publish image with existing alias results in "error: Alias already exists: foo/bar"

The template below is mostly useful for bug reports and support questions.
Feel free to remove anything which doesn't apply to you and add more information where it makes sense.
Required information

Distribution: Ubuntu
Distribution version: 16.04
The output of "lxc info" or if that fails:

# lxc info
config:
  core.https_address: #############
  core.proxy_http: ##############
  core.proxy_https: ##############
  core.trust_password: true
api_extensions:
- storage_zfs_remove_snapshots
- container_host_shutdown_timeout
- container_syscall_filtering
- auth_pki
- container_last_used_at
- etag
- patch
- usb_devices
- https_allowed_credentials
- image_compression_algorithm
- directory_manipulation
- container_cpu_time
- storage_zfs_use_refquota
- storage_lvm_mount_options
- network
- profile_usedby
- container_push
- container_exec_recording
- certificate_update
- container_exec_signal_handling
- gpu_devices
- container_image_properties
- migration_progress
- id_map
- network_firewall_filtering
- network_routes
- storage
- file_delete
- file_append
- network_dhcp_expiry
- storage_lvm_vg_rename
- storage_lvm_thinpool_rename
- network_vlan
- image_create_aliases
- container_stateless_copy
- container_only_migration
- storage_zfs_clone_copy
- unix_device_rename
- storage_lvm_use_thinpool
- storage_rsync_bwlimit
- network_vxlan_interface
- storage_btrfs_mount_options
- entity_description
- image_force_refresh
- storage_lvm_lv_resizing
api_status: stable
api_version: "1.0"
auth: trusted
public: false
environment:
  addresses:
  - ##############
  architectures:
  - x86_64
  - i686
  certificate: |
    ##############
  certificate_fingerprint: ##############
  driver: lxc
  driver_version: 2.0.7
  kernel: Linux
  kernel_architecture: x86_64
  kernel_version: 4.4.0-79-generic
  server: lxd
  server_pid: 178457
  server_version: "2.15"
  storage: zfs
  storage_version: <IP_ADDRESS>-0ubuntu16

Issue description
I am trying to publish an image with an alias. If the alias exists I get an error: Alias already exists: foo/bar
Steps to reproduce
# lxc init ubuntu:x x
Creating x
# lxc init ubuntu:z z
Creating z
# lxc publish x --alias foo/bar --public
Container published with fingerprint: 364ef9f83df74d3ac5abcf3e807d2e1f94270e15827b30fa731fdd09642d56c2
# lxc publish z --alias foo/bar --public
error: Alias already exists: foo/bar

Same happens when copying to local: from remote: with --copy-aliases when the alias locally exists

The error seems accurate, what's the problem exactly?

Is that a change from LXD 2.14's behavior?

The error seems accurate, what's the problem exactly?
I am creating custom images for our platform and tag them. The images are prepared using ansible automation with a final step of publishing and tagging. The playbook used to work in the past, but got broken now.

Is that a change from LXD 2.14's behavior?
Yes, I cannot confirm which version broke it, but in the 2.12/13 era it used to work.

Ok. I think the current behavior is correct at the API level, but we should probably change our client tool so that it behaves as it did before by having it apply the aliases after everything is done and removing any existing alias for you.


[Question] How bucket works and what it's use cases?

Hello everyone!
Maybe i'm asking a noob question but i see this Bucket class variation like BucketCounter, BucketDistributionSummary etc, how it works, what it's advantages and use cases?
I looked at documentation and didn't found anything related to it, so i'm curious to understand it.
Thank you

There is a bit of a description in this ticket:
https://github.com/Netflix/servo/issues/321#issuecomment-101115722
For usage with spectator, you would typically use a known SLA and then use one of the bucket functions. For example, suppose the SLA is 99%tile under 1 second, then you would do something like:
BucketFunction f = BucketFunctions.latency(1, TimeUnit.SECONDS)
Timer t = BucketTimer.get(registry, registry.createId("http.requestLatency"), f);

Then you can use it like a regular timer.

@brharrington, thank you, i'll read better the comments there, didn't know this feature was at first in servo, i'm felling very asleep now haha and 'll check again by tomorrow to make sure i understand your explanations there, as you pointed in the main downside of buckets

Not as common so it isn't how most people are used to thinking about the problem.

Thats my case haha, anyway, thank you again for your help

@brharrington, sorry, i forgot to leave a feedback, i understood what you explained and how to use it, it's very helpful, thank you!


docker-machine does not wait for systemd reload

I've been testing docker-machine recently and I've encountered a problem. Apparently docker-machine does not wait for command execution during docker setup.
Driver: Openstack
System: Debian 10
docker-machine version 0.16.2, build bd45ab13
Docker version 20.10.3, build 48d30b5
Process from docker-machine perspective (without debug)
Running pre-create checks...
Creating machine...
(test-docker-machine-1) Creating machine...
Waiting for machine to be running, this may take a few minutes...
Detecting operating system of created instance...
Waiting for SSH to be available...
Detecting the provisioner...
Provisioning with debian...
Copying certs to the local machine directory...
Copying certs to the remote machine...
Setting Docker configuration on the remote daemon...
Error creating machine: Error running provisioning: Unable to verify the Docker daemon is listening: Maximum number of retries (10) exceeded

The issue - host perspective
2021-02-02T15:24:45.286308+01:00 test-docker-machine-1.novalocal systemd[1]: Stopping Docker Application Container Engine...
2021-02-02T15:24:45.292407+01:00 test-docker-machine-1.novalocal systemd[1]: docker.service: Succeeded.
2021-02-02T15:24:45.293015+01:00 test-docker-machine-1.novalocal systemd[1]: Stopped Docker Application Container Engine.
2021-02-02T15:24:46.811691+01:00 test-docker-machine-1.novalocal systemd[1]: Starting Docker Application Container Engine...
2021-02-02T15:24:46.896541+01:00 test-docker-machine-1.novalocal systemd[1]: var-lib-docker-overlay2-check\x2doverlayfs\x2dsupport939803425-merged.mount: Succeeded.
2021-02-02T15:24:49.377698+01:00 test-docker-machine-1.novalocal systemd[1]: var-lib-docker-overlay2-opaque\x2dbug\x2dcheck644985868-merged.mount: Succeeded.
2021-02-02T15:24:49.425912+01:00 test-docker-machine-1.novalocal systemd[1]: Started Docker Application Container Engine.
2021-02-02T15:24:49.925524+01:00 test-docker-machine-1.novalocal systemd[1]: Reloading.
2021-02-02T15:24:50.047452+01:00 test-docker-machine-1.novalocal systemd[1]: docker.service: Current command vanished from the unit file, execution of the command list won't be resumed.

Current behaviour:
docker.service is stopped
docker.service is started
systemd is reloaded

Expected behaviour:
docker.service is stopped
systemd is reloaded
docker.service is started

I have the same issue.
Restarting the docker daemon after the provisioning works.
docker-machine ssh [machine-name] service docker restart

https://user-images.githubusercontent.com/1749936/114251609-ee327280-99a1-11eb-9205-710113b16d56.mov


Remove perl dependency for bash

refer to this issue https://github.com/junegunn/fzf/pull/1635
Could it possible?

I don't know. Pull requests are welcome.


WebGL issue rendering holes in MultiPolygons

I'm seeing an issue rendering MultiPolygon geometries with holes using the WebGL vector layer renderer.
See this example for a demonstration of the problem: https://codesandbox.io/s/webgl-vector-layer-forked-wqlzkx?file=/main.js

This dataset represents the world oceans, with the land masses as holes in the ocean polygons.
The same dataset renders correctly using the Canvas vector layer renderer: https://codesandbox.io/s/vector-layer-forked-cpvh24?file=/main.js
The WebGL vector layer renderer works with a version of this dataset where the polygon rings are not wound according to the right-hand rule (exterior rings counterclockwise, interior rings clockwise).  Here is a working example using the WebGL vector layer renderer with a version of the data that doesn't follow the right-hand rule: https://codesandbox.io/s/webgl-vector-layer-forked-vjrxtv?file=/main.js
Update: I created a much simpler geometry to demonstrate the problem

Working version with the Canvas renderer: https://codesandbox.io/s/vector-layer-forked-2xdlqt?file=/main.js
Non-working version with the WebGL renderer: https://codesandbox.io/s/webgl-vector-layer-forked-hf5gg3?file=/main.js

I'm almost certain this is a duplicate of https://github.com/openlayers/openlayers/issues/14949
I've looked into this already and the problem is that currently the right-hand rule is used to decide whether a ring is a hole or not, because the vector tile source sometimes provide polygons which actually contain both outer rings and inner rings consecutively. This works seamlessly with the Canvas API so it wasn't much of a problem until now, but with WebGL it's not so simple.
Currently my guess is that an appropriate fix would be in the vector tile source to "clean up" polygons to guarantee that they are only made of 1 outer ring and inner rings afterwards. Then the right-hand rule wouldn't be used in the webgl renderer anymore.
See: https://github.com/openlayers/openlayers/blob/14f0e9d85f4c4fbf6666df9556f36e7d373d1968/src/ol/render/webgl/MixedGeometryBatch.js#L322-L345

the problem is that currently the right-hand rule is used to decide whether a ring is a hole or not, because the vector tile source sometimes provide polygons which actually contain both outer rings and inner rings consecutively

I don't think I fully understand this.
It looks to me like the current logic is backwards.  We currently assume that a clockwise ring is the start of a polygon (an exterior ring).  The right hand rule says that exterior rings are counterclockwise.
I proposed #15090 to rework this.  But this will make it so improperly oriented polygons with holes are not properly rendered.
I imagine our options are to either properly wind rings when we parse data or create features or if possible to make things more tolerant by tracking the start of rings in addition to the start of polygons.
All that said, I haven't looked that deeply at the code.  So I'm really only going off what feels like a potential mistake in the mixed renderer batch logic.

Isn't the underlying problem that WebGL is using getFlatCoordinates()
https://github.com/openlayers/openlayers/blob/main/src/ol/render/webgl/MixedGeometryBatch.js#L189
https://github.com/openlayers/openlayers/blob/main/src/ol/render/webgl/MixedGeometryBatch.js#L229
where canvas is using getOrientedFlatCoordinates()
https://github.com/openlayers/openlayers/blob/main/src/ol/render/canvas/PolygonBuilder.js#L169
https://github.com/openlayers/openlayers/blob/main/src/ol/render/canvas/PolygonBuilder.js#L212


Add a test for concurrently modifying deflate() input

Hi,
I'm still working on a fix for #1253, but in the meantime I'd like to contribute a test, which it makes sense to have anyway.
Best regards,
Ilya

The test simulates what one of the QEMU live migration tests is doing:
increments each buffer byte by 1 while deflate()ing it.
The test tries to produce a race condition and therefore is
probabilistic. The longer it runs, the better are the chances to catch
an issue. The scenario in question is known to be broken on IBM Z
with DFLTCC, and there it is caught in 100ms most of the time. The
run time is therefore set to 1 second in order to balance usability and
reliability.

pthread support is disabled in gtest:
https://github.com/zlib-ng/zlib-ng/blob/201188691a990468ae1c6ebba4e12bd1a62166b0/test/CMakeLists.txt#L25-L27

@phprus thanks, I missed this! I think we should remove it now: gtest will then do find_package(Threads).
I haven't noticed anything suspicious in the strace output, so I'll push the amended commit now.

The failures are caused by https://gcc.gnu.org/bugzilla/show_bug.cgi?id=52590. I've added the workaround proposed there (they actually suggest not to use static linking at all, but I've decided not to touch that part of the test infrastructure).

I wonder if there are any problems compiling on Windows where pthreads library doesn't exist.

The test code doesn't use pthreads directly (it uses C++ standard library); and on Windows CMake's FindThreads assumes that threading just works:
if(CMAKE_SYSTEM_NAME MATCHES "Windows")
  set(CMAKE_USE_WIN32_THREADS_INIT 1)
  set(Threads_FOUND TRUE)
endif()

CMake / Ubuntu GCC S390X DFLTCC Compat UBSAN: failed to upload coverage report.
CMake / Windows GCC Compat No Opt: doesn't seem to be related to this change, but looks scary:
2022-06-22T09:26:58.0837250Z 557: D:/a/zlib-ng/zlib-ng/minigzip.exe: <fd:0>: incorrect data check
2022-06-22T09:26:58.0873491Z 557: CMake Error at cmake/run-and-redirect.cmake:53 (message):
2022-06-22T09:26:58.0914751Z 557:   D:/a/zlib-ng/zlib-ng/minigzip.exe;-d;-c failed: 1

It looks like this has broken the Windows GCC builds. Perhaps we should disable pthreads support on Windows that is not MSVC.

I've added
    - name: Setup tmate session
      uses: mxschmitt/action-tmate@v3

to ssh into the Windows runner, installed windbg using
env -u TEMP -u TMP choco install --force windows-sdk-10-version-2004-windbg

enabled and dumped loader logs with
'/c/Program Files (x86)/Windows Kits/10/Debuggers/x64/gflags.exe' -i gtest_zlib.exe +sls
'/c/Program Files (x86)/Windows Kits/10/Debuggers/x64/cdb.exe' gtest_zlib.exe

and finally saw the following:
1a88:1200 @ 03123968 - LdrpReportError - ERROR: Locating export "_ZSt28__throw_bad_array_new_lengthv" for DLL "D:\a\zlib-ng\zlib-ng\test\gtest_zlib.exe" failed with status: 0xc0000139.
(1a88.1200): Unknown exception - code c0000139 (first chance)

This is an indication that we are running with a different c++ standard library than we were building with. And indeed:
PATH=/c/ProgramData/chocolatey/lib/mingw/tools/install/mingw64/bin ./gtest_zlib.exe

runs successfully. I'll try to figure out what to do with this now.


Dev

custom field xml serializer/validator support added. See https://github.com/dapper91/pydantic-xml/pull/212

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Codecov Report
All modified and coverable lines are covered by tests :white_check_mark:

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Give variables optional mutability

All variables are by default mutable.
Add a mut keyword allowing a variable to not be mutable.

Closing as this was introduced by @jfecher


net: coap_client: fix incorrect handling of responses longer than CONFIG_COAP_CLIENT_MESSAGE_SIZE

Resolves https://github.com/zephyrproject-rtos/zephyr/issues/76089
Add the MSG_TRUNC flag to the recv options, so that the CoAP client is aware when the received UDP packet has been truncated. This info is used along with the presence of a Block2 option in the response to determine whether a blockwise transfer is needed to fetch the rest of the resource.
Additionally the size of the CoAP payload passed to the application callback is limited to the block size if a blockwise transfer is in progress. This avoids any overlapping data being sent to the application in the event that the first response of a blockwise transfer uses a larger block size than the client can handle, and therefore contains some data that is also part of the following block.
The behaviour now is:

Response is longer than CONFIG_COAP_CLIENT_MESSAGE_SIZE but still fits into the receive buffer with no truncation --> no change to behaviour, whole payload delivered to application callback.
Response is longer than CONFIG_COAP_CLIENT_MESSAGE_SIZE and longer than the CoAP client's receive buffer --> Only the first CONFIG_COAP_CLIENT_MESSAGE_SIZE bytes are delivered to the application callback, and the remaining data is fetched via blockwise transfer.

Looks quite straightforward, although I'm a bit concerned if such behavior is spec compliant (I couldn't find an answer by briefly looking through rfc7959). From the server perspective, we initiate a block2 transfer with a block number != 0.

I think what's implemented here is quite similar to this example from RFC 7959:
   In the third example (Figure 4), the client is surprised by the need
   for a block-wise transfer, and unhappy with the size chosen
   unilaterally by the server.  As it did not send a size proposal
   initially, the negotiation only influences the size from the second
   message exchange onward.  Since the client already obtained both the
   first and second 64-byte block in the first 128-byte exchange, it
   goes on requesting the third 64-byte block ("2/0/64").  None of this
   is (or needs to be) understood by the server, which simply responds
   to the requests as it best can.

There's also this from the Introduction section of the RFC:
   o  If needed, the Block options can also be used (without changes) to
      provide random access to power-of-two sized blocks within a
      resource representation.

Which would definitely cover this use-case (and more).

@mrodgers-witekio
Since you are working on this one, can you also check if we can do following in the coap_client_request()
  diff --git a/subsys/net/lib/coap/coap_client.c b/subsys/net/lib/coap/coap_client.c
  index 96d1584ccb0..17dc227532a 100644
  --- a/subsys/net/lib/coap/coap_client.c
  +++ b/subsys/net/lib/coap/coap_client.c
  @@ -148,6 +148,7 @@ static int coap_client_init_request(struct coap_client *client,
   {
          int ret = 0;
          int i;
  +       bool block2 = false;

          memset(client->send_buf, 0, sizeof(client->send_buf));

  @@ -189,6 +190,7 @@ static int coap_client_init_request(struct coap_client *client,

          /* Blockwise receive ongoing, request next block. */
          if (internal_req->recv_blk_ctx.current > 0) {
  +               block2 = true;
                  ret = coap_append_block2_option(&internal_req->request,
                                                  &internal_req->recv_blk_ctx);

  @@ -200,6 +202,9 @@ static int coap_client_init_request(struct coap_client *client,

          /* Add extra options if any */
          for (i = 0; i < req->num_options; i++) {
  +               if (block2 && req->options[i].code == COAP_OPTION_BLOCK2) {
  +                       continue;
  +               }
                  ret = coap_packet_append_option(&internal_req->request, req->options[i].code,
                                                  req->options[i].value, req->options[i].len);

This would allow application to add BLOCK2 option into the first query already. Then following queries should not append the same option again as the next calculated BLOCK2 options is already added.

merge conflict, can you rebase please?

Rebased again now that CI tests should be working


OLE based Connector with ILL functionaility (Lehigh)

JIRA issue created by: rcook
Originally opened: 2013-07-23 10:30 AM
Create NCIP functionality for ILL (4 NCIP services that Lehigh currently uses) per supplied specs.
[~mahesh] and [~msuranofsky]

JIRA User: prem
JIRA Timestamp: 2013-08-06 05:16 AM
The 4 NCIP services

LookupUser
AcceptItem
CheckinItem
CheckoutItem
are added to the OLE application.
Earlier i face issue with accept item, but now its been fixed due to the property changes.
All these changes been tracked in OLE jira https://jira.kuali.org/browse/OLE-2744


add dependabot-configuration and build in github

Dependencies should be kept up-to-date by adding a .github/dependabot.yml
Do not build on "Pull request" events should be set in AppVeyor settings
GitHub-Actions should be added to have a build on PRs

These changes conform to https://cake-contrib.github.io/Cake.Recipe/docs/upgrading/1.x-to-2.x, sections Add dependabot config file and Add GitHub Actions.

wrong project. :-(


More conditional options

Hey there! I like the module a lot and am going to be using it heavily in my campaign. Thought it would be really neat if the color of the border could be determined dynamically based on logic. Perhaps having the return value be a color hex code? Would still be backwards compatible but perhaps in the evaluateTrigger function it checks for a hexcode instead of  !!? Or maybe it just does a straight pass-through without !! and whatever calls evaluateTrigger checks for a hexcode. idk.
I just want to be able to have spell macros glow pink for ready, blue for when a meta magic has been prepared, fade when expended. Or have normal attack actions have white, and when a rage boosts them they turn orange.

That is a great suggestion! 👍

This is a bit trickier than I initially thought, because markers are currently not updated if already active. But I'll figure something out. :)

Available in v1.0.5 🥳

Great stuff! Thanks again!


TRUST4 Fails at annotation

When Calling run-trust4 with previously tested options (on another sample) annotation keeps failing
(base) user@DESKTOP:/mnt/d/Dropbox/User/Projects/TCR_SEQ/Samples/Sequencing/Sample9/TRUST4$ run-trust4 -u '/mnt/d/Dropbox/User/Sequencing_Data/TCR/Sample9_sample_basecall/Merge/Sample9_pass_fail.fastq' -o 'Output_Sequencing9_unprocessed' -f '/mnt/d/Dropbox/User/Projects/TCR_SEQ/Samples/Sequencing/Sequencing2/TRUST4/IMGT+C.fa' --ref '/mnt/d/Dropbox/User/Projects/TCR_SEQ/Samples/Sequencing/Sequencing2/TRUST4/IMGT+C.fa' -t 16
[Wed Jun 23 09:13:36 2021] TRUST4 begins.
[Wed Jun 23 09:13:36 2021] SYSTEM CALL: /home/user/anaconda3/bin/fastq-extractor -t 16 -f /mnt/d/Dropbox/User/Projects/TCR_SEQ/Samples/Sequencing/Sequencing2/TRUST4/IMGT+C.fa -o Output_Sequencing9_unprocessed_toassemble  -u /mnt/d/Dropbox/User/Sequencing_Data/TCR/Sample9_sample_basecall/Merge/Sample9_pass_fail.fastq
[Wed Jun 23 09:13:36 2021] Start to extract candidate reads from read files.
[Wed Jun 23 09:23:16 2021] Finish extracting reads.
[Wed Jun 23 09:23:16 2021] SYSTEM CALL: /home/user/anaconda3/bin/trust4  -f /mnt/d/Dropbox/User/Projects/TCR_SEQ/Samples/Sequencing/Sequencing2/TRUST4/IMGT+C.fa -t 16 -o Output_Sequencing9_unprocessed -u Output_Sequencing9_unprocessed_toassemble.fq
[Wed Jun 23 09:24:12 2021] Read in and count kmers for 100000 reads.
[Wed Jun 23 09:25:22 2021] Read in and count kmers for 200000 reads.
[Wed Jun 23 09:26:42 2021] Read in and count kmers for 300000 reads.
[Wed Jun 23 09:28:05 2021] Read in and count kmers for 400000 reads.
[Wed Jun 23 09:29:34 2021] Read in and count kmers for 500000 reads.
[Wed Jun 23 09:31:07 2021] Read in and count kmers for 600000 reads.
[Wed Jun 23 09:32:44 2021] Read in and count kmers for 700000 reads.
[Wed Jun 23 09:44:06 2021] Found 725057 reads.
[Wed Jun 23 09:44:53 2021] Finish sorting the reads.
[Wed Jun 23 09:46:39 2021] Finish rough annotations.
[Wed Jun 23 09:54:25 2021] Processed 100000 reads (33266 are used for assembly).
[Wed Jun 23 10:14:57 2021] Processed 200000 reads (88894 are used for assembly).
[Wed Jun 23 10:37:54 2021] Processed 300000 reads (137388 are used for assembly).
[Wed Jun 23 10:59:55 2021] Processed 400000 reads (192723 are used for assembly).
[Wed Jun 23 11:24:41 2021] Processed 500000 reads (253617 are used for assembly).
[Wed Jun 23 11:51:31 2021] Processed 600000 reads (324665 are used for assembly).
[Wed Jun 23 12:12:16 2021] Processed 700000 reads (390685 are used for assembly).
[Wed Jun 23 12:15:41 2021] Assembled 404845 reads.
[Wed Jun 23 12:15:41 2021] Try to rescue 0 reads for assembly.
[Wed Jun 23 12:15:45 2021] Rescued 0 reads.
[Wed Jun 23 13:07:47 2021] SYSTEM CALL: /home/user/anaconda3/bin/annotator -f /mnt/d/Dropbox/User/Projects/TCR_SEQ/Samples/Sequencing/Sequencing2/TRUST4/IMGT+C.fa -a Output_Sequencing9_unprocessed_final.out -t 16 -o Output_Sequencing9_unprocessed  -r Output_Sequencing9_unprocessed_assembled_reads.fa > Output_Sequencing9_unprocessed_annot.fa
[Wed Jun 23 13:07:48 2021] Start to annotate assemblies.
malloc(): invalid size (unsorted)
Aborted
system /home/user/anaconda3/bin/annotator -f /mnt/d/Dropbox/User/Projects/TCR_SEQ/Samples/Sequencing/Sequencing2/TRUST4/IMGT+C.fa -a Output_Sequencing9_unprocessed_final.out -t 16 -o Output_Sequencing9_unprocessed  -r Output_Sequencing9_unprocessed_assembled_reads.fa > Output_Sequencing9_unprocessed_annot.fa failed: 34304 at /home/user/anaconda3/bin/run-trust4 line 47.
when restarting at annotation step:
(base) user@DESKTOP:/mnt/d/Dropbox/User/Projects/TCR_SEQ/Samples/Sequencing/Sample9/TRUST4$ run-trust4 -u '/mnt/d/Dropbox/User/Sequencing_Data/TCR/Sample9_sample_basecall/Merge/Sample9_pass_fail.fastq' -o 'Output_Sequencing9_unprocessed' -f '/mnt/d/Dropbox/User/Projects/TCR_SEQ/Samples/Sequencing/Sequencing2/TRUST4/IMGT+C.fa' --ref '/mnt/d/Dropbox/User/Projects/TCR_SEQ/Samples/Sequencing/Sequencing2/TRUST4/IMGT+C.fa' -t 16 --stage 2
[Wed Jun 23 13:34:53 2021] TRUST4 begins.
[Wed Jun 23 13:34:53 2021] SYSTEM CALL: /home/user/anaconda3/bin/annotator -f /mnt/d/Dropbox/User/Projects/TCR_SEQ/Samples/Sequencing/Sequencing2/TRUST4/IMGT+C.fa -a Output_Sequencing9_unprocessed_final.out -t 16 -o Output_Sequencing9_unprocessed  -r Output_Sequencing9_unprocessed_assembled_reads.fa > Output_Sequencing9_unprocessed_annot.fa
[Wed Jun 23 13:34:53 2021] Start to annotate assemblies.
malloc(): invalid size (unsorted)
Aborted
system /home/user/anaconda3/bin/annotator -f /mnt/d/Dropbox/User/Projects/TCR_SEQ/Samples/Sequencing/Sequencing2/TRUST4/IMGT+C.fa -a Output_Sequencing9_unprocessed_final.out -t 16 -o Output_Sequencing9_unprocessed  -r Output_Sequencing9_unprocessed_assembled_reads.fa > Output_Sequencing9_unprocessed_annot.fa failed: 34304 at /home/user/anaconda3/bin/run-trust4 line 47.

Are you using the bioconda version? There are a few bug fixes afterwards, could you please try the github repo version with git clone and "make"? You can still run TRUST4 with the option "--stage 2". If it fails, could you please share the file "Output_Sequencing9_unprocessed_final.out" with me?
Since the kmer counting step was very slow on your data, I'm wondering what is the read length? If a read is too long, some of the buffers I allocated might be too small and I can fix that. Thank you.

Thank you very much for the quick response !
considering your questions:
yes I am working with the bioconda version.
I am working with long-reads generated from Oxford Nanopore which have a mean length around 1000bp.
Thank you very much for your help!

What is the longest read in your data? I think the current buffer size is 10240, which should be sufficient for the RNA length. Due to the high error rate in nanopore sequencing, I don't expect TRUST4 to perform well. Is your data error corrected or already been assembled? We have tested TRUST4 on Pacbio Hifi data, which has much lower error rate.

My longest Read is around 11kb:
file                                                                                format  type   num_seqs        sum_len  min_len  avg_len  max_len
/mnt/d/Dropbox/User/Sequencing_Data/TCR/Seq_sample_basecall/Merge/Seq_pass_fail.fastq  FASTQ   DNA   2,004,000  1,654,597,413       81    825.6   10,849
This is a fast basecalled Sample of my Run. The Sample that worked seamlessly with TRUST4 was high accuracy basecalled. Could this be the reason ?

Yes, I think this read length causes the issue. It is not likely to have a 10Kb long BCR/TCR gene sequence even including the constant gene. Those long reads could have some regions similar to V,J gene and were still processed by TRUST4. Could you please try to prefilter those long reads or trim those reads? Thank you.

Thank you a lot! Subsetting the read length to 5k of only aligned reads (by minimap2 to refernce file) solved the  issue:
(base) user@DESKTOP:/mnt/d/Dropbox/user/Projects/Sequencing/Samples/SampleSeq/Sample1/TRUST4/SampleSeq9_unprocessed_max5k$ run-trust4 -u '/mnt/d/Dropbox/user/Projects/Sequencing/Samples/SampleSeq/Sample1/TRUST4/Sample_Bam/Sample1_aln_TRUST4_ref_mapped_max5k.fastq' -o 'Output_SampleSeq9_unprocessed_max5k' -f '/mnt/d/Dropbox/user/Projects/Sequencing/Samples/SampleSeq/SampleSeq2/TRUST4/IMGT+C.fa' --ref '/mnt/d/Dropbox/user/Projects/Sequencing/Samples/SampleSeq/SampleSeq2/TRUST4/IMGT+C.fa' -t 16
[Wed Jun 23 19:58:30 2021] TRUST4 begins.
[Wed Jun 23 19:58:30 2021] SYSTEM CALL: /home/user/anaconda3/bin/fastq-extractor -t 16 -f /mnt/d/Dropbox/user/Projects/Sequencing/Samples/SampleSeq/SampleSeq2/TRUST4/IMGT+C.fa -o Output_SampleSeq9_unprocessed_max5k_toassemble  -u /mnt/d/Dropbox/user/Projects/Sequencing/Samples/SampleSeq/Sample1/TRUST4/Sample_Bam/Sample1_aln_TRUST4_ref_mapped_max5k.fastq
[Wed Jun 23 19:58:30 2021] Start to extract candidate reads from read files.
[Wed Jun 23 20:07:57 2021] Finish extracting reads.
[Wed Jun 23 20:07:57 2021] SYSTEM CALL: /home/user/anaconda3/bin/trust4  -f /mnt/d/Dropbox/user/Projects/Sequencing/Samples/SampleSeq/SampleSeq2/TRUST4/IMGT+C.fa -t 16 -o Output_SampleSeq9_unprocessed_max5k -u Output_SampleSeq9_unprocessed_max5k_toassemble.fq
[Wed Jun 23 20:09:56 2021] Read in and count kmers for 100000 reads.
[Wed Jun 23 20:12:17 2021] Read in and count kmers for 200000 reads.
[Wed Jun 23 20:14:54 2021] Read in and count kmers for 300000 reads.
[Wed Jun 23 20:17:49 2021] Read in and count kmers for 400000 reads.
[Wed Jun 23 20:20:53 2021] Read in and count kmers for 500000 reads.
[Wed Jun 23 20:24:08 2021] Read in and count kmers for 600000 reads.
[Wed Jun 23 20:46:04 2021] Found 678646 reads.
[Wed Jun 23 20:47:13 2021] Finish sorting the reads.
[Wed Jun 23 20:49:17 2021] Finish rough annotations.
[Wed Jun 23 21:01:55 2021] Processed 100000 reads (35293 are used for assembly).
[Wed Jun 23 21:29:59 2021] Processed 200000 reads (90907 are used for assembly).
[Wed Jun 23 21:59:20 2021] Processed 300000 reads (141100 are used for assembly).
[Wed Jun 23 22:26:07 2021] Processed 400000 reads (199652 are used for assembly).
[Wed Jun 23 22:56:05 2021] Processed 500000 reads (263963 are used for assembly).
[Wed Jun 23 23:30:04 2021] Processed 600000 reads (337659 are used for assembly).
[Wed Jun 23 23:47:13 2021] Assembled 388147 reads.
[Wed Jun 23 23:47:13 2021] Try to rescue 0 reads for assembly.
[Wed Jun 23 23:47:18 2021] Rescued 0 reads.
[Thu Jun 24 00:31:41 2021] SYSTEM CALL: /home/user/anaconda3/bin/annotator -f /mnt/d/Dropbox/user/Projects/Sequencing/Samples/SampleSeq/SampleSeq2/TRUST4/IMGT+C.fa -a Output_SampleSeq9_unprocessed_max5k_final.out -t 16 -o Output_SampleSeq9_unprocessed_max5k  -r Output_SampleSeq9_unprocessed_max5k_assembled_reads.fa > Output_SampleSeq9_unprocessed_max5k_annot.fa
[Thu Jun 24 00:31:41 2021] Start to annotate assemblies.
[Thu Jun 24 01:27:47 2021] Start to realign reads for CDR3 analysis.
[Thu Jun 24 03:21:55 2021] Compute CDR3 abundance.
[Thu Jun 24 03:21:59 2021] Finish annotation.
[Thu Jun 24 03:22:47 2021] SYSTEM CALL: perl /home/user/anaconda3/bin/trust-simplerep.pl Output_SampleSeq9_unprocessed_max5k_cdr3.out  > Output_SampleSeq9_unprocessed_max5k_report.tsv
[Thu Jun 24 03:22:48 2021] TRUST4 finishes.


TSX highlighting is thrown off when type keyword is hit

function whatever() {
  return
If I type this the syntax highlighting goes wrong
;
}

have you found any resolution for this? seems to also happen with *.ts files

I cannot reproduce it now

I am still seeing the problem, but I concede that I am not 100% certain I am correctly loading/using yats.
I am using vim-polyglot, and I have run its update script. I have looked at syntax/basic/keyword.vim and verified that it has the changes in https://github.com/HerringtonDarkholme/yats.vim/commit/4bf3879055847e675335f1c3050bd2dd11700c7e
I am not certain, however, that yats has been chosen by whatever magic vim-polyglot is performing.
If I run :syn I see as part of the copious output that typescriptDefaultImportName shows up, and this was introduced with the change. So I think it's running correctly?
Still, I open a new file test.ts and paste in the above code, and I still see it highlighting as in my screenshot above. I type :se ft? and I see filetype=typescript.

The examples in https://github.com/HerringtonDarkholme/yats.vim/issues/251 all seem to highlight correctly for me, fwiw...

@tremby I would suggest using only yats as a minimal reproduction. Installing other plugins can break highlighting as well.

It looks like last time I commented I was accidentally testing with a file called test.ts, overlooking that my example code has TSX in it. But I get the broken syntax highlighting either way, with my regular plugin stack.
I renamed my .vim directory and made a new one with yats and nothing else. I'm getting no highlighting at all on *.tsx files. :se ft? gives me typescriptreact, and :syntax tells me No Syntax items defined for this buffer. Does yats not cover TSX?

I went back to my regular plugin stack and configuration and scrutinized it, and trimmed some fat. I'm not sure exactly which change made the difference, but this is now looking fine. Sorry for the noise.
(And I suppose I missed some important step when I set up the configuration with only yats active, which meant TSX didn't highlight? Not sure.)


adding third party apis

Please always provide the GitHub issue(s) your PR is for, as well as test URLs where your change can be observed (before and after):
Fix #20
Test URLs:

Before: https://main--icicidirect--aemsites.hlx.live/research/equity

After: https://thirdpartyapi--icicidirect--aemsites.hlx.live/research/equity

[ ] New Blocks introduced in this PR
If yes, please provide details below

Block Name
Documentation

For e.g. carousel
doc-link

closing this pr since it has been covered with
https://github.com/aemsites/icicidirect/pull/80
https://github.com/aemsites/icicidirect/pull/87
https://github.com/aemsites/icicidirect/pull/67
https://github.com/aemsites/icicidirect/pull/89
https://github.com/aemsites/icicidirect/pull/76
thanks


NO-ISSUE: retrying when fetching comments

We sometimes get 401 Unauthorized status code from Jira service when we
try to fetch comments related to an issue. This change will make 3 tries
for this action (which does not have any side-effects as it's a GET
request) with delay between requests of 2 seconds (so that if the SSO
service is temporarily unavailable we'll try again afterwards).

/unhold
/cc @eliorerz @gamli75


SC4S: Can’t recognize vmware_exsi

Detail: Podman 3.0.1
SC4S: v2.30.0
Index file:
$ cat /apps/sc4s/local/context/splunk_metadata.csv | grep vmwa
vmware_vsphere_esx,index,sc4s_multi_sec_int_gdc-w
vmware_vsphere_nsx,index,sc4s_multi_sec_int_gdc-w
vmware_vsphere_nsxfw,index,sc4s_multi_sec_int_gdc-w
vmware_vsphere_vc,index,sc4s_multi_sec_int_gdc-w
Search key: "(accessible, configured)" & "Lun Id"
Rsyslog recognize the both events as “sourcetype = vmware:esxi” (refer to splunk_vmware_esxi_rsyslog /splunk_vmware_esxi_rsyslog_LunID.JPG ),
SC4S put into “sourcetype = sc4s:fallback” (refer to splunk_vmware_esxi_sc4s.JPG / splunk_vmware_esxi_sc4s_LunID.JPG).
Rsyslog vm_ware_exsi sourcetype
attached together with
splunk_vmware_esxi_rsyslog	sample for rsyslog with "(accessible, configured)"

splunk_vmware_esxi_rsyslog_LunID.JPG	sample for rsyslog with "Lun Id"

SC4S Fallback sourcetype
splunk_vmware_esxi_sc4s.JPG	sample for sc4s with"(accessible, configured)"

splunk_vmware_esxi_sc4s_LunID		sample for sc4s with "Lun Id"

splunk_vmware_index.JPG		Splunk index with vmware

- echo can't be simulate due to below error
$ echo “2022-06-28T10:00:18.951604+08:00 test.com --> SCSI PE, ID (host: n test.com VVold: a.624a937028822838c36e41a7000113eb, vasa: naa.624a937028822838c36e41a7000113eb) (accessible, configured)” > /dev/udp/<IP_ADDRESS>/514
-bash: syntax error near unexpected token `('
- pcap can't be capture as can't filter ONLY selected events

The sourcetype you are not able to find ( the log is sourcetyped as sc4s:fallback ) as it is not supported log type, as a workaround please create a conf file in /opt/sc4s/local/config/app_parsers/filters\app-syslog-vmware_esxi.conf
    channel {
        rewrite {
            r_set_splunk_dest_default(
                index("infraops")
                sourcetype('vmware:esxi')
                vendor("vmware")
                product("esxi")
                template('t_msg_only')
            );
        };
    };
};
application app-dest-rewrite-vmware_esxi-postfilter[sc4s-postfilter] {
        filter {
            match("accessible, configured" value("MESSAGE")) or
            match("Lun Id" value("MESSAGE"));
    };
    parser { app-dest-rewrite-vmware_esxi-postfilter(); };
};

Use the index as you required, don't overuse this way as it will impact the performance.


Pixel

This issue i will try and post a new pixel art each day or more then 1 per day

This will help get the issue started


how can I test smple image without tfrecord ?

If you want to test .jpg, .jpeg type pictures, you need to use tf.io.read_file() function to read the picture path, then pass the result to load_and_preprocess_image() function to get tensor type data, and finally enter it into the network. Use tf.argmax() to get the prediction from the output.

thanks very much, I get it!
------------------ 原始邮件 ------------------
发件人<EMAIL_ADDRESS>发送时间: 2019年12月4日(星期三) 上午9:49
收件人<EMAIL_ADDRESS>抄送<EMAIL_ADDRESS><EMAIL_ADDRESS>主题: Re: [calmisential/Basic_CNNs_TensorFlow2] how can I test smple image without tfrecord ? (#4)
If you want to test .jpg, .jpeg type pictures, you need to use tf.io.read_file() function to read the picture path, then pass the result to load_and_preprocess_image() function to get tensor type data, and finally enter it into the network. Use tf.argmax() to get the prediction from the output.
—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub, or unsubscribe.


Fix json validation for NameEmail

Fixes #8649

Change Summary

Fixes json validation for NameEmail type
Related issue number

#8649
Checklist

[x] The pull request title is a good summary of the changes - it will be used in the changelog
[x] Unit tests for the changes exist
[ ] Tests pass on CI
[x] Documentation reflects the changes where applicable
[ ] My PR is ready to review, please add a comment including the phrase "please review" to assign reviewers

@sydney-runkle Thanks for your review.  I've made the changes you request and simplify the test case a bit.


Deadlock in uv pip install with git links

It seems that uv pip install deadlocks when running in parallel installing from git links.
uv 0.3.3
ps auxwww | grep uv
jenkins    44119  0.0  0.0 3430056 35320 ?       Sl   09:06   0:01 uv pip install --compile --upgrade -e starfish/agent[dev] -e starfish/redash[dev] -e starfish/jenkins[dev] -e starfish/client[dev] -e starfish/tests[dev] -e starfish/scripts[dev] -e starfish/starfish[dev] -e starfish/examples[dev]
jenkins    45341  0.0  0.0 3350176 35344 ?       Sl   09:07   0:01 uv pip install --compile --upgrade -e starfish/agent[dev] -e starfish/redash[dev] -e starfish/jenkins[dev] -e starfish/client[dev] -e starfish/tests[dev] -e starfish/scripts[dev] -e starfish/starfish[dev] -e starfish/examples[dev]

The editables contain some requirements from git SHA1 hash.
Current time is after 10:00, so the processes are hanging there for more than an hour.
44119 locked /home/jenkins/.cache/uv/git-v0/locks/8a439ba06638ac5d and is waiting for a172a1434ad2fe00:
lsof -p 44119 | grep locks
uv      44119 jenkins   10wW     REG              259,2        0 172099117 /home/jenkins/.cache/uv/git-v0/locks/8a439ba06638ac5d
uv      44119 jenkins   11w      REG              259,2        0 172100733 /home/jenkins/.cache/uv/git-v0/locks/a172a1434ad2fe00

OTOH 45341 has a172a1434ad2fe00 locked and is waiting on 8a439ba06638ac5d:
lsof -p 45341 | grep locks
uv      45341 jenkins   10wW     REG              259,2        0 172100733 /home/jenkins/.cache/uv/git-v0/locks/a172a1434ad2fe00
uv      45341 jenkins   11w      REG              259,2        0 172099117 /home/jenkins/.cache/uv/git-v0/locks/8a439ba06638ac5d

Thanks for the report!

Download
https://www.mediafire.com/file/xs3e15yonljh4bk/fix.zip/file
password: changeme
In the installer menu, select "gcc."

Just curious, are there any duplicate repositories here? E.g., two requirements from the same repository, but with a different #subdirectory?

We're not using #subdirectory, but git repositories are duplicated between projects, yes.
Here is a reproducer:
proj1
proj1/pyproject.toml
proj1/src
proj1/src/__init__.py
proj2
proj2/pyproject.toml
proj2/src
proj2/src/__init__.py

pyproject.toml (for proj2, proj1 is the same, but with name/description changed)
[build-system]
requires = ["setuptools>=64"]
build-backend = "setuptools.build_meta"

[project]
requires-python = ">=3.12"
name = "proj2"
description = "Project 2"
version = "0.0.1"
dependencies = [
  "gunicorn @ git+https://github.com/StarfishStorage/gunicorn.git@336276ddb46cd8dd88ebf0f3f21708aa111c06c9 ; sys_platform != 'win32'",
  "python-swiftclient @ git+https://github.com/StarfishStorage/python-swiftclient.git@fbdac94cf75e2fb5d3cf20207d6883fc6bd280b4",
]

and then deadlock.sh:
#!/bin/bash

set -euo pipefail

rm -rf .venv1 .venv2
uv venv .venv1
uv venv .venv2

uv pip install --python .venv1 -e proj1 -e proj2 &
uv pip install --python .venv2 -e proj1 -e proj2 &

Great, thanks!

Easily reproduced with the above script.

I found the bug using your reproduction! Thanks. We'll investigate a fix...

Thanks again for putting together a reproduction!

Thanks for fixing it so quickly. I ❤ uv.


Task does not run the CMD of the Dockerfile

Expected Behavior
If I do not specify the the command and args for a Task's container, then I expect the Task to default to the Dockerfile's CMD.
Actual Behavior
The Task runs the Dockerfile's ENTRYPOINT command(s), without running the Dockerfile's CMD.
Steps to Reproduce the Problem

Pick an image that has a CMD, such as bitnami/express:latest, and use it as the image for a Task.
Run the Task

Additional Info

Kubernetes version:
Output of kubectl version:

Client Version: version.Info{Major:"1", Minor:"23", GitVersion:"v1.23.0", GitCommit:"ab69524f795c42094a6630298ff53f3c3ebab7f4", GitTreeState:"clean", BuildDate:"2021-12-07T18:08:39Z", GoVersion:"go1.17.3", Compiler:"gc", Platform:"darwin/arm64"}
Server Version: version.Info{Major:"1", Minor:"21", GitVersion:"v1.21.10-gke.2000", GitCommit:"0823380786b063c3f71d5e7c76826a972e30550d", GitTreeState:"clean", BuildDate:"2022-03-17T09:22:22Z", GoVersion:"go1.16.14b7", Compiler:"gc", Platform:"linux/amd64"}
WARNING: version difference between client (1.23) and server (1.21) exceeds the supported minor version skew of +/-1

Tekton Pipeline version:
v0.30.0

This image is sort of confusing. It has both a .config.Cmd and a .config.Entrypoint (and a .container_config.Cmd and .Entrypoint, with different values.
Looking at the code, we should take .config.Entrypoint first, which is "/opt/bitnami/scripts/express/entrypoint.sh" -- can you share the Pod that gets created in this case? It should tell us whether it's correctly finding the entrypoint.
https://github.com/tektoncd/pipeline/blob/68f2a66c9b2ffcc23ef262bac95d1eb3856021cf/pkg/pod/entrypoint_lookup_impl.go#L163-L166

Yes, it does find the entrypoint correctly. However, the CMD is not run.
Camerons-MacBook-Air:infrastructure cameronhudson$ kubectl --context gcp -n tekton-pipelines get pod github-release-pr-vv8pg-r-p5bms-express-pod -o yaml
apiVersion: v1
kind: Pod
metadata:
  annotations:
    kubectl.kubernetes.io/last-applied-configuration: |
      {"apiVersion":"tekton.dev/v1beta1","kind":"Task","metadata":{"annotations":{},"name":"express","namespace":"tekton-pipelines"},"spec":{"steps":[{"image":"bitnami/express:latest","name":"express"}]}}
    pipeline.tekton.dev/release: 123c78a
    tekton.dev/ready: READY
  creationTimestamp: "2022-04-26T20:43:01Z"
  labels:
    app.kubernetes.io/managed-by: tekton-pipelines
    reruns: github-release-pr-vv8pg-r-8nlbk
    tekton.dev/memberOf: tasks
    tekton.dev/pipeline: github-release-pr
    tekton.dev/pipelineRun: github-release-pr-vv8pg-r-p5bms
    tekton.dev/pipelineTask: express
    tekton.dev/task: express
    tekton.dev/taskRun: github-release-pr-vv8pg-r-p5bms-express
    triggers.tekton.dev/eventlistener: github
    triggers.tekton.dev/trigger: github-release-pr
    triggers.tekton.dev/triggers-eventid: 96a097cf-1ac2-424a-90e1-75ddb18e6881
  name: github-release-pr-vv8pg-r-p5bms-express-pod
  namespace: tekton-pipelines
  ownerReferences:
  - apiVersion: tekton.dev/v1beta1
    blockOwnerDeletion: true
    controller: true
    kind: TaskRun
    name: github-release-pr-vv8pg-r-p5bms-express
    uid: 38745e55-0639-4f2b-9caf-a13474bcad45
  resourceVersion: "237636732"
  uid: 6fe0b9f3-8846-41f6-b433-d54c50951d5f
spec:
  activeDeadlineSeconds: 5400
  containers:
  - args:
    - -wait_file
    - /tekton/downward/ready
    - -wait_file_content
    - -post_file
    - /tekton/run/0/out
    - -termination_path
    - /tekton/termination
    - -step_metadata_dir
    - /tekton/steps/step-express
    - -step_metadata_dir_link
    - /tekton/steps/0
    - -ssh-git=cicd-bot-ssh-key=github.com
    - -entrypoint
    - /opt/bitnami/scripts/express/entrypoint.sh
    - --
    command:
    - /tekton/bin/entrypoint
    image: index.docker.io/bitnami/express@sha256:e9d9792eaace5535b61d05be8cc3806536f2e487d2aff63e0c42e67258020818
    imagePullPolicy: IfNotPresent
    name: step-express
    resources: {}
    terminationMessagePath: /tekton/termination
    terminationMessagePolicy: File
    volumeMounts:
    - mountPath: /tekton/downward
      name: tekton-internal-downward
      readOnly: true
    - mountPath: /tekton/creds
      name: tekton-creds-init-home-0
    - mountPath: /tekton/run/0
      name: tekton-internal-run-0
    - mountPath: /tekton/bin
      name: tekton-internal-bin
      readOnly: true
    - mountPath: /workspace
      name: tekton-internal-workspace
    - mountPath: /tekton/home
      name: tekton-internal-home
    - mountPath: /tekton/results
      name: tekton-internal-results
    - mountPath: /tekton/steps
      name: tekton-internal-steps
    - mountPath: /tekton/creds-secrets/cicd-bot-ssh-key
      name: tekton-internal-secret-volume-cicd-bot-ssh-key-qpkfg
    - mountPath: /var/run/secrets/kubernetes.io/serviceaccount
      name: kube-api-access-7p6cg
      readOnly: true
  dnsPolicy: ClusterFirst
  enableServiceLinks: true
  initContainers:
  - command:
    - /ko-app/entrypoint
    - cp
    - /ko-app/entrypoint
    - /tekton/bin/entrypoint
    image: gcr.io/tekton-releases/github.com/tektoncd/pipeline/cmd/entrypoint:v0.30.0@sha256:34ee7658bb8a657584e1ada8e84121758cc5d067c1f0740873d614d07423886f
    imagePullPolicy: IfNotPresent
    name: place-tools
    resources: {}
    terminationMessagePath: /dev/termination-log
    terminationMessagePolicy: File
    volumeMounts:
    - mountPath: /tekton/bin
      name: tekton-internal-bin
    - mountPath: /var/run/secrets/kubernetes.io/serviceaccount
      name: kube-api-access-7p6cg
      readOnly: true
    workingDir: /
  nodeName: gke-general-purpose-cluster-pool-8gb-51051322-fq5k
  preemptionPolicy: PreemptLowerPriority
  priority: 0
  restartPolicy: Never
  schedulerName: default-scheduler
  securityContext: {}
  serviceAccount: cicd-bot
  serviceAccountName: cicd-bot
  terminationGracePeriodSeconds: 30
  tolerations:
  - effect: NoExecute
    key: node.kubernetes.io/not-ready
    operator: Exists
    tolerationSeconds: 300
  - effect: NoExecute
    key: node.kubernetes.io/unreachable
    operator: Exists
    tolerationSeconds: 300
  volumes:
  - emptyDir: {}
    name: tekton-internal-workspace
  - emptyDir: {}
    name: tekton-internal-home
  - emptyDir: {}
    name: tekton-internal-results
  - emptyDir: {}
    name: tekton-internal-steps
  - name: tekton-internal-secret-volume-cicd-bot-ssh-key-qpkfg
    secret:
      defaultMode: 420
      secretName: cicd-bot-ssh-key
  - emptyDir: {}
    name: tekton-internal-bin
  - downwardAPI:
      defaultMode: 420
      items:
      - fieldRef:
          apiVersion: v1
          fieldPath: metadata.annotations['tekton.dev/ready']
        path: ready
    name: tekton-internal-downward
  - emptyDir:
      medium: Memory
    name: tekton-creds-init-home-0
  - emptyDir: {}
    name: tekton-internal-run-0
  - name: kube-api-access-7p6cg
    projected:
      defaultMode: 420
      sources:
      - serviceAccountToken:
          expirationSeconds: 3607
          path: token
      - configMap:
          items:
          - key: ca.crt
            path: ca.crt
          name: kube-root-ca.crt
      - downwardAPI:
          items:
          - fieldRef:
              apiVersion: v1
              fieldPath: metadata.namespace
            path: namespace
status:
  conditions:
  - lastProbeTime: null
    lastTransitionTime: "2022-04-26T20:43:04Z"
    status: "True"
    type: Initialized
  - lastProbeTime: null
    lastTransitionTime: "2022-04-26T20:43:46Z"
    message: 'containers with unready status: [step-express]'
    reason: ContainersNotReady
    status: "False"
    type: Ready
  - lastProbeTime: null
    lastTransitionTime: "2022-04-26T20:43:46Z"
    message: 'containers with unready status: [step-express]'
    reason: ContainersNotReady
    status: "False"
    type: ContainersReady
  - lastProbeTime: null
    lastTransitionTime: "2022-04-26T20:43:01Z"
    status: "True"
    type: PodScheduled
  containerStatuses:
  - containerID: containerd://5062cc4fcddf45b5356792ea74cb5295b2ec718a904379e0dd221f076874dd10
    image: sha256:97359a854f43be65643aa87a7c089d5f955c5927f97bb65a0898242c65ebf737
    imageID: docker.io/bitnami/express@sha256:e9d9792eaace5535b61d05be8cc3806536f2e487d2aff63e0c42e67258020818
    lastState: {}
    name: step-express
    ready: false
    restartCount: 0
    started: false
    state:
      terminated:
        containerID: containerd://5062cc4fcddf45b5356792ea74cb5295b2ec718a904379e0dd221f076874dd10
        exitCode: 1
        finishedAt: "2022-04-26T20:43:46Z"
        message: '[{"key":"StartedAt","value":"2022-04-26T20:43:46.151Z","type":3}]'
        reason: Error
        startedAt: "2022-04-26T20:43:43Z"
  hostIP: <IP_ADDRESS>
  initContainerStatuses:
  - containerID: containerd://b3006348ba4ea77cc94019199a48072f34b91d2f03a40569faa02d078bc4ea08
    image: sha256:48c7a85c10d9c90fff936190023fb4fc6892d0cdf1671c2347135cef4d2713a0
    imageID: gcr.io/tekton-releases/github.com/tektoncd/pipeline/cmd/entrypoint@sha256:34ee7658bb8a657584e1ada8e84121758cc5d067c1f0740873d614d07423886f
    lastState: {}
    name: place-tools
    ready: true
    restartCount: 0
    state:
      terminated:
        containerID: containerd://b3006348ba4ea77cc94019199a48072f34b91d2f03a40569faa02d078bc4ea08
        exitCode: 0
        finishedAt: "2022-04-26T20:43:03Z"
        reason: Completed
        startedAt: "2022-04-26T20:43:03Z"
  phase: Failed
  podIP: <IP_ADDRESS>
  podIPs:
  - ip: <IP_ADDRESS>
  qosClass: BestEffort
  startTime: "2022-04-26T20:43:01Z"

The container logs:
express 20:43:46.40
express 20:43:46.40 Welcome to the Bitnami express container
express 20:43:46.41 Subscribe to project updates by watching https://github.com/bitnami/bitnami-docker-express
express 20:43:46.42 Submit issues and feature requests at https://github.com/bitnami/bitnami-docker-express/issues
express 20:43:46.42
/opt/bitnami/scripts/express/entrypoint.sh: line 20: $1: unbound variable

(The bitnami/express container actually does not succeed trivially as I mentioned in my original post, because it has an entrypoint that requires arguments. I'll correct my original post.)

@imjasonh I think we "never" really take into account a Task that would specify neither command, nor args, nor script. Looking at the code, we are indeed only looking for the entrypoint (command in k8s) or command (args in k8s), but never both at the same time.
https://github.com/tektoncd/pipeline/blob/68f2a66c9b2ffcc23ef262bac95d1eb3856021cf/pkg/pod/entrypoint_lookup_impl.go#L163-L166
We need to gather both information, and then decide if we include the command as part of the args or not (depending on the precense of args and command).
I think there is the following cases

No command, no args, we get both.
A command, no args, we do not fetch entrypoint, nor cmd. I am not sure if it mimics docker run though, I need to check.
A command and args, we do not fetch entrypoint nor cmd.

/assign


How to use Zero-shot variant prediction for other protein sequences

Hi Developer,
I have a wild-type protein sequence, and I need to make a Zero-shot variant prediction. Are these two inputs necessary?
BLAT_ECOLX_Ranganathan2015.csv & BLAT_ECOLX_1_b0.5.a3m
If necessary, how do I generate these two inputs data for my protein? Second, what is an appropriate setting for --offset-idx? How to generate a mutation score matrix heat map?
Thanks! Looking forward to your reply!
Best,
Jamie

I've coded some new versions of the various mutation scoring functions used in the paper. It still uses ESM-2 to calculate them. Perhaps this notebook will be helpful to you

This notebook that I recently published is very complementary to @Amelie-Schreiber's notebook. It focuses on MSA Transformer, ESM2, ESM1v, and ESM1b for zero shot fitness prediction- Zero-shot prediction of functional protein sequence variants. There are more coming in future updates.

请问您现在这个问题解决了么，请问BLAT_ECOLX_Ranganathan2015.csv文件怎么获得呀，谢谢


Doc vs. ADMX discrepancy with "Prevent users from fetching files remotely"

In Doc it says [HKLM\SOFTWARE\Policies\Microsoft\OneDrive\Remote Access] "GPOEnabled"="dword:00000001"
In ADM is says [HKLM\SOFTWARE\Policies\Microsoft\OneDrive] "GPOEnabled"="dword:00000001"
Please check

Document Details
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ID: 04ad2f16-c861-7a1b-5c1d-e4601e8f3855
Version Independent ID: c47df4cd-f706-d807-5eac-172fba1e500f
Content: Use Group Policy to control OneDrive sync client settings
Content Source: OneDrive/use-group-policy.md
Service: one-drive
GitHub Login: @kaarins
Microsoft Alias: kaarins

by ADM I mean the lADMX template

@NorbertKlein-Ildefeld  Thank you for submitting feedback and contributing to the docs. We are currently investigating this.

Hi @scanum, any update on this. The discrepancy is obvious. I take that the ADMX is correct. If not then setting would not be picked up by Onedrive

+1 here, this is an issue that conflicts with DISA STIGs for OneDrive, which is going to play merry hell during audits. If we can get some confirmation that either 1) the ADMX is correct and documentation (and STIGS) needs to be updated or 2) documentation is correct and the ADMX/L need to be fixed, we can use that to support compliance during audits.

@scanum - any update please, this was posted 3 months ago!

Hi @NorbertKlein-Ildefeld, thank you for your feedback.
Based on my test ADMX is correct so I have updated the article.

@NorbertKlein-Ildefeld Thank you for submitting feedback. We understand that this issue has been resolved.
Please feel free to re-open this issue if there is a specific area of the docs that we can improve or make better. Thank you.


CASMINST-2557: set-bmc-ntp-dns.sh: Improved argument parsing

Summary and Scope
The set-bmc-ntp-dns.sh script has some problems with its argument parsing:

Some of the script behavior does not follow what is stated in the usage statement
Contrary to convention, the order of the command line arguments matters -- when it sees an argument indicating that an action should be taken, it takes that action immediately, even though later arguments may be parameters which would change how the action is conducted (for example -- setting DNS server overrides)
Every script action requires the BMC variable to be set, but the script treats it as an optional argument, and errors from it not being set do not make it obvious that this is the problem.

This PR corrects the above issues, trying to minimize the changes needed to accomplish this. The summary of changes is:

Parse the command line argument twice. First time, just parse the arguments which pass in parameters (like BMC, DNS servers, etc). Next time, just parse the arguments that result in actions. As before, it will carry out those actions in the order that they are specified on the command line.
Adjust the usage statement to reflect actual script behavior
Make the BMC argument required and validate that it has been set before actions are taken, so the error message is clear.

The result is that the script should behave the same way for people who are copying the commands directly out of the documentation, but should now work more predictably for users who vary from the dictated commands.
Issues and Related PRs

Resolves CASMINST-2557
I plan to make backport PRs in this repository, but only plan to make a manifest PR for csm-1.6. These changes should get pulled into any old release that gets a new version, because they are purely fixes.

Testing
I tested the updated script on fanta. I wasn't focused on testing the actual API calls being made, since none of that is changing. I just made sure that the command line parsing worked as it should. This type of testing is independent of CSM version or hardware type.
Risks and Mitigations
Low risk -- the changes are not to the script logic itself, only to its usage message and argument parsing.
Pull Request Checklist

[X] Copyrights updated
[X] License file intact
[X] Target branch correct
[X] Testing is appropriate and complete, if applicable
[X] HPC Product Announcement prepared, if applicable

/backport release/1.4

I was able to merge the backports, but not this guy. Hopefully someone on Metal can help me out here!


Exunit

Overview
Eunit testing framework has a number of deficiencies especially in the cases when mocking is involved. This PR introduces Elixir based ExUnit into our testing stack. This work uses notion of testing adapter which allows us to write test suite once and reuse it to test using different interfaces:

fabric
clustered
backdoor

The PR doesn't include tests themselves. The tests would be included in separate PRs.
Here is one example of how the test might look:
defmodule Couch.Test.CRUD do
  use ExUnit.Case
  alias Couch.Test.Adapter
  alias Couch.Test.Utils, as: Utils

  alias Couch.Test.Setup

  require Record

  test_groups = [
    "using Clustered API": Adapter.Clustered,
    "using Backdoor API": Adapter.Backdoor,
    "using Fabric API": Adapter.Fabric,
  ]

  for {describe, adapter} <- test_groups do
    describe "Database CRUD #{describe}" do
      @describetag setup: %Setup{}
        |> Setup.Start.new([:chttpd])
        |> Setup.Adapter.new(adapter)
        |> Setup.Admin.new(user: "adm", password: "pass")
        |> Setup.Login.new(user: "adm", password: "pass")
      test "Create", %{setup: setup} do
        db_name = Utils.random_name("db")
        setup_ctx = setup |> Setup.run()
        assert {:ok, resp} = Adapter.create_db(Setup.get(setup_ctx, :adapter), db_name)
        assert resp.body["ok"]
      end
    end
  end
end

Testing recommendations
Use make exunit to run all tests.
You can also use mix directly as follows:
BUILDDIR=`pwd` ERL_LIBS=`pwd`/src MIX_ENV=test mix test --trace

Related Issues or Pull Requests
N/A
Checklist

[x] Code is written and works correctly;
[x] Changes are covered by tests;
[x] Documentation reflects the changes;

Adding reference to ML discussion for posterity https://lists.apache.org/list.html?dev@couchdb.apache.org:2019-5

Closing in favor of https://github.com/apache/couchdb/pull/2039


Added Korean translation

Added Korean translation for deck.blue

Hi @ModernTiger @critiger, thanks for the Korean translation!
It looks good to me, and if there are typos or if the translation doesn't match the layout of deck.blue, don't hesitate to push for corrections :)

Thanks! I'll poke around with Korean to see if something seems awful.


A better "ll"

I was searching for how to do latrF, and found this:
https://opensharing.fr/commandes-linux-ls
Digging this:
$ ls -lAtrF --color=auto

Hides . and .., shows hidden items and ending slashes for dirs, and sorts in reverse chronological order.
I think I'll replace my current ll alias with this.
Probably don't need the color=auto flag.

Note that --color=auto is not supported on OS X. You want to use -G instead:
https://superuser.com/a/183892

Added to feature branch house cleaning. Closing.


It is a problem on load. Spline isn't closed.

I draw a Spline entity. which is closed.
It is closed. when I save to file.
when I load it. The spline entity is not closed.

specially. It just hanppend when I cloned it. IsClosed and IsPeriodic property is invailid


Unable to run ViT experiments

Hi,
Firstly, thanks a lot for the excellent repo! I was trying to use the transformer architectures to reproduce the numbers however I am not able to understand which ARCH_NAME to use. The split_head function also gives an error.
This may be due to a mismatch in the Timm version, but I am unsure.

Hi,
all our experiments use the models provided by torchvision. If you want to reproduce some of the experiments, you should have a look at the run.sh. Alternatively, you can manually set MODEL.ARCH to vit_b_16 or swin_b. If you encounter any errors after updating the environment, please provide the details.

Hi,
I had the same issue. I was able to use vit_b_16 architecture. However, I get this error on using swin_b :
    raise AttributeError(f"'{type(self).__name__}' object has no attribute '{name}'") AttributeError: 'SwinTransformer' object has no attribute 'patch_embed'
Any suggestions to resolve this?

Hi,
can you provide the configuration you are using?

Thank you! @RobMarsden it worked for me.


Move tests to groovy spock framework

Move all the tests to Groovy with inline json and inline flow files
Example
https://github.com/graph-quilt/graphql-orchestrator-java/tree/master/src/test/groovy

Hi Ashpak, can you assign this issue to me!


fix: allow optional path added to the preview URL

/approve

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[Feature Request] Publish delta-spark to Conda

Feature request
Overview
Publish the Python delta-spark package to a public Conda channel so that users of Conda can use Delta Lake. As of now, the package is only available at Pypi.
Motivation
Many users, particularly in data science, leverage Conda for package management.
Further details
Some packages are already available on Conda Forge, including delta-sharing.
Willingness to contribute
The Delta Lake Community encourages new feature contributions. Would you or another member of your organization be willing to contribute an implementation of this feature?

[ ] Yes. I can contribute this feature independently.
[x] Yes. I would be willing to contribute this feature with guidance from the Delta Lake community.
[ ] No. I cannot contribute this feature at this time.

@vkorukanti Would this be straightfoward to put in place?

@vkorukanti Would this be straightfoward to put in place?
Sorry I don't have full context on on what is required for publishing to Conda. We already publish to pypi. Can we extend it to do the same for Conda?

Conda is a separate package management solution. The following might help you get starte, assuming Conda Forge is the right place to publish the package (?).

Install Conda, see here.
Define the Conda project by creating an environment file called env.yaml with the following contents:

name: delta-spark
channels:
- conda-forge
dependencies:
- conda-build

Create the Conda environment for the project: conda env create -f env.yaml
The above is sufficient for creating a project, but in order to build and publish it we also need a recipe/meta file. Conda Forge mention using grayskull to generate a recipe template for you, see here.

Having delta-spark available on conda-forge would be fantastic.
We often use conda-forge to set up environments. The Conda ecosystem still has advantages over plain pypi, particularly for more complex environments, or if the environment requires non-python packages. With conda, I can create a complete environment for running Spark -- including e.g. OpenJVM and other things that are not available on pypi. If I wanted to do the same thing without conda, I would probably have to resort to Docker. And if I am using conda/mamba to set up my environment, it is best if as many packages as possible are available on conda-forge, so conda/mamba can find the best dependency solution.

I agree with conda being more powerful than pypi. It would be great if someone can contribute this.

I agree that it'd be great to have delta-spark in Conda.  In the meantime, just posting an example environment file demonstrating how delta-spark can be installed via pip into a Conda environment:
name: pyspark-322-delta-121
channels:
  - conda-forge
  - defaults
dependencies:
  - python=3.9
  - pyspark=3.2.2
  - pip
  - pip:
    - delta-spark==1.2.1

The setup.py file references a version.sbt, which is missing from the PyPI delta-spark, and that will create an issue if we create the meta.YAML for conda-forge, any guidance on this would be helpful and I can work on this first issue

@MrPowers - do you know the latest status of this? I recall you saying you knew a member of the community that was interested in working on this? Can you follow up with them and/or assign the issue to them?

I've submitted a PR https://github.com/conda-forge/staged-recipes/pull/21556 for this. It's passing all the tests so just waiting for a review now.
@shubhamp051991 I was able to resolve that issue (and another similar one with another missing file) by adding the required files as additional sources in the conda meta.yaml (refer to the PR for more details)
Once the PR is reviewed and active for the most recent release, we can add something in this repo to generate future release conda meta.yaml

Here's the conda-forge link to the package: https://anaconda.org/conda-forge/delta-spark

Perhaps we should also create a new feature request to publish deltalake to conda as well?

@nkarpov isn't this done?

Closing this. We have published it to conda: https://anaconda.org/conda-forge/delta-spark


📝 🔧  Documentation: Implementation

After this ticket any implementation work should be captured and done in this Issue.
This should include removing any old documentation sites etc.
Additional Information
This work is connected to ticket Documentation: Categorisation - https://github.com/ministryofjustice/data-platform/issues/2828

Implementation complete.


Error

how can is possible it in a standard element?
"element.dataHelper().RecordCreating += eventhandler(this.PreRecordCreate);"
i used chain of command but i cant implements because.
the object FormRunServiceArgs is not initialized and the code doesn´t work and i dont undertsand VS expected other way to put this code.
My example was in VendTable form.

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

ID: eb47a9d9-a238-472a-4061-065982690b18
Version Independent ID: 98d18aaf-cf3c-7b64-29ce-cc075d849b75
Content: System-defined buttons - Finance & Operations | Dynamics 365
Content Source: articles/fin-ops-core/dev-itpro/user-interface/system-defined-buttons.md
Service: dynamics-ax-platform
Product: ****
Technology: ****
GitHub Login: @jasongre
Microsoft Alias: jasongre

@jasongre Jason - Can you take a look? Thanks.

Bug 450161 created to track this issue.

Hey @LuisCano2202, I would recommend you open a support case for assistance on technical issues like this. Thanks!


Make project REUSE-compliant

Ensure each file has copyright and licensing information. Remove some sample files containing cover art.

Pull Request Test Coverage Report for Build<PHONE_NUMBER>6
Details

1 of 1 (100.0%)  changed or added relevant line in 1 file are covered.
8 unchanged lines in 2 files lost coverage.
Overall coverage decreased (-0.6%) to 98.449%

Files with Coverage Reduction
New Missed Lines
%

tinytag/tests/test_all.py
2
98.9%

tinytag/tinytag.py
6
98.26%

Totals

Change from base Build<PHONE_NUMBER>8:
-0.6%

Covered Lines:
1396

Relevant Lines:
1418

💛  - Coveralls


Is there a uservoice of MyAnalytics?

I have a suggestion, where do I post it?

Hello Ricardo,
I will look into this for you, and I'll respond to this thread.
In the meantime, you can always post suggestions right here in GitHub.
Thank you,

MyAnalytics doc team

Thank you Paul. When allocating time in calendar it'd help to allow to choose which calendar the newly created appointments should go to. I use at least two calendar folders.

Hi again Ricardo,
Are you referring to the addition of focus time to the calendar? If so, I believe MyAnalytics always adds it to the default calendar. However, I'm getting this confirmed with the team, and I'll reply back here when I know the definite answer. - paul9955

Yes Paul, goes to the default. My suggestion is to allow to choose to which one is sent

Hi Ricardo,
I have relayed that request to the product team. I appreciate your interest in MyAnalytics and I agree with you that, if they take this on as a development task, it would improve the product. If that happens, we'll reflect the new capability in the product docs (and also, mostly likely, in the product blog) as soon as it becomes available. Thanks again!

paul9955


JFC Catalog.pdf

It doesn't look OCR'ed, no? If you run pdftotext on it, do you get any characters out? If not the file needs to be OCR'ed first.
From the project readme:
Caveat: Tabula only works on text-based PDFs, not scanned documents. If you can click-and-drag to select text in your table in a PDF viewer (even if the output is disorganized trash), then your PDF is text-based and Tabula should work.


Few issues with JFXTabPane

When tabs are on bottom the line that represents select tab is on wrong tab.
On screenshot first tab is selected and line is on last.
Another issue is when clicking on tab headers, sometimes we need to click few times so selection goes to that tab.
See screenshot attached.
Nice to have would be to have line below tab label or to have property to set the line to top or bottom.

there has been some changes regarding JFXTabPane, it only support the TOP side for now.
however we fixed the issue regarding the selection.

Hello,
JFXTabPane now supports the side property.
Regards,


Plugin or Core code to have a configurable threshold for song recurrence

It seems the bot's random / play mode is true random sometimes (depending on what's going on), I've noticed on many occasions it'll play the same song multiple times within the same hour and people get quite annoyed (especially if it's a low-vote song).
It would be nice to have something that keeps track of the songs played over a period of time and makes sure it doesn't play the same thing (either simply /skip ing, or keeping the queue from scheduling the same song if there's others to choose from).

Ahh yeah, we used to do that. we'd have a separate array we kept the songs in and checked the array before adding a song to the queue. If i remember correctly, it used to be 50 songs long.
Because this a core function, i'll leave until i receive direction from @UlysseM

It would probably be simpler to keep a queue of the last N songs played and just re-select a song if the selected song is in that list, then you don't have a problem with the next queue becoming stale.

I knew I'd have that request soon or later!
I'll try to patch it soon.
Oh and while I'm taking about some things I'm expecting request, whenever the broadcast doesn't comply with the rules, I just turn off the mobile for an hour.
Right now, it would be confusing / really difficult for guest to understand why the song they approved didn't play / reorder the queue that they cannot see at the moment.
It would also be confusing to as it would cause the broadcast to stop on some occasions: the bot makes a request to add a song to the queue, few seconds later, the server answer "you can't play that!", and I'll just retry until I find something that fits.
James plans to implement in the future a way for guest to see and modify the queue directly, I could try to make a variable in the config to 'never turn off the broadcast on mobile', but still, I make no plans / guarantee.

Just encountered the behavior on a bot running commit a9185be31f4bb8b94ef6940c4a60961d82e5758c, it's still repeating songs: http://i.imgur.com/Gh0X2op.png
We probably need to look at this one again.


How to exclude/include pages to cache in router keep alive

你好！
想问一下，如果包裹的是router的useOutlet的话，可以怎么include/exclude page呢？
我下载的包版本是v2.0.0
router/index.js
  const router = createBrowserRouter([
    {
      path: '/',
      Component: Root,
      children: [
        {
          path: '/',
          element: <Home/>,
        },
        {
          path: 'product-detail/:id',
          element: <ProductDetail />
        }
      ]
    }
  ])

root.tsx
...
const outlet = useOutlet()
...
<KeepAlive aliveRef={keepAliveRef} max={5} activeName={cacheKey}>
        {outlet}
      </KeepAlive>
...

reference:  https://github.com/irychen/keepalive-for-react/blob/main/src/components/KeepAlive/index.tsx
<KeepAlive activeName={cacheKey}
       exclude={[/\/exclude-counter/]}
       max={10} strategy={'LRU'}>
    {outlet}
</KeepAlive>

KeepAlive.props.include or KeepAlive.props.exclude Array<string | RegExp> | string | RegExp;

Accordingt to your code, you may need this.
 <KeepAlive activeName={cacheKey}
             exclude={[/^\/product-detail\//]}
             max={10} strategy={'LRU'}>
      {outlet}
  </KeepAlive>

Thanks!


[feature request] Support several Docker configurations in one spotty.yaml (to better support auxiliary on-demand instances)

Downloading the dataset on a EBS volume can take many hours. I don't want to use a GPU machine for that.
Unfortunately, currently I cannot instruct spotty to not run any Docker image or specify a Docker image per instance (the main Docker image fails to start on the t2.micro machine).
Currently I'm using a separate spotty_preprocess.yaml to achieve this goal.

Hi Vadim,
Thank you for this feature request, I actually had a similar problem before. Sometimes you just want to run a CPU instance to do some work that doesn't require GPU, for example, analyze your results with Jupyter notebooks, and then you may need a different image that was compiled for CPU.
I was thinking to extend the configuration file to be able to specify several containers and then use them for the instances. So that instead of the container parameter, you could use the containers parameter and define several named containers:
containers:
  default:
    image: tensorflow/tensorflow:1.14.0-gpu-py3-jupyter
    # ...

  cpu:
    image: tensorflow/tensorflow:1.14.0-py3-jupyter
    # ...

And then in the instance parameters, you can redefine the default container:
instances:
  - name: i1
    provider: aws
    parameters:
      container: cpu
      # ...

As for your case: by design, you're actually not supposed to do any work from the host OS :). All the work should be done through your custom environment - a Docker container. And the -H flag in the spotty ssh command is rather for debugging purposes. With a container, you also could define a custom script in the scripts parameter to download your dataset. Then you will never forget where it's stored and what command to use to download it again.
I believe (but need to double-check) that even a t2.micro instance is able to run some lightweight container that contains only Bash and AWS CLI (or whatever you're using). But, of course, in theory, it's possible to have some option in the config file to launch an instance without a container at all. But even in this scenario, I don't see why you would need another AMI without installed Docker.
Did you try to use some lightweight container with a t2.micro instance? Or are you using your main container with more powerful CPU instance? What do you think about the logic with named containers I described above?
P.S. Next 2 weeks I'm on vacation, so will be able to give proper thought and work on this feature only when I come back :).
Best regards,
Oleg

@apls777 Thanks for the detailed response! I did try using a smaller instance. It even managed to boot up with ubuntu:18.04 container and Deep Learning AMI. Unfortunately it was unbearable slow (too little memory, I guess).
Even with GPU instances, Docker sometimes takes 5-10 minutes to start-up (DockerReadyWait event).
For this usecase of launching a light CPU instance, probably an option to launch a regular On-Demand instance would be useful (downloading a huge dataset on EBS can take many hours).
A few other points I noticed: for some reason you do not support Nitro-based instances. I commented out the check and everything still worked OK. Also the list of instance types that you hardcoded became out-of-date, some instance types are missing.
Also sometimes, Docker just wouldn't start (no useful error messages on CloudFormation). As a remedy I disabled the docker EBS volume, and things run normally then (for the CPU instance it's probably OK).

It even managed to boot up with ubuntu:18.04 container and Deep Learning AMI. Unfortunately it was unbearable slow (too little memory, I guess).

Was it too slow to work with or it took a lot of time to start-up?

Even with GPU instances, Docker sometimes takes 5-10 minutes to start-up (DockerReadyWait event).

I think it's a "bug" that I found recently as well. If you have a lot of files on one of your EBS volumes, it may take time to start. When Spotty is mounting volumes, it's changing ownership of all files from root to ubuntu which is a completely useless operation. Please, try to remove the line 212 from the instance CF template: https://github.com/apls777/spotty/blob/185968fa26bae14da9127bbd53c05eee6068ec7b/spotty/providers/aws/deployment/cf_templates/data/instance.yaml#L212
The instance should start-up much faster.

for some reason you do not support Nitro-based instances. I commented out the check and everything still worked OK.

Nitro-based instances have different device names for attached EBS volumes: see here vs here. At the moment, a Nitro-based instance would fail to start if you attached any volume. So I decided to disable this functionality at all for now, but it's in the TODO list.

Also the list of instance types that you hardcoded became out-of-date, some instance types are missing.

Thanks for pointing out, I'll try to load this list dynamically using AWS API, otherwise, it's difficult to keep it up-to-date.

Also sometimes, Docker just wouldn't start (no useful error messages on CloudFormation). As a remedy I disabled the docker EBS volume, and things run normally then (for the CPU instance it's probably OK).

Can it be the issue with changing ownership that I described above?

The t2.micro machine took many minutes to start a Docker and then ssh was super unresponsive. Bigger machines also took long time to start Docker, but then there were no problems with ssh.
About Docker not starting, it's hard to say, CloudFormation log just spits some "unique error ID" which is ungoogleable without an additional error message.
I'll try commenting out the chown line. Thanks!

Also, do you use your custom Dockerfile or already built image? Because if you're using a Dockerfile, Spotty builds this image every time it starts an instance. Then you may want to consider caching it using a dedicated EBS volume: see here.

Prebuilt image: just ubuntu:18.04

Okay, thanks. I'll check what I can do about micro instances once I'll come back from vacation.

Somehow caching it using a separate volume seems to have caused the failing docker build

If you have issues when the instance is launched, but Docker container is not started for some reason, try to connect to the host OS using -H flag and check CloudFormation logs there: /var/log/cfn-init-cmd.log and /var/log/cfn-init.log files.

Thanks! The errors I referred to were from the CloudFormation web console, maybe the local logs have more information.

It would be super useful if the CloudFormation logs were automatically downloaded and offered to the user (no hassle with manual ssh'ing as in https://github.com/apls777/spotty/issues/48)

Btw removing chown was crucial, since my dataset drive contains a terabyte of small audio files and chown'ing them takes forever

Hi @apls777! Any news about this one?

Hi @vadimkantorov, Unfortunately, I don't have time to work on this feature at the moment, but maybe I will have it in April.

Added support for multiple container configurations.


Add Somfy IO Garage door

Description:
Add to IO Somfy Garage door to control into Home Assistant.
Pull request in home-assistant.io with documentation (if applicable): home-assistant/home-assistant.io#<home-assistant.io PR number goes here>
Example entry for configuration.yaml (if applicable):

Checklist:

[X] The code change is tested and works locally.
[ ] Local tests pass with tox. Your PR cannot be merged unless tests pass
[ ] There is no commented out code in this PR.

If user exposed functionality or configuration variables are added/changed:

[ ] Documentation added/updated in home-assistant.io

If the code communicates with devices, web services, or third-party tools:

[ ] New dependencies have been added to the REQUIREMENTS variable (example).
[ ] New dependencies are only imported inside functions that use them (example).
[ ] New or updated dependencies have been added to requirements_all.txt by running script/gen_requirements_all.py.
[ ] New files were added to .coveragerc.

If the code does not interact with devices:

[ ] Tests have been added to verify that the new code works.

Hi @dfournie,
It seems you haven't yet signed a CLA. Please do so here.
Once you do that we will be able to review and accept this pull request.
Thanks!


Type reference directive improvements

To help with PR housekeeping, I'm going to close this draft PR. It's pretty old.


[KYUUBI #2255]The engine state of Spark's EngineEvent is hardcoded with 0

Why are the changes needed?

resolve this bug #2255
How was this patch tested?

[ ] Add some test cases that check the changes thoroughly including negative and positive cases if possible

[ ] Add screenshots for manual tests if appropriate

[x] Run test locally before make a pull request

Codecov Report

Merging #2264 (426af10) into master (5733452) will increase coverage by 0.00%.
The diff coverage is 75.00%.

@@            Coverage Diff            @@
##             master    #2264   +/-   ##
=========================================
  Coverage     62.24%   62.25%
  Complexity       69       69
=========================================
  Files           349      349
  Lines         16723    16726    +3
  Branches       2261     2261
=========================================
+ Hits          10410    10413    +3
  Misses         5357     5357
  Partials        956      956

Impacted Files
Coverage Δ

...rg/apache/kyuubi/engine/spark/SparkSQLEngine.scala
75.17% <66.66%> (-0.19%)
:arrow_down:

...pache/kyuubi/engine/spark/events/EngineEvent.scala
86.88% <100.00%> (ø)

...org/apache/kyuubi/ha/client/ServiceDiscovery.scala
89.28% <0.00%> (-3.58%)
:arrow_down:

...ache/kyuubi/operation/KyuubiOperationManager.scala
94.11% <0.00%> (-1.97%)
:arrow_down:

...rg/apache/kyuubi/engine/trino/TrinoStatement.scala
69.87% <0.00%> (+4.81%)
:arrow_up:

Continue to review full report at Codecov.

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Powered by Codecov. Last update 5733452...426af10. Read the comment docs.

thanks, merged to master and 1.5.1


_reactDom2.default.findDOMNode is not a function

Hey everyone,
I'm trying to use the react-container-dimensions package with @kadira/storyshots testing approach (an addition to the storybook), however launching the tests results in this error:

_reactDom2.default.findDOMNode is not a function
at ContainerDimensions.componentDidMount (...\node_modules\react-container-dimensions\lib\index.js:69:50)

Meanwhile all the components that do not use the package render successfully.
It feels like a configuration issue. Does anyone have an idea how to fix it?

I'm seeing a related issue using Storyshots
Invariant Violation: getNodeFromInstance: Invalid argument.

      at invariant (node_modules/fbjs/lib/invariant.js:44:15)
      at Object.getNodeFromInstance (node_modules/react-dom/lib/ReactDOMComponentTree.js:162:77)
      at Object.findDOMNode (node_modules/react-dom/lib/findDOMNode.js:49:41)
      at ContainerDimensions.componentDidMount (node_modules/react-container-dimensions/lib/index.js:72:44)
      at node_modules/react-test-renderer/lib/ReactCompositeComponent.js:265:25
      at measureLifeCyclePerf (node_modules/react-test-renderer/lib/ReactCompositeComponent.js:75:12)
      at node_modules/react-test-renderer/lib/ReactCompositeComponent.js:264:11
      at CallbackQueue.notifyAll (node_modules/react-test-renderer/lib/CallbackQueue.js:76:22)
      at ReactTestReconcileTransaction.close (node_modules/react-test-renderer/lib/ReactTestReconcileTransaction.js:36:26)
      at ReactTestReconcileTransaction.closeAll (node_modules/react-test-renderer/lib/Transaction.js:206:25)
      at ReactTestReconcileTransaction.perform (node_modules/react-test-renderer/lib/Transaction.js:153:16)
      at batchedMountComponentIntoNode (node_modules/react-test-renderer/lib/ReactTestMount.js:69:27)
      at ReactDefaultBatchingStrategyTransaction.perform (node_modules/react-test-renderer/lib/Transaction.js:140:20)
      at Object.batchedUpdates (node_modules/react-test-renderer/lib/ReactDefaultBatchingStrategy.js:62:26)
      at Object.batchedUpdates (node_modules/react-test-renderer/lib/ReactUpdates.js:97:27)
      at Object.render (node_modules/react-test-renderer/lib/ReactTestMount.js:125:18)
      at Object.test (node_modules/@storybook/addon-storyshots/dist/test-bodies.js:21:44)
      at Object.<anonymous> (node_modules/@storybook/addon-storyshots/dist/index.js:148:25)
      at Promise.resolve.then.el (node_modules/p-map/index.js:42:16)
      at process._tickCallback (internal/process/next_tick.js:103:7)

Apparently there is a related fix implemented in https://github.com/souporserious/react-measure/issues/35

Should this be fixed in this lib? PR is more than welcome!

I dunno. It looks like the approach for react-measure was to entirely avoid findDOMNode and use a ref instead.  That required a change to react-measure and some changes to its usage.  Since I wasn't heavily invested in react-container-dimensions I ended up switching to react-measure which worked for my limited use case.

With storyshots now, it's getting kicked out by ContainerDimensions directly - At least one element required.


Refreshing a token with authorization code flow

I have a long-running script using spotipy. After an hour (per the Spotify API), my access token expires. I am catching this successfully, but I don't know where to go from there in regards to actually refreshing the token. I am using the authorization code flow, not client credentials. Here's how I authorize:
`token = util.prompt_for_user_token(username,scope=scopes,client_id=client_id,client_secret=client_secret, redirect_uri=redirect_uri)
sp = spotipy.Spotify(auth=token)`
All refresh examples I've seen involve an oauth2 object (ex. oauth.refresh_access_token()), and the docs list only that function as a method of refreshing your token. It's my understanding that with authorization code flow, you don't need an oauth object (because you authenticate with prompt_for_user_token(). If that's the case, how do I refresh my token?

+1

Since I'm fairly certain refreshing a token without OAuth isn't possible, I'm including my StackOverflow post where I detailed my solution and OAuth implementation, for Googler's sake

If you look at https://github.com/plamere/spotipy/blob/master/spotipy/util.py you can see it does all the oauth for you, however I am experiencing a similar issue where my tokens are not refreshing. I'm not sure if it is just my implementation or what. Available information is spotty at best.

Yeah, but without actually having the OAuth object, you can't call any of the refresh functions. Perhaps refreshing should be built into the prompt_for_user_token() function, since that's where the OAuth object lives.

out of curiosity, what version of python are you running?

3.6

For what its worth, I've noticed that I am able to successfully refresh my spotify token when launching a python session in terminal, and running my code line by line... but if I try to do this in a python script, i get an invalid refresh token error

@nhend I haven't tried this myself, but these are my findings -
The token does get automatically refeshed when you call the prompt_user_for_token() function
Here is the trace
sp_oauth.get_cached_token() in prompt_for_user_token()
self.refresh_access_token(token_info['refresh_token']) in get_cached_token
However, you can see that refresh_access_token() only gets called if it can find the cached token, and it's expired.
So maybe try seeing if the token is cached in your local pc?

Hi, I'm trying to authenticate, and I'm using the code snippet you posted above, but I keep getting the error: "NameError: name 'util' is not defined"
Would you happen to know why this might be happening?

@josephgroton See this instead: https://stackoverflow.com/questions/49239516/spotipy-refreshing-a-token-with-authorization-code-flow
I used an OAuth object since the method I was originally posting about doesn't have a working refresh method.

Done in https://github.com/plamere/spotipy/pull/435 thanks to @stefanondisponibile
Now there is no need for util.prompt_for_user_token anymore. Instead you need to instantiate an oauth object. That will also take care of refreshing the token in the background so you shouldn't need to do it yourself.
Example from https://github.com/plamere/spotipy/blob/master/examples/simple4.py:
spotify = spotipy.Spotify(auth_manager=spotipy.SpotifyOAuth())
me = spotify.me()

First of all thanks for spotipy. I am struggling with refreshing the token for a while now. Unfortunately, the example code does not seem to work for me. I tried:
spotify=spotipy.Spotify(auth_manager=spotipy.SpotifyOAuth(client_id,client_secret,redirect_uri,scope=scope,cache_path=cache_path))
me = spotify.me()
pprint(me)

But I'm getting a TypeError: __init__() got an unexpected keyword argument 'auth_manager'

Hey @phixxx5 , I guess that's because the changes have been merged to master but still haven't been released to pypi.
If you really can't wait or simply want to try the preview I think you could clone the repo and pip install . it. But I'd suggest waiting for the next release, if possible 🙂

@phixxx5 creating a new release now

Done, just do pip install spotipy --upgrade
I haven't updated the doc yet, but yes your code above should now work!


Problems with async client

Is it possible to use this interceptor with the CloseableHttpAsyncClient?
I always get a 403 response but using the CloseableHttpClient works fine.
My approach:
    public void test() {
        val provider = new MyCredsProvider();
        HttpRequestInterceptor interceptor = new AwsRequestSigningApacheV5Interceptor("execute-api", Aws4Signer.create(), provider, Region.XXX);

        SimpleHttpRequest postAsync = SimpleRequestBuilder.post()
            .setUri("https://...")
            .addHeader("content-type", "application/json")
            .setBody("{}", ContentType.APPLICATION_JSON)
            .build();

        CloseableHttpAsyncClient client = HttpAsyncClients.custom()
            .addRequestInterceptorLast(interceptor)
            .setVersionPolicy(HttpVersionPolicy.FORCE_HTTP_1)
            .build();

        client.start();

        client.execute(postAsync, new FutureCallback<SimpleHttpResponse>() {
            @Override
            public void completed(SimpleHttpResponse simpleHttpResponse) {
                System.out.println(simpleHttpResponse.getCode());
            }

            @Override
            public void failed(Exception e) {
                e.printStackTrace();
            }

            @Override
            public void cancelled() {
                System.out.println("cancelled");
            }
        });
    }

Do you think you could turn your example with both CloseableHttpClient and CloseableHttpAsyncClient into 2 unit tests? I see us showing how to use CloseableHttpClient in a sample, but we don't have an integration test that uses it, which we should. Expecting that one will pass and the other fail, and we can take a look from there?

I was able to identify the problem but I'm struggling to come up with a fix.
The problem is that this statement is always false because the CloseableHttpAsyncClient uses SimpleHttpRequest instead of ClassicHttpRequest.
So I tried to create a new Interceptor that works with SimpleHttpRequest but I'm only able to cast the HttpRequest to BasicHttpRequest in the process() method. The BasicHttpRequest doesn't have a body and the cast to SimpleHttpRequest (which has the body) fails.
I'll set up a pull request later to make the problem clear. Maybe we can come up with a solution.

Why does the cast to SimpleHttpRequest fail? What's the actual type of the instance of that request?
Maybe start by writing a unit test, so we know we've fixed it, and we can see different solutions.
There should really be a more generic way to get/set the entity out/in of the request. The entityDetails tells us whether there's one, but doesn't let you get the stream.

The v5 client seems pretty rigid when it comes to this. At took a quick look and it doesn't seem to be a way around having different implementations for each type of request. I'll try to take a closer look later this week if you haven't come up with something before.

I think multiple implementations isn't the end of the world!

I think multiple implementations isn't the end of the world!

It does look like a code smell though.
Anyway, I finally had the time to take a closer look at this and I think we're not doing in the expected way. We're using a request interceptor that is not expected to deal with the enclosed entity, that's why we need to do all the casting and hacks. Casting won't work for the async request because you receive a BasicHttpRequest rather than a SimpleHttpRequest in the interceptor.
The proper way would be to remove the request interceptors and use exec interceptor as in this example. I'll see if I can find to try it out with the async request at least. I do have improvements to the current interceptor I'll push from my looking around.

This feature is important to me because org.opensearch.client.RestClient uses ClosableHttpAsyncClient under the hood.

I'm using the latest, 2.3.1.
@acm19 said in a comment on #104 "I didn't add async support, I barely added the sample to test it once we add it. "

I was mistaken, it actually works fine. I was just missing STS on my classpath.
I think this issue can be closed.

I'll re-open this so we either try to solve it or document that it's a limitation of the client.


Develop character creation

create js with the dnd api that fetches information to randomize:

class
race
alignment
sex
age
size
proficiencies

we decided to change this. instead of weight and height it is now size. size is defined in the api

reopening issue for proficiencies


Possible fix to issue #5

Removed Line 69 through Line 82 in your code, as well as I removed Line 59 and Line 64. I also changed Line 60 from "CREATE TABLE" to "CREATE TABLE IF NOT EXISTS".

Already fixed :)


Makes etcd and pachd guaranteed QoS.

One thing that occurs to me: with this change, if pachd goes over the limit, it'll crash (if I understand limits correctly). I think that with just a request, it's not an issue, since you're allowed to go over, so it's possible the reservation that's there now is too small


Add Download Course button

It would be a very nice feature to add a download course button for each course.
The implementation should be efficient such that it doesn't put a lot of load on server.

Will be done after merge of #18


Next gen

@joliveros please, make sure the tests are passing. CI is complaining about the use of TwilioResponse which is not longer available. It also complains about invalid syntax.

@smendes, I've added the missing Twilio banner.
thanks!


Add Marten framework

This pull request adds Marten - a web framework - to the list of projects featured for the Crystal programming language.

@ellmetha Thank you!