hdf5-threadsafe: 1.10.3 -> 1.10.4

Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools. This update was made based on information from https://repology.org/metapackage/hdf5-threadsafe/versions.
meta.description for hdf5-threadsafe is: '"Data model, library, and file format for storing and managing data"'.

Checks done (click to expand)

built on NixOS
/nix/store/g6mcnn0j5z38lvwdkk9zcm17q683ilyd-hdf5-1.10.4/bin/h5diff passed the binary check.
/nix/store/g6mcnn0j5z38lvwdkk9zcm17q683ilyd-hdf5-1.10.4/bin/h5ls passed the binary check.
/nix/store/g6mcnn0j5z38lvwdkk9zcm17q683ilyd-hdf5-1.10.4/bin/h5dump passed the binary check.
Warning: no invocation of /nix/store/g6mcnn0j5z38lvwdkk9zcm17q683ilyd-hdf5-1.10.4/bin/h5debug had a zero exit code or showed the expected version
/nix/store/g6mcnn0j5z38lvwdkk9zcm17q683ilyd-hdf5-1.10.4/bin/h5repart passed the binary check.
/nix/store/g6mcnn0j5z38lvwdkk9zcm17q683ilyd-hdf5-1.10.4/bin/h5mkgrp passed the binary check.
/nix/store/g6mcnn0j5z38lvwdkk9zcm17q683ilyd-hdf5-1.10.4/bin/h5clear passed the binary check.
/nix/store/g6mcnn0j5z38lvwdkk9zcm17q683ilyd-hdf5-1.10.4/bin/h5import passed the binary check.
/nix/store/g6mcnn0j5z38lvwdkk9zcm17q683ilyd-hdf5-1.10.4/bin/h5repack passed the binary check.
/nix/store/g6mcnn0j5z38lvwdkk9zcm17q683ilyd-hdf5-1.10.4/bin/h5jam passed the binary check.
/nix/store/g6mcnn0j5z38lvwdkk9zcm17q683ilyd-hdf5-1.10.4/bin/h5unjam passed the binary check.
/nix/store/g6mcnn0j5z38lvwdkk9zcm17q683ilyd-hdf5-1.10.4/bin/h5copy passed the binary check.
/nix/store/g6mcnn0j5z38lvwdkk9zcm17q683ilyd-hdf5-1.10.4/bin/h5format_convert passed the binary check.
/nix/store/g6mcnn0j5z38lvwdkk9zcm17q683ilyd-hdf5-1.10.4/bin/h5stat passed the binary check.
/nix/store/g6mcnn0j5z38lvwdkk9zcm17q683ilyd-hdf5-1.10.4/bin/h5perf_serial passed the binary check.
Warning: no invocation of /nix/store/g6mcnn0j5z38lvwdkk9zcm17q683ilyd-hdf5-1.10.4/bin/h5redeploy had a zero exit code or showed the expected version
/nix/store/g6mcnn0j5z38lvwdkk9zcm17q683ilyd-hdf5-1.10.4/bin/h5cc passed the binary check.
15 of 17 passed binary check by having a zero exit code.
12 of 17 passed binary check by having the new version present in output.
found 1.10.4 with grep in /nix/store/g6mcnn0j5z38lvwdkk9zcm17q683ilyd-hdf5-1.10.4
directory tree listing: https://gist.github.com/c068e52b5560aeff117ef3b8c0bea12f
du listing: https://gist.github.com/ac2bf885adef11f6a66c2b4b32d2771d

Rebuild report (click to expand)

815 total rebuild path(s)
223 package rebuild(s)
222 x86_64-linux rebuild(s)
205 i686-linux rebuild(s)
176 x86_64-darwin rebuild(s)
212 aarch64-linux rebuild(s)
First fifty rebuilds by attrpath
EBTKS
alembic
armadillo
bicgl
bicpl
caffe
caffe2
cdo
cntk
conglomerate
digikam
eccodes
enblend-enfuse
ezminc
fast-neural-doodle
fenics
freecad
gazebo
gazebo-headless
gazeboSimulator.gazebo6
gazeboSimulator.gazebo6-headless
gazeboSimulator.gazebo7
gazeboSimulator.gazebo7-headless
gdal
gnss-sdr
grass
grib-api
h5utils
haskellPackages.hdf5-lite
hdf5
hdf5-cpp
hdf5-fortran
hdf5-mpi
hdf5-threadsafe
hugin
inormalize
kallisto
kdeApplications.kdenlive
kdenlive
kst
libLAS
libminc
libreoffice
libreoffice-fresh
libreoffice-fresh-unwrapped
libreoffice-still
libreoffice-still-unwrapped
libreoffice-unwrapped
libsForQt5.mlt
libsForQt511.mlt

Instructions to test this update (click to expand)

Either download from Cachix:
nix-store -r /nix/store/g6mcnn0j5z38lvwdkk9zcm17q683ilyd-hdf5-1.10.4 \
  --option binary-caches 'https://cache.nixos.org/ https://r-ryantm.cachix.org/' \
  --option trusted-public-keys '
  r-ryantm.cachix.org-1:gkUbLkouDAyvBdpBX0JOdIiD2/DP1ldF3Z3Y6Gqcc4c=
  cache.nixos.org-1:6NCHdD59X431o0gWypbMrAURkbJ16ZPMQFGspcDShjY=
  '

(r-ryantm's Cachix cache is only trusted for this store-path realization.)
Or, build yourself:
nix-build -A hdf5-threadsafe https://github.com/r-ryantm/nixpkgs/archive/250c35002108da2715c005264f839397d9bc51c9.tar.gz

After you've downloaded or built it, look at the files and if there are any, run the binaries:
ls -la /nix/store/g6mcnn0j5z38lvwdkk9zcm17q683ilyd-hdf5-1.10.4
ls -la /nix/store/g6mcnn0j5z38lvwdkk9zcm17q683ilyd-hdf5-1.10.4/bin

Success on aarch64-linux (full log)
Attempted: hdf5-threadsafe
Partial log (click to expand)
shrinking /nix/store/bl9df00nnd3c6aw37gabzbs1dxfybj4r-hdf5-1.10.4/lib/libhdf5.so.103.0.0
strip is /nix/store/1jprj383qnzd50vn8qq3a0id6a08a9fi-binutils-2.30/bin/strip
stripping (with command strip and flags -S) in /nix/store/bl9df00nnd3c6aw37gabzbs1dxfybj4r-hdf5-1.10.4/lib  /nix/store/bl9df00nnd3c6aw37gabzbs1dxfybj4r-hdf5-1.10.4/bin
patching script interpreter paths in /nix/store/bl9df00nnd3c6aw37gabzbs1dxfybj4r-hdf5-1.10.4
/nix/store/bl9df00nnd3c6aw37gabzbs1dxfybj4r-hdf5-1.10.4/share/hdf5_examples/run-all-ex.sh: interpreter directive changed from " /bin/sh" to "/nix/store/vg9477j4nafj505cr9agvgndxys7743x-bash-4.4-p23/bin/sh"
/nix/store/bl9df00nnd3c6aw37gabzbs1dxfybj4r-hdf5-1.10.4/share/hdf5_examples/c/run-c-ex.sh: interpreter directive changed from " /bin/sh" to "/nix/store/vg9477j4nafj505cr9agvgndxys7743x-bash-4.4-p23/bin/sh"
/nix/store/bl9df00nnd3c6aw37gabzbs1dxfybj4r-hdf5-1.10.4/bin/h5redeploy: interpreter directive changed from " /bin/sh" to "/nix/store/vg9477j4nafj505cr9agvgndxys7743x-bash-4.4-p23/bin/sh"
/nix/store/bl9df00nnd3c6aw37gabzbs1dxfybj4r-hdf5-1.10.4/bin/h5cc: interpreter directive changed from " /bin/sh" to "/nix/store/vg9477j4nafj505cr9agvgndxys7743x-bash-4.4-p23/bin/sh"
checking for references to /build/ in /nix/store/bl9df00nnd3c6aw37gabzbs1dxfybj4r-hdf5-1.10.4...
/nix/store/bl9df00nnd3c6aw37gabzbs1dxfybj4r-hdf5-1.10.4

Timed out, unknown build status on x86_64-darwin (full log)
Attempted: hdf5-threadsafe
Partial log (click to expand)
cannot build derivation '/nix/store/9wz7d7nxi2yhvi5dhq0nzgwlsc0c14vn-clang-5.0.2.drv': 1 dependencies couldn't be built
cannot build derivation '/nix/store/372n5gnp6088yk92cikmdnsrqh6gb1zq-compiler-rt-5.0.2.drv': 1 dependencies couldn't be built
cannot build derivation '/nix/store/pna9s3cspkkx7qfbwl09dblwjgwn08hq-cctools-binutils-darwin.drv': 1 dependencies couldn't be built
cannot build derivation '/nix/store/5rzbmkg7za1rqbcv7blhjj0gqjwklcdh-cctools-binutils-darwin-wrapper.drv': 1 dependencies couldn't be built
cannot build derivation '/nix/store/w2j5zljrlpj07cgc4hq5xw0kl97b9hp4-clang-wrapper-5.0.2.drv': 3 dependencies couldn't be built
cannot build derivation '/nix/store/0fyjbzdcda241j1ibh68gv5f25rslyrb-stdenv-darwin.drv': 6 dependencies couldn't be built
cannot build derivation '/nix/store/10i596kkwacnza4fh2vqc5r0gmzx18wj-remove-references-to.drv': 1 dependencies couldn't be built
cannot build derivation '/nix/store/9y8c66lbibw5hic2bnc7pzpgkvc5pwwk-stdenv-darwin.drv': 7 dependencies couldn't be built
cannot build derivation '/nix/store/kaac8jhadwb48mr3czj479vbk2yv59mi-hdf5-1.10.4.drv': 3 dependencies couldn't be built
error: build of '/nix/store/kaac8jhadwb48mr3czj479vbk2yv59mi-hdf5-1.10.4.drv' failed

But this is already in staging --> #50100
@ryantm


fix docs

[x] fix build docs
[x] add rtd CI
[x] add pre-commit CI

@timtreis @sagar87 I will merge this if you approve, even if tests don't pass cause not sure how to fix them (this PR is just to do things described above), but few additional comments:

noticed you have "sandbox" notebooks in the root of the projects. I would remove them and add them in spatial sandbox repo or even in others but not here, diffs for notebooks, especially with many images, can get very heavy and then it's a pain to remove them to git history.
notebooks here should just be the ones for the docs, and actually we might not even want that, but we might want to just put them in spatialdata-notebooks repo. For now the simple one I would live but would not modify extensively until API is ready
now there is CI for docs, meaning you can check how the docs build in URL (click details next to the job). You can also build them locally with make html in docs folder, but anyway useful to check out how they render.
we might want to have branch protection in main, please feel free to add it following how it's done in other spatialdata repos
I think we want mypy checks as well. Adding it now will be problematic (probably many fixes to be added), but adding it later also potentially. more difficult. It's gonna be quite some work, so you decide when you think is best.

will merge regardless of pre-commit, @timtreis @sagar87 you could fix in separate PR?

Yeah, I will fix this next


Support for<EMAIL_ADDRESS>

I set "KexAlgorithms<EMAIL_ADDRESS>on my servers and now I cant connect with CB.
I get errors "key exchange was not finished, connection is closed. Cannot negotiate, proposals do not match". I have CM 12.1 running on OnePlus One

I would also appreciate this.

Fixed by #370


Use Maven for Unit Testing

Instead of the existing way to run the unit tests in the GitHub Actions workflow, it seems that we can just run mvn clean test (or just mvn test) to run all the unit tests. We should see if this will work for us.
This would require:

Check that this does in fact run all the unit tests (and not that some are missing).

If there are any missing, I think we can fix that by adding it to one of the pom.xml files.

Check that this is compatible with the code coverage reporting.
Update the GitHub workflow file to use this instead
Optional: we may be able to switch to a simpler container/runner for building everything.

This issue may be more work than it's worth, and PR #88 drastically reduces the time tests take- the only issue is that we have to continually add any new tests to the pom file, which is easy enough to do. Consider closing?

Yes, let's just stick with the solution from PR #88.


git pull failing with "fatal: protocol error: bad line length character"

This has been happening on one of my private git repos since around the beginning of this week:
$ git pull --verbose
fatal: protocol error: bad line length character: Port

From some cursory searching, I can see that this might happen when a request is too large (source). I also see
$ keybase git gc $REPO
This may take several minutes...
▶ ERROR file does not exist

My log id: e1a420afae023c425c601d1c

Never mind - https://stackoverflow.com/q/8170436/207384 tells me it's more likely to be an SSH error. And indeed, upon investigating further, it seems it's due to an issue with another remote in the same repo that's accessed over SSH.

Fixed it by opening the ssh agent of putty and adding the key.


Improve bash completions

Fix lxc file completion.
Fallback to default bash file/path completion if we do not provide
any. Useful with lxc file push and lxc file pull, maybe with
others.

Signed-off-by: Yura Pakhuchiy<EMAIL_ADDRESS>

This pull request didn't trigger Jenkins as its author isn't in the whitelist.
An organization member must perform one of the following:

To have this branch tested by Jenkins, use the "ok to test" command.
To have a one time test done, use the "test this please" command.

Those commands are simple Github comments of the format: "jenkins: COMMAND"


Milestone 1: Client Setup

Discussed in  Node meeting 23.4.2020, see DST/PERUN Node GDoc.
Description

For setting up a minimal go-perun frame, the following steps serve as guideline:

[ ] Import and initialize the ethereum backend
[ ] (Inject levelDB persistence adapter)) not yet needed
[ ] Set up a client.Client:

[ ] Create an Adjudicator
[ ] Create a Funder
[ ] Create a Listener and listen on it
[ ] Create a Dialer

[ ] Inject a logger, for example logrus

To make the client work, a handler for ChannelProposalReq needs to be added and started, see and.
Look at the Implementation hints section below for examples.

Some reminders for the specifications:

[ ] Derive specifications for remaining components

[ ] What do we want to specify? (wallet, identity management and rpc interface, …)
[ ] How/Where do we want to specify? (maybe the Wiki?)

Context  This Task should make all new developers familiar with the usage of go-perun and help to plan future milestones.
All options that need to be hard-coded here can be directly used to specify Milestone 2.
Testing  Was not discussed, but tests are always appreciated.
Acceptance criteria
Implementation hints
client usage
logger injection
slightly outdated godoc
ethereum backend import

Hi @ggwpez ,
This issue covers many tasks, that can itself constitute a milestone.  So I have created a milestone and specific issues to address each task described here. Does the new issues (#38, #39) cover all the points specified here ? In that case, can we close this in the favor of new ones ?

@manoranjith yes these issues seem to cover it. Thanks for the split up.


Disappearing back button

Describe the bug
The back button likes to disappear on my iPhone SE. It happens a lot, but here's one set of repro steps.
To Reproduce
Steps to reproduce the behavior:

Go offline
Start a new obs w/ the sound recorder
Record a sound but don't leave the recorder
Tap the play button
The Media viewer pops up, and the back button disappears. If you tap the space where the back button should be, the media viewer closes

Expected behavior
The back button should appear, and being offline should not change that.
Screenshots

Context (please complete the following information):

Device: iPhone SE (3rd gen)
OS: iOS 17.5.1
App version: 0.36.1 (102)

Amanda can replicate in dev but not in prod.


[Feature] Support instance  list command

works like this:
./swctl --debug --base-url=http://<IP_ADDRESS>:8080/graphql --display=yaml instance ls --service-id=4 --start=2019-11-09 --step=MONTH
DEBUG Debug mode is enabled
DEBUG Using configurations:
 global:
   base-url: http://<IP_ADDRESS>:8080/graphql
DEBUG Start time: 2019-11-09 end time:
DEBUG >> variables: map[duration:{2019-11-09 2019-12-09 DAY} serviceId:4]
DEBUG >> query:
                query ($serviceId: ID!, $duration: Duration!) {
                instances: getServiceInstances(duration: $duration, serviceId: $serviceId) {
                        id
                        name
                        language
                                instanceUUID
                        attributes {
                                name
                                value
                        }
                        }
                }

DEBUG >> headers: map[Accept:[application/json; charset=utf-8] Content-Type:[application/json; charset=utf-8]]
DEBUG << {"data":{"instances":[{"id":"4","name":"projectA-pid:4771@skywalking-server-0001","language":"JAVA","instanceUUID":"d54c4f5b5094419c9f0d12b8445730c0","attributes":[{"name":"os_name","value":"Linux"},{"name":"host_name","value":"skywalking-server-0001"},{"name":"process_no","value":"4771"},{"name":"ipv4s","value":"<IP_ADDRESS>"}]}]}}
- id: "4"
  name: projectA-pid:4771@skywalking-server-0001
  attributes:
  - name: os_name
    value: Linux
  - name: host_name
    value: skywalking-server-0001
  - name: process_no
    value: "4771"
  - name: ipv4s
    value: <IP_ADDRESS>
  language: JAVA
  instanceuuid: d54c4f5b5094419c9f0d12b8445730c0

================================================

./swctl --debug --base-url=http://<IP_ADDRESS>:8080/graphql --display=yaml instance ls --service-name=projectB --start=2019-11-09 --step=MONTH

DEBUG Debug mode is enabled
DEBUG Using configurations:
 global:
   base-url: http://<IP_ADDRESS>:8080/graphql
DEBUG Start time: 2019-11-09 end time:
DEBUG >> variables: map[serviceCode:projectB]
DEBUG >> query:
                query searchService($serviceCode: String!) {
                service: searchService(serviceCode: $serviceCode) {
                                id name
                        }
                }

DEBUG >> headers: map[Accept:[application/json; charset=utf-8] Content-Type:[application/json; charset=utf-8]]
DEBUG << {"data":{"service":{"id":"2","name":"projectB"}}}
DEBUG >> variables: map[duration:{2019-11-09 2019-12-09 DAY} serviceId:2]
DEBUG >> query:
                query ($serviceId: ID!, $duration: Duration!) {
                instances: getServiceInstances(duration: $duration, serviceId: $serviceId) {
                        id
                        name
                        language
                                instanceUUID
                        attributes {
                                name
                                value
                        }
                        }
                }

DEBUG >> headers: map[Accept:[application/json; charset=utf-8] Content-Type:[application/json; charset=utf-8]]
DEBUG << {"data":{"instances":[{"id":"2","name":"projectB-pid:4713@skywalking-server-0001","language":"JAVA","instanceUUID":"55a7a0af57f64c1da0b7c44063ddc8c0","attributes":[{"name":"os_name","value":"Linux"},{"name":"host_name","value":"skywalking-server-0001"},{"name":"process_no","value":"4713"},{"name":"ipv4s","value":"<IP_ADDRESS>"}]}]}}
- id: "2"
  name: projectB-pid:4713@skywalking-server-0001
  attributes:
  - name: os_name
    value: Linux
  - name: host_name
    value: skywalking-server-0001
  - name: process_no
    value: "4713"
  - name: ipv4s
    value: <IP_ADDRESS>
  language: JAVA
  instanceuuid: 55a7a0af57f64c1da0b7c44063ddc8c0
================================================================
./swctl --debug --base-url=http://<IP_ADDRESS>:8080/graphql --display=yaml instance ls --service-name=projectB --service-id=4 --start=2019-11-09 --step=MONTH

DEBUG Debug mode is enabled
DEBUG Using configurations:
 global:
   base-url: http://<IP_ADDRESS>:8080/graphql
DEBUG Start time: 2019-11-09 end time:
DEBUG >> variables: map[duration:{2019-11-09 2019-12-09 DAY} serviceId:4]
DEBUG >> query:
                query ($serviceId: ID!, $duration: Duration!) {
                instances: getServiceInstances(duration: $duration, serviceId: $serviceId) {
                        id
                        name
                        language
                                instanceUUID
                        attributes {
                                name
                                value
                        }
                        }
                }

DEBUG >> headers: map[Accept:[application/json; charset=utf-8] Content-Type:[application/json; charset=utf-8]]
DEBUG << {"data":{"instances":[{"id":"4","name":"projectA-pid:4771@skywalking-server-0001","language":"JAVA","instanceUUID":"d54c4f5b5094419c9f0d12b8445730c0","attributes":[{"name":"os_name","value":"Linux"},{"name":"host_name","value":"skywalking-server-0001"},{"name":"process_no","value":"4771"},{"name":"ipv4s","value":"<IP_ADDRESS>"}]}]}}
- id: "4"
  name: projectA-pid:4771@skywalking-server-0001
  attributes:
  - name: os_name
    value: Linux
  - name: host_name
    value: skywalking-server-0001
  - name: process_no
    value: "4771"
  - name: ipv4s
    value: <IP_ADDRESS>
  language: JAVA
  instanceuuid: d54c4f5b5094419c9f0d12b8445730c0

Set both --service-id and --service-name,  --service-name is ignored

Codecov Report

Merging #10 into master will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff           @@
##           master      #10   +/-   ##
=======================================
  Coverage   51.85%   51.85%
=======================================
  Files           2        2
  Lines          54       54
=======================================
  Hits           28       28
  Misses         22       22
  Partials        4        4

Continue to review full report at Codecov.

Legend - Click here to learn more
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help works like this:
./bin/swctl i ls -h

NAME:
   swctl instance list - List all available instance by given --service parameter

USAGE:
   swctl instance list [command options] [arguments...]

OPTIONS:
   --start TIME  query start TIME
   --end TIME    query end TIME
   --service ID  query service ID

As I commented at the issue, how could do separated ID and name in --service both? This seems not right.

@wu-sheng  Support both Name and ID in the latest code.

How do you know it is ID? Try to parse int?

How do you know it is ID? Try to parse int?

First through the name search services. If the query result is not empty, get serviceId from the query result, or else take the --service value as the serviceId

First through the --service value search services. If the query result is not empty, get serviceId from the query result, or else take the --service value as the serviceId

If a service name is an integer, then you may face ambiguity issue.
Such as swctl instance --service 123 meaning service name = 123 or service id = 123?
I would say swctl instance --service 123 must be service name = 123. If id is expected to be supported, choose maybe swctl instance --service-id 123 or something we could discuss later.
CLI is a command line tool, I want it has clear meaning.

First through the --service value search services. If the query result is not empty, get serviceId from the query result, or else take the --service value as the serviceId

If a service name is an integer, then you may face ambiguity issue.
Such as swctl instance --service 123 meaning service name = 123 or service id = 123?
I would say swctl instance --service 123 must be service name = 123. If id is expected to be supported, choose maybe swctl instance --service-id 123 or something we could discuss later.
CLI is a command line tool, I want it has clear meaning.

Agree to provide --service-name and --service-id.

@wu-sheng @kezhenxu94  please review

I will submit a new PR to resolve conflicts.

Why do you need a new PR? You could update this branch and PR. New PR will make the context lose.

We are using squash and merge, you should not worry about multiple commit logs.

@kezhenxu94 @heyanlong Please recheck.


PriceCheck window opens automatically upon login

PriceCheck's window currently opens automatically upon logging in which isn't particularly useful; this doesn't reflect the behavior of most other Dalamud addons and is more of a nuisance since you're unlikely to need to use PriceCheck every time you log in. This should either be disabled or an option should be added to do so.

That's fair, I'll add this in next release.

This is now available in testing as a toggle in settings.


plotting derived values

It seems it is not possible to plot derived values using ggcyto aesthetics
ggcyto(fs,aes(y= `PerCP.A` / `PE.A`,x=`PE.A`)) +
geom_hex(bins=64)+
scale_x_log10(breaks = trans_breaks("log10", function(x) 10^x),
              labels = trans_format("log10", math_format(10^.x))) +
scale_y_log10(breaks = trans_breaks("log10", function(x) 10^x),
              labels = trans_format("log10", math_format(10^.x))) +
annotation_logticks()+                # Default: log ticks on bottom and left
facet_grid( Protein * Domain ~ Mutated ) +
ggtitle('liveSubset')

Am I missing something?
My workaround now is to add derived columns using fsApply and cbind2:
fs<= fsApply(fs,function(ff) cbind2(ff,with(as.data.frame(ff@exprs),{ SOME EXPRESSION RETURNING A MATRIX})))
And I now see also I can use transform to similar effect.
But is there a better way?
Thanks!

Currently we don't support derived variable in aes at ggcyto level. The better workaround is to use ggplot directly on flowSet, e.g.
ggplot(fs,aes(y= `PerCP.A` / `PE.A`,x=`PE.A`))

Some layers (e.g  facet and scale_color_gradientn ) must be added by user at ggplot level (they were added automatically by ggcyto wrapper )
Since you were already having customized facet_grid, you then only need to take care of gradientn, which can be retrieved from hex_fill element of ggcyto_par_default(). (i.e. + ggcyto_par_default()[["hex_fill"]])
see [here] for more examples of operating flowSet at ggplot level, (https://github.com/RGLab/ggcyto/blob/master/vignettes/ggplot.flowSet.2d.md)


Add flatland ros1

Please add the following dependency to the rosdep database.
Package name:
flatland (metapackage), flatland_server, flatland_msgs, flatland_plugins, flatland_viz
Package Upstream Source:
https://github.com/avidbots/flatland (? or n/a)
Purpose of using this:
Flatland is lightweight 2d simulator (2.5d) built on Box2D and tightly integrated with ROS. It can serve as a gazebo alternative.
Distro packaging links:
Links to Distribution Packages

n/a?

Please Add This Package to be indexed in the rosdistro.
noetic
(a ros2 port is in mostly done works but one thing at a time).
The source is here:
https://github.com/avidbots/flatland
Checks

[x] All packages have a declared license in the package.xml
[x] This repository has a LICENSE file
[x] This package is expected to build on the submitted rosdistro

New package review:

[x] At least one of the following must be present

[x] Top level license file: https://github.com/avidbots/flatland/blob/master/LICENSE
[ ] Per package license files

[x] License is OSI-approved: BSD-3-Clause
[x] License correctly listed in package.xmls

[x] flatland: https://github.com/avidbots/flatland/blob/master/flatland/package.xml#L9
[x] flatland_msgs: https://github.com/avidbots/flatland/blob/master/flatland_msgs/package.xml#L6
[x] flatland_plugins: https://github.com/avidbots/flatland/blob/master/flatland_plugins/package.xml#L6
[x] flatland_server: https://github.com/avidbots/flatland/blob/master/flatland_server/package.xml#L6

[x] Public source repo: https://github.com/avidbots/flatland/tree/master/
[x] Source repository contains ROS packages and each package meets REP-144 naming conventions

[x] flatland
[ ] flatland_msgs
[ ] flatland_plugins
[ ] flatland_server

Replaced with https://github.com/ros/rosdistro/pull/36035


Support usage of Numaplane without ArgoCD

Summary
There is a desire to use Cloud Workspaces to create a development environment on a VM where there is a k3d environment running.
What @kohlisid has in mind is that when somebody spins up one of these, it would deploy the Numaflow AddOn, and then deploy everything identical to that which is being deployed to other environments. While Cloud Workspaces does not require the "no data loss" features of Numaplane, the deployment through this means is seen as being more seamless.
There is no ArgoCD. One issue I can think of is that we no longer have the Sync Waves in that case. This would mean that a Pipeline can in fact be deployed without a corresponding isbsvc, and thus would enter a "Failed" state.
Perhaps, we could add a check before creating a Pipeline that the isbsvc exists and has been fully reconciled.

Message from the maintainers:
If you wish to see this enhancement implemented please add a 👍 reaction to this issue! We often sort issues this way to know what to prioritize.

cc @xdevxy FYI.
BTW, @kohlisid and I did discuss the potential of not using Numaplane at all, but that seemed less seamless (he would need to go fetch the numaflow manifest himself, he would deploy differently from the other environments).


Can use nuscenes mini to train？

Thank you for your good job!!
I tried to use nusenes mini to run a training demo, but raise error "No such file or directory: 'data/nuscenes/maps/expansion/singapore-onenorth.json', so i wonder if this version can only train on full nuscenes dataset?
"

you should download Map expansion in https://www.nuscenes.org/nuscenes， and put them in maps folder.

It is compatible with Pytorch==1.10.2, just follow the steps of the author.
cd ${floder of xformers}; pip -vvv install .

Thank you. I have trird to cd ${floder of xformers}; pip -vvv install .
but raise error "No such file or directory: '/code/third_party/xformers/xformers/version.py', i didn't find the version.py, have you meet the same problem?

I have solve the problem. Before installing xformer, you should cd /root/miniconda3/envs/magicdrive/lib/python3.8/subprocess.py, line425, change check=True to check=False.
But wneh i train with nuscenes mini, raise error:packaging.version.InvalidVersion: Invalid version: '0.0.19+.d20240506'

Definitely, it is because you are downloading the zip rather than cloning this project repo.
Please check #8.


 renders below modals on iOS

Before reporting this bug, please...

Check the latest documentation: https://docs.nativebase.io/
Check for existing open/closed issues for a possible duplicate before creating a new issue: https://github.com/GeekyAnts/NativeBase/issues
Use the latest NativeBase release: https://github.com/GeekyAnts/NativeBase/releases
Check examples from NativeBase KitchenSink https://github.com/GeekyAnts/NativeBase-KitchenSink
For discussion purpose make use of NativeBase discord: https://discord.gg/TSgCw2UPmb

Describe the bug
If I click to open a  rendered inside an iOS modal, the select is rendered below the modal.
To Reproduce
Steps to reproduce the behaviour:
As description.
Expected behaviour
The Select should float above the modal.
CodeSandBox/Snack link
Screenshots
Platform

NativeBase version [e.g. 3.0.1] latest
Device: [e.g. iPhone6] any
OS: [e.g. iOS8.1] iOS 15
Browser [e.g. stock browser, safari] N/A
Browser version [e.g. 22] N/A
React Native version [e.g. sdk-42]
Expo sdk version [e.g. 41] 42
node [e.g. 14.16.1] 14.17.4
yarn or npm [e.g. 6.1] Yarn 3.0.2

Additional information

Add any other context about the problem here.
Is the bug present in both iOS and Android or in any one of them?
If you want your issue to be looked at quicker, please attach a snack reproducible with your issue. Makes it easier for us!

The Modal components in NativeBase uses a JavaScript portal implementation and it doesn't render on top of the Native Stack Navigator screens. We're actively looking into this issue. I'll update once we come up with a solution.
Current hacky solution to make it work would be to wrap each screen with a NativeBaseProvider.

Any updates on this? Or any workarounds I can try?

I'm running into this too.

I had the same issue while using Select and Popover (NativeBase v3.2.2).
The only solution that worked for me was to replace @react-navigation/native-stack with @react-navigation/stack.

Don't close this issue. This is an automatic message by Fresh - a bot against stale bots.

I have the same issue, using 3.3.5

I have the same issue, using 3.3.7

i am having the same issue with 3.2.2

still same 3.4.1

We're working on this. Hope to fix this in the coming release. Thanks for your patience.

Would be helpful to mention this restriction in the docs for the time being.

ANy update on this yet i am still facing same issue>

Any update? Need this urgently...

any update ??

Any update? same issue

We've been working on some workaround. This issue is coming from our internal Overlay component. We've to change our component render pattern to solve this issue.  This may take some time.
Thanks for your patience.

Thanks @surajahmed.
Same here. any suggestion or workaround for the time being?

FIX: upgrade to version 3.4.6 (or higher)
Replace import { Modal } from "react-native";
with import { Modal } from 'native-base';
Select should now render above modal on iOS. https://docs.nativebase.io/select

this is still happening and I am on 3.4.20
Is any one else still having this? or can you guys confirm at least if this is working for you now? I have spent days on this and planning to completely take off the nativebase unfortunately.

@byberkan I managed to get it working when using the "presentation" prop for Stack Navigator Screen Options but couldn't get it working for general purposes (it seemed very on-off and sometimes it would work).
In the end, we changed the design to get around this.

FIX: upgrade to version 3.4.6 (or higher)
Replace import { Modal } from "react-native"; with import { Modal } from 'native-base';
Select should now render above modal on iOS. https://docs.nativebase.io/select

this is working perfectly
Thanks @olamigokayphils

Hi, same probleme here. When using createNativeStackNavigator (react-navigation ) and having one of my screen with presentation option prop set to "modal", the select displays behind the screen modal.

Hi, same probleme here. When using createNativeStackNavigator (react-navigation ) and having one of my screen with presentation option prop set to "modal", the select displays behind the screen modal.

Does this solve your issue? It solved mine which was kind of the same as yours: https://github.com/GeekyAnts/NativeBase/issues/4864#issuecomment-1240632661

Hi, same probleme here. When using createNativeStackNavigator (react-navigation ) and having one of my screen with presentation option prop set to "modal", the select displays behind the screen modal.

Reporting same issue using native-base 3.4.28.
Wrapping surfaces that have modal as presentation option with <NativeBaseProvider> seems to be a good workaround. Will continue doing so till this issue is resolved.


Add compatibility for Pan-ukbb external data, make column names configurable.

This PR aims to make newly matched pan-ukbb data usable in the pheweb browser.
Changes

Make external data column names configurable

For matrix data, pval and beta are configurable, single files have c:p:r:a + pval and beta

Add both pval and beta to phenoview tables

Beta should now be usable as pan-ukbb scans were made with saige

In case only matrix DAO or file DAO is available, use that for both operations, otherwise use both (previously matrix DAO was saved to jeeves.ukbb_matrix_dao and file DAO was saved to jeeves.ukbb_dao, so you had to have both for full ukbb functionality. Now they are saved similarly, but if one is missing then either ukbb_matrix_dao or okbb_dao is pointed to be the existing DAO.)
Example config for pan-ukbb data in config.r5.py

Possible changes to be made before merge

Due to the fact that our data has changed quite a lot since R1 when the previous ukbb data was created (remove chr from vars, change to numerical chromosomes from XYMT), the data differ by quite a bit. I had to add a few variables and checks to the DAO initialization & configs. We should see whether this could be done better.

file DAO config has chrom_is_numeric flag for whether chromosomes are XYMT or 23,24,25
matrix DAO has column_names dict for pval and beta names, file DAO has c:p:r:a also
Whether chrom has "chr" prefix is figured out at runtime

Config file format could be changed
Frontend table can be prettier

R6 data with pan-ukbb data can be seen in dev.finngen.fi

@Lipastomies  add OR also to gene page main table and coding variant table

@Lipastomies  add OR also to gene page main table and coding variant table

I think its good enough to runtime figure the chr dickery as you have done.
Also table is pretty enough

I think its good enough to runtime figure the chr dickery as you have done.
Also table is pretty enough

@Lipastomies add OR also to gene page main table and coding variant table.
also gene report download seems to error out .... UKBB beta needed there also: http://dev.finngen.fi/gene/CLCN6

Checked the error, seems to be related to latex not being available?
[2021-01-20 07:13:45,458] ERROR in app: Exception on /genereport/CLCN6 [GET]
Traceback (most recent call last):
  File "/home/lehisart/ext_venv/lib/python3.5/site-packages/flask/app.py", line 2447, in wsgi_app
    response = self.full_dispatch_request()
  File "/home/lehisart/ext_venv/lib/python3.5/site-packages/flask/app.py", line 1952, in full_dispatch_request
    rv = self.handle_user_exception(e)
  File "/home/lehisart/ext_venv/lib/python3.5/site-packages/flask/app.py", line 1821, in handle_user_exception
    reraise(exc_type, exc_value, tb)
  File "/home/lehisart/ext_venv/lib/python3.5/site-packages/flask/_compat.py", line 39, in reraise
    raise value
  File "/home/lehisart/ext_venv/lib/python3.5/site-packages/flask/app.py", line 1950, in full_dispatch_request
    rv = self.dispatch_request()
  File "/home/lehisart/ext_venv/lib/python3.5/site-packages/flask/app.py", line 1936, in dispatch_request
    return self.view_functions[rule.endpoint](**req.view_args)
  File "/home/lehisart/pheweb/pheweb/serve/server.py", line 468, in gene_report
    gene_top_assoc_threshold=conf.report_conf["gene_top_assoc_threshold"], func_var_assoc_threshold=conf.report_conf["func_var_assoc_threshold"] )
  File "/home/lehisart/pheweb/pheweb/serve/reporting/report.py", line 43, in render_template
    return build_pdf(tmpl.render(**params))
  File "/home/lehisart/ext_venv/lib/python3.5/site-packages/latex/build.py", line 234, in build_pdf
    raise RuntimeError('No available builder could be instantiated. '
RuntimeError: No available builder could be instantiated. Please make sure LaTeX is installed.

Seems like the error is just missing LaTeX on the dev machine.
We'll have to test this on a docker for sure, but I wouldn'ẗ be too worried about this right now.

@Lipastomies add OR also to gene page main table and coding variant table.
also gene report download seems to error out .... UKBB beta needed there also: http://dev.finngen.fi/gene/CLCN6

Checked the error, seems to be related to latex not being available?
[2021-01-20 07:13:45,458] ERROR in app: Exception on /genereport/CLCN6 [GET]
Traceback (most recent call last):
  File "/home/lehisart/ext_venv/lib/python3.5/site-packages/flask/app.py", line 2447, in wsgi_app
    response = self.full_dispatch_request()
  File "/home/lehisart/ext_venv/lib/python3.5/site-packages/flask/app.py", line 1952, in full_dispatch_request
    rv = self.handle_user_exception(e)
  File "/home/lehisart/ext_venv/lib/python3.5/site-packages/flask/app.py", line 1821, in handle_user_exception
    reraise(exc_type, exc_value, tb)
  File "/home/lehisart/ext_venv/lib/python3.5/site-packages/flask/_compat.py", line 39, in reraise
    raise value
  File "/home/lehisart/ext_venv/lib/python3.5/site-packages/flask/app.py", line 1950, in full_dispatch_request
    rv = self.dispatch_request()
  File "/home/lehisart/ext_venv/lib/python3.5/site-packages/flask/app.py", line 1936, in dispatch_request
    return self.view_functions[rule.endpoint](**req.view_args)
  File "/home/lehisart/pheweb/pheweb/serve/server.py", line 468, in gene_report
    gene_top_assoc_threshold=conf.report_conf["gene_top_assoc_threshold"], func_var_assoc_threshold=conf.report_conf["func_var_assoc_threshold"] )
  File "/home/lehisart/pheweb/pheweb/serve/reporting/report.py", line 43, in render_template
    return build_pdf(tmpl.render(**params))
  File "/home/lehisart/ext_venv/lib/python3.5/site-packages/latex/build.py", line 234, in build_pdf
    raise RuntimeError('No available builder could be instantiated. '
RuntimeError: No available builder could be instantiated. Please make sure LaTeX is installed.

Seems like the error is just missing LaTeX on the dev machine.
We'll have to test this on a docker for sure, but I wouldn'ẗ be too worried about this right now.

@Lipastomies add OR also to gene page main table and coding variant table.
also gene report download seems to error out .... UKBB beta needed there also: http://dev.finngen.fi/gene/CLCN6

It seems UKBB data is not fetched for coding variant table, so I'll have to touch the jeeves function/frontend data grathering a bit. @juhis Do you have any opinions on whether it's better to add a call to ukbb data in the jeeves coding() function or handle it in frontend?

@Lipastomies add OR also to gene page main table and coding variant table.
also gene report download seems to error out .... UKBB beta needed there also: http://dev.finngen.fi/gene/CLCN6

It seems UKBB data is not fetched for coding variant table, so I'll have to touch the jeeves function/frontend data grathering a bit. @juhis Do you have any opinions on whether it's better to add a call to ukbb data in the jeeves coding() function or handle it in frontend?

@Lipastomies add OR also to gene page main table and coding variant table.
also gene report download seems to error out .... UKBB beta needed there also: http://dev.finngen.fi/gene/CLCN6

It seems UKBB data is not fetched for coding variant table, so I'll have to touch the jeeves function/frontend data grathering a bit. @juhis Do you have any opinions on whether it's better to add a call to ukbb data in the jeeves coding() function or handle it in frontend?
If I were to do it in frontend, I'm thinking maybe make a separate function for downloading the relevant UKBB variants and then join these in another function. In any case, I think I'll need to touch frontend columns & download header.

Discussed with Mitja and Mutaamba and we decided to leave the change for later. IF/When we do the change at some point, trhe data wrangling should be in the backend, and frontend should pretty much only render stuff.

@Lipastomies add OR also to gene page main table and coding variant table.
also gene report download seems to error out .... UKBB beta needed there also: http://dev.finngen.fi/gene/CLCN6

It seems UKBB data is not fetched for coding variant table, so I'll have to touch the jeeves function/frontend data grathering a bit. @juhis Do you have any opinions on whether it's better to add a call to ukbb data in the jeeves coding() function or handle it in frontend?
If I were to do it in frontend, I'm thinking maybe make a separate function for downloading the relevant UKBB variants and then join these in another function. In any case, I think I'll need to touch frontend columns & download header.

Discussed with Mitja and Mutaamba and we decided to leave the change for later. IF/When we do the change at some point, trhe data wrangling should be in the backend, and frontend should pretty much only render stuff.

Changed in d58c356:

Added UKBB OR to latex template & gene report page
Changed ukbb_dao and ukbb_matrix_dao init to be inside DataFactory, as discussed above
Added cpra to config for matrix dao

Changed in d58c356:

Added UKBB OR to latex template & gene report page
Changed ukbb_dao and ukbb_matrix_dao init to be inside DataFactory, as discussed above
Added cpra to config for matrix dao

I believe all of this will be happening in the new import Mutaamba is finishing so I believe we can delete this PR?
@Lipastomies @majorseitan


[Bug] Share intent should use setClipData(uri) for content:// uris

Issue Summary
I'm the developer of Sharedr, a share menu replacement app.
One of my users pointed out that Sharedr doesn't work when trying to share a file from your app.
While I can't be sure, I suspect that your app is relying on the legacy EXTRA_STREAM to supply a content:// uri to the destination app. I'll try to give more details below but I can imagine your time is valuable so here's the quick fix:
Instead of only setting Intent.EXTRA_STREAM...
Intent intent = new Intent();
intent.putExtra(Intent.EXTRA_STREAM, uri);
Intent chooserIntent = Intent.createChooser(intent, null);
startActivity(chooserIntent);

..please also use setClipData() and - optionally, Android should do this for you as long as you use setClipData() - then call addFlags(FLAG_GRANT_READ_URI_PERMISSION):
Intent intent = new Intent();
intent.setClipData(ClipData.newRawUri(null, uri));
intent.addFlags(Intent.FLAG_GRANT_READ_URI_PERMISSION);
intent.putExtra(Intent.EXTRA_STREAM, uri); // keep this for compatibility with old applications
Intent chooserIntent = Intent.createChooser(intent, null);
startActivity(chooserIntent);

Please also see the issue I filed on the AOSP bug tracker regarding this (little known) problem: https://issuetracker.google.com/issues/176280829
If you want to test if it works, you could download and install Sharedr (https://sharedr.rejh.nl/).
Now, for some background information and why this change is needed to support 3rd party share menu apps.
With Android Jelly Bean (API 16) Intent.setClipData(android.content.ClipData) was introduced:

As of Build.VERSION_CODES.JELLY_BEAN, the data being sent can be supplied through setClipData(android.content.ClipData). This allows you to use FLAG_GRANT_READ_URI_PERMISSION when sharing content: URIs and other advanced features of ClipData. If using this approach, you still must supply the same data through the EXTRA_TEXT or EXTRA_STREAM fields described below for compatibility with old applications. If you don't set a ClipData, it will be copied there for you when calling Context#startActivity(Intent).

Source: https://developer.android.com/reference/android/content/Intent#ACTION_SEND
As stated in the docs, Android will copy the uri to a ClipData if you don't set it. What the docs don't tell you is that Android's Intent.createChooser() will not copy the EXTRA_STREAM and the FLAG_GRAND_READ_URI_PERMISSION flag to the so called chooser intent. This makes sense, as this flag only works on ClipData: If an app doesn't use setClipData() but instead only uses the legacy EXTRA_STREAM method, that implies the flag will not work, thus is not needed, and the system should not add those flags.
In case you wonder why this is a problem for 3rd party share menu replacement apps while it's working fine with the system share menu: From what I've learned from the Android system share menu's source code, it leverages its system app privileges to add the flag and then starts the destination app on your app's behalf. That way the system share menu can grant read permission for content:// uris that actually belong to your app. As you can probably imagine, 3rd party apps are not allowed to pull these kinds of shenanigans.
Again, please also see the issue I filed on the AOSP bug tracker regarding this (little known) problem:https://issuetracker.google.com/issues/176280829
If you've read this far: Many thanks for your time, I hope you will find the time to fix the problem. If you have any further questions I'll do my best to answer them.
Steps to Reproduce the Problem
Not entirely sure as this issue was reported to me by a user of my app.
Specifications
Again, not entirely sure as this issue was reported to me by a user of my app, but if my assumption is correct, this problem should be reproducible on Android 4.1 and up.

Fixed in #113


Remove Irmin.Basic

The Basic functor makes things confusing for users by hiding what's going on, and restricts all back-ends to providing only the base API.
This branch removes it, changing the examples to use the more explicit form. As back-ends can now provide additional functions, Irmin_git.Internals is moved inside the store and the hacks removed (or, at least, moved to just the unit-tests). i.e. you can now only ask for a Git commit object from a Git store.
I also deleted Ir_bc.Make and Ir_bc.MAKER because a) they were confusing me, b) they aren't used within Irmin, and c) they are not exposed to users of the API.
Code needs to be updated from e.g.
module S = Irmin.Basic(Irmin_git.FS)(Irmin.Contents.String)

to
module S = Irmin_git.FS(Irmin.Contents.String)(Irmin.Ref.String)(Irmin.Hash.SHA1)

This branch is on top of the BC.Repo branch #275 (so the diff isn't quite as big as it looks).

Although this makes the API indeed simpler, I think we need something else to simplify user code, e.g.:
-module Store = Irmin.Basic(Irmin_git.FS)(Irmin.Contents.String)
+module Store = Irmin_git.FS(Irmin.Contents.String)(Irmin.Ref.String)(Irmin.Hash.SHA1)

make Irmin yet more verbose than it was.

I'm happy to merge anyway, we can re-add higher level facing APIs later.

Does the user code need to be shorter? Typically, we'd be saving only 23 characters per program, but making it harder to understand in the process. Doesn't seem like a good trade-off.

Examples (and perhaps aliases for commonly-referenced modules) would go a long way here.  It's a lot to expect a new user of Irmin to generate a string like
module Store = Irmin_git.FS(Irmin.Contents.String)(Irmin.Ref.String)(Irmin.Hash.SHA1)

from looking at the API documenttion, but I do agree that it's easier to understand as a result of being more explicit.

@yomimono Yeah, there's an example in the page next to BASIC (which is still there), but it probably needs some reorganisation. The actual code examples in the docs need updating for the new API (should probably wait for the rest of the changes), but the ones in the examples directory work. Suggestions welcome...

Does the user code need to be shorter?

It doesn't, but we should have something simpler for the 90% use-case, ie. when users want to use JSON and/or strings and/or cstruct as contents, and don't want to worry about the type of references and SHA1.
then I guess that then next 9% of users want to specify some custom merge function.
(disclaimer: these numbers are completely random :p )


error 403 while accepting offer

hi,
i created a bot that has to accept all offers with no items from me.
while bot try to accept offer returns error 403. i read that can be problem with my api key, but i regenerated it many times, deleted it or setup() generated key.
I'm sure accepting is performing after successful login.
I don't know what is cause of my problem.
thanks for help.

probably you have one week ban on your system.

sometimes bot accept a few offers and after error comes again


install script fails on Creality K1 with klipper

I am trying to run the install script but it fails as below:
root@K1-4158 /root/mobileraker_companion/scripts [#] ./install-mobileraker-companion.sh
-sh: ./install-mobileraker-companion.sh: not found
root@K1-4158 /root/mobileraker_companion/scripts [#] cd ..
root@K1-4158 /root/mobileraker_companion [#] ./scripts/install-mobileraker-companion.sh
-sh: ./scripts/install-mobileraker-companion.sh: not found
root@K1-4158 /root/mobileraker_companion [#]

forget this. I found the correct install script


networkpolicies code tuning

there has got to be something wrong with networkpolicies too.  there's no way the policy data is actually changing.  it appears you are doing an update when nothing has in fact changed in the data.

Closing in favor of: https://github.com/rancher/rancher/issues/14372


Add useful error message when redirect from http to https occurs

When App Service Authentication is turned on and the mobile app URL is using http, the mobile app server will issue a 302 for every request. We should provide a useful error message for this so the user knows what is going on.

Hi there, please have a look at the Readme section for the future of Azure Mobile Apps. Closing this issue for now. Thanks!


Use direct routing device only when tunneling is disabled and BPF Host Routing or NodePort are enabled.

Please see the commit for details.
Fixes: #17480
Use direct routing device only when tunneling is disabled and BPF Host Routing or NodePort are enabled.

/test

/test

/test

/test-1.23-net-next

Travis CI failure seems relevant to my changes. Let me check.

I shouldn't skip InitDefaultPrefix in here even if the DirectRoutingDevice is missing.
https://github.com/cilium/cilium/pull/18815/files#diff-9143180298a1f5ba5dc10fd98d87945d1381ef45b7347a639f85e13e84285ca2R363-R367
Actually, in the case of the IPv6, we are handling the missing case here.
https://github.com/cilium/cilium/blob/8034fd57180a7ebc8284a9b099d17db7404e45c9/pkg/node/address.go#L113
Background: https://github.com/cilium/cilium/commit/41805e4aaf6da9f10932cc360b9caeb8370747b8
I'll revert this change.

/test


is it possible to cluster points and paths

I'm wondering if we can clusters the points and paths using markerclusterGroup. As far as I understood from this libraey its suing canvas elements, and not markers to render the flows. Is there any way you can think of to add the markerclustergroup to this one it would be wonderful. Grouping points and flows while zooming out.

@Zahma neat idea.  Specifically you mean Leaflet.markercluster, right?
As a first step in looking into this--in your own use of that plugin--did you try to see if it would support drawing to the canvas automatically, via the L.canvas LeafletJS conventions?  Such as:
var canvasRenderer = L.canvas();
var markers = L.markerClusterGroup({
  renderer: canvasRenderer
});

Although I'm unsure if it even supports that and if you have to do it at the L.markerClusterGroup level or at its individual marker layers that get added to it.  First I'd want to know if that is supported with that lib to help decide how to technically implement this.  I would want to lean on an already established clustering plugin to help with the to/from points.
With Leaflet.Canvas-Flowmap-Layer when it comes to "clustering" the flow lines I could see that being pretty straightforward once we have the clustered markers figured out.
cc @sarahbellum

@jwasilgeo  I'm pretty sure markerclusterGroup doesn't support canvas it only gets Markers as parameter.
One Idea I thought about is to have both libraries each working on its side. Canvas Flow Map Layer takes a Feature collection, whereas markerclustergroup takes Markers. So what I'm thinking about basically is to draw the Markers without displaying them, apply the clustering, and then do some calculations to finally construct a featurecollection object that will be then served to CanvasFlowMap for display. But
this is not the best way to do it in terms of efficiency. If you have any idea or contribution I'll be grateful.

@Zahma Hi, I'm chiming in on behalf of the visualization implications of clustering. One consideration is the complexity that clustering might add to creation of the Bezier curve line, especially if you allow zooming, where the clustering would change. The Bezier curve lines will potentially become far fewer when zoomed out, and more abundant as the user zooms in and point declustering occurs. This could be super cool!

@Zahma I think I follow what you're saying above.   "...then do some calculations to finally construct a featurecollection object that will be then served to CanvasFlowMap for display..." could totally work.
@sarahbellum thanks for bringing up the visualization feedback and concerns.  Is this the behaviour you envisioned, @Zahma?

@sarahbellum @jwasilgeo .Thank you both for your interest.  In fact i'm working on it right now, I'll let you know of the implications.


Move over most recent changes from MS3 repository

This will probably require a manual merge due to rebasing in the main branch there

[ ] support for grouped documents input
[ ] re-enables namespace override xml read test
[ ] re-enable mappertest
[ ] import repository issues

Header issues:

[ ] unrecognized line should not throw an exception, forwards compatibility
[ ] unrecognized version should not throw an exception, forwards compatibility
[ ] the value of default outputs is still not clear

We won't need to re-enable the namespace override test, that's been re-enabled in this repo since I added namespace support. All the others in the first section look fine (though of course, importing issues from your repository is a meta issue). I propose we de prioritize the github pages bit (though it shouldn't be hard) as it doesn't affect the exported functionality. Will someone on your team be doing them or should I undertake to do so?
I am strongly against unrecognized lines not throwing an exception. An unrecognized header line being ignored virtually guarantees behavior will not be what's expected. Furthermore, if unrecognized header lines are accepted, and then the underlying datasonnet engine is updated to include support for that line, then the behavior of existing scripts that have not changed at all will  suddenly change due to the header line now being recognized, which is a very bad thing. Also, if have a typo in a header line (at least the first part), you won't be told there's an issue, you'll just have mysterious missing behavior.
I am slightly less strongly against unrecognized versions not throwing an exception, since (if every header line is understood), then there's a decent possibility all the code in the script is acceptable, and it could be tested and run. I am still against it, because some issues might not be apparent on brief testing (such as code paths that use nonexistent functions, but don't come up in a quick check that the script still works), and also because one of the points of the version is to be a strong signal on runtime compatibility.
Re: default outputs, the reason "default" was added to the output is to resolve the question of "what gets done if any/any is provided as the output", which needs to be one of the configured outputs. As for why there are multiple outputs, that's a pretty definite requirement for us. Some scenarios that have come up for us are to want to configure some options for eg both Java and JSON, or Java and CSV. If we want to remove the "accepts any/any for output type" possibility I'm fine with getting rid of the default output functionality

Btw, I don't see anything in the above around the XML functionality, did we still want to talk through some of that?

Thanks for the reply :)
On the namespace test, I guess we missed it when we cherry picked that piece. It's checkmarked now.
On the github pages CI, this is definitely not as high priority as others, but still a must. We have developers making use of the docs and the ci is the only way to guarantee they're looking at the right info.
On the header exceptions, ultimately graceful degradation is better than simply not working. This W3C document is where I'm coming from Forwards Compatibility: Must Accept Unknowns. It's kinda standard.
On default output, I've changed my mind and see the multiple outputs support does have value. Could we instead of introducing another keywork default output just take whichever is last? It'd leave the standard use case simple, plus prevents the complexity on the Header API. I'm thinking we could encapsulate the defaulting logic within the Header and preserve the previous signatures.
On XML mixed content, I think the new format deviates from the badgerfish convention, at least as I understand it. For example, in this online converter if you put the input for the mixed content test, you'll get back what we had before, which is what I would expect after reading the badgerfish convention docs. Plus I think as it was before it should still preserve order in a round trip, no? Since the writer iterates on the elements in the right order, regardless of the type... I think.
Some of this stuff is probably easier to discuss verbally, so if you want to jump on a call let me know.

I'll post a few things here to document some thoughts, but would be glad to hop on a call.
Forward compatibility is only standard in certain contexts.  When transforming data for a financial transaction, that's not the case. Numerous major standards are not forward compatible. Two that spring to mind are, Apache Arrow specifically calls out that if an older client library finds file structure it can't handle it will fail completely (because silently reading wrong data is very bad), SQLite has had several non-forwards-compatible file format changes (deliberately, because integrity of the database would fail if they didn't), and I can provide others as needed.
It's useful to note the caveat at the beginning of what you link: "A language whose syntax allows additional unknown text"--this isn't a general rule to follow, it is opting into a practice in a specific context.
Imagine folks out there running Camel, and they move a script over to another Camel deployment, and it works... except for some reason no matter what they change the output is never XML like the docs say it should be, it is always JSON. They double check the headers, they triple check the headers, everything is perfect, yet it doesn't work? Well, maybe we changed something about how outputs are specified (as just happened across these versions), and their perfect lines, that perfectly match the newest version of DataSonnet's docs, don't match the older version of DataSonnet that the second Camel uses, but the older version is just silently ignoring the headers it doesn't recognize. Heck, even if for some reason some of their functions don't work, imagine how mystified they'll be. The functions are documented, and they've got the right version header, why aren't those functions working?
The story is much better if we are strict about the headers. They get a message saying that the version of DataSonnet they're using doesn't support 3.0, only 1.0 and 2.0,  and they should either upgrade or attempt to modify the script for use with 2.0. If they choose the latter and change the script header to 2.0, then they're told which header lines don't work, and can fix them.

Re: default as a keyword, I like explicit better. Someone only occasionally reading or writing the headers can't be expected to have memorized a behavior like "last as default". The most common use case is a single output configuration, and that will still be treated as the default. There won't be anything wrong with specifying multiple without a default, either, there just won't be a default if used in an any/any situation, so all existing headers using the new format will continue working.

For XML, a few things.
First, with the previous setup, tags that are the same will end up in the same array, so even if ordering is relied on, it won't be possible to reconstitute the mixed content.
Second, probably the most common use case I'm aware of for mixed content in data transformation would be working with the mixed content exactly and completely. For example, someone might well have XML something like:
<comments>
  <comment>
    You can go to here to find out more about platypuses specifically, or over here to find out more about monotremes in general.
  </comment>
</comments>

Someone when transforming that is generally going to want to bring along the whole mixed content and put it in some other place in the output structure. That isn't possible with the previous output.
Third, even if relying on ordering did allow round tripping, JSON objects aren't ordered (to quote from json.org, "An object is an unordered set of name/value pairs."). If someone used another tool to generate sections of JSON they expect DataSonnet to turn into XML, we can't rely on any particular ordering.

Btw, something I realized I might not have made clear with the version header in the DataSonnet files: it isn't intended to tick anywhere near as rapidly as the DataSonnet main version. I could see it being several major versions of the java code before the header changes even one major version.
Additionally, I'd be very open to modifying the code so not-specifically-understood minor versions are still allowed to run (with a warning logged of course), and reserving header version rejection only for major version changes.

Hey Russell.
So on the header, you make good points about compatibility. Though I still prefer to leave the debugging to developers if something doesn't work, I think compromising on allowing forward minor versions is fair. I'll strike those through once we make those changes.
I think the default output and xml changes are more significant, because they are big changes in functionality and API, that I'm not sure we should be doing at this moment as we're trying to ship in Camel 3.7. On XML, we're basically discussing an entirely different format than badgerfish in order to enable round tripping, which is valuable, but it's a breaking change. And for the header I think the implicit behavior of 'last output' is a fine tradeoff for keeping the Header API simple. After all the use case of multiple outputs is a very minimal fraction.

Or we could rely on the quality factor media type parameter to signal which is preferred. I think that'd achieve both the functionality and leave the Header API as it is.

I think the quality idea for default might be a good solution, I'll review the RFCs to make sure I'm understanding it fully

Re: the badgerfish convention, we're already diverging from the original badgerfish convention (which didn't have indexed text at all), and the example implementation of the one variant we're looking at has various bugs and oddities (for example, it does strange things when xml tags are single characters). Several of the other implementations seem to be minor variants as well.
I think getting to a badgerfish implementation that supports round tripping XML--which is the same as complete support for XML semantics--is a good idea even if it ends up being a slight updating of one variant of the convention. We have to document our implementation fully, either way, the quick description on the converter page isn't enough.

so apparently there's no way to migrate issues across orgs so will need to replicate the issues

All merged!


Add twine setup for PyPI

From discussions in meeting on 04/13/2021, came up with following bullet items:

[x] Create the PyPi account that will host the SciDataLib package (@JohnsonDylan will lead this)
[x] Figure out the description for the package on PyPi and update the long_description in setup.py (@stuchalk will lead this). Currently, we are using the entire README in the setup.py lines , which is probably a bit too verbose)
[x] Need to create an API token using the PyPi account. This is under "Account Settings" -> "API Tokens" to create the token. We only need scope for the SciDataLib project.
[x] Once we have that API token, we need to place it in the GitHub Secrets (in GitHub under "Settings" -> "Secrets") Then we create a "Repository Secret" with the token.
[x] Use the name of that secret in the GitHub Actions yaml to add a deploy stage to PyPi following the below example:

   - name: Build Python package and Upload to PyPi
        shell: bash -l {0}
        if: startsWith( github.ref, 'refs/tags/v') && matrix.python-version == env.PYTHON_MAIN_VERSION
        env:
            PYPI_TOKEN_PASSWORD: ${{ secrets.PYPI_TOKEN }}
        run: |
          pip install wheel twine
          python setup.py sdist bdist_wheel
          twine upload --username "__token__" --password $PYPI_TOKEN_PASSWORD dist/*

Well I decided to go with the verbose description after all.  We can fix this in a future release :)


Fix typo in instructions for adding target to EventBridge

Fixes a grammatical error and makes the filename in the prose match the one in the command below.
Relevant page/section: https://docs.localstack.cloud/user-guide/aws/eventbridge/#add-the-lambda-function-as-a-target

Thanks 🙏


Provide the readInt8 function call in plain_dictionary codec with arguments

In codec/plain_dictionary.js, we are calling: readInt8() without argument:

opts.bitWidth = cursor.buffer.slice(cursor.offset, cursor.offset+1).readInt8();

This is fine for node.js, because its readInt8()method has a default argument of offset = 0. See https://github.com/nodejs/node/blob/master/lib/internal/buffer.js#L411.
But when using this package in browser, it breaks because the buffer method (provided by shim packages) does not have such a default argument. For example: https://github.com/feross/buffer/blob/master/index.js#L1221
Accepting this change will make this package compatible to use in browser.

Excellent @FZSS thank you!

appreciate the prompt response! If you haven’t done so, can you consider publishing an updated version to npm?

published as +<EMAIL_ADDRESS>Keep in mind that the branch published is parquetjs-lite


fvm support

Hi. Thanks for creating this great extension.
My only problem with this extension is that it does not support fvm.
Can you please add some kind of settings "useFvm" that will replace "dart run build_runner build --delete-conflicting-outputs..." with "fvm dart run build_runner build --delete-conflicting-outputs..."? That will be great
Greetings
Kamil

Wait, people are actually using this? Haha. Please feel free to make a PR, shouldn't take too long.

Maybe a "dartCommand" which defaults to "dart" and could be changed to "fvm dart"?

It's a practice now to set flutterSdk in the settings.json
So, i created a PR to get sdk path from workspace settings, this way when jumping between projects with and without fvm plugin will always get right path.

Closing as stale, please reopen if needed


A problem with glob syntax

I have following tree structure of folders:
src/
|_ public/
   |_ first/
      |_ readme.txt

and a simple flyfile.js:
export default async function () {
  await this.start(["build"])
}

export async function build() {
  await this.start(["resources"])
}

export async function resources() {
  await this
    .source('src/public/**/*.*')
    .target('build', {depth: 1})
}

And everything is ok! But if the readme.txt don't have a file extension .txt (readme) and I rewrite .source('src/public/**/*.*') as .source('src/public/**/*') it will cause the EISDIR error:
[16:25:26] Starting "resources"
~~[~3~2~m~s~t~a~c~k~:~ ~~[~3~9~m~
~ ~ ~~[~3~2~m~-~ ~~[~3~9~m~E~r~r~o~r~:~ ~E~I~S~D~I~R~:~ ~i~l~l~e~g~a~l~ ~o~p~e~r~a~t~i~o~n~ ~o~n~ ~a~ ~d~i~r~e~c~t~o~r~y~,~ ~r~e~a~d~
~ ~ ~~[~3~2~m~-~ ~~[~3~9~m~ ~ ~ ~ ~a~t~ ~E~r~r~o~r~ ~(~n~a~t~i~v~e~)~
~~[~3~2~m~m~e~s~s~a~g~e~:~ ~~[~3~9~m~E~I~S~D~I~R~:~ ~i~l~l~e~g~a~l~ ~o~p~e~r~a~t~i~o~n~ ~o~n~ ~a~ ~d~i~r~e~c~t~o~r~y~,~ ~r~e~a~d~
~~[~3~2~m~e~r~r~n~o~:~ ~~[~3~9~m~ ~ ~~[~3~4~m~-~4~0~6~8~~[~3~9~m~
~~[~3~2~m~c~o~d~e~:~ ~~[~3~9~m~ ~ ~ ~E~I~S~D~I~R~
~~[~3~2~m~s~y~s~c~a~l~l~:~ ~~[~3~9~m~r~e~a~d~
[16:25:26] resources failed due to Error: EISDIR: illegal operation on a directory, read

How to solve this problem?

For now, I'd go with the following:
this.source(['src/public/**/*.*', 'src/public/first/readme'])

Or, just rename your readme to readme.md, since that's more the standard.
The EISDIR error is fixed in<EMAIL_ADDRESS>which is still being tested.

I understand that I can rename it, but I want not to think about things like this) I look forward to v1.0.
Thank you!

No worries, totally understandable. Closed this just because of the 1.0 fix :)
No problemo


Funnel responds with 'Closed explicitly'

Hi,
I am getting the following message in the funnel logs, and neither command line requests nor the web interface work
{"err":"Closed explicitly","level":"debug","msg":"responding: /tes.TaskService/ListTasks","ns":"server","resp":null,"time":"2019-06-03T18:55:42Z"}
{"error":"Closed explicitly","level":"error","msg":"Calling ListTasks","ns":"aws-batch","time":"2019-06-03T18:56:11Z"}

When I try on the command line
$curl': curl http://<IP_ADDRESS>:8001/v1/tasks/bjpfhrq0fs0g00dn4is

{
  "error": "Closed explicitly",
  "code": 2
}

The same queries used to work a day ago. If I restart the server it works, but eventually ends up in this state.
What does this mean? and what causes it?
Is there any configuration option that needs to be considered?
The funnel server is interacting with mongodb (located on a different server), and submits jobs to AWS batch.
Thanks

Funnel wasn't handling mongo sessions properly. I'm guessing the session was becoming stale and was being closed by the mongo server.
Try the fix reference in the PR above.

The new version does not seem to work properly.
The jobs are submitted and immediately go to state 'SYSTEM_ERROR' without being sent to AWS batch.
In the log files (with the debug enabled) there is no information.
Using the previous version (which eventually gets to the 'Closed explicitly' state) the jobs are submitted as expected and go to states QUEUED and RUNNING etc

The changes I made shouldn't have affected jobs being submitted to batch.  Nonetheless I found a spot where I wasn't logging a potential error in the CreateTask method.  I pushed up a new commit to that branch that should provide this missing error logging.

Hmm,
the problem is still there.
If I use the 0.9.0 version my jobs get submitted to AWS batch.
If i switch to the latest commit I submit the job and it does not even make it to aws batch. Instead in the logs i see:
{"error":"RequestError: send request failed\ncaused by: Post https://batch.us-east-1.amazonaws.com/v1/describejobs: x509: failed to load system roots and no roots provided","level":"error","msg":"Calling DescribeJobsWithContext","ns":"aws-batch","time":"2019-06-17T18:35:24Z"}

Thanks, there is still the same problem
This version is still not able to submit jobs to AWS Batch. (the previous version v0.9.0 can on teh same node, with the same config files)
The only relevant error I can see is
{"error":"RequestError: send request failed\ncaused by: Post https://batch.us-east-1.amazonaws.com/v1/submitjob: x509: failed to load system roots and no roots provided","level":"error","msg":"error submitting task to compute backend","ns":"server","taskID":"bk3ut6qi76gg008vei1g","time":"2019-06-17T19:48:44Z"}

Thanks
K

Are you running your funnel server in a docker container? If so, I think the problem may have been with the base image I was using. Try rebuilding the container (make docker) using the branch in #613.

I am using it in an image, but I compiled it myself.
FROM ubuntu:18.04

RUN apt-get update &&\
    apt-get -y install git golang go-dep

ENV GOROOT=/usr/lib/go-1.10/
ENV GOPATH=/opt/
ENV PATH=$PATH:$GOROOT/bin

WORKDIR /opt

WORKDIR /opt/src/github.com/ohsu-comp-bio/
RUN git clone https://github.com/ohsu-comp-bio/funnel.git
WORKDIR /opt/src/github.com/ohsu-comp-bio/funnel
#RUN git checkout mongo-session && git pull origin mongo-session
RUN make && go build

FROM ubuntu:18.04

RUN mkdir -p /opt/funnel/funnel-work-dir
COPY --from=0 /opt/src/github.com/ohsu-comp-bio/funnel/funnel /opt/funnel/funnel

ENTRYPOINT ["/opt/funnel/funnel"]

CMD []

Nevertheless, I will try your suggestion and let you know

Ah ok. I the source of the error is that the ubuntu:18.04 image doesn't com with ca-certificates. See https://blog.cloud66.com/x509-error-when-using-https-inside-a-docker-container

Perfect, thanks for the pointer.
This solved the problem...

For completion the docker file is now:

FROM ubuntu:18.04

RUN apt-get update &&\
    apt-get -y install git golang go-dep

ENV GOROOT=/usr/lib/go-1.10/
ENV GOPATH=/opt/
ENV PATH=$PATH:$GOROOT/bin

WORKDIR /opt

WORKDIR /opt/src/github.com/ohsu-comp-bio/
RUN git clone https://github.com/ohsu-comp-bio/funnel.git
WORKDIR /opt/src/github.com/ohsu-comp-bio/funnel
RUN make && go build

FROM ubuntu:18.04

RUN mkdir -p /opt/funnel/funnel-work-dir
COPY --from=0 /opt/src/github.com/ohsu-comp-bio/funnel/funnel /opt/funnel/funnel

RUN apt-get update
RUN apt-get install -y ca-certificates

ENTRYPOINT ["/opt/funnel/funnel"]

CMD []


resetOdometry does not reset thetaController/lastHeadingRadians

Sorry, I guess this is probably fine because the odometry should only be reset when the robot is still, and if the robot is still then it will set it.


Update OCP AWS scripts for master->devel rename

Update the prep_for_subm.sh OCP AWS install script and docs to reflect
the rename of the "master" branch to "devel" for all Submariner repos.
Signed-off-by: Daniel Farrell<EMAIL_ADDRESS>

Updated the commit message to reflect the narrower scope of this PR now that other PRs have dealt with other similar renames.


Update folder structure to work with new build tooling

demo content and other stuff can be kept on root level now, we centrally ignore everything outside the library namespace folder with the latest version of UI5Lab-central!
Only index.json needs to be moved to test-resources/it/designfuture


Micro Front Ends -- Agent can report Global and Local Errors

Outcomes

[ ] Traditional Agent builds can report errors as they do now
[ ] Modular agent builds can report global errors, if not disabled
[ ] Modular agent builds can report local errors, if enabled
[ ] Any error reported by the agent will be harvested and sent to the configurations defined in the agent configuration object
[ ] API access should be standardized across all build types of the agent

Is there any progress on these MFE topics? I think this is what we are waiting for: The ability for MFE components, hosted in a shell application that ALSO reports to NewRelic, to report their own metrics and events to their own application. Right now any and all metrics are "intercepted" by the hosting application and collected in their NewRelic application.

I was wondering the same things actually. It looks like there is some initial work done and available here, but the feature set is fairly limited by the looks of it. Is this still being worked on?

@MartijnKooij @jmezach Following up on this, thank you for your continued interest. Work on this topic was shelved for some time, but ha nows been prioritized, and is on our board to be completed by next quarter. This will likely include NPM  agent loaders that mirror what is available via New Relic's UI, APM and copy/paste, a custom agent loader that can be configured for custom features as plugins, as well as an initial MFE loader that supports page actions, metrics, and error capturing.


Kingdom Hearts II Map Studio

Adds a tool called Map Studio, which is responsible to modify different aspects of information from MAP and ARD files. It also serves as a viewer.

Planned functionalities:

[X] Free camera movement
[X] BOB editing
[ ] Verify if BOBs can be edited by attaching to PCSX2
[x] View collisions
[ ] Edit collision properties (flags, etc.)
[x] Switch to different COCT files
[ ] Handle DOCT files
[x] Export collision layer
[ ] Import collision layer
[ ] Export MAP meshes
[ ] Import MAP meshes
[ ] UVSC implementation
[ ] TEXA implementation
[x] Enumerate SpawnPoint files
[x] Allow to modify SpawnPoint objects
[x] Show and edit event collisions
[ ] Show and edit walk paths
[x] Show decompiled SpawnScript
[x] Allow to compile SpawnScript
[ ] Simulate SpawnScript

Marked the pull request as Ready. I know I implemented half of the functionality I actually wanted, but many of them depends from aspects of the game that has not been reversed engineered yet. A second pull request can always be opened in the future to add the "missing" functionalities.

The ability to change the key bindings would be handy for people who don't have qwerty layout.

maybe allow the option to move the camera up or down with "Q" and "E" respectively, this saves time having to turn the camera upwards and move up that way

Shift should increase the speed by a lot more, and highlighting a selected object + targeting the camera on that object would be a much appreciated feature. As it is, there's no way to tell which instance of PLAYER.mdlx you want to edit without moving every instance in the map until the one you want to edit moves. Same goes for bounding boxes.

I'm sorry it's taken me this long to write the review, anyway, I'd say it's all good to be integrated with the main branch, all the main functions work perfectly fine, and any changes can simply be pushed in future iterations

Thank you so much for your feedback Tom!


bug(server): Incorrectly set environment variables

This PR fixes the Incorrectly set environment variables in the server plugin.

const RR_RPC = "RR_RPC" (value was empty)
RR_HTTP moved to the HTTP plugin
closes #479

linked #368


Bedtools intersect truncates name column to 1000 chars?

Hello,
I hope you're well.
We're using bedtools (v2.30.0) in some additional camouflaged gene work and are running into an issue where it appears bedtools intersect truncates the name field to 1000 chars, though we're also missing the subsequent column, so not sure exactly what's happening.
The name column is where we list the set of all genomic regions that are identical, and some of the sets are quite large.
Here's the command I'm running:
bedtools intersect -a mini_align_to.bed -b mini_camo_annotations.bed > mini_intersect.bed
I have attached the two input files and the resulting truncated output. Had to change file extensions to .txt to satisfy GitHub requirements.
mini_align_to.txt
mini_camo_annotations.txt
mini_intersect.txt
Can you help?
Really appreciate it.

Hi @mebbert, this limitation does not exist in master.  You can clone and compile and be GTG.


Bar chart needs it's own documentation section

Should make sure to include a thorough explanation of the "cluster" and "stack" mechanisms

#321 Addresses this topic, if there needs to be more docs, don't hesitate to reopen!


Consider removing Buffer from node code, replace with native array type

More info: https://sindresorhus.com/blog/goodbye-nodejs-buffer
Also would provide a better fix for: https://github.com/ericblade/quagga2/issues/509
The current fix is just to install the type, because it doesn't matter... but it could matter in user code.

added PR https://github.com/ericblade/quagga2/pull/539

side observations:  root tsconfig.json has types ["mocha", "node"]
probably consider tsconfig.test.json for the mocha tests inside src/

good idea.  there's been some recent upgrades to typescript's handling of nested tsconfig files, too, an update to current ts is probably a good idea too


Make repo size better

This is one we've discussed a lot, it's a tricky tradeoff between complexity of computing the value and accuracy. Hopefully we can find something fast that's pretty accurate. We shouldn't consider anything too slow for this since it's not crucial that this value be correct.

Perhaps the list-commit view could show the total size, and incremental size (what was added in this commit)..
I'm not sure what the SIZE column in list-commit is  right now.

Upon commit, that could be saved somewhere, and summed up easily for list-repo ?
I understand we could be tempted to list the size of the backing store, but most of the time, I'll want to know if my data is right, if I've been receiving the right amount of data, to assess if my pipelines are properly working, etc.. that's going to be day-to-day. Backing-storage will be a concern once in a while.. but I wouldn't put that first and foremost. Perhaps behind -o wide  ? :)


Website/Documentation 404

Readme currently shows "Website" as http://dustinfarris.com/ember-django-adapter/, which returns a 404. As far as I know, the documentation is not hosted anywhere else.

Thanks, I'll work on getting this back up

Wanted to give this a bump. In need of this addon but can't get to the documentation.

That must have been a huge outage... @dustinfarris

Yeah still down, do you need help at all?

Hi @Parrryy, maybe the documentation could be re-posted as a wiki on GitHub. Do you have any experience setting them up?

Sorry for the radio silence.  Yes I need help with this.  Open to ideas and happy to do whatever needed administratively.  I will open a general request for maintainers in a separate issue.
Dustin
Sent from my iPhone

On Jul 7, 2021, at 19:01, Jeff Kerr @.***> wrote:

Hi @Parrryy, maybe the documentation could be re-posted as a wiki on GitHub. Do you have any experience setting them up?
—
You are receiving this because you were mentioned.
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@dustinfarris Happy to help where I can. @gojefferson Not particularly but happy to look into and help out.

I've updated the domain/url to dustinfarris.github.io/ember-django-adapter which should solve the http error issues.  The formatting and content of the docs could use some love if anyone cares to contribute.


Adding market to all event broadcast

This change adds the subscribing market as the second argument for event handlers. This is preferable to including the market in the primary event payload as it would add unnecessary properties to that object.
If a user wishes to receive the subscribe market for the event, they simply need to handle the second property:
binance.on('trade', (trade, market) => {

});

all markets were modified to support this behavior
all markets now have test coverage to ensure the market event is supplied as the second argument.

Pull Request Test Coverage Report for Build 264

295 of 315 (93.65%)  changed or added relevant lines in 21 files are covered.
10 unchanged lines in 5 files lost coverage.
Overall coverage decreased (-0.1%) to 86.449%

Changes Missing Coverage
Covered Lines
Changed/Added Lines
%

src/exchanges/binance-client.js
26
27
96.3%

src/exchanges/bitflyer-client.js
12
13
92.31%

src/exchanges/bitmex-client.js
13
14
92.86%

src/exchanges/cex-client.js
0
17
0.0%

Files with Coverage Reduction
New Missed Lines
%

src/exchanges/cex-client.js
1
13.79%

src/exchanges/ethfinex-client.js
1
96.45%

src/exchanges/bitfinex-client.js
1
93.64%

src/exchanges/gemini-client.js
3
84.11%

src/exchanges/bitflyer-client.js
4
85.71%

Totals

Change from base Build 262:
-0.1%

Covered Lines:
2017

Relevant Lines:
2205

💛  - Coveralls


ESP32: Integrate SCD30 Sensor Library

As part of the effort to create an EPS32 based Golioth Frog Sensor https://github.com/Ribbit-Network/ribbit-network-frog-sensor/issues/126 , we need to find and integrate drivers for the Frog Sensors into the ESP-IDF framework stared in this branch: (https://github.com/Ribbit-Network/ribbit-network-frog-sensor/tree/esp32_golioth)
Sensors
SCD-30 - NDIR CO2 Temperature and Humidity Sensor - https://www.adafruit.com/product/4867
There's a common set of sensor drivers UncleRus/esp-idf-lib which has support for the SCD-30.

There is an example project here showing how to integrate the SCD-30 library
https://github.com/UncleRus/esp-idf-lib/tree/master/examples/scd30/default

The basic proof of concept code is now complete for reading data from the SCD30 sensor. Will validate with hardware shortly.

Build log is here: https://github.com/Ribbit-Network/ribbit-network-frog-sensor/actions/runs/3271380897/jobs/5381101675

I'm attempting to test this with the hardware and discovered that the Adafruit dev board we are using has a switchable power source for the I2C connector that gets disabled when I flash the board.

I'm trying to set the pin controlling that power source to high, but I can't seem to make it work. Perhaps you have some insight into what I might be doing incorrectly @beriberikix?
https://github.com/Ribbit-Network/ribbit-network-frog-sensor/blob/esp32_golioth/software_esp32/main/app_main.c#L178-L181

Oooh, I didn't know they added that. Very useful for future battery readings as well as low-power mode. I think there's a bit of initialization missing, which is probably masked by scd30 library. Fortunately there's also a library for the battery gauge that will be useful for future features, not just enabling: https://esp-idf-lib.readthedocs.io/en/latest/groups/lc709203f.html
I would suggest breaking this up a bit further - just getting each one of the I2C devices working in a standalone example, integrate them one at a time and then add Golioth.
If that fails, or just because, hop over to our forum :)

I tried flashing a few more times and I actually believe this is an issue with the debugger not resetting the esp32 properly after the flash. When I manually power cycle after the flash, this works as expected. Will need to investigate more.

Yes, that’s the way I get it to flash most of the time unfortunately. Is
that why I have to manually power cycle after to get it out of programming
mode at the boot loader level?
Any work around a or documentation that better explains the interactions
between the boot loader, esp-idf and everything I should read?
On Tue, Oct 25, 2022 at 2:59 AM Jonathan Beri @.***>
wrote:

Ah yes, that's one annoying thing about the ESP32 Feathers - you have to
put it in "programming mode"...sometimes. Have you put it into bootloader
mode
<
https://learn.adafruit.com/adafruit-esp32-s2-feather/factory-reset#step-2-enter-rom-bootloader-mode-3106832

?
On Mon, Oct 24, 2022 at 7:12 AM Keenan Johnson @.***>
wrote:

I tried flashing a few more times and I actually believe this is an issue
with the debugger not resetting the esp32 properly after the flash. When
I
manually power cycle after the flash, this works as expected. Will need
to
investigate more.
—
Reply to this email directly, view it on GitHub
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,
or unsubscribe
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You are receiving this because you were mentioned.Message ID:
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linkedin.com/in/jonathanberi https://www.linkedin.com/in/jonathanberi/
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Reply to this email directly, view it on GitHub
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Nevermind, after reading the adafruit docs on this board, the behavior is quite clear.
I have a consistent process to flash using the reset button, however, I believe I have two separate problems.

The scd30 code from the example in doesn't seem to function. I have filed an issue to get to the bottom of that here: https://github.com/UncleRus/esp-idf-lib/issues/464
I'm having some problems setting the golioth nvm wifi credentials using the terminal program.

I get this error from the terminal and no commands seem to produce any change or output in the terminal.
Type 'help' to get the list of commands.
Use UP/DOWN arrows to navigate through command history.
Press TAB when typing command name to auto-complete.
Press Enter or Ctrl+C will terminate the console environment.

Your terminal application does not support escape sequences.
Line editing and history features are disabled.
On Windows, try using Putty instead.
esp32> W (1646) golioth_example: WiFi and golioth credentials are not set
W (1646) golioth_example: Use the shell settings commands to set them, then restart

I've completed this task.
I have created an esp-idf project that integrates the SCD30 library and the latest golioth firmware from https://github.com/golioth/golioth-firmware-sdk
I have validated that the code does talk to the SCD30, connects to golioth, etc
See PR for code details: https://github.com/Ribbit-Network/ribbit-network-frog-sensor/pull/184
ESP-ROM:esp32s3-20210327
Build:Mar 27 2021
rst:0x15 (USB_UART_CHIP_RESET),boot:0x8 (SPI_FAST_FLASH_BOOT)
Saved PC:0x420a4b6a
0x420a4b6a: esp_pm_impl_waiti at /Users/keenan/esp/esp-idf/components/esp_pm/pm_impl.c:839

SPIWP:0xee
mode:DIO, clock div:1
load:0x3fce3808,len:0x1650
load:0x403c9700,len:0xb9c
load:0x403cc700,len:0x2f98
entry 0x403c994c
I (24) boot: ESP-IDF v4.4.2 2nd stage bootloader
I (24) boot: compile time 12:56:53
I (25) boot: chip revision: 0
I (26) boot.esp32s3: Boot SPI Speed : 80MHz
I (31) boot.esp32s3: SPI Mode       : DIO
I (36) boot.esp32s3: SPI Flash Size : 4MB
I (40) boot: Enabling RNG early entropy source...
I (46) boot: Partition Table:
I (49) boot: ## Label            Usage          Type ST Offset   Length
I (57) boot:  0 nvs              WiFi data        01 02 00009000 00004000
I (64) boot:  1 otadata          OTA data         01 00 0000d000 00002000
I (72) boot:  2 phy_init         RF data          01 01 0000f000 00001000
I (79) boot:  3 factory          factory app      00 00 00010000 00100000
I (87) boot:  4 ota_0            OTA app          00 10 00110000 00100000
I (94) boot:  5 ota_1            OTA app          00 11 00210000 00100000
I (101) boot: End of partition table
I (106) boot: Defaulting to factory image
I (110) esp_image: segment 0: paddr=00010020 vaddr=3c0b0020 size=22f1ch (143132) map
I (145) esp_image: segment 1: paddr=00032f44 vaddr=3fc97180 size=0426ch ( 17004) load
I (149) esp_image: segment 2: paddr=000371b8 vaddr=40374000 size=08e60h ( 36448) load
I (158) esp_image: segment 3: paddr=00040020 vaddr=42000020 size=a8d10h (691472) map
I (283) esp_image: segment 4: paddr=000e8d38 vaddr=4037ce60 size=0a31ch ( 41756) load
I (292) esp_image: segment 5: paddr=000f305c vaddr=50000000 size=00010h (    16) load
I (300) boot: Loaded app from partition at offset 0x10000
I (301) boot: Disabling RNG early entropy source...
I (302) cpu_start: Pro cpu up.
I (305) cpu_start: Starting app cpu, entry point is 0x40375370
0x40375370: call_start_cpu1 at /Users/keenan/esp/esp-idf/components/esp_system/port/cpu_start.c:160

I (0) cpu_start: App cpu up.
I (320) cpu_start: Pro cpu start user code
I (320) cpu_start: cpu freq: 160000000
I (321) cpu_start: Application information:
I (321) cpu_start: Project name:     golioth-esp-idf-external-app
I (321) cpu_start: App version:      hw_v2-93-g1f33572-dirty
I (321) cpu_start: Compile time:     Nov 27 2022 12:56:47
I (322) cpu_start: ELF file SHA256:  aeb0a1ec7b541b07...
I (322) cpu_start: ESP-IDF:          v4.4.2
I (322) heap_init: Initializing. RAM available for dynamic allocation:
I (322) heap_init: At 3FCA2688 len 0003D978 (246 KiB): D/IRAM
I (323) heap_init: At 3FCE0000 len 0000EE34 (59 KiB): STACK/DRAM
I (323) heap_init: At 3FCF0000 len 00008000 (32 KiB): DRAM
I (323) heap_init: At 600FE000 len 00002000 (8 KiB): RTCRAM
I (324) spi_flash: detected chip: generic
I (325) spi_flash: flash io: dio
I (325) sleep: Configure to isolate all GPIO pins in sleep state
I (326) sleep: Enable automatic switching of GPIO sleep configuration
I (327) cpu_start: Starting scheduler on PRO CPU.
I (0) cpu_start: Starting scheduler on APP CPU.

Type 'help' to get the list of commands.
Use UP/DOWN arrows to navigate through command history.
Press TAB when typing command name to auto-complete.
I (649) pp: pp rom version: e7ae62f
I (659) net80211: net80211 rom version: e7ae62f
                                                                                I (669) wifi:wifi driver task: 3fce75d0, prio:23, stack:6656, core=0
I (669) system_api: Base MAC address is not set
I (669) system_api: read default base MAC address from EFUSE
I (669) wifi:wifi firmware version: eeaa27d
I (669) wifi:wifi certification version: v7.0
I (669) wifi:config NVS flash: enabled
I (669) wifi:config nano formating: disabled
I (679) wifi:Init data frame dynamic rx buffer num: 32
esp32> I (679) wifi:Init management frame dynamic rx buffer num: 32
I (679) wifi:Init management short buffer num: 32
I (679) wifi:Init dynamic tx buffer num: 32
I (679) wifi:Init static tx FG buffer num: 2
I (679) wifi:Init static rx buffer size: 1600
I (679) wifi:Init static rx buffer num: 10
I (679) wifi:Init dynamic rx buffer num: 32
I (679) wifi_init: rx ba win: 6
I (689) wifi_init: tcpip mbox: 32
I (689) wifi_init: udp mbox: 6
I (689) wifi_init: tcp mbox: 6
I (689) wifi_init: tcp tx win: 5744
I (689) wifi_init: tcp rx win: 5744
I (689) wifi_init: tcp mss: 1440
I (689) wifi_init: WiFi IRAM OP enabled
I (689) wifi_init: WiFi RX IRAM OP enabled
I (689) phy_init: phy_version 503,13653eb,Jun  1 2022,17:47:08
I (729) wifi:mode : sta (f4:12:fa:59:ab:58)
I (729) wifi:enable tsf
I (739) wifi:new:<1,0>, old:<1,0>, ap:<255,255>, sta:<1,0>, prof:1
I (1699) wifi:state: init -> auth (b0)
I (1719) wifi:state: auth -> assoc (0)
I (1719) wifi:state: assoc -> run (10)
I (1739) wifi:connected with Bill Wi the Science Fi, aid = 1, channel 1, BW20, bssid = 28:bd:89:de:66:df
I (1739) wifi:security: WPA2-PSK, phy: bgn, rssi: -39
I (1749) wifi:pm start, type: 1

I (1749) wifi:set rx beacon pti, rx_bcn_pti: 0, bcn_timeout: 0, mt_pti: 25000, mt_time: 10000
W (1749) wifi:<ba-add>idx:0 (ifx:0, 28:bd:89:de:66:df), tid:6, ssn:2, winSize:64
I (1829) wifi:BcnInt:102400, DTIM:2
W (1959) wifi:<ba-add>idx:1 (ifx:0, 28:bd:89:de:66:df), tid:0, ssn:0, winSize:64
I (2649) esp_netif_handlers: sta ip: <IP_ADDRESS>, mask: <IP_ADDRESS>, gw: <IP_ADDRESS>
I (2649) example_wifi: WiFi Connected. Got IP:<IP_ADDRESS>
I (2649) example_wifi: Connected to AP SSID: Bill Wi the Science Fi
I (2649) golioth_mbox: Mbox created, bufsize: 1144, num_items: 10, item_size: 104
I (2659) golioth_example: SCD30 Firmware Version: 3.2
I (2659) golioth_example: Starting continuous measurement
I (2699) golioth_coap_client: Start CoAP session with host: coaps://coap.golioth.io
I (2709) libcoap: Setting PSK key

I (2709) golioth_coap_client: Entering CoAP I/O loop
I (2959) golioth_example: Golioth client connected
I (2959) golioth_coap_client: Golioth CoAP client connected
I (4669) golioth_example: CO2: 838 ppm
I (4669) golioth_example: Temperature: 24.89 °C
I (4669) golioth_example: Humidity: 35.14 %
I (6679) golioth_example: CO2: 942 ppm
I (6679) golioth_example: Temperature: 24.82 °C
I (6679) golioth_example: Humidity: 35.24 %
I (8689) golioth_example: CO2: 967 ppm
I (8689) golioth_example: Temperature: 24.80 °C
I (10699) golioth_example: CO2: 974 ppm24 %


Fix custom fields bug

When custom fields referenced a ListReference and there was no GUID in the Mongo data, and the custom field had a wsSelector that was a negative number (a "magic" ws), Send/Receive would crash. This fixes that bug and includes a regression test to ensure the bug stays fixed.
This is commit f9d002d6abb4de8351a92bc7e924ff55e7614e1e from the master branch, rewritten for the fieldworks8-master branch.

This change is

Unit tests are passing locally, and this bugfix is already merged into master, so I'll merge it without waiting for a code review.


Integration of jsonata-moment for support of correct timely based conditions in summer and winter time

📑 I have found these related issues/pull requests

🏷 Feature Request Type
Other
🔖 Feature description
Some JSON validations require a time based condition e.g. device states with time based states.
But in countries like Germany we have summer and winter time difference in offsets and the default $now() only supports a fixed timezone offset.
e.g.: $now('[H01]:[m01]', '+0200')
✔ Solution
Integration of jsonata-moment for support of correct timely based conditions in summer and winter time with $moment()
https://github.com/elasticio/jsonata-moment
❓ Alternatives
No response
📝 Additional Context
https://github.com/jsonata-js/jsonata/issues/347

I'd like to not add jet another datetime library.
I would prefer if jsonata would get the functionality to localize dates upstream instead.

Yes, it has been a few years, but without anybody contributing a PR.
If someone contributes a PR upstream, I'd assume that they will review it.
As said:
I'd prefer if you'd contribute the functionality you need upstream.
we can add the plugin if upstream

rejects your PR or
comments that they'd like to keep it in a separate plugin

Monkeypatching functionality without a reason is not maintainable for us, sorry.


a (short) set of instructions on how to build the validation jars from the repo

a (short) set of instructions on how to build the validation jars from the repo

PR https://github.com/IBM/FHIR/pull/292


Include a simple footer for all pages

In order to conform to SEO standards, we need to include a footer for all pages

version is without Sanity. Create component/s in Storybook.

Questions

Is RSS REALLY needed in 2021?
Is the design in Figma up to date? Ask @BirteThornquist

Acceptance criteria

A working component in Storybook according to Figma sketches
Must be accessible

In order to ensure good quality we should (Keep the ones we need for this US)

[ ] Perform integration testing
[ ] Perform functional testing
[ ] Extra focus on usability
[ ] Test for portability
[ ] Test for accessibility
[ ] Create automated acceptance test/smoke test
[ ] Perform performance and load test
[ ] Perform user testing
[ ] Perform security testing

Related to #359 for a version with data from Sanity.

Only include links in the footer. Do not spend time on RSS service