stimulating inter-MT contacts."
I deleted the nup154 annotation

so it was referring to  the assembly/polymerization of
GO:0061673  mitotic spindle astral microtubule
In that case good to obsolete because it's meaning was ambiguous (i.e a type of spindle, or part of the spindle)

I believe so.

Action
obsolte
GO:0055049    astral spindle assembly
and make it a related synonym of
GO:0051225  spindle assembly

Also GO:0055050    astral spindle assembly involved in male meiosis

I didn't create an annotation spreadsheet as annotation were removed during the discussion.

authors: Antonialock ValWood hattrill


text:
Obsoletion request: cell surface bile acid receptor signaling pathway

cell surface bile acid receptor signaling pathway
has the same meaning as G protein-coupled bile acid receptor activity

Yes, they are related as the MF is part_of BP. Which one should be obsoleted?

'cell surface bile acid receptor signaling pathway'
G protein signaling is more specific
Thanks, Pascale

Sorry, I don't understand. You want to merge the pathway, a BP into the receptor activity, an MF? They don't have the same meaning. As of now, MF is part of BP, which seems to be correct.
Although at the moment the only annotations to the BP "GO:0038184 cell surface bile acid receptor signaling pathway" are the receptors, there is more known about the pathway, e.g. PMID:36409000. If we obsoleted it now, we may have to resurrect it soon.

Hi @raymond91125
Sorry I pasted the wrong terms. We need to fix both MF and BP here
MF

[ ] obsolete grouping class bile acid receptor activity
with CONSIDER G protein-coupled bile acid receptor activity and  (lithocholic acid receptor activity).
[ ] add synonym 'farnesoid X receptor activity' and  'farnesoid X nuclear receptor activity'
[ ] (lithocholic acid receptor activity): add parent: nuclear receptor activity (please also keep the signaling receptor activity parent)  (see for example https://pubmed.ncbi.nlm.nih.gov/12016314  and https://pubmed.ncbi.nlm.nih.gov/11248085/ )
[ ] check references for both terms
[ ] add the new PubMed you cite (PMID:36409000) as a reference to both terms

BP

[ ] obsolete grouping class bile acid signaling pathway (used inconsistently) with CONSIDER cell surface bile acid receptor signaling pathway and intracellular bile acid receptor signaling pathway
[ ] cell surface bile acid receptor signaling pathway >> change label to 'adenylate cyclase-activating G protein-coupled bile acid receptor signaling pathway'
[ ] >> move as a child of adenylate cyclase-activating G protein-coupled receptor signaling pathway
[ ] >> fix definition like that of siblings
[ ] >> add reference PMID:36409000

I hope this is clearer!
Thanks, Pascale

lithocholic acid receptor activity, by its definition and references cited, actually is a grouping term of vitamin D receptor (PMID:12016314) and G-protein coupled receptor (PMID:12419312).
PMID:35415765 and PMID:32480317 are more recent review articles.

Note that PMID:32480317 Table 1 shows that there are cell surface bile acid receptors other than TGR5 (adenylate cyclase pathway), e.g.  S1PR2, PMID:28120434, muscarinic receptor, PMID:12924634.

I think the muscarinic receptor is G protein-coupled acetylcholine receptor signaling pathway involved in heart process

Do we want to retain a grouping BP term?

For bile acid receptor? If this is what you're asking, no; this is too confusing; people should be able to pick which pathway it is.

@pgaudet I understand that your desire to reduce inconsistent annotations by obsoleting bile acid receptor activity and bile acid signaling pathway. However, once they are gone, the two general types of bile acid receptor/response will then not be linked together in the ontology. Wouldn't this be a potential issue for enrichment analyses by reducing recall? A more conservative approach would be to make these two terms do_not_annotate and request that annotations be moved to terms more specific. Would that work?

Hi,
I made the changes suggested above, added referenced from the comment https://github.com/geneontology/go-ontology/issues/26958#issuecomment-1942924038
I kept the BP 'bile acid signaling pathway' to group both pathway (and the MFs), but made that term 'do not annotate'.
I have added logical definitions for the signaling pathway terms:
GO:0038184  adenylate cyclase-activating G protein-coupled bile acid receptor signaling pathway
is_a adenylate cyclase-activating G protein-coupled receptor signaling pathway
and starts_with GO:0038182 ! G protein-coupled bile acid receptor activity
GO:0038185  intracellular bile acid receptor signaling pathway
is_GO:0141193 ! nuclear receptor signaling pathway
and starts_with GO:0038186 ! bile acid nuclear receptor activity
Thanks, Pascale


text:
add synonym to pigment cell diff

Please add chromatophore differentiation as a synonym
for pigment cell differentiation GO:0050931.  Also add
the comment:
Note that this process is distinct from the pigment
bearing structure found in certain photosynthetic
bacteria and cyanobacteria, or the chromoplast of
plants, which are also sometimes called chromatophores.
Reported by: mellybelly
Original Ticket: "geneontology/ontology-requests/3176":https://sourceforge.net/p/geneontology/ontology-requests/3176

thanks www.movied.org


text:
Document ObjectProperties/patterns for use in TC plugin

Which OPs/patterns does the plugin work for?
This is a good opportunity to standardize across OBO

all instances of C must be in T: C SubClassOf in-taxon some T // no need for only-in-taxon if in-taxon is functional
no instances of C are in T: C SubClassOf in-taxon only not T
there exists some instance of C in T (currently only used in Uberon): keep as annotation assertion for now?

Will the PTC plugin would with 1 + 2?
Note for 2 we have historically used an AP. This will still be necessary if ontology maintained in .obo. But we can standardize to the most precise OWL for use with this tool

+1

Modification of the above, allowing for a canonical logical representation and a canonical shortcut

all instances of C must be in T:
a. Logical: C SubClassOf in-taxon some T // no need for only-in-taxon if in-taxon is functional
b. Shortcut: no need
no instances of C are in T:
a. Canonical logical representation: C SubClassOf in-taxon only not T
b. Alternative EL logical representation: C disjointWith in-taxon some T (depends on injecting GCIs into NCBITaxon)
c. Canonical Shortcut: AnnotationAssertion: C never-in-taxon T
there exists some instance of C in T
a. Canonical logical representation: [a C]  Type in-taxon some T
b. Canonical shortcut: C present-in-taxon T

Note: none of the above can be considered to be statements about evolutionary gain or loss
It's important for us in GO to be able to indicate

gain in ancestral node X
lost in ancestral node X

@thomaspd's proposal here:
https://docs.google.com/presentation/d/1Z3d8SBz-BWHPV5a9oaniPypZIYzV7VzBwVcleLdpk_c/edit#slide=id.p
This essentially adds a qualifier to a TC such that it can be declared GLOBAL strengthening the meaning

Only in = Gained at the specified branch in evolution
Never in = Lost at the specified branch in evolution

These could be represented by paired statements. cc @balhoff

authors: cmungall matentzn

repo: geneontology/protege-taxon-constraints


text:
Abandoned?

Noticed the recent dependabot PR merges but your NPM repo was updated 8 months ago. Has this project been abandoned? Are you planning to push these changes to NPM any time soon?
Just wondering because it looks like a fantastic project.

@FacePalmDev not abandoned. Thank you :).

authors: FacePalmDev generalpiston

repo: generalpiston/typeorm-encrypted

license: MIT


text:
Net connections not closing automatically

When we drop the server, the socket is not unbound
When we drop client, connection is not killed

not sure what this was about LUL

repo: geng-engine/geng


text:
Add checklist of how to structure a pull request

Feel free to suggest improvements to this checklist.

@romunov There are additional aspects that might be included in PR checklists. Please consider adding them:

image testing: test build should still be done on a local computer, to validate that the image builds OK (cannot be done from PR)
image validation: one should attempt to use the test build of the image in a resolwe-bio test (or similar). This is shared responsibility between the one making the PR and the review-er.
for new image folders, the corresponding image folder/project needs to be created beforehand on AWS ECR for image push to succeed.

Thank you @jkokosar and @AnzeLovse for the comments. After thinking a bit more about this, I have split the document into two sections. One is about building a Docker image from scratch, the other one is updating the existing image. I believe these two processes are different enough to warrant at least their own section.

Commits are now squashed. Feel free to merge if there's nothing else.

source: gharchive/pull-request

authors: jkokosar romunov

repo: genialis/resolwe-docker-images


text:
Remove in-memory tableInfoStore

This PR simplifies how we are handling table information. Currently, table information is loaded in memory on database startup. This was done to fix issues with concurrent table creation with the badger engine, but I believe this is not the right solution for that problem.
With this change, table information is not cached anymore and directly fetched from the engine.

Codecov Report

Merging #322 (df665b6) into main (707824d) will decrease coverage by 0.38%.
The diff coverage is 51.89%.

@@            Coverage Diff             @@
##             main     #322      +/-   ##
==========================================
- Coverage   61.94%   61.56%   -0.39%
==========================================
  Files          74       74
  Lines        6877     6816      -61
==========================================
- Hits         4260     4196      -64
- Misses       2056     2069      +13
+ Partials      561      551      -10

Impacted Files
Coverage Δ

database/config.go
61.45% <35.84%> (-7.58%)
:arrow_down:

database/database.go
56.14% <71.42%> (-1.49%)
:arrow_down:

database/transaction.go
62.56% <89.47%> (-0.08%)
:arrow_down:

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update 707824d...df665b6. Read the comment docs.

authors: asdine codecov-io

repo: genjidb/genji


text:
Possibly support MAF file with all upper case column headers?

Some centers submit MAF files with all capitalized headers.  Due to this, in my processing code I actually capitalizes the headers to resolve this issue.
Do you know if Genome Nexus will annotate a maf file with all capitalized headers?  I know vcf2maf also accepted all capitalized headers.

I will need to double check this... off the top of my head I want to say that no, the annotator will not work for these. I will follow up with the answer.

@thomasyu888 I annotated a MAF with all uppercase column headers and technically the answer to whether Genome Nexus will annotate these kinds of MAFs is yes HOWEVER, certain columns that are added by the Genome Nexus annotator will be duplicated..
The standard MAF headers will be adjusted to their proper casing in the output annotated file. However, there are extra columns that the annotator adds that will basically be duplicated.
For example, if you are running a MAF through the annotator that has a column "CODONS", then the annotator will generate a file with columns "Codons" and "CODONS". "Codons" is a field that is added by the annotator and "CODONS" is the field that existed in the input file.
I see 2 possible solutions... either (1) adjust the standardize_mutation_data.py script to ignore case when resolving data from a MAF (so either HUGO_SYMBOL or Hugo_Symbol) would be treated the same way or (2) adjust the annotator so that duplicate columns are not introduced.

Hmm... would standardize_mutation_data.py remap the columns?  I feel like this could be cumbersome.
Do you know if Genome Nexus duplicates all of the columns or just the ones it also writes out?  For instance, if the maf file had the column COLUMN_NOT_EXIST, does GenomeNexus write this out?

the script does not currently remap uppercase headers to their standard form.
Genome Nexus would retain a column such as COLUMN_NOT_EXIST since it is not part of the standard MAF header and it is not one of the fields that gets added due to annotation.

I see, so technically Genome Nexus would retain HUGO_SYMBOL because it is not a standard MAF header correct?   Instead of remapping, would it be better to add a flag to Genome Nexus to not retain such columns?

HUGO_SYMBOL would be remapped to Hugo_Symbol because the annotator will ignore case for the standard MAF columns

Hmmm, I think if we just turned the maf headers uppercase, then we would only have to worry about removing the duplicated columns

We won't be changing the casing of the MAF headers on our end as we want to continue following the MAF specifications. Another thing I would want to consider as well is if you're going to be removing duplicate columns as a post-processing step then you would just need to make sure that you retain a column like "Consequence" and not "CONSEQUENCE" as the former is how the Genome Nexus annotation is going to write out that data during annotation.

Thanks, so sounds like the solution for me is to map the column headers to the MAF specifications during an added preprocess step.  I wouldn't just be able to download the MAF and run it through the annotation scripts.
The advantage of this is that I wouldn't need to remove any duplicated columns as all the column headers will all have been remapped.  The downside is that script would have to updated alongside the growing MAF spec.

I believe the MAF specs have been stable for several years now, I dont think it'll be changing any time soon as it was defined as part of the TCGA project.

Closing and filed an issue for myself.

repo: genome-nexus/annotation-tools


text:
Making sure ARGextender uses the last version of PanRes

ARGextender uses an outdated version of the PanRes data. Make sure it uses the latest version by updating the database download and rules.

Using this as test case: https://www.ebi.ac.uk/ena/browser/view/ERR4678687

repo: genomicepidemiology/ARGprofiler


text:
when uploading layers reuse token so reader isn't closed premature.

closes #94
The idea is to save the token from r.initiateUpload so it can be reused for the layout PUT request. which saves one roundtrip, and doesn't close the reader.
Also in Basic Transport we don't set basic auth if Token exists, which is set in UploadLayer L:43 I don't know how to pass data to the caller other then adding header data to the response.

awesome
ci is failing because of gofmt: you can run:
gofmt -s -w registry/*.go

to fix... also there are some tests in the root of the project if you want to add one that would ensure this will not break in the future.

Since I'm hitting this issue:
@Vad1mo Can you recheck this? It looks like you put the wrong commit here or you force push the master before this pr was closed...
https://github.com/Vad1mo/reg/commit/75924f5572e192567c44efba1bb846f52acaf64a should be the correct. ?

yes Vad1mo/reg@75924f5  is correct, the function PutManifest  alone is not enough.

authors: Vad1mo jessfraz jkroepke

repo: genuinetools/reg


text:
fix overview deletion

[ ] I added an entry to CHANGELOG.md if knowledge of this change could be valuable to users.

Here is a brief summary of what I did:

Pull Request Test Coverage Report for Build 9977246456
Details

28 of 34 (82.35%)  changed or added relevant lines in 4 files are covered.
16 unchanged lines in 11 files lost coverage.
Overall coverage decreased (-0.002%) to 90.657%

Changes Missing Coverage
Covered Lines
Changed/Added Lines
%

services/src/pro/datasets/external/netcdfcf.rs
0
6
0.0%

Files with Coverage Reduction
New Missed Lines
%

services/src/pro/api/handlers/users.rs
1
95.75%

services/src/datasets/external/edr.rs
1
85.72%

services/src/datasets/external/netcdfcf/ebvportal_api.rs
1
89.32%

services/src/datasets/external/aruna/mock_grpc_server.rs
1
85.37%

services/src/pro/layers/postgres_layer_db.rs
1
96.09%

services/src/datasets/external/netcdfcf/ebvportal_provider.rs
1
92.36%

services/src/pro/datasets/external/netcdfcf.rs
1
0.0%

operators/src/processing/raster_vector_join/mod.rs
1
91.78%

services/src/api/handlers/layers.rs
2
88.8%

services/src/pro/contexts/postgres.rs
3
96.79%

Totals

Change from base Build 9957948370:
-0.002%

Covered Lines:
133339

Relevant Lines:
147081

💛  - Coveralls

authors: coveralls michaelmattig

repo: geo-engine/geoengine


text:
Correction

corretion

correction

repo: geoffreyarthaud/oc-install-ide-cours


text:
Invalid Polygons and Points are reported valid

Polygons without coordinates and Points with multiple Points are reported as valid, but the spec says it's not.
Examples:
{
  "id": "ABC",
  "type": "Feature",
  "bbox": [-70.275032,-64.72924,-65.087479,-51.105831],
  "geometry": {
    "type": "Polygon",
    "coordinates": [
    ]
  }
}

Building on @m-mohr's example.
This example with a single point with a single coordinate passes validation:
test.json
{
  "id": "ABC",
  "type": "Feature",
  "geometry": {
    "type": "Point",
    "coordinates":
        [-122.308150179]
  },
  "properties": {
    "name": "Dinagat Islands"
  }
}

Python script to test validation using jsonschema library
import jsonschema
import json

# Geojson schema to validate against
with open('geojson.json')as fp:
    geojson = json.load(fp)

# Test geojson to validate
with open('test.json')as fp:
    test = json.load(fp)

jsonschema.validate(test, geojson)

This issue is rather old, but since I'm currently analysing the latest JSON Schema draft, and came across this issue, I had a closer look at the examples, the GeoJSON schemas, and the GeoJSON spec:
Regarding the polygon example from @m-mohr : Section 3.1 of the spec appears to allow empty coordinate arrays:

A GeoJSON Geometry object of any type other than "GeometryCollection" has a member with the name "coordinates". The value of the "coordinates" member is an array.  The structure of the elements in this array is determined by the type of geometry.  GeoJSON processors MAY interpret Geometry objects with empty "coordinates" arrays as null objects.

So the example appears to be valid GeoJSON, minus the missing "properties" key. This is valid on https://www.jsonschemavalidator.net/ against the Feature schema:
{
  "id": "ABC",
  "type": "Feature",
  "geometry": {
    "type": "Polygon",
    "coordinates": [
    ]
  },
  "properties" : null
}

Regarding the point example from @jbants : On https://www.jsonschemavalidator.net/ the example is invalid against the Feature schema.

Yes, polygons with empty coordinates are valid.  And the current schema treats point coordinates with fewer than two values as invalid.  #28 adds the above examples to the test fixtures.

authors: jbants jechterhoff m-mohr tschaub

repo: geojson/schema


text:
Rectangle tool shows only three handles and won't finish on click.

Hi, I ran into a problem with the rectangle tool. Didn't manage to get it working on fiddle but here's a zipped folder with all code involded.
Run testbug.html and the problem reproduces.
As far as I can tell the other tools work as expected.
testbug.zip
l

Sorry for the late replay ... I have fixed this with the PR #993.
This is happening because of your custom CRS

No worries, I am mainly using the polygon tool.
Happy to have been able to offer a chance to further improve this excellent tool.
cheers Rene
On Sunday, October 3, 2021, 10:00:43 PM GMT+2, Falke Design ***@***.***> wrote:

Sorry for the late replay ... I have fixed this with the PR #993.
This is happening because of your custom CRS
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Fixed with Release 2.11.3

authors: Falke-Design renewestenberg

repo: geoman-io/leaflet-geoman


text:
KeyError on optional inputs

Description
I created a process with some optional inputs:
inputs = [LiteralInput('offset',
                       'Pagination offset',
                       data_type='integer',
                       default=0,
                       min_occurs=0)]

Running this in Apache/mod_wsgi, the apache log gives me:
[Tue Aug 16 12:03:11.269690 2016] [wsgi:error] [pid 11211:tid 140561246181120] [remote 127.0.0.1:42484] mod_wsgi (pid=11211): Exception occurred processing WSGI script '/var/www/html/wps/pywps.wsgi'.
[Tue Aug 16 12:03:11.269739 2016] [wsgi:error] [pid 11211:tid 140561246181120] [remote 127.0.0.1:42484] Traceback (most recent call last):
[Tue Aug 16 12:03:11.269761 2016] [wsgi:error] [pid 11211:tid 140561246181120] [remote 127.0.0.1:42484]   File "/usr/local/lib/python2.7/dist-packages/Werkzeug-0.11.10-py2.7.egg/werkzeug/wrappers.py", line 291, in application
[Tue Aug 16 12:03:11.270088 2016] [wsgi:error] [pid 11211:tid 140561246181120] [remote 127.0.0.1:42484]     return f(_args[:-2] + (request,))(_args[-2:])
[Tue Aug 16 12:03:11.270111 2016] [wsgi:error] [pid 11211:tid 140561246181120] [remote 127.0.0.1:42484]   File "/usr/local/lib/python2.7/dist-packages/pywps-4.0.0a2-py2.7.egg/pywps/app/Service.py", line 585, in call
[Tue Aug 16 12:03:11.270238 2016] [wsgi:error] [pid 11211:tid 140561246181120] [remote 127.0.0.1:42484]     request_uuid
[Tue Aug 16 12:03:11.270258 2016] [wsgi:error] [pid 11211:tid 140561246181120] [remote 127.0.0.1:42484]   File "/usr/local/lib/python2.7/dist-packages/pywps-4.0.0a2-py2.7.egg/pywps/app/Service.py", line 304, in execute
[Tue Aug 16 12:03:11.270278 2016] [wsgi:error] [pid 11211:tid 140561246181120] [remote 127.0.0.1:42484]     response = self._parse_and_execute(process, wps_request, uuid)
[Tue Aug 16 12:03:11.270293 2016] [wsgi:error] [pid 11211:tid 140561246181120] [remote 127.0.0.1:42484]   File "/usr/local/lib/python2.7/dist-packages/pywps-4.0.0a2-py2.7.egg/pywps/app/Service.py", line 338, in _parse_and_execute
[Tue Aug 16 12:03:11.270313 2016] [wsgi:error] [pid 11211:tid 140561246181120] [remote 127.0.0.1:42484]     inpt, wps_request.inputs[inpt.identifier])
[Tue Aug 16 12:03:11.270342 2016] [wsgi:error] [pid 11211:tid 140561246181120] [remote 127.0.0.1:42484] KeyError: 'offset'
It appears the parser is expecting an input for the offset parameter, but it's optional.
I was able to fix this with this simple change in the code:
diff --git a/pywps/app/Service.py b/pywps/app/Service.py
index 66b8843..67f10bf 100644
--- a/pywps/app/Service.py
+++ b/pywps/app/Service.py
@@ -330,7 +330,7 @@ class Service(object):

             # Replace the dicts with the dict of Literal/Complex inputs
             # set the input to the type defined in the process
-            if isinstance(inpt, ComplexInput):
+            elif isinstance(inpt, ComplexInput):
                 data_inputs[inpt.identifier] = self.create_complex_inputs(
                     inpt, wps_request.inputs[inpt.identifier])
             elif isinstance(inpt, LiteralInput):

Not sure if that was the intended behaviour or if there's more going on here...
Environment

operating system: Ubuntu 16.04
Python version: 2.7.12
PyWPS version: 4.0.0-alpha2
source/distribution

[x] git clone
[ ] Debian
[ ] PyPI
[ ] zip/tar.gz
[ ] other (please specify):

web server

[x] Apache/mod_wsgi
[ ] CGI
[ ] other (please specify):

Steps to Reproduce
Additional Information

@bstdenis I'm unable to reproduce with (in master):
        inputs = [
            LiteralInput('name', 'Name', data_type='string', default=0, min_occurs=0)
        ]

Any chance you can provide a class as a minimum test case?

@tomkralidis I currently have problems testing with the master branch because of #183 but it seems the problematic part I was mentioning is going to be modified by pull request #188
I will wait for that to do further testing, thanks.

@bstdenis could you please confirm, that both #183 and #154 issues are ok in current master?

@jachym Yes, everything now works as expected in my limited tests. Thanks!

I also had a similar issue #203, but after updating the latest version, I could solve that.

authors: bstdenis geoslegend jachym tomkralidis

repo: geopython/pywps

license: mit

license_source: bigquery


text:
🛑 NYCResistor Wiki is down

In 690fff3, NYCResistor Wiki (https://wiki.nycresistor.com) was down:

HTTP code: 0
Response time: 0 ms

Resolved: NYCResistor Wiki is back up in 0918a1f after 11 minutes.


text:
PreparedGeometry::contains is not thread safe before run at least once

Hi,
It seems that prepared geometry contains is not thread safe before run at least once. Easiest to provoke on large geometries. Not able to provoke on example in docs.
Regards, Gaute

Can you provide me a code having this issue so I can fix it and enforce it through tests please?

https://github.com/gauteh/roaring-landmask/pull/6/files#diff-6423871468d8d2f4ebf2a85e879f9ba388c361b859c9191d62d4571685c95f58 , I think you need a big geometry for this to trigger.

Ok, I'll try to take a look when I have a bit of time.

:+1: thanks. I can work around this atm by using a warmup call. It is most likely an upstream bug. But would be a pity to !Send/!Sync Geometry/PreparedGeometry just because of that.

Don't hesitate to take a look in the meantime. If yu can find a way to go around this limitation without removing Send and Sync, it'd be perfect. :)

If we can afford a warmup call to contains, that is the only way I can
think of at the moment (without fixing upstream). From the backtrace in
geos it seems like the segfault happens somewhere in sorting of a vector in
the geometry. I'll take a further look if(/when..?) I find the time!
On Wed, Sep 8, 2021 at 8:33 PM Guillaume Gomez @.***>
wrote:

Don't hesitate to take a look in the meantime. If yu can find a way to go
around this limitation without removing Send and Sync, it'd be perfect. :)
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Thanks, greatly appreciated! A bit under the water currently. ^^'

No problem, thanks for the effort!

In version 9 with geos 3.11 it is no longer reliable to warm up the prepared geometry to make it thread safe.

This is still the case, I don't know how to fix this. PreparedGeometry is not thread-safe.
This test fails: https://github.com/gauteh/roaring-landmask/blob/main/src/lib.rs#L328
While this is ok: https://github.com/gauteh/roaring-landmask/blob/main/src/lib.rs#L283

Maybe related:

https://github.com/libgeos/geos/pull/826
https://github.com/libgeos/geos/issues/825

authors: GuillaumeGomez gauteh

repo: georust/geos


text:
Client - Implement ActionNavbar plugin

We should introduce a custom plugin used as container for links or toggle for other plugins that will be used for each editor route. This plugin will be placed on top of the page right after the brand navbar with following requirements:

allow configurations of links/dropdowns via localConfig.json
allow configuration of buttons/link/dropdowns from other plugin using the plugin container

If others plugins will be configured properly this plugin should recieve their configuration inside the items prop. See the Detail Panel #92 for an example of configuration.
The configuration for the menu items should follow the current structure provided by homepage described here https://github.com/GeoNode/geonode-mapstore-client/blob/master/geonode_mapstore_client/client/README.md but within this implementation we should start to normalize and make the configuration consistent among the menu components.
Important: This plugin/component is shared on all routes of the applications

Some additional notes:

1 we should evaluate how to refactor the current MenuIndex to be used inside the ActionNavbar plugin and in the search page as component. The ActioNavabar should be composed by two menu one on the left the other on the right. The left menu should fill all the available width space (flex 1 ?) while the right one only its own actual content.

2 Remove the current swipe behaviour in favor of a dropdown. The menu should compute if all the menu item are visible or not and show them in a dropdown based on this computation. The dropdown should show the items as a flat list so no nested dropdown. The right menu is should be used only for a small counts of item so they should be always all visible. (the draggable and tabindex on current tag and link component were needed only for the swipe menu so they can be removed)

3 We should evaluate on how we should controls the margin/padding on this navbar because in the current mockup the homepage/search expect a margin while the editors the navbar on the full extent of the width

We discussed and agreed that the previous proposed solution it's not working as expected and it has a bad UI/UX for a web page.

so we agreed to make something more simple such as this sketch

repo: geosolutions-it/nexus-geonode


text:
The size of entity labels with title h2/h3

Resolves #107

won't do

authors: joschne perrauda

repo: geovistory/design-system


text:
Replay button

Hi @gereleth! We were chatting about recording videos of solve strategies, so I started experimenting with a "replay" button. The advantage is it doesn't record the time spent thinking. (Also I think it's better not to record the panning and zooming.)
I was surprised how easy this was to implement.
Code on my replay branch is rather rough, but it basically works. Preview here: https://penrosepipes-git-replay-gordonwoodhull.vercel.app
Here is a video of a partial solve of a trihexa in "proofs mode":
https://www.youtube.com/watch?v=FS926PZWwPI
Here's a complete trihexa solve, recorded on my tablet, where I prefer to play:
https://youtu.be/hpJTyRG_Y2k?feature=shared
Would be glad to clean up this code you're interested.
Known bug: if you click replay twice it goes haywire replaying every move twice!

This looks somewhat similar to the undo feature I worked on. And I just realized I never published that branch...
I have this video of a full undo/redo of a puzzle: https://x.com/gereleth/status/1706761417838231581
But I got bogged down trying to come up with how zoom/pan should be handled when undoing and never finished it.
Regarding solve videos I think it's more interesting to watch a sped up actual solve =). I made this recording for comparison (3x my actual speed). I think the cursor hovering around makes it more obvious where your attention is so the process is easier to follow.
https://github.com/gereleth/hexapipes/assets/6080076/1ba907bf-7009-460f-9f72-e7b72a851c64

Undo/redo would be nice!  IMO zoom/pan are orthogonal & should not be put in the history, but that's just my opinion.
Huh, yeah the cursor is nice. I mostly play on tablet,  and I spend a lot of time just looking for things, so I wouldn't record that way.
Oh well.

authors: gereleth gordonwoodhull

repo: gereleth/hexapipes


text:
add "design-evolution" to documentation

show how the internal design evolved over time with additional requirements

created evolution.adoc, need to hyperlink from other parts of documentation

repo: gernotstarke/cirQlizr


text:
Reorganize "University Course Programs" Section and Add USA PhD Programs

For issue #59

thanks for your efforts!


text:
[Suggestion] Don't Delete convex.json When Running npx convex dev

Background Information
I'm developing a project within a team wherein our React client consumes the Convex API. As of the moment, the onboarding process and development environment setup is quite cumbersome due to unintended(?) actions caused by npx convex dev.
We have a client/convex.json file that specifies the following information that is crucial to the functionality of the client side:
{
    "functions": "./src/_convex"
}

Running npx convex dev and going through the setup wizard deletes this file and then results in a [CONVEX Q(files:getFilesByDocumentId)] Could not find public function for 'files:getFilesByDocumentId'. Did you forget to run `npx convex dev` or `npx convex deploy`? error.
Demo

The Suggestion
If it's possible, npx convex dev shouldn't delete these configuration files on directories without .env.local's Convex files. Or perhaps, the wizard can ask questions if there is an existing configuration files or if there are files to ignore during the initialization process.
Also, an npx convex dev --verbose flag would be nice to see explicit updates on any file changes.

@Luzefiru that sounds like a bug. We'll look into it. Meanwhile make sure you are on the latest version of convex, as the issue might have already been fixed.

I think this was fixed a while ago, testing with 1.13.1 it is no longer an issue.

authors: Luzefiru thomasballinger xixixao

repo: get-convex/convex-js


text:
feat: Add emergency kit screen to set pending orders to failed

Introduces an emergency kit section to the settings to cleanup pending orders. I think this pattern might be useful in the future to selectively fix broken states on the app site.
https://github.com/get10101/10101/assets/382048/451155d8-b11a-4ebf-8a8c-1be8e3be7845

What's the side effect of setting Filling orders to failed`? If we get a match later on, we would simply fail right?

Can't predict all side effects, but in the case if we would have a regular order which gets executed. We would get an error when trying to set the order to Filled as the Filling order was not found. That would also prevent the position from getting created on the app side, but the dlc channel would be set up.


text:
post 返回直接是 byte类型 咋用？

post 返回直接是 byte类型 咋用？

小伙子，你试试看这样行不行？

EasyHttp.post(this)
        .api(new XxxApi())
        .request(new HttpCallback<Byte>(this) {

            @Override
            public void onSucceed(Byte result) {

            }
        });

超过三天没有响应，关闭此 issue。

repo: getActivity/EasyHttp


text:
语言切换错乱

我下载代码运行测试了一下，发现以下问题：
1.MultiLanguages Demo   杀掉程序 -> 进入应用 -> 切换语言：有不小概率出现切换错乱的问题，如本来要切换到繁体，实际切成了简体
2.在AndroidProject项目中使用MultiLanguages，发现杀掉程序再次进入应用，应用语言恢复成了系统语言。我拷贝了以前自己写的语言切换代码用到AndroidProject项目中，仍然有杀掉程序再次进入应用，应用语言恢复成了系统语言的问题。

框架版本号是多少，手机的品牌、型号、Android 版本是什么

小伙子，根据你提供的复现步骤，我并不能复现这个问题，能否录个视频过来我看一下

问题已经解决，后续会发布修复版本

authors: ChunmingWu getActivity

repo: getActivity/MultiLanguages


text:
[BUG] Hard to see three dots on Accounts page (Dark Mode)

Is there an existing issue for this?

[X] I have searched the existing issues

Describe the bug
It's hard to see the three dots to edit an account on the Accounts page when in Dark Mode.
Please increase the contrast on the three dots so it is easier to see.
Screenshots [optional]

Steps To Reproduce

Enable dark mode (browser/OS)
Go to settings
Click on Manage accounts
Look for the three dots

Expected behavior
It should be easy to see that there are three dots for each account so the user can edit/remove them.
Alby information

Version 1.18.0
Installed manually

Device information

OS: Mac OS
Firefox Developer Edition 107.0b2 (64-bit)

Additional context
No response
Are you working on this?
No

@secondl1ght any idea how to make this more prominent in dark mode?

Maybe add a border and make the dots a bit whiter?

Maybe add a border and make the dots a bit whiter?

Love it! wdyt @reneaaron @dvoroneca ?

+1

authors: Cameri bumi escapedcat im-adithya

repo: getAlby/lightning-browser-extension


text:
Guru Claim Request (trame+vtk)

Guru: https://gurubase.io/g/trame

Guru: https://gurubase.io/g/vtk

Done! 🚀

I'm closing this one. Feel free to reach out here or on Discord if you need any help

authors: jourdain kursataktas

repo: getanteon/gurubase


text:
Run tests on GitHub Actions against earliest and latest SDK

As discussed at https://github.com/getappmap/appmap-intellij-plugin/pull/553, it would be helpful to not just run tests against the earliest supported SDK.

:tada: This issue has been resolved in version 0.73.0 :tada:
The release is available on:

v0.73.0
GitHub release

Your semantic-release bot :package::rocket:

authors: appland-release jansorg

repo: getappmap/appmap-intellij-plugin


text:
Error response are gibberish \u001f\b\u0000\u0000\u0000\u0000\u0000\u0000\u00004»\u000eÂ0\fEÅ\nk\u001fRÅÔ\u001f\bi-µq°ÝJ¨ê¿\n\u0018,ÝáÜ{¼95oºþÜu3²\t]ïn¤Ji\u0000\u0016 \u0014X\

Do you no why my error responses from BigCommerce are not readable?

"error": "Error: Request returned error code: 422 and body: \u001f\b\u0000\u0000\u0000\u0000\u0000\u0000\u00004»\u000eÂ0\fEÅ\nk\u001fRÅÔ\u001f\bi-µq°ÝJ¨ê¿\n\u0018,ÝáÜ{¼95oºþÜu3²\t]ïn¤Ji\u0000\u0016 \u0014X\u0004àk!Á\bOÂ)ª+ø;\u001fôhµoÛ+NQ\u0007\rç\u0019%`SBë3ÊÕ_Y\u001d8âÑG\u0011âÞÜê|²2v\u001fI!\u000bÇ¥(G¯ÀÙVðcàzü¿qûþ\u0001\u0000\u0000ÿÿ\u0003\u0000ÿ\u001byÇÅ\u0000\u0000\u0000"

That's a gzipped response. You are likely not setting the version to v3 (default is v2)

@ohabash You're likely using Ngrok to test the API. You can see the responses in Ngrok's console. (That was my case at least)

2 things that really helped me out @ohabash....

For the instance of new BigCommerce, make sure you're using the one that corresponds to the BigCommerce documentation.  So like for /v2/stores, set it to v2.

Make sure you only use the characters after the '/' (slash) when passing the store hash to make sure it forms the URL correctly.

I hope this helps you, and anyone else that may be having issues.

the solution for me was to switch my version of node-bigcommerce to 3.0.0

My errors are "gibberish" aswell.
This code returns the error message which I added as an image.
const BigCommerce = require('node-bigcommerce');
const bigCommerce = new BigCommerce({
    logLevel: 'info',
    clientId: `${ENV.CLIENT_ID}`,
    secret: `${ENV.CLIENT_SECRET}`,
    storeHash: `${ENV.CLIENT_STOREHASH}`,
    accessToken: `${ENV.CLIENT_ACCESSTOKEN}`,
    responseType: 'json',
    callback: `/auth`,
    apiVersion: 'v3' // Default is v2
});

bigCommerce.post(`/checkouts/${checkoutId}/orders`)
    .then(orderId => {
        console.log(orderId);
        // req.session.orderId = orderId
        resolve(orderId)
    })
    .catch(err => reject(err))

Is there something I can do about this?

@meesrutten Go to: http://127.0.0.1:4040/inspect/http and inspect the requests (if you're using ngrok, that's what helped me debug the responses)

I'm not using Ngrok, just Nodemon...

@meesrutten Yeah, I believe you're right. I think my case was a bit different. This one is probably due to this way content-encoding is handled inside the library itself.  Someone mentioned that using version 3.0.0 works for them.

Hmm, problem is still not resolved

@meesrutten This just came up to my mind but check on your app settings if you have the right scope. It's in #3 technical details when you choose edit app. I hope that's what's going on for you.

@youssseeef, I think you may have found the issue he was having, but not that the error response was gibberish.  I opened https://github.com/getconversio/node-bigcommerce/pull/71 to address this, as well as any future issue regarding BigCommerce request headers.

I have same gibberish problem...  In Postman the Error is correctly rendered.  I'm sucessfully firing off on the same path so it is not a config or a "v3" setting.  I'm purposefully firing an error to see the result.   The status codes are correct.. the Gibberish is present in the Error Message.

I believe that the error handling may not handle decompression...
      if (res.statusCode >= 400 && res.statusCode <= 600) {
        const error = new Error(`Request returned error code: ${res.statusCode} and body: ${body}`);
        error.code = res.statusCode;
        error.responseBody = body;  <==== ERROR NOT DECOMPRESSED??

        return reject(error);
      }

      // Use GZIP decompression if required
      if (shouldUnzip) {
        const unzip = contentEncoding === 'deflate' ? zlib.deflate : zlib.gunzip;
        return unzip(Buffer.from(body, encoding), (err, data) => {
          if (err) {
            return reject(err);
          }
          return parseResponse(res, data.toString('utf8'), resolve, reject);
        });
      }

      return parseResponse(res, body, resolve, reject);
    });
  });

Version 4.0.1 of this library still returns gibberish:

authors: meesrutten napalm272 ohabash philspitler richardkeller411 youssseeef

repo: getconversio/node-bigcommerce


text:
Windows 10 need --vs2015 for building

In the readme it is asking to use this command line for windows;
$ npm install --global windows-build-tools // Windows 10
$ npm install --global windows-build-tools --vs2015 // Windows 7

but I just did a build of Ferdi with this commit 4cb24eb and I was getting error when using this line;
npm run rebuild
So I used the command line for windows 7 (in my windows 10 machine) and after re-using rebuild and build.. everything worked.
So my suggestion is to do
this
$ npm install --global windows-build-tools // Windows 10
$ npm install --global windows-build-tools --vs2015 // Windows 7

to this
$ npm install --global windows-build-tools --vs2015

Addressed via https://github.com/getferdi/ferdi/commit/33a1daa4dc0a01a8d2fd68300ddd63503aab8d41. Thank you for testing on Windows 10 and reporting.

For more information in the error log it was saying that the build was needing Visual Studio v140 (so VS2015) and not 2017 for windows 10

authors: Makazzz kytwb

repo: getferdi/ferdi


text:
Not working in 3.4

Latest update causes the following error:
Please select one or two layers.
Even if i select two layers.

here too

Yup, same!

I think this can be closed, as it seems to be working in latest Sketch 41.2

authors: A7DC Arkkimaagi chrleon ultradeck


text:
[add-resource] New Widget Plugin

I would like to add my new widget plugin to the Grav Repository.
Here are the project details: sojimaxi/grav-plugin-widget
The plugin works by using modular templates and pages as reusable widgets to displayed in various page templates.
It's a cool plugin i created to help me with my current project
Thanks
Soji

Thanks, you need to make the version in the blueprint match the release tag: https://github.com/sojimaxi/grav-plugin-widget/blob/master/blueprints.yaml#L2 (re-release and make it 1.0.1

Thanks a lot @flaviocopes. The plugin has been updated to version 1.1.0 with a new feature

Added for next GPM update.

authors: flaviocopes rhukster sojimaxi

repo: getgrav/grav


text:
WIP: Convert all node compilers

This PR shows how I intend to convert the remaining node compilers. This one has all the node compilers converted, using a few techniques:

Added a NodeCompilationContext to bundle the various arguments passed to node compilers.
Added a from_node_with_rhs() trait method that can be used to pass is_rhs when desired.
As a bonus, all node compilers now take a NodeWithSource instead of Node. This, plus, the NodeCompilationContext enabled a lot of code simplifications.

Of course this PR is too large now and the tests still fail, so I’ll start cutting out some smaller pieces and submit those for review instead. But the updating of the signatures will remain a large PR regardless.
cc @morgante

This approach looks reasonable, happy to review a PR switching the signatures over.

authors: arendjr morgante

repo: getgrit/gritql


text:
Pointing assets to http:// instead of https:// when loading https:// domain

Describe the bug
Hi, I don't know why this is happening but the indiekit server is pointing to http version of assets when loading https://
    <link rel="icon" href="http://server.rafaj.dev/assets/icon.svg"/>
    <link rel="mask-icon" href="http://server.rafaj.dev/assets/icon.svg" color="#0055ee"/>
    <link rel="stylesheet" href="http://server.rafaj.dev/assets/app.css"/>

I am using nginx in front of the server and redirecting with 301 everything http to https but firefox keeps blocking http requests.
To reproduce
Steps to reproduce the behavior:
https://github.com/danielstaleiny/rafaj.dev-micropub/blob/master/config.js
Expected behaviour
Load resources from https://
Screenshots or logs
because my browser is blocking http assets, result page looks like this

(ignore the yellowish background-color instead of white (I am overriting it in defaults.))
Environment

Indiekit version: [e.g. v0.1.0-alpha.9]
Browser: [Firefox 85.0]
Server/host: [DigitalOcean/NixOS]
Content store URL: [
https://github.com/danielstaleiny/rafaj.dev]
Publication URL: [rafaj.dev]

Additional context
beside this, Do I need to setup anything to accept micropub request on the endpoint ?

Same behaviour on Chromium 88.0.4324.146 , blocked mixed content.

Ah, think I might have an idea what’s happening here, will investigate.
As to set up; you don’t need to define the mediaEndpoint value if you want to use the one that’s already built in to Indiekit; that conflict value exists only if you want to use another URL for media uploads.

My requests were failing so I added it but I thought that is the case. I will remove it. :)) thank you. Let me know if you need any more information.

So this is where the URL gets set: https://github.com/getindiekit/indiekit/blob/b4f0ff94d244d0adcdff60a8100265a0402d9f64/packages/indiekit/lib/middleware/locals.js#L17

I am using nginx in front of the server and redirecting with 301 everything http to https but firefox keeps blocking http requests.

I’m wondering if this is the request from which Express is determining the request and its various properties before it’s all redirected to https. Why are you using nginx? You shouldn’t need any server for Indiekit to run.

Could you please elaborate why I don't need server for the indiekit to run ? I was in believe that if I want to post content from anywhere Mobile/desktop/laptop/web I would need to host it to reach indiekit instance.
For the issue:
Internal protocol might be http:// because I proxy to http://localhost:PORT which could cause this to resolve to http being the protocol. I will see if I can override the protocol on nginx side and report back.
Otherwise it would be maybe nice to force http/https by options {protocol: 'https'} or something like that. This would go into server(options)

Alright, setting X-Forwarded-Proto to 'https' on nginx side fixed the issue and everything routes to https instead :). Learned something new today.

Glad you got it sorted!

Could you please elaborate why I don't need server for the indiekit to run?

Indiekit is a server. Without getting into definitions of what a server is, it’s built upon ExpressJS, which is an application that, when run on a port, listens for and responds to HTTP requests. I’m hosting Indiekit on Heroku, so most of the setup is taken care off, but having a little experience of using NodeJS apps on my own web server, you just need to ensure Indiekit is running on a given port; maybe that’s what you’re doing here with nginx?
Can I ask, how have you got your server setup? Keen to make sure Indiekit works in different setups!

Yes, I am more than happy to.
I often host more than 1 app on server so 1 IPS instance is good enough to host everything there.
If you want to reduce downtime while your app is restarting you load balance it with nginx. (1 instance is updating/restarting while other one is serving content).
Because you want to have control what you have accessible from outside and how you want to integrate nginx. Nginx will take care of SSL, CORS, HEADERS, load balance, you can setup subdomains, you can setup subsection on your domain eg. domain.com serving website domain.com/api/ is serving api server. There is so much what you can do in terms of security, caching and other things with nginx that there are even frameworks like openresty which I use to secure my postgREST api.
So in nutshell, I often server multiple application and different types on server so I need to use nginx to take care of what is good at.
The endgoal is to create server with all the things you need to setup modern indieweb website with its own micropub microsub, reader, website, cms, api if needed. All this while being cloud agnostic. So I based everything on NixOS which is like orchestration tool operating system.
and by the way you also use load balancer but it balance trafik to your 1 instance of heroku, which does it for you out of the box.

Different topic.
Is there any community behind this which I can join ? where do you hang out ? I might have couple of questions.

Just worth noting, this project has not been designed to handle the levels of traffic where you’d need a load balancer! In most cases it should have a user base of 1!

Is there any community behind this which I can join ? where do you hang out ? I might have couple of questions.

No, and I’m reluctant to start one, as I’ve not got the time to moderate it. Happy to respond to issues and pull requests however. More general queries about IndieWeb can be posted on the IndieWeb chat, I’m on there sometimes, but not often.

authors: danielstaleiny paulrobertlloyd

repo: getindiekit/indiekit


text:
[Bug] - Wrong hash value is displayed in UI and sent in an (sub) environment

Insomnia Version: v5.12.0-beta.3
Operating System: Microsoft Windows 10, Version 1703 (Build 15063.632)

Details
When I create a second environment with different values for a handful of keys, the calculated hash value (SHA512) is wrong in the UI (URL preview and referenced environment variable), also in the sent request.
My Workspace: [Bug]-Wrong-hash-value-in-sub-environment_2017-11-27.zip
Environments
Base Environment
{
    "hash_input": "{{ orderid }}{{ secret  }}",
    "orderid": 123456789012345,
    "password": "{% hash 'sha512', 'hex', hash_input %}",
    "secret": "ThisIsATopSecretValue"
}

Expected password value
ea84d15f33d3f9e9098fe01659b1ea0599d345770bba20ba98bf9056676a83ffe6b5528b2451ad04badbf690cf3009a94c510121cc6897045f8bb4ba0826134c
Sub Environment
{
    "hash_input": "{{ orderid }}{{ secret  }}",
    "orderid": 987654321098765,
    "password": "{% hash 'sha512', 'hex', hash_input %}",
    "secret": "ThisIsASecondTopSecretValue"
}

Expected password value
2ce08c40004d7630ceca5065f9f9352cce228bba1ca192956e957c8ac65bea6d75c845107c6bef166646dc47648e15ba36b2631ca237d057d82cef34eac9f486
Wrong password value in UI
Independent from the selected environment the wrong password value is shown in the user interface. In my case there is neither the one from the base environment nor the one from the sub environment shown. The shown password is that old one before I change two values (password and secret) in the environment.
Also a restart of Insomnia does not change this behaviour.
Old password shown in UI
1d52c84df98483f75e166378f87721e0ec9a4b4edb0a1602c16e332e9d2febfb147ecf760bef5e74cb3a85bf501920261f887474d7e3e5f2ca0d177d6198ec51
Finally
I expect that a hash value is calculated properly for displaying it in the user interface and also for sending a correct request - depending on the selected environment.

I figured out the problem. It looks like Insomnia is not rendering the variable value first before being passed into the template tag. I printed out the arguments within the hash plugin and this is what I found:
HASHING sha512 hex {{orderid}}{{ secret  }}

I would expect it to be this instead:
HASHING sha512 hex 123456789012345ThisIsATopSecretValue

I'll see if I can get this fixed for the next beta

Should be fixed now in 5.12.0

authors: gschier op-mime

repo: getinsomnia/insomnia


text:
Figure out how the authentication mechanisms in go-swagger work

The swagger definition contains a securityDefinition:
securityDefinitions:
  bearer:
    type: apiKey
    in: header
    name: x-tfs-auth

With this enabled, adding security: [bearer: [] ] to a resource results in errors like:
server/restapi/operations/modules/list_modules.go:17:54: undefined: models.Principal
server/restapi/operations/modules/list_modules.go:20:78: undefined: models.Principal
server/restapi/operations/modules/list_modules.go:26:29: undefined: models.Principal
server/restapi/operations/modules/list_modules.go:59:17: undefined: models.Principal
server/restapi/operations/modules/list_modules.go:61:24: undefined: models.Principal

How authentication in go-swagger works needs to be figure out. There's a demo of the broken state in https://github.com/drewsonne/terraform-server/tree/feature/authentication
Deliverables:

A PR with the list-modules operation using an API key token.

This works now, and the auth structures are handled by the ApiKey handler, and users in the database.

repo: getlunaform/lunaform


text:
Account for text overflow in tables

Right now we account for possible text overflow in table cells in several places. However, I think there are other places in table cells where we still need to account for possible text overflow. (Example: The Created column of the app users table.) To account for overflow, we have typically used CSS like the following:
overflow: hidden;
text-overflow: ellipsis;
white-space: nowrap;

I'm going to go ahead and close out this issue. We've accounted for possible text overflow in more places since I first filed this issue three years ago, and we don't know of specific places where we don't account for it. This is something that the QA team seems to look for, which also gives me confidence. It's definitely possible that there are still places where we don't account for overflow, but I think we can just fix them as we discover them.

repo: getodk/central-frontend


text:
cassandra - Datastax4x upgrade

Fixes #2090
Problem
Cassandra Datastax driver upgrade - 4.x version APIs and configuration adjustments
Solution
Implemented changes and and refactoring in the modules:

quill-cassandra
quill-cassandra-zio
quill-cassandra-monix

the module origina library (lagom) uses oder (3.6x) version of datastax driver/
quill-cassandra-lagom

Adjusted sbt options to be able to run unit tests locally
https /apache site for the cassandra 3.11 binaries
minor/cosmetic changes to docker files.

Notes
Additional notes.
Checklist

[x] Unit test all changes
[X] Update README.md if applicable
[ ] Add [WIP] to the pull request title if it's work in progress
[x] Squash commits that aren't meaningful changes
[x] Run sbt scalariformFormat test:scalariformFormat to make sure that the source files are formatted

@getquill/maintainers

Also, thanks so much for this really, really great work!!!

Looks like the CI failed. Could you please double check the test configs?

could it be due to missing entries in docker-compose-m1?
I ran all tests locally last night...

Slightly different scripts are used for the Github Actions CI. It's the setup_bigdata.sh and some others. I don't think docker-compose-m1 is used.

Be sure to include CASSANDRA_CONTACT_POINT_0, CASSANDRA_CONTACT_POINT_1 and other new env vars into build.sh.

Be sure to include CASSANDRA_CONTACT_POINT_0, CASSANDRA_CONTACT_POINT_1 and other new env vars into build.sh.
Thank you for the lead!
added. definitely missed the point - I ran the tests via docker-compose sbt directly.

repo: getquill/quill


text:
Add a changelog in both packages to satisfy the pub.dev analyzer

the pub.dev analysis score removes 5 points when there is no changelog file in a package.
cf. #96

We could use a symlink (if pub publish supports that). And have a shared CHANGELOG.
Otherwise we'll need to maintain two changelogs, I'm afraid.

Once the Flutter package will use the native plugins, will the 2 packages be impact by the same changes ?

we already have symlinks, if pub publish doesn't support it, we'll reopen it

authors: bruno-garcia marandaneto rxlabz

repo: getsentry/sentry-dart


text:
Add sentry-electron cli command which uploads symbols for current electron dependency

You might want to add this to sentry-cli instead but it would be great to have a cli command somewhere which:

Downloads all symbols for the version of electron referenced in package.json using electron-download
Uploads these symbols to Sentry

So we already have such command in sentry-cli we basically only have to integrate it in a script.
https://docs.sentry.io/learn/cli/dsym/
We were also thinking about adding support for https://github.com/getsentry/sentry-wizard and help with the setup process like adding the DSN to the package.json and add a script for uploading symbols etc.

Ok having this in the wizard could make more sense.
I did see the sentry-cli commands to upload symbols but wanted something to automate the process, especially if I change the version of electron we're using.
Currently I'd have to run:
electron-download --version=1.7.11 --dsym --platform=darwin
sentry-cli upload-dif -t dsym  C:\Users\tim\AppData\Local\electron\Cache\
electron-download --version=1.7.11 --symbols --platform=win32 --arch=ia32
electron-download --version=1.7.11 --symbols --platform=win32 --arch=x64
electron-download --version=1.7.11 --symbols --platform=linux --arch=x64
sentry-cli upload-dif -t breakpad C:\Users\tim\AppData\Local\electron\Cache\

Having said that, with symbol server support maybe none of the above is required.

I will reopen this until we have that automated somehow.

ref: https://github.com/getsentry/sentry-wizard/pull/4

authors: HazAT timfish

repo: getsentry/sentry-electron


text:
fix: Sync global scope to main process

Closes #1022
To PR reviewers... am I merging the scopes with the correct hierarchy?

Perfect, thanks for the link!


text:
Should User ID be a String vs. Number?

When I have a user object, and pass the id property to addSession like so:
zep.memory.addSession({
  sessionId: sessionId,
  userId: user.id,
});

I get the following error:
Type 'number | undefined' is not assignable to type 'string'.
Type 'undefined' is not assignable to type 'string'. ts(2322)
• CreateSessionRequest.d.ts(20, 5): The expected type comes from property
'userId' which is declared here on type 'CreateSessionRequest'

Should this be a string? https://github.com/getzep/zep-js/blob/main/src/api/types/User.ts#L10

Ah, I'm guessing I should use the userId property.

Hi, thank you for bringing this to our attention, since the id field would seem confusing here.
It looks like using userId: user.userId! should work, assuming you have a setup like this:
const userId = "typescript-test-user1";
const sessionId = "typescript-test-session1";
const user = await client.user.add({userId: userId});
const session = await client.memory.addSession({
    sessionId: sessionId,
    userId: user.userId!,
});

Let us know if this works for you.

authors: jackaldenryan metaskills

repo: getzep/zep-js


text:
How to write back to sheets?

I know this is reading, but map sounds like a transform operation, where you take the original input and change it to something else :)

Hi, can you create a PR, that creates a writing function?

one of these days I will. For now I just used sheetsDB instead.

authors: adminy gglukmann

repo: gglukmann/google-sheets-mapper


text:
Black dots & Unable to decode on ST3 / Mac

The plugin shows black dots and "Unable to decode" messages in the ST console. See image for details.

@knightq
thank you. got that problem again, on Yosemite now, and that solved.

Reinstalling as @KNIGHTQ commented, and run also Brew list ImageMagick and look for the "convert". In my case: "/usr/local/Cellar/imagemagick/7.0.5-9/bin/convert"
Before
{
“convert_path” : “/usr/local/bin/convert”
}
Now:
{
“convert_path” : “/usr/local/Cellar/imagemagick/7.0.5-9/bin/convert”
}
I hope this works!

authors: fabianmu isaacalves luis3dms

repo: ggordan/GutterColor


text:
Automation shortcuts/URL

Edit: wrong section to be written in
Hi,
using Firefox, as you know we can't keep track of local files.
But what i'm doing is :
1 - using a localhost server to make a grabbable URL for FF,
2 - edit with vim with autoCmd to start a FF page on :w
3 - on FF, click install confirm on the updated script and ^+w to close the tabs opened.
Here's what my alias looks like for those interested in doing so:
cd ~/soft/scripts/***
http-server -c-1 -a 127.0.0.1 >/dev/null &
vim '+normal Go' -c 'autocmd BufWritePost * !firefox localhost:8080/***.user.js && qdbus org.kde.KWin /KWin setCurrentDesktop 3' ***.user.js

NB: qdbus command is to change to Firefox virtual desktop.
QUESTION: is there a URL or a shortcuts to automate the install confirmation of a script ? So i don't have each update to click "confirm install" and close those tabs.
Thanks.

Just saying hi so you don't think I'm ignoring this issue. I have no idea, sorry. Maybe someone else can help (and I'm assuming this is relevant to this repo?)

Hi @Thorin-Oakenpants , thanks for showing some life =)
It should be relevant to the features, either hidden or not yet implemented. Making a register API/URL should be doable.

I have no idea what you're asking or what you're trying to do.
Just based on the title, maybe Marionette is what you're looking for but I've never dabbled with that and couldn't really help you, sorry.

wrong section to be written in

and what does that mean?

authors: Bumbadawg Thorin-Oakenpants earthlng


text:
Where does ‘bak’ come from in ”--srcdict $fseq/bak/dict.${src}.txt“ in extract_alignment.sh?

The scripts are sa follows:
echo "Start processing alignment data into fairseq data format"
python preprocess.py -s $src -t $tgt --dataset-impl lazy
--workers 8 --destdir $fseq --align-suffix align --joined-dictionary
--trainpref $fseq/bpe/train --validpref $fseq/bpe/valid
--srcdict $fseq/bak/dict.${src}.txt --process-only-alignment

Does --srcdict $fseq/bak/dict.${src}.txt means to use the vanilla data dictionary?


text:
ROOT minimizer fail

I'm still looking to the cause of this... though debug is providing no traceback. In the basic test notebook:
jl = JointLikelihood( model, data_list, verbose=False )
jl.set_minimizer('ROOT')
res = jl.fit()

Out:
IndexErrorTraceback (most recent call last)
<ipython-input-9-d30b697cf86b> in <module>()
      1 jl = JointLikelihood( model, data_list, verbose=False )
      2 jl.set_minimizer('ROOT')
----> 3 res = jl.fit()

/Users/jburgess/coding/3ML/threeML/classicMLE/joint_likelihood.pyc in fit(self, quiet, compute_covariance)
    212             # Perform the fit
    213
--> 214             xs, log_likelihood_minimum = self._minimizer.minimize(compute_covar=compute_covariance)
    215
    216             if log_likelihood_minimum == minimization.FIT_FAILED:

/Users/jburgess/coding/3ML/threeML/minimizer/ROOT_minimizer.pyc in minimize(self, compute_covar)
     78         if compute_covar:
     79
---> 80             covariance_matrix = self._compute_covariance_matrix(best_fit_values)
     81
     82         else:

/Users/jburgess/coding/3ML/threeML/minimizer/minimization.pyc in _compute_covariance_matrix(self, best_fit_values)
    593             if minima[i] is None:
    594
--> 595                 minima[i] = best_fit_values[i] / 1000.0
    596
    597             if maxima[i] is None:

IndexError: index 0 is out of bounds for axis 0 with size 0

Ok, as @giacomov pointed out to me, the problem is ROOT6. For Mac installation, it is best to build from source. If using a python virtualenv, then you need to make sure to build ROOT against the venv which contains the 3ML distribution.


text:
unknown error

When running using gulp, i am getting following error
node_modules\bluebird\js\release\async.js:48
        fn = function () { throw arg; };
                           ^
Error: Cannot communicate with PhantomJS process: Unknown reason
    at Phantom._afterExit (D:\xampp\htdocs\globals\node_modules\phridge\lib\Phantom.js:353:17)
    at emitTwo (events.js:111:20)
    at ChildProcess.emit (events.js:191:7)
    at Process.ChildProcess._handle.onexit (internal/child_process.js:204:12)

any help would be great,
thanks.

@lorvent Have you tried deleting node_modules, running npm cache clean, followed by npm i?

i think that fixed the problem

authors: RyanZim lorvent

repo: giakki/uncss


text:
Add instance type/VM size spec to info endpoint response

Towards https://github.com/giantswarm/giantswarm/issues/6697
This spec change should allow the info endpoint to provide all details about AWS instance types or Azure machine sizes required by our UIs.
Preview
          "workers": {
            "count_per_cluster": {
              "max": null,
              "default": 3
            },
            "instance_type": {
              "options": [
                "m5.xlarge", "m5.2xlarge", "m5.4xlarge"
              ],
              "default": "m3.large",
              "specification": [
                {
                  "name": "m5.xlarge",
                  "description": "M5 series with medium resources",
                  "cpu_cores": 4,
                  "memory_size_gb": 16
                }
              ]
            }
          }

TODO

Make the spec provider-agnostic. instance_type is AWS terminology.
[ ] Update definitions
[ ] Check attribute naming for consistency

Obsolete

repo: giantswarm/api-spec


text:
Add chartconfig resource chart

Towards https://github.com/giantswarm/giantswarm/issues/1902

Yep, TIL you can have multiple charts but their names must match <project-name>-*-chart, fixed.

repo: giantswarm/chart-operator


text:
cluster chart: render Cluster resource

towards https://github.com/giantswarm/giantswarm/issues/31697
this PR:

renders the Cluster resource from the shared cluster chart

Checklist

[x] Update changelog in CHANGELOG.md.
[x] Make sure values.yaml and values.schema.json are valid.
[x] Update /examples if required.

I ran the test suite locally based on the last commit and this branch of standup https://github.com/giantswarm/cluster-standup-teardown/pull/124
Everything is fine as long as the value is added on upgrade as can be read in the changelog.
CAPVCD/Standard

CAPVCD/Upgrade

authors: anvddriesch glitchcrab

repo: giantswarm/cluster-cloud-director


text:
Teleport: Create /etc/teleport-join-token.

What does this PR do?
Enables early SSH access by creating the Teleport token file during node boot. Kubernetes automatically takes over the token file by mounting the secret over it when ready.
Effect on users

SSH access available immediately during node bootstrap
No service restarts needed
Clean transition to secret-based tokens
No changes needed for existing clusters

Background
Currently, nodes require Kubernetes to be ready and nodes rolling before allowing SSH access.
This creates issues when troubleshooting Kubernetes nodes while bootstraping.
Reviewer focus needed on

Secret mount behavior

Release notes
- Added support for early SSH access during node bootstrap

[x] CHANGELOG.md has been updated (if it exists)

Ok, now the confusion is complete. What's the point of having two different PRs, which - to me as someone who's not very familiar with the Teleport agent - look the same or at least feel like they could be one? 😅

Ready to be reviewed

LGTM if tested!

Tested in cluster-aws using mc-bootstrap if you want you can take a look on my PRs there too

authors: Gacko ssyno

repo: giantswarm/cluster


text:
Add authorized API calls to get list of repo tags

Code starts to be super messy. It worth to have some generic interface and implement those listing/authorization methods for interface.
But as we have two repos for now, this covers our use-case.
Comparing to pulling every tag, this version obviously works much faster and is safe from rate-limiting perspective as we do only one request to get tags

I've refactored code a bit to have registry client as interface and moved then all the logic into interface implementation per registry.
There is still this weird part of credentials duplication, but I like now this better. Even if it still looks terrible :D

repo: giantswarm/crsync


text:
Add docs on sharing secrets with GS

Closes https://github.com/giantswarm/giantswarm/issues/22237

@marians do you think this looks a bit better for the age section?

repo: giantswarm/docs


text:
Work with GHC 8.2.1

I'd like to support GHC 8.2 by the time the Stackage LTS package set including it is released. I've updated the package bounds and now I'm running into a GHC API change between <=8.0 and 8.2 where extraPkgConfs seems to have been removed and the order of the list it expects has reversed.
To check the current progress, run nix-build release821.nix.

Ready for testing! nix-build release821.nix should create a working notebook environment!

I am confused by the test failures and wondering what I changed to cause them.

I was hoping that upgrading to a new enough resolver would make the problem go away, but I no longer think it will and there's an issue in the codebase that needs to be addressed. I've added a small failure.hs that demonstrates the failure on GHC 8.2:
$ stack ghci failure.hs
*Main> eval "1 + 1"
*** Exception: Not in scope: ‘IHaskell.Display.displayFromChanEncoded’
No module named ‘IHaskell.Display’ is imported.

The issue appears to be that packages in GHC 8.0 and below are named e.g ihaskell-1.2.3.4 but in 8.2 they're just ihaskell. I'm getting a different error now, so I'll call that progress :tada:

:tada: :fireworks: :champagne:

I'm going to split out release821.nix and the newer stack.yaml into a separate PR, and try to figure out how to test both 8.0 and 8.2 as part of the CI process.

repo: gibiansky/IHaskell


text:
NB2 cropsimulation输出为0

Hello, I have some questions that I would like to ask you to answer below, this has been bothering me for a long time.
Firstly, when NB2 calls UtilitiesCalc to interpolate monthly data to daily scale data, there is an error "x and y arrays must be equal in length along interpolation axis". The parameters involved are monthly_vector, cycle_begin, what should I change?

Secondly, when I modified the first problem, I added the code "monthly_vector = np.zeros(12)", it can be executed, but the results of crop yield under rainfed and irrigated are all 0. Is it related to the invalid value of -999 in the output of NB1 for the LGP and other data?

Looking forward to your answer, appreciate it! Last but not least, have a nice life!

I ran with the Laos example data and the output is also 0, what is the reason? How should I change it? Your help is highly appreciated!

Hi @maobw12,
If you're interpolating from monthly to daily, the format of code setting should be:
daily[i_row, i_col, :] = obj_utilities.interpMonthlyToDaily(monthly[i_row, i_col,:], 1, 365)
where: daily = 1-D Numpy array (365 elements)
monthly = 1-D Numpy array (12 elements)
For the M2 outputs, it's hard to say, probably because of the input zero array of monthly data being fed into PyAEZ, you might encounter M2 results obtaining zeroes. But I suggest revising daily interpolation like the code above the see the results again.
Regards,
Swun Wunna Htet

Hello The interpolation does work as you say：daily[i_row, i_col, :] = obj_utilities.interpMonthlyToDaily(monthly[i_row, i_col,:], 1, 365) ，but it calls the "interpMonthlyToDaily" method in UtilitiesCalc.py with an error. I am interpolating from monthly to daily data and the result is as shown above. I tried using the example data from Laos and found the same result. Do you mean to use day by day data instead of month by month data?

Hey @maobw12,
Please provide a sample of your data and the notebook you used. I need to investigate more about this particular mishap.
Regards,
Swun Wunna Htet

Hello, I've sent you the data and the code, and I've also sent you the package.
NB2_issue_MAO.zip
Greetings.
Bingwan MAO

Hello , I don't know why this error is not reported anymore, the error is as shown in the following picture.Thank you very much for your letter.

Regards,
MAO

@maobw12,
After reviewing your data, I noticed some data not aligned with. The sample notebook is not provided as well, so I don't know exactly what error you've encountered. Here's the list of data inconsistency.

Why are your precipitation values obtaining negative values?
Relative humidity value must be between 0 -1 as required by PyAEZ and your data values have exceeded these minimum and maximum limits.
Your original geotiff files have Albert Lambertian Projection with meters as units, I wonder how you obtain minimum and maximum latitude? Please note that recent PyAEZ version focus primarily on Northern Latitude. Southern latitude extented implementation is currenting in development stage. As you didn't provide me minimum and maximum latitude, I tested with 0 and 40 as inputs (for experiment).

With all these changes, the simulation is running in my PC. Up until now, I haven't encountered any errors yet. In any case, I've attached an example notebook with your dataset.

NB2_CropSimulation.zip

Thank you very much for your letter, I will look at my data again and give it a try. Regarding latitude and longitude, I was looking at the lowest and highest dimension values for the study area.
Also, I would like to ask about the input of climate scenario data is it in the input climate data portal in Module 1?
Regards,

After I did it again on the notebook you returned, it shows that the yield_of_all_crop_cycles_rainfed array may not have been populated with data correctly, it's an array of zeros. What could be the cause of this please? Thank you for your letter, best wishes!

Hi @maobw12,
This is getting strange, because the simulation is successful in my pc. I believe it's a matter of python package version, which need to be updated. Here's a list of python package versions which I used to simulate with you data. Example M2 result attached as image.
Numpy 1.24.4
GDAL 3.5.1
Scipy 1.11.1
Numba 0.57.1
Pandas 1.5.3
Python 3.9.13

Ah, that's so weird, ok, I'll check my version, thank you very much.

Hello, I tried again after changing the version, and got the crop yield under irrigation conditions, but the yield filling under rain-fed conditions was still 0.

@maobw12,
I'll check it out again.
Regards,
Swun Wunna Htet

@maobw12,
I ran with v2.2 again, and no errors were observed for the cause of having rainfed conditions having zeros, nor any big mishaps happened during M2 simulation.
Apart from rainfed zero case, the only thing I've noticed is all your raster layers have Albert Lambertian Projection. In PyAEZ model, we used GCS coordinates of Latitudes which I assumed you preprocessed all your climate data with Lambertian projection which is not correct.
When using PyAEZ, we suggest all the raster layers to be preprocessed with EPSG:4326 as PyAEZ requires to create latitude maps. Later after the simulations, you can reproject back to Lambertian projection.
These are the latitudes I obtained from reprojection into EPSG:4326.
Lat_max = 47.65
Lat_min = 43.66
I'm sending a zipped file of the results of M2, including the settings I applied for simulations for your information.
NB2_issue_MAO_SWUN.zip
Sincerely yours,
Swun Wunna Htet

What 's the version of your anaconda3 ? I want to confirm whether this is the problem.

@maobw12,
I don't use anaconda, but conda only. Here's the version of installed conda.

i have the same question . i carefully check is there difference between my climate data and sample lao's climatedata，the precipitation data have some problems，in monthly simulation , should it  be (one month's pre accumaltion) or (one month's pre /30)?
but i'm afraid this problem is  not the reason of  simulation result is zero

@yelvk,
I can't say for sure. Generally in AEZ, all crop simulation has to be evaluated with daily climatic data. If you use daily data, the problem would be the data itself. But if you use monthly, the monthly values representing each month of year will undergo daily interpolation to obtain daily interpolated values, which might not be accurate as daily data.
Especially when it comes to rainfed yield simulation, the obtained biomass for a particular crop cycle will be reduced depending on the moisture conditions of the soil, subsequently the crop evapotranspiration.
At any time, whenever you encounter zero maximum yield (rainfed/irrigated), please check with your crop calendar, fc1, and fc2 factor maps. If fc1 or fc2 is zero, that indicates 100% thermal unsuitability or moisture deficit. But if the crop calendar (starting date) returned zero, that means existence of one of unsuitability characteristics due to thermal climate, permafrost classes, or cycle length not being supportive for the entire growing period.

@NokuzaSezo97
the fc1&fc2 exactly is zero ,but i dont think it is reasonable.
LAO's sample data can be simulated successfully,while use my data in the same environment  got zero again.
this is the result caculated from NB1,and the crop parameter xlsx ,should it be all zero?

my climate data is clipped by region border(used as simulation mask), the LAOsample data include the whole rectangle.
do nodata value out of mask would confilct simulation result?

@yelvk, I suspect returning fc1, fc2 returning (assuming yield and crop calendar returning zeroes) could indicate that simulations meet with unsuitable characteristics (thermal climate, permafrost classes,
Could you provide me the zip folder containing:

the crop parameter excel sheet, including each LUT's not-suitable thermal climate classes' list,
Module I outputs
Six climatic variables in 3-D Numpy cubes

Regards,
Swun Wunna Htet

@NokuzaSezo97 thanks for your review
in GAEZ data-reviewer website ,this area has specific value ,i think there are something wrong in my simulation rather than the area cant harvest anything

the data inclued the whole region is out of the github's size limitation
so i clip a part of region's data  for you
harbin-aez.zip
in NB2 module,i have tried each crops in my xlsx,they all have same outputs,
thank you again

@NokuzaSezo97
maybe i have find the problem , i add two line codes in here and the simulation result looks well out of my expection

but it is not tally with the facts, the tem in this area will drop below zero in winter normally. does not pyAEZ model take this situation into account?

@yelvk,
The list of unsuitable thermal climate classes for four LUTs are missing in the data provided. Could you provide me the missing data?
Swun Wunna Htet

@NokuzaSezo97
is this parameter what you're referring to？

unsuitable thermal climate classes for  maize  and  soy  are [1,2,9,10,11,12] ,which for rice is [1,9,10,11,12]

repo: gicait/PyAEZ


text:
Update

Breaking Change:

Description:
Related issue (if applicable): fixes #
Pull request in home-assistant.io with documentation (if applicable): home-assistant/home-assistant.io#<home-assistant.io PR number goes here>
Example entry for configuration.yaml (if applicable):

Checklist:

[ ] The code change is tested and works locally.
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If user exposed functionality or configuration variables are added/changed:

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If the code does not interact with devices:

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@giefca, you should consider to rebase instead of merging..
https://developers.home-assistant.io/docs/en/development_catching_up.html

authors: fredrike giefca

repo: giefca/home-assistant


text:
The documentation link on crates.io leads to a 404

When following the documentation link on crates.io (https://gifnksm.github.io/union-find-rs) the result is a 404 page:

I mean the link in the sidebar:

The link to docs.rs in the readme works as normal.

Thank you for reporting!
The crates.io link will be fixed in the next release.

authors: JSorngard gifnksm

repo: gifnksm/union-find-rs


text:
Amazon Prime "No Video Detected"

The extension didn't detect a video that is on the page.

Hey @TymurGubayev, thanks for reporting this issue!
Could you add some more detail? For me, it works flawlessly on amazon.de! Is it possible that you clicked the Movie Subtitle icon too soon? Before the page was fully loaded?

authors: TymurGubayev gignupg

repo: gignupg/Movie-Subtitles


text:
Add TYPO3 logo

Hi Gil,
thanks for your wonderful work by providing supervised SVGs to the world and specifically to PlantUML standard lib. The TYPO3 association would like to add the TYPO3 logo to your set. TYPO3 CMS is an Open Source Enterprise Content Management System with a large global community.
Preview

Zipped SVG
typo3.zip
Greetings
Alex

Added in 17261479e64d27613dfd2f71e66eefae38b3d698
Thanks

Added in 17261479e64d27613dfd2f71e66eefae38b3d698
Thanks

authors: alexander-nitsche gilbarbara

repo: gilbarbara/logos


text:
Add Cardano Logo

Logo
Website
Wikipedia Page

Added in de8fdaf0ce10dc9f0c41e7f0612da5d2d36f4e74
Thanks

authors: Redxtorm gilbarbara


text:
Laravel

Laravel recently released version 6.0 which introduced a brand new logo.

Hello,
Thanks for your PR but as described in the CONTRIBUTING guideline we do not accept PRs since this repo is generated from another data source.
I've added the new logo in my backlog and will update it as soon as possible.
[s]

authors: gilbarbara jirkavrba


text:
The Ning client starts too many thread pools

Every time a client instance is created it starts a new cached thread pool instance. When running tests in another project I observed OOMs as a result. I propose that the generated client for Ning come with a default singleton thread pool, and allow client overrides in the constructor.

This has actually been a problem in production for me. Unfortunately, I had to create multiple clients of my service - for sending authentication via cookie - and didn't realize that under the hood one it was also instantiating one AsyncHttpClient. Needless to say, this approach starved the machine from resources - it couldn't create more threads.

fixed in 0.8 release which should be online next week

authors: emersonloureiro haywood mbryzek

repo: gilt/apidoc


text:
Must close connection on masked server->client frame

http://tools.ietf.org/html/draft-ietf-hybi-thewebsocketprotocol-17#section-5.1

A client MUST close a connection if it detects a masked frame.

Related: #102

In WebSocket.as line 491, add:
if (buffer[1]>127)
{
dispatchCloseEvent(false, 1002, "Server must not mask.");
return null;
}

Thanks. Pulled at https://github.com/gimite/web-socket-js/commit/14023075bfa7350a3a2268cb6d7e38e046b24bcf

authors: gimite ranc

repo: gimite/web-socket-js


text:
ETQ Analyst, je veux créer des dashboard interne directement via du code pour plus de flexibilité

:thinking: Contexte et problématique
Récemment nous avons eu de grosse lenteur sur Metabase et plusieurs fois j'ai eu des demandes sur dashboards interne à la plateforme pour des fonctionnalités qui n'étaient pas vraiment possible sur l'outil donc il a fallu trouver une solution de contournement.
:tada: Proposition de solution
Je voudrais pouvoir créer des tableaux via du code, qui permettrait d'intégrer les tableaux internes à IF directement dans le parcours utilisateur.

système de pagination à créer ex nihilo. Quid du DSFR pour créer des tableaux de pilotage ? Utilisation de class utilitaires.

Doublon avec #1672 ????

authors: Master-Touks bbohec nathalie-reyre

repo: gip-inclusion/immersion-facile


text:
Arm processor

it can be made available for users with arm processor?

Docker Desktop for mac will automatically use qemu in case of x86 images

install x86 version of brew
arch --x86_64 zsh -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install.sh)"

Install node v12
brew install node@12


text:
MERN_MongoDB: 3.1 Creating Database in MongoDB(V)

Description
Creating Database in MongoDB

Explain all the steps for creating a MongoDB Database with the CLI.

It should include basic commands to insert data, show and use the database.

Explain all the steps for creating a MongoDB Database with Compass.

Project Directory
Branch MERN>MERN/Topic/Backend/MongoDB/
Name the File as 3.1_Creating_Database_in_MongoDB(V).md
Domain
MERN
Type of Contribution
Video
Code of Conduct

[X] I follow Contributing Guidelines & Code of conduct of this project.

/assign

/assign

repo: girlscript/winter-of-contributing


text:
Duplicate in an Array using Floyd's Cycle detection

Description
The problem statement is that, given an array of n+1 elements whose values are in range [1,n]. All the elements occur just once except for a number which occurs 2 or more times. I'd like to include more details on this problem statement, and how this can be done using Floyd's cycle detection algorithm.
Domain
DSA
Type of Contribution
Documentation
Code of Conduct

[X] I follow Contributing Guidelines & Code of conduct of this project.

I am eswari priya repaka and i belong dsa batch2. pls review it and assign me this issue @goelesha @vikhyatsingh123

/assign


text:
ML 4.3: SARSA (D)

Description 📜
This document contains the explanation of SARSA along with its Algorithm and application.
Fixes #5332

Type of change 📝

[ ] Au#dio (Should be in mp3 format Includes speech clarity, Concise ,Low distortion)
[ ] Vi#deo (Animations, screen-recordings, presentations and regular explanatory films are all possibilties etc)
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[ ] Android Dev #(Flutter)
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[ ] Go#lang
[ ] Interview #Prep
[ ] Java_#Domain
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[ ] ME#RN
[x] Machine Learning
[ ] Open #Source
[ ] Python_#Domain
[ ] Ru#st
[ ] Statis#tics
[ ] UI/#UX

Checklist ✅

[x] I follow Contributing Guidelines & Code of conduct of this project.
[x] I have performed a self-review of my own code or work.
[x] I have commented my code, particularly in hard-to-understand areas.
[x] My changes generates no new warnings.
[x] I'm GWOC'21 contributor

Screenshots / Gif (Optional) 📸

@abhisheks008