"Perieți" is listed in the drop-down menu

Description:
When user writes "Perieți" the location appears in the drop-down menu next to the comune and the county witch is a part according to the law
Precondition:
The website is up an running.

Step 1
Write in the search bar "Perieți"
Expected results
The location appears in the drop-down menu as "Comuna Perieți, OLT"


Test compilation failed

When I tried to update #125 and do a full compilation including tests, I saw this line fails to compile.
https://github.com/64bit/async-openai/blob/f28303b3867b62d57722bc3867942baf6fc39bbd/async-openai/src/file.rs#L87
The error is

A quick fix is
let list_files = client.files().list("").await.unwrap();

but I don't know what you want to test and I see the code came from you, so probably you can fix it yourself? @64bit

Dang, this is my bad. yeah anything empty works including empty [] for query param.
Tests in file.rs were to test all file related APIs. I'll add fix for this.

This is fixed in https://github.com/64bit/async-openai/commit/30f8b6a326ffe89e1698f36df631adeaadf7c498


Add demo component for the jsonforms web page

Coverage decreased (-1.1%) to 66.043% when pulling e77f0c6089f60fd6410a5f820df49f6721784a3b on hecforga:master into 1fad442fe907f5141c2ee091b10b419d5bfc2aa8 on eclipsesource:master.

Coverage decreased (-1.2%) to 65.945% when pulling 5839725a56d9d4649515b0e489b2645209c1e5cd on hecforga:master into 1fad442fe907f5141c2ee091b10b419d5bfc2aa8 on eclipsesource:master.

Coverage decreased (-1.1%) to 65.945% when pulling d431f6c1241c5863fa243b40366e34558e563fa7 on hecforga:master into 3e684d7ba5b52160f759442bdbf98ff9a6b18527 on eclipsesource:master.

Coverage decreased (-1.3%) to 65.713% when pulling e930e7b740381cebd97f241b41cd08aebc32462a on hecforga:master into 3e684d7ba5b52160f759442bdbf98ff9a6b18527 on eclipsesource:master.

Coverage decreased (-1.4%) to 65.647% when pulling 88c21b6202d575be57466cd398a0cd7930801590 on hecforga:master into 3e684d7ba5b52160f759442bdbf98ff9a6b18527 on eclipsesource:master.

Coverage decreased (-1.4%) to 65.307% when pulling 0b60f75f65b2032ff791c19dceca8feee020e5a2 on hecforga:master into 04d55e822f8a3b2e0b04d257cde381d983d5d9f1 on eclipsesource:master.


On the dataset configuration

First of all, thank you for your wonderful project and congrats your acceptance!
I have a few questions about the NSD dataset.

It is stated that there are 24,980 training examples and 2,770 test samples in your paper. Does it mean that there are 24,980 training pairs of (voxel, img) and 2,770 for text per subject? I give you this question as the num_train = 8557 + 300 and num_val = 982 in your code and the number does not match. 8857 * 3 = 26571, 982 * 3  = 2946. So, could you clarify where these numbers come from?

After I scrutinize the training data of subject1, I found that there are duplicates of images. That is, for example, images for 0th tuple and 400th tuple are the same. I checked that all 982 pairs in the test set and it does have all distinct images. However, training set does not. So I wonder if these duplicates in the training dataset are okay. (I checked that there are 5970 unique tuples in the training dataset)

In addition, your codes seem to have an error on making validation loader. If 982 % batch_size != 0, then the last incomplete batch seems to be dropped. I think it has to be fixed and wonder if there can be a change in your reported results in the paper.
https://github.com/MedARC-AI/fMRI-reconstruction-NSD/blob/4d02ab3b63e45bb4e35c15f5d433a1ad0569ee77/src/utils.py#L336

Thank you.

@beotborry Hi, I encountered the same issue while training. The actual training steps are four times larger than the expected ones (1104 vs. 276). How did you solve this problem? Do I need to change the values of num_train and num_test variables? I appreciate your help.

Sorry for the delay, all images in the Natural Scenes Dataset were seen up to 3 times by the subjects. During training we train the model using every sample (which explains there being 3 duplicates) but during testing we averaged across the same-image repeats (which explains the lack of 3 duplicates). Given that the validation is the test set, there are 982 unique test images so there shouldnt be an incomplete batch (in which case partial should probably be set to True to allow incomplete batches to go through). num_train should actually be multiplied by 3 because of how we are processing the not-averaged-across-repeats, so that's a mistake on our part... I dont know how much that would tangibly affect results.

Sorry for the delay, all images in the Natural Scenes Dataset were seen up to 3 times by the subjects. During training we train the model using every sample (which explains there being 3 duplicates) but during testing we averaged across the same-image repeats (which explains the lack of 3 duplicates). Given that the validation is the test set, there are 982 unique test images so there shouldnt be an incomplete batch (in which case partial should probably be set to True to allow incomplete batches to go through). num_train should actually be multiplied by 3 because of how we are processing the not-averaged-across-repeats, so that's a mistake on our part (and was used for the results in the paper) ... I dont know how much that would tangibly affect results, probably not much.

In the provided JSON file (metadata_subj01.json), the values for num_train, num_val, and num_test are as follows:
"train": 8559,
"val": 300,
"test": 982

However, in the initial code snippet, the default values for num_train, num_val, and num_test are specified as follows:
"num_train": 8859,
"num_val": 982,

I have the following questions regarding the differences:
Why is there a discrepancy between the values of train in the JSON file and num_train in the default code?
Additionally, why is num_val equal to test in the JSON file?

Because when we were developing the model we used the validation set as our test set. For final models used in paper we consolidated the validation set into the training set and used the test set as our test set. 8559 + 300 = 8859


Mapping WebApiCompatShim routes

Is there anything special I need to do to get SwashBuckle to recognize ApiControllers from WebApiCompatShim without attribute routing? My routes are currently setup like this
Startup.cs
 routes.MapWebApiRoute(
                    name: "apiRoute",
                    template: "api/{controller}/{action}");

Controller
 public class RegistationController : ApiController
    {
        [HttpGet]
        public HttpResponseMessage List()
        {
            var results = .... ;
            if (results.Any()) return Request.CreateResponse(HttpStatusCode.OK, results);

            return Request.CreateErrorResponse(HttpStatusCode.NotFound, "Nobody Registered" );
        }
    }

MVC 6/Core matches the route but it doesn't get picked up by swagger

+1

There's no support for ApiExplorer/Swashbuckle using conventional routing.  We strongly recommend using attribute routing for building any API. If you want to, as @ruben0909 suggested you can use a route like [Route("api/[controller]/[action]")] to do something similar and keep it DRY.

Ok. Thanks guys


Support orderBy on JSONB columns / Json fields in PostgreSQL

Problem
I need to be able to sort by values inside of the Postgres JSONB column, right now, I have to query the database using raw SQL and am not able to utilize Prisma's functionality to do so.
Suggested solution
Using the in-built Postgres jsonb ordering field->key would work, and having it just work like the JSON filtering would work in terms of actual client implementation.
Alternatives

Additional context

I believe the title of this issue should read Support "OrderBy" on JSONB columns in Postgres. I am also interested in this feature

I just stumbled upon this as well. I really have a need for a project I am using at work.

Potential duplicate: https://github.com/prisma/prisma/issues/9130


Retry CI on test crash

Improves CI tests to better handle runner instability without creating false negatives with a blind retry mechanism.

The main instability addressed is with enumerating the window collection from the WindowUtilities.GetWindows() method:

This has since been improved in fa61cfabbbcd03dd0d9373001d2b183d6a0ee52d which removes the need for an external retry mechanism.
Still, this PR hardens the SDK's handling of client startup for low resource environments.


Decay Flag

If there is a decay flag on the item, the item taken into the bag gives a warning. I think the flag should be canceled.
12:27:ERROR:Timer expired without DECAY flag 'Katana' (UID=04000b8a6)?

I don't understand the issue.
If you are overriding the @timer trigger, you should always return 1 to block the default behavior.
The default behavior is to delete an item when the timer expires, and only if there's the decay flag. If it expires but the item doesn't have the flag, then you get a warning

ignore my first message that there is a misunderstanding.

( .add i_box_wood ) target ground.
throw the created box into your bag.
display the time with the .xshow timer and you will see that the timer is not -1.
When the timer is 0 you will get a warning in the consol.

Another situation.

( .add i_box_wood ) target ground.
throw the created box into your bag.
then take it out of the bag again and put it on the floor.
Check the attr_Decay flag and you will see that it does not come.
Reset the timer with .xtimer 1 and you will see that it is not deleted.

I confirm this issue..
.add i_dagger
Select ground
PickUP item and palace in backpack
Timer still running.. In old release when pickup item from ground timer go to -1 in backpack
and if put back on ground start normal decay timer

True.. I have some weird error on shard. Probably link to that

I make some test a work good..
I make this test:

Create item on ground (normal decay time work)
Pick up item on ground and place in backpack timer stop -1
Drop item from backpack to ground and normal decay timer start
Drop item from backpack to container on ground timer still -1

I've tested this trouble and now it works like should be.

good job.


⚠ Bofrost.at has degraded performance

In 837781a, Bofrost.at (https://www.bofrost.at) experienced degraded performance:

HTTP code: 200
Response time: 1121 ms

Resolved: Bofrost.at performance has improved in 6fab712 after 8 minutes.


Strategy is not defined

File "c:\Users\sheik\AppData\Local\Programs\Python\Python38\Scripts\meanrevertingstrategy.py", line 183, in
class MeanRevertingStrategy(Strategy):
NameError: name 'Strategy' is not defined
Kindly look into.
Thank you.
Sheikh

Never mind.


Issue with reassignment of variable

var b = {test: ''};
var a = '';
a = {test: function() {}};
a.test();

This produces an error "'test' is not a function" on the last line, since it thinks that a.test is a string.
This appears to be a bug in Tern itself. When autocompleting, it lists test as a function on a. However, afterwards, it thinks a.test is a string.
This issue is not critical, since it only happens when a variable is reassigned to something of a different type.

@rkistner could you retry it please, it seems that with last version of ternjs, I have not your problem?

@rkistner  it seems that tern has resolved this problem.@rkistner  it seems that tern has resolved this problem. I have added a test https://github.com/angelozerr/tern-lint/commit/aa2c3e1afd7f6060fcc4aeda898b1ee4505ef97a for this issue.
I close this issue.


try upgrade max compression to 40

If only it was that simple...

If only it was that simple...

We had to try, search, reflect on it :) could be better if anyone actually doing it will do it open source ofc ;)

It's like asking contractors to build a house for you for free. Nobody does serious work like that for free.

It's like asking contractors to build a house for you for free. Nobody does serious work like that for free.
You do get open source "for free" if it's a fun project and something else is paying the bills already. But neither applies here.

What you said is not applicable.
I'm not gonna debate on it. You did an amazing work for sure. Sadly that do not deserves people as it should.


Add CI job to validate the Katas on the current M.Q.Katas package

Currently all CI build jobs in the Katas CI build use the latest released Microsoft.Quantum.Katas package (the version defined in the .csproj files). E2E builds build the package currently defined in the code and then update the katas to use that package before running the validations. This means that when a bad change is introduced to the M.Q.Katas package, Katas CI build can pass but the E2E build can fail.
We need to add a new CI build job that follows the same pattern as the E2E builds:

Build the M.Q.Katas package from the latest code
Use that package to test a subset of katas that use the QuantumSimulator and the various features of the CounterSimulator (don't have to test all the katas, since most of them rely on the same functionality)

An example of the change that brought this up is https://github.com/microsoft/QuantumKatas/tree/mariia/count-nary-operations (in particular, changing CounterSimulator's _operationsCount key from ICallable to String), which causes the later cells in DeutschJozsaAlgorithm kata to fail validation, but the katas that don't use CounterSimulator functionality still passed.
https://github.com/microsoft/QuantumKatas/pull/690 attempted to fix this, but with that PR the CI build fails on the first cell of each notebook, including the ones which use only QuantumSimulator.

We will be migrating the Katas to the new QDK that will use a different infrastructure (see https://devblogs.microsoft.com/qsharp/introducing-the-azure-quantum-development-kit-preview/ for the announcement), so we won't continue to improve the existing infrastructure of Q# notebooks magics. Closing this issue as "won't fix".


feat: support undefined process

Related: https://github.com/holepunchto/tiny-paths/issues/3

Would like to see this happen. I got to add process to the top of all my bundles because of this.


Droid cleanups

Please select one of the following

[x] I am removing an existing difference between facebook/react-native and microsoft/react-native :thumbsup:
[ ] I am cherry-picking a change from Facebook's react-native into microsoft/react-native :thumbsup:
[ ] I am making a fix / change for the macOS implementation of react-native
[ ] I am making a change required for Microsoft usage of react-native

Deleting a few changes/files which are not present in the FB repository.
Focus areas to test
build
Microsoft Reviewers: Open in CodeFlow

I assume this means that the checkbox that is checked in the PR description is wrong?

I assume this means that the checkbox that is checked in the PR description is wrong?

Ah yes.. Wrong box was cheched .. :)


Issue with Multi-GPU Distributed Computing Using UCE Model

Hi there,
I encountered a problem while calculating embeddings with the UCE model and setting args.multi_gpu=True. I received an error: AttributeError: 'TransformerModel' object has no attribute 'module'. Could you please help me understand what might be causing this and how to resolve it?
Thank you!

Hi, are you launching the command with hugging face accelerator?


Report via check when a project does not use semantic versioning

This may need further investigation before it can be addressed.
One benefit to having such a check would be allowing users to see when their project is relying on dependencies that do not communicate breaking changes in the semver way.
In cases where the commit finder is not invoked, this check would be limited to analysing the singular version of the artefact being examined. However, whether it actually makes sense to analyse the full list of tags from a repository is also open to debate as some repositories may have only used non-semver schemes at some point in the past, meaning their most recent versions (as tags) are fine.

I think it’s important to consider a version number like 1.2.3 and a semantic version number 1.2.3. The difference? There is none.
Semantic versioning is about interpreting the version number, it’s not inherently built into it.
Case in point: up until v2 Pydantic did not use semantic versioning and v1.10.0 broke v1.9.x (Changelog). As of v2, those folks plan to be more diligent with their version numbers 🤞🏼 I’ve seen projects document in their Changelog that their version numbers follow semver (can’t find an example right now), but at least Python package metadata (docs) doesn’t seem to communicate how to interpret the version number (docs) wrt. semver.

If a Changelog is available for a release, we could also consider a lightweight text processing to detect breaking changes, features, and patches to see if the project has followed semantic versioning for a particular version. What do you think?

Also, I think it would make sense to bring this up with the Python discussion forum and suggest additional package metadata that identifies the version schema. Won’t solve your problem here right now, but… 🤷🏻♂


[ADP-3030] Remove prune from DBLayer

Overview
We want to remove functions from the DBLayer record until essentially all DB access is done through the walletsState :: DBVar.
This task is about removing prune from the DBLayer record.
Issue number
ADP-3030

bors merge


Poor editor performance and high memory usage on macOS compared to 3.2.2

Godot version:
3.2.3, 3.2.4
OS/device including version:
MacBook Pro (Retina, 15-inch, Mid 2015)
macOS Catalina
2.2 GHz Quad-Core Intel Core i7
16 GB 1600 MHz DDR3
Intel Iris Pro 1536 MB
Issue description:
I have noticed significantly degraded editor performance and higher memory usage on recent versions of Godot compared to 3.2.2 stable. Basically 3.2.2 is great, while 3.2.3 and 3.2.4 are far less responsive in general and use way more memory. 3.2.4 RC2 seems even worse than 3.2.3, though I'm not sure if stable builds are more optimized which might account for that.
The issue does not seem project specific, and here I made a new project containing only a simple scene with a sprite animated using vertex shader. I am not running the game but just in the 2D scene preview.
Memory usage on 3.2.2:

Same scene in 3.2.3 stable:

And 3.2.4 RC2:

As you can see 3.2.3 and 3.2.4 are using 2 to 2.5 times as much memory compared to 3.2.2. Interestingly, I have not noticed any significant difference in CPU usage or energy.

@djrain Can you try reproducing this with all the released 3.2.3 betas and RCs? You can download them here.

The issue is present in 3.2.3 beta 1. It's using around twice as much memory as 3.2.2 stable and editor runs noticeably slower.

Does it use less memory if you turn off 2D batching in the project settings?

Does it use less memory if you turn off 2D batching in the project settings?

Nope, no difference.

Any clue on how to debug this @godotengine/macos?

For some reason, I am no longer able to reproduce this as before. Maybe my computer had been acting up, though it is odd considering I was experiencing the issue for some time... In any case, now the editor is snappy across versions, and I don't see any alarming differences in memory usage. So unless anyone else is having the issue, I think we can go ahead and close this for now.


Environment builds but some packages have libstdc++.so.6 errors

I'm migrating one of my repositories to this cookie cutter and I've run into an error that has me stymied. I've been testing the cookiecutter branch of my repository on a few systems before merging into master; they all behave as expected, except in one case: on the head node of a large cluster. My general strategy is to clone my repository, build the conda environment, activate it, run pip install -e ., and then run the test suite, just like what happens on Travis. (I have made one change to the default conda environment YAML, which is to specify python=3.6 for pytraj.) When I do this on TSCC/SDSC, I have no problems building the environment or installing my module, but my tests fail with libstdc++.so.6 problems (see below). Does this suggest that something went wrong building the dynamically linked (?) C code in scipy and mdtraj? I don't modify any paths in my .bashrc. Any suggestions for how to debug things? I can manually import pymbar and mdtraj despite these errors.
(base) [davids4@tscc-login1 pAPRika]$ conda env create -f devtools/conda-envs/test_env.yaml
[...]
#
# To activate this environment, use
#
#     $ conda activate paprika-debug-tleap-dummy
#
(base) [davids4@tscc-login1 pAPRika]$ conda activate paprika-debug-tleap-dummy

(paprika-debug-tleap-dummy) [davids4@tscc-login1 pAPRika]$ pip install -e .
Obtaining file:///home/davids4/paprika-debug-tleap-dummy/pAPRika
Installing collected packages: paprika
  Running setup.py develop for paprika
Successfully installed paprika

(paprika-debug-tleap-dummy) [davids4@tscc-login1 pAPRika]$ pytest -v paprika/tests/
=========================================================== test session starts ============================================================
platform linux -- Python 3.6.7, pytest-4.2.1, py-1.7.0, pluggy-0.8.1 -- /home/davids4/anaconda3/envs/paprika-debug-tleap-dummy/bin/python
cachedir: .pytest_cache
rootdir: /home/davids4/paprika-debug-tleap-dummy/pAPRika, inifile:
plugins: cov-2.6.1
collected 18 items / 2 errors / 16 selected

================================================================== ERRORS ==================================================================
_____________________________________________ ERROR collecting paprika/tests/test_analysis.py ______________________________________________
ImportError while importing test module '/home/davids4/paprika-debug-tleap-dummy/pAPRika/paprika/tests/test_analysis.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
paprika/tests/test_analysis.py:7: in <module>
    from paprika import analysis
paprika/analysis.py:6: in <module>
    import pymbar
../../anaconda3/envs/paprika-debug-tleap-dummy/lib/python3.6/site-packages/pymbar/__init__.py:31: in <module>
    from pymbar import timeseries, testsystems, confidenceintervals, version
../../anaconda3/envs/paprika-debug-tleap-dummy/lib/python3.6/site-packages/pymbar/confidenceintervals.py:25: in <module>
    import scipy.stats
../../anaconda3/envs/paprika-debug-tleap-dummy/lib/python3.6/site-packages/scipy/stats/__init__.py:367: in <module>
    from .stats import *
../../anaconda3/envs/paprika-debug-tleap-dummy/lib/python3.6/site-packages/scipy/stats/stats.py:173: in <module>
    from . import distributions
../../anaconda3/envs/paprika-debug-tleap-dummy/lib/python3.6/site-packages/scipy/stats/distributions.py:10: in <module>
    from ._distn_infrastructure import (entropy, rv_discrete, rv_continuous,
../../anaconda3/envs/paprika-debug-tleap-dummy/lib/python3.6/site-packages/scipy/stats/_distn_infrastructure.py:16: in <module>
    from scipy.misc import doccer
../../anaconda3/envs/paprika-debug-tleap-dummy/lib/python3.6/site-packages/scipy/misc/__init__.py:68: in <module>
    from scipy.interpolate._pade import pade as _pade
../../anaconda3/envs/paprika-debug-tleap-dummy/lib/python3.6/site-packages/scipy/interpolate/__init__.py:175: in <module>
    from .interpolate import *
../../anaconda3/envs/paprika-debug-tleap-dummy/lib/python3.6/site-packages/scipy/interpolate/interpolate.py:32: in <module>
    from .interpnd import _ndim_coords_from_arrays
interpnd.pyx:1: in init scipy.interpolate.interpnd
    ???
../../anaconda3/envs/paprika-debug-tleap-dummy/lib/python3.6/site-packages/scipy/spatial/__init__.py:98: in <module>
    from .kdtree import *
../../anaconda3/envs/paprika-debug-tleap-dummy/lib/python3.6/site-packages/scipy/spatial/kdtree.py:8: in <module>
    import scipy.sparse
../../anaconda3/envs/paprika-debug-tleap-dummy/lib/python3.6/site-packages/scipy/sparse/__init__.py:231: in <module>
    from .csr import *
../../anaconda3/envs/paprika-debug-tleap-dummy/lib/python3.6/site-packages/scipy/sparse/csr.py:15: in <module>
    from ._sparsetools import csr_tocsc, csr_tobsr, csr_count_blocks, \
E   ImportError: /opt/gnu/gcc/lib64/libstdc++.so.6: version `CXXABI_1.3.9' not found (required by /home/davids4/anaconda3/envs/paprika-debug-tleap-dummy/lib/python3.6/site-packages/scipy/sparse/_sparsetools.cpython-36m-x86_64-linux-gnu.so)
______________________________________________ ERROR collecting paprika/tests/test_openmm.py _______________________________________________
ImportError while importing test module '/home/davids4/paprika-debug-tleap-dummy/pAPRika/paprika/tests/test_openmm.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
paprika/tests/test_openmm.py:7: in <module>
    from paprika.openmm_simulate import *
paprika/openmm_simulate.py:9: in <module>
    from mdtraj.reporters import NetCDFReporter
../../anaconda3/envs/paprika-debug-tleap-dummy/lib/python3.6/site-packages/mdtraj/__init__.py:29: in <module>
    from .formats.registry import FormatRegistry
../../anaconda3/envs/paprika-debug-tleap-dummy/lib/python3.6/site-packages/mdtraj/formats/__init__.py:15: in <module>
    from .dtr import DTRTrajectoryFile
E   ImportError: /opt/gnu/gcc/lib64/libstdc++.so.6: version `CXXABI_1.3.9' not found (required by /home/davids4/anaconda3/envs/paprika-debug-tleap-dummy/lib/python3.6/site-packages/mdtraj/formats/dtr.cpython-36m-x86_64-linux-gnu.so)
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Interrupted: 2 errors during collection !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
========================================================= 2 error in 4.71 seconds ==========================================================

I might have an idea, but will need some more information. Can you post your test_env.yaml file?
I will point out that the cookiecutter does not do anything with compilation, so this might be an upstream package issue, not necessarily the cookiecutter itself. For instance, the line /home/davids4/anaconda3/envs/paprika-debug-tleap-dummy/lib/python3.6/site-packages/scipy/sparse/_sparsetools.cpython-36m-x86_64-linux-gnu.so indicates it might be an issue with the scipy download, which seems unlikely.
Are there additional packages in your base/root conda environment which may get overwritten or temporarily removed when you activate the new environment?

Hi Levi, thanks for your thoughts. Here is the test_env.yaml file:
(paprika-debug-tleap-dummy) [davids4@tscc-login1 pAPRika]$ cat devtools/conda-envs/test_env.yaml
name: paprika-debug-tleap-dummy
channels:
  - conda-forge
  - omnia
  # AmberTools seem to live at this repository...
  - http://ambermd.org/downloads/ambertools/conda/
dependencies:
    # Base depends
  - python=3.6
  - pip
  - numpy
  - scipy
  - parmed
  - mdtraj
  - pymbar
  - openmm
  # Eventually we can/should migrate away from this, once AMBER gets onto omnia/conda-forge.
  # See https://openforcefieldgroup.slack.com/archives/C8NE3J96U/p1549403299386500
  - ambertools=18

    # Testing
  - pytest
  - pytest-cov

    # Pip-only installs
  - pip:
    - codecov

I'm not sure if there's anything in base that might be overwritten by this test environment. It's been a few months since I've worked on TSCC with this code, so I just did a conda update conda and conda update before trying to test my cookiecutter branch. I'm running conda 4.6.3 now. FWIW, here's the output of conda list in my test environment:

`conda list`
```
(paprika-debug-tleap-dummy) [davids4@tscc-login1 pAPRika]$ conda list
# packages in environment at /home/davids4/anaconda3/envs/paprika-debug-tleap-dummy:
#
# Name                    Version                   Build  Channel
ambertools                18.0                          0    omnia
atomicwrites              1.3.0                      py_0    conda-forge
attrs                     18.2.0                     py_0    conda-forge
blas                      1.1                    openblas    conda-forge
blosc                     1.15.1            hf484d3e_1002    conda-forge
bzip2                     1.0.6             h14c3975_1002    conda-forge
ca-certificates           2018.11.29           ha4d7672_0    conda-forge
certifi                   2018.11.29            py36_1000    conda-forge
chardet                   3.0.4                    pypi_0    pypi
codecov                   2.0.15                   pypi_0    pypi
coverage                  4.5.2           py36h14c3975_1000    conda-forge
fftw3f                    3.3.4                         2    omnia
hdf5                      1.10.4          nompi_h11e915b_1105    conda-forge
idna                      2.8                      pypi_0    pypi
libffi                    3.2.1             hf484d3e_1005    conda-forge
libgcc                    7.2.0                h69d50b8_2    conda-forge
libgcc-ng                 7.3.0                hdf63c60_0    conda-forge
libgfortran-ng            7.2.0                hdf63c60_3    conda-forge
libstdcxx-ng              7.3.0                hdf63c60_0    conda-forge
lzo                       2.10              h14c3975_1000    conda-forge
mdtraj                    1.9.2           py36hff88cb2_1000    conda-forge
mmpbsa-py                 16.0                     pypi_0    pypi
more-itertools            4.3.0                 py36_1000    conda-forge
ncurses                   6.1               hf484d3e_1002    conda-forge
numexpr                   2.6.9           py36h637b7d7_1000    conda-forge
numpy                     1.16.1          py36_blas_openblash1522bff_0  [blas_openblas]  conda-forge
openblas                  0.3.3             h9ac9557_1001    conda-forge
openmm                    7.3.0           py36_cuda92_rc_1    omnia
openssl                   1.0.2p            h14c3975_1002    conda-forge
packmol-memgen            0.9.9a0                  pypi_0    pypi
pandas                    0.24.1           py36hf484d3e_0    conda-forge
paprika                   0.0.3+87.g1ecf2fe.dirty           dev_0
parmed                    3.0.0+57.g74a84d30          pypi_0    pypi
pdb4amber                 1.6.dev0                 pypi_0    pypi
pip                       19.0.2                   py36_0    conda-forge
pluggy                    0.8.1                      py_0    conda-forge
py                        1.7.0                      py_0    conda-forge
pymbar                    3.0.3            py36h3010b51_3    conda-forge
pymsmt                    18.0                     pypi_0    pypi
pytables                  3.4.4           py36h5d69a80_1004    conda-forge
pytest                    4.2.1                    py36_0    conda-forge
pytest-cov                2.6.1                      py_0    conda-forge
python                    3.6.7             hd21baee_1001    conda-forge
python-dateutil           2.8.0                      py_0    conda-forge
pytraj                    2.0.3                    pypi_0    pypi
pytz                      2018.9                     py_0    conda-forge
readline                  7.0               hf8c457e_1001    conda-forge
requests                  2.21.0                   pypi_0    pypi
sander                    16.0                     pypi_0    pypi
scipy                     1.2.0           py36_blas_openblash1522bff_1201  [blas_openblas]  conda-forge
setuptools                40.8.0                   py36_0    conda-forge
six                       1.12.0                py36_1000    conda-forge
sqlite                    3.26.0            h67949de_1000    conda-forge
tk                        8.6.9             h84994c4_1000    conda-forge
urllib3                   1.24.1                   pypi_0    pypi
wheel                     0.33.0                   py36_0    conda-forge
xz                        5.2.4             h14c3975_1001    conda-forge
zlib                      1.2.11            h14c3975_1004    conda-forge
```

I think this might actually be an issue with some pointer to old linkers which the scipy library is looking at, but expecting a newer version which should get shipped with Conda.
I don't have a good answer for you, but here is a link to someone having this exact same issue: https://github.com/ContinuumIO/anaconda-issues/issues/5191#issuecomment-406029140
From what I am reading on that issue, it looks like it might be your LD_LIBRARY_PATH variable is set to point at some old libgcc files and so the SciPy binaries are looking there first instead of at the ones installed in the Conda Environment.

Hmm, yes indeed, good sleuthing. I didn't have anything overriding LD_LIBRARY_PATH in my .bashrc but it is set by the cluster and some of those look kinda old. If I manually add the conda libraries to the front of that, things do work. For example:
(paprika-debug-tleap-dummy) [davids4@tscc-login1 lib]$ LD_LIBRARY_PATH=/home/davids4/anaconda3/lib:$LD_LIBRARY_PATH

(I guess I could have used the environment specific lib directory, but the base one worked). It's not ideal, but it's a viable workaround.

Glad to hear. Can we close this issue then as it seems to be beyond the scope of Cookiecutter?

Yep, thanks.

Possibly need the same compiler toolchain for building the local package as was used to build the env packages. Another suspect is that the c-f compiler toolchain has switched over the past months, so old envs may behave differently than new envs.


IE9 videos fail to load fully

Hi,
I am using the Wordpress plugin version of mediaelement.js and it is fantastic! However, we have just discovered that when using IE9 (Win 7 and Vista) that video files were failing to fully load in the player. I have tried updating the plugin and downgrading the plugin to see if that would change the functionality at all, this hasn't work.
Interesting, when I view your website http://mediaelementjs.com on IE9 Win7 I experience the same issue with the video shown at the top of the page - the player reports that the file is 44 seconds long, but only loads as far as 17 seconds. Once 17 seconds is reached the video stops and goes back to the start again. The amount of loading on the video file seems to vary with the size of the file - ie when trying to load a 389MB file that should play for 45min, you are shown the first 10seconds.
The workarounds we have found so far are to a) change browsers or b) use F12 Developer Tools in IE and change to either IE8 browser mode or IE9 Compatibility View.
Let me know what other information you need provided and I will try to help,
Many thanks!

Hmm. If you turn off JavaScript, do you get the same effect (i.e. with the native <video> tag).

Hi John,
Thanks for the rapid reply. When JavaScript is turned off I get the same effect with the added bonus of no video being displayed until you click play (looks just like an audio player) and the audio player is missing completely.
Kimberley

So it sounds like it's a problem with IE9 and not so much mediaelementjs. Are you having problems with other HTML5 sites or players, or just MEjs?

Perhaps there some kind of throttling going on in your machine.
You could see if forcing Flash helps.
$('video').mediaelementplayer({mode: 'shim'});
JD

Will do - where abouts exactly does that line go in the Wordpress Plugin.
For what it is worth, it isn't just my machine that is having issues so
far I have tested on 10 separate machines.
K

Kimberley Johnston
eLearning Support Specialist
ITS Teaching and Learning Facilities
University of Otago
New Zealand
www.otago.ac.nz/elearning

On 8/02/12 12:04 PM, "John Dyer"
<EMAIL_ADDRESS>hub.com> wrote:

Perhaps there some kind of throttling going on in your machine.
You could see if forcing Flash helps.
$('video').mediaelementplayer({mode: 'shim'});
JD

Reply to this email directly or view it on GitHub:
https://github.com/johndyer/mediaelement/issues/376#issuecomment-3858858


[Feature Request] ZenStack CLI syntax checking for ZModel

requested by Marblism.

Fixed in 2.5.0


JENKINS-45038: Add Folder Listing Section

This plugin allows the creation of 'View Listing Sections'.  These contain panels which displayed nested
views as tree structures.
Unfortunately the 'View Listing Section' does not support generating tree structures based on folder
hierarchies.
This new section type emulates the functionality of the 'View Listing Section' using folders.

I've rebased this onto master to get the fix for relative jobs names, and added another small fix. We're now running this in our pre-production Jenkins 2 instance.

Decided this was all against the wrong issue. So amended the commit message and branch name and now have to create a new PR for the new branch name.


Fix #2152

Fixes #2152 .

Pull Request Test Coverage Report for Build 7553

6 of 7 (85.71%)  changed or added relevant lines in 2 files are covered.
10 unchanged lines in 3 files lost coverage.
Overall coverage decreased (-0.002%) to 54.536%

Changes Missing Coverage
Covered Lines
Changed/Added Lines
%

sharding-core/sharding-core-execute/src/main/java/org/apache/shardingsphere/core/execute/sql/execute/result/QueryResultMetaData.java
5
6
83.33%

Files with Coverage Reduction
New Missed Lines
%

sharding-core/sharding-core-parse/sharding-core-parse-common/src/main/java/org/apache/shardingsphere/core/parse/antlr/sql/segment/dml/expr/FunctionExpressionSegment.java
1
0.0%

sharding-core/sharding-core-parse/sharding-core-parse-common/src/main/java/org/apache/shardingsphere/core/parse/antlr/sql/segment/dml/expr/PropertyExpressionSegment.java
2
0.0%

sharding-core/sharding-core-parse/sharding-core-parse-common/src/main/java/org/apache/shardingsphere/core/parse/antlr/sql/segment/dml/expr/SubquerySegment.java
7
0.0%

Totals

Change from base Build 7552:
-0.002%

Covered Lines:
8608

Relevant Lines:
15784

💛  - Coveralls


feat: added functionality to obatain minimum and maximum feasible inp…

methods for computing minimum and maximum feasible input resolution based on the receptive field
updated images

Codecov Report

Merging #30 (dfbc914) into main (2a4d8ee) will increase coverage by 0.37%.
 Consider uploading reports for the commit 29d9af4 to get more accurate results

@@            Coverage Diff             @@
##             main      #30      +/-   ##
==========================================
+ Coverage   89.03%   89.40%   +0.37%
==========================================
  Files          20       20
  Lines        1313     1369      +56
==========================================
+ Hits         1169     1224      +55
- Misses        144      145       +1

Impacted Files
Coverage Δ

rfa_toolbox/utils/graph_utils.py
73.68% <100.00%> (+10.72%)
:arrow_up:

tests/test_graph/test_utils.py
98.26% <100.00%> (+0.60%)
:arrow_up:

tests/test_encodings/test_pytorch.py
98.24% <0.00%> (-1.76%)
:arrow_down:

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LOAD PAINT annotations

for these we will only display the
Panther node ID:
PANTHER:PTN000678822)
from
https://github.com/geneontology/go-annotation/issues/2055#issuecomment-413174441
I'll 'activate' this ticket when appropriate

(The PANTHER ID should be the first in the list)

maybe we could try loading the panther data while you are here. Although we have a lot to do so probably unlikely. Anyway I will remove "future" now.

Hi Kim,
Could  you load the PAINT annotation on dev at some point  ( I only really need the  post filtering GO GAF with the PAINT data that we would retain). After that you can delete it  again. I don't want it to go on the live site yet.
Once I have the filtered list I will do some QC checking to see if  we are happy for it to go live.

I'll give it a go.  It's easiest to do a Chado load on my desktop with the PAINT data so I don't need to mess with the main load.
Where is the GAF file for PAINT?  Is there a pombe-only file?

It will just be the normal GAF that is exported. Hang on I missed some important information here. Although there did used to be a ticket with this in, I just can't find it.
Essentially, we want to load the PAINT data from the GO file  (we must presumably have a filter not to load at present?)
Then we want to make IBA  the lowest priority evidence code in the filter  (temporarily), this is just to give everything else precedence (Including IEA NAS, TAS which I believe are largely OK).
This will give me fewer to check.
I'm hoping that after the filters there will not be very much left, otherwise we have missed a lot of stuff that it would be possible to annotate by ISS. I have no idea really, it will be very interesting ;)
Does that make sense or do you need more info?

Essentially, we want to load the PAINT data from the GO file

Do you mean from the GOA/UniProt GAF file?  I can't see any annotation that looks like it's from PAINT.  What should I look for?

Anthing with  the pombe taxon that we don't load currently should include it. I can't think of anything else that we don't load.
It will have "PANTHER" somewhere in the with file,  IBA evidence. I think the assignee is GOC...

contributer is GO_Central
Also, I realise I did not answer the whole question.  Yes GOA/GAF. We will take them from there because it's easiert.
Can you see them?

Like this
UniProtKB:A6X980 | sfc7 | part_of | GO:0000127    transcription factor TFIIIC complex | ECO:0000318   IBA | PMID:21873635 | PANTHER:PTN001474144 more... | 284812 Schizosaccharomyces pombe (strain 972 / ATCC 24843) | GO_Central

No, not the GOA/UniProt GAF; use the PomBase file that's been through the GO pipeline.
Get the file from http://snapshot.geneontology.org/annotations/pombase.gaf.gz (there's also a .gpad.gz) and grep for evidence IBA and/or assigned by GO_Central.

Currently we use the Uniprot GAF for everything else, so this will be easier to test from (the differences  between the 2 sources should be small)
We can switch once I have done the bulk of the testing to mop up the residual stuff (if there is any). This is quick and dirty before we alter the pipelines (which we should do).
We would also need to  switch to get other GO derived stuff from GO (function process links which we also get currently from GOA)
Kim: We will always need to get the  InterPro and Uniprot from GOA (because we  filter a lot of stuff before Pombe data  goes into GO)

(which we  probably should do)

I'm hoping that in the long term there is no need for these inferences, so it might not be worth switching just for this. Although  I suspect we are a way off that with the IBA

Thank you both.  Got it now.
I've just tried a quick test to make sure those annotations can be loaded.  It's mostly OK except for these lines where the systematic ID (P50525) looks like a UniProt ID instead of a pombe ID:
UniProtKB	P50525	apn1		GO:0003906	PMID:21873635	IBA	PANTHER:PTN000485019|SGD:S000001597|WB:WBGene00000151	F	DNA-(apurinic or apyrimidinic site) lyase 1	UniProtKB:P50525|PTN000485041	protein	taxon:284812	20170228	GO_Central
UniProtKB	P50525	apn1		GO:0005634	PMID:21873635	IBA	PANTHER:PTN000485021|SGD:S000001597	C	DNA-(apurinic or apyrimidinic site) lyase 1	UniProtKB:P50525|PTN000485041	protein	taxon:284812	20170228	GO_Central
UniProtKB	P50525	apn1		GO:0006284	PMID:21873635	IBA	PANTHER:PTN000485019|SGD:S000001597|WB:WBGene00000151	P	DNA-(apurinic or apyrimidinic site) lyase 1	UniProtKB:P50525|PTN000485041	protein	taxon:284812	20170228	GO_Central
UniProtKB	P50525	apn1		GO:0005739	PMID:21873635	IBA	PANTHER:PTN000485021|SGD:S000001597	C	DNA-(apurinic or apyrimidinic site) lyase 1	UniProtKB:P50525|PTN000485041	protein	taxon:284812	20170228	GO_Central
UniProtKB	P50525	apn1		GO:0008081	PMID:21873635	IBA	PANTHER:PTN000485019|SGD:S000001597|WB:WBGene00000151	F	DNA-(apurinic or apyrimidinic site) lyase 1	UniProtKB:P50525|PTN000485041	protein	taxon:284812	20170228	GO_Central

Apart from those 5 lines, there are no other warnings.  Tomorrow I'll look more closely at what got loaded to check that it's OK.
In case it needs reporting, there are also these lines which also have a UniProt systematic ID but the pombe systematic ID is in column 3, so they load OK:
UniProtKB	Q9P3E3	SPAC750.08c		GO:0005739	PMID:21873635	IBA	PANTHER:PTN001157969|SGD:S000001512	C	NAD-dependent malic enzyme (Predicted), partial (Fragment)	UniProtKB:Q9P3E3|PTN002361248	protein	taxon:284812	20170228	GO_Central
UniProtKB	Q9P3E3	SPAC750.08c		GO:0006108	PMID:21873635	IBA	FB:FBgn0002719|PANTHER:PTN000601050|PomBase:SPCC794.12c|TAIR:locus:2017854|TAIR:locus:2052045|TAIR:locus:2054085|TAIR:locus:2127038|TAIR:locus:2180547|TAIR:locus:2181980|UniProtKB:P48163|UniProtKB:Q16798	P	NAD-dependent malic enzyme (Predicted), partial (Fragment)	UniProtKB:Q9P3E3|PTN002361248	protein	taxon:284812	20170228	GO_Central
UniProtKB	Q9P3E3	SPAC750.08c		GO:0004470	PMID:21873635	IBA	FB:FBgn0002719|MGI:MGI:97043|PANTHER:PTN000601050|PomBase:SPCC794.12c|RGD:3074|SGD:S000001512|TAIR:locus:2017854|TAIR:locus:2052045|TAIR:locus:2054085|TAIR:locus:2127038|TAIR:locus:2180547|TAIR:locus:2181980|UniProtKB:P23368|UniProtKB:P26616|UniProtKB:P48163|UniProtKB:Q16798	F	NAD-dependent malic enzyme (Predicted), partial (Fragment)	UniProtKB:Q9P3E3|PTN002361248	protein	taxon:284812	20170228	GO_Central
UniProtKB	Q9P3E3	SPAC750.08c		GO:0004471	PMID:21873635	IBA	PANTHER:PTN001157969|PomBase:SPCC794.12c	F	NAD-dependent malic enzyme (Predicted), partial (Fragment)	UniProtKB:Q9P3E3|PTN002361248	protein	taxon:284812	20170228	GO_Central
UniProtKB	Q9P3E3	SPAC750.08c		GO:0005829	PMID:21873635	IBA	PANTHER:PTN002361249|UniProtKB:P26616	C	NAD-dependent malic enzyme (Predicted), partial (Fragment)	UniProtKB:Q9P3E3|PTN002361248	protein	taxon:284812	20170228	GO_Central
UniProtKB	Q9P3E3	SPAC750.08c		GO:0006090	PMID:21873635	IBA	PANTHER:PTN000601050|PomBase:SPCC794.12c|SGD:S000001512|UniProtKB:Q16798	P	NAD-dependent malic enzyme (Predicted), partial (Fragment)	UniProtKB:Q9P3E3|PTN002361248	protein	taxon:284812	20170228	GO_Central

One thing that will need a code change is processing the "with" column (col 8).  There are lots of IDs in each field and the loader only knows how to store the first ID.  Should we store just the PANTHER ID from the with fields?
Here's an example:
FB:FBgn0013674|PANTHER:PTN000046096|SGD:S000007260

There are lots of IDs in each field and the loader only knows how to store the first ID.

Sorry, that's not right.  The loader can store all the IDs and there's also an option to store just the first ID.

For display we will need to do something to reduce this field (possibly only dispolaying the panther ID but letting people maybe see the others in mouse over, if that is possible). I don't think we will want to see these e long strings of IDs by default.
But we can chat about that after the preliminary  clean up, there is no hurry (I won't be doing this quickly I suspect I will chug through them over a few Friday afternoons when I am braindead from curation session checking).

For display we will need to do something to reduce this field (possibly only dispolaying the
panther ID but letting people maybe see the others in mouse over, if that is possible).

We can do that but I think initially it's easier to just store and display the PANTHER ID.  There's less code to change that way.  Displaying the other IDs can be a task for latter.

But we can chat about that after the preliminary clean up, there is no hurry

I'm doing a test Chado load now on my Desktop.  Tomorrow you'll be able to see the initial results of loading the PANTHER annotations with all the usual annotation and filtering.

I'm doing a test Chado load now on my Desktop.

There are 5211 annotations from PAINT after loading everything and filtering.  The input file has 14560 PAINT annotations.
You can see the results on my desktop until 1pm or so.
Here's an example of a more specific PAINT term filtering an existing term:
original: https://www.pombase.org/gene/SPBC336.04
with PAINT: http://desktop.kmr.nz:4242/gene/SPBC336.04
("3'-5'-exodeoxyribonuclease" activity instead of "3'-5' exonuclease activity")
This is the gene with the largest number of annotations from PAINT (14 after GO filtering):
http://desktop.kmr.nz:4242/gene/SPAC57A7.12
To speed things up I disabled most of the non-GO annotation loading for this test so only the GO annotation will be complete on my desktop.

Great. Let me know when. I started work early today. My new working pattern seems to be early start, siesta.

It's ready!
http://desktop.kmr.nz:4242

That's great!
Can I get a GAF?

I  can manage with it like this if not. I can check a slim process a day probably .
Just one thing. I think the IBA are given precedence over ISS?
At least
mug14 has
GO:0030036 | actin cytoskeleton organization | ISO with P35611 | GO_REF:0000024
in PomBAse
but
this is not visible here
http://desktop.kmr.nz:4242/gene/SPBC359.06

I think the IBA are given precedence over ISS?

IBD is lowest priority, IBA is second lowest.

mug14 has
GO:0030036 | actin cytoskeleton organization | ISO with P35611 | GO_REF:0000024

mug14 has
GO:0051017 | actin filament bundle assembly | IBA with PTN000072560 , P35611 , P35612
which is a descendant of GO:0030036 actin cytoskeleton organization.

IBD is lowest priority, IBA is second lowest.

Here's the full priority list, with the highest priority first:
 inferred by curator
 inferred from sequence orthology
 inferred from sequence or structural similarity
 inferred from sequence model
 traceable author statement
 non-traceable author statement
 inferred from expression pattern
 inferred from electronic annotation
 inferred from reviewed computational analysis
 inferred from biological aspect of ancestor
 inferred from biological aspect of descendant

That list is from this issue: https://github.com/pombase/pombase-chado/issues/594#issue-184221717

Oh yes, ignore me!

Here's the GAF file: https://send.firefox.com/download/704965af26d3bfd6/#5IlTGHbsK7v8UpbmcBOoVA

Do you know why
http://desktop.kmr.nz:4242/gene/SPBC409.09c
GO:0000941 | condensed nuclear chromosome inner kinetochore 10
  | IBA with PTN001804338 , mis13
is showing?
there is also an IDA

Looks like a bug!  I'll investigate.

Oddly I didn't spot any others. I wonder if i. should have an extension of some sort? or something?

I've found a bug and I think it's the bug that causing the problem you found.  It's a slightly embarrassing bug that's been there for ages: the redundant annotation filtering is currently done before the GO term remapping (using pombe-embl/chado_load_mappings/GO_mapping_to_specific_terms.txt).
mis13 has this annotation in the contig file:
FT                   /GO="aspect=C; term=inner kinetochore of condensed
FT                   chromosome; GOid=GO:0000939; evidence=IDA;
FT                   db_xref=PMID:15502821; date=20040914"

And the mapping file has:
GO:0000939      GO:0000941      condensed nuclear chromosome inner kinetochore

When the filtering is done the annotation is still to GO:0000939 so the IBA annotation isn't filtered.  At the remapping stage GO:0000939 is changed to GO:0000941 so we get the redundant annotation.  I'll run a local test to make sure that's all true.
I'll also change the load script to do the re-mapping before filtering.

OK no need to  do anything else with this ticket for a while. I opened a load of tickets and it will l clearly take a  while until those are fixed.
There are a few more process and component slim terms I would like to check but I made good progress this morning:
https://github.com/pombase/curation/issues/2739
https://github.com/pombase/curation/issues/2737
and this covers most of the processes where fission yeast is a major model so I'm a bit fussier
I'm expecting  metabolism etc will be fine anyway...

I'll also change the load script to do the re-mapping before filtering.

Doing the filtering after the mapping has fixed the PAINT test load:
http://desktop.kmr.nz:4242/gene/SPBC409.09c
I've fixed the nightly load script too so the main site should be fixed in the morning.

It's giving an error right now. Although I'm not going to do any more on this right now so that is good;)
Back to curation...

It's giving an error right now

Yep, it's slightly in flux.  :-)
Let me know when you get back to this and I'll make sure the latest GO/PAINT annotations are loaded.  I'll also make sure the site isn't broken on my desktop.  I'm happy to leave my machine on overnight (my time) if you need access.

How many PAINT annotation remain after that filter is applied?

no hurry, just curious...

After filtering there are 5199 PAINT annotations.  There are 14560 before filtering.

Oh it was 5211  before the bug, so it only dropped by 12. shame !

Assigned to me for the checking phase

I did quite a lot of checking  a while ago, at least an the slim tem level.I reported a lot of errors, but further checking wold be diminishing returns. These were the. checks I did
https://github.com/pombase/curation/issues/2739
https://github.com/pombase/curation/issues/2737
I  went through the  GO annotation tracker and added filters  for any PANTHER ids where there are outstanding  queries about annotation valididyy (and just checked this in)
next:

[ ] make sure the latest GO/PAINT annotations are loaded. Using this priority list:
inferred by curator
inferred from sequence orthology
inferred from sequence or structural similarity
inferred from sequence model
traceable author statement
non-traceable author statement
inferred from expression pattern
inferred from electronic annotation
inferred from reviewed computational analysis
inferred from biological aspect of ancestor
inferred from biological aspect of descendant
(Note that eventually we might change the priority but for now we still want the smallest possible number of PAINT annotation)

[ ]  Last time I asked "After filtering there are 5199 PAINT annotations. There are 14560 before filtering." It will be useful to know  these numbers with eh current evidence heirarchy filtering  after the new PANTHER family filters are applied (out of curiosity).

[ ] PANTHER annotations have a long list of supporting IDs . Long term it might be better to display only for the Panther node ID: (e.g. PANTHER:PTN000678822) - but at fist we will display the  complete lists, might be interesting for people, and it would be good if there was a way to make these accessible (I will look into panther external  links which might provide this detail), or make visible in mouse over (THIS CAN HAPPEN LATER- POSSIBLY MOVE TO A NEW TICKET?)

make sure the latest GO/PAINT annotations are loaded.

Do you mean add PAINT to the main load?  Or would you like another test load?

I think maybe do one more test load and I will validate the numbers and do a very quick sanity check. Then we can move to live.
It's a lot of annotation so I think there will be a lot of  annotation issues  but hopefully  we can squash them pretty quickly.

I think maybe do one more test load and I will validate the numbers and do a very quick sanity check. Then we can move to live.

OK, I'll run a full load with PAINT on my desktop early next week.  I'll let you know when it's done.

make sure the latest GO/PAINT annotations are loaded. Using this priority list:

I just checked and that's the priority list we're currently using.
I'm running a test load now.  It should be ready by the morning.

The load finished on my desktop.  It will be here until midday UK time or so: http://desktop.kmr.nz:4242/
The load doesn't include all datatypes because I wanted it finish quickly.

It will be useful to know these numbers with eh current evidence hierarchy filtering after the new PANTHER family filters are applied (out of curiosity).

Before filtering: 14168.  After: 4975

If you'd like to look at the GAF from this load it's (temporarily) here: http://desktop.kmr.nz/pombase/dumps/builds/pombase-build-2020-10-19-d1/pombase-build-2020-10-19-d1.gaf.gz

Thanks I won't have time to check this a.m as I'll be working with Alayne until about 1.
So I will probably do this tomorrow.

The load finished on my desktop. It will be here until midday UK time or so: http://desktop.kmr.nz:4242/

New and faster link: https://desktop.kmr.nz/

So I will probably do this tomorrow.

OK.  My desktop will be on until noon-ish tomorrow.

I won't get to this today, or possibly even tomorrow as I need to finish a CC session and prepare/record my sys biol lecture (that will likely take a full day).
I will let you know which day I plan to do checking the evening before.

I will let you know which day I plan to do checking the evening before.

I can re-run the load when you need it.
In the meantime I've copied the current data and website from my desktop to oliver1.  So you can now access it even when my desktop is off using this URL: http://paint.pombase.kmr.nz/

wow thanks. i shouldn't be doing this today. need to record talk...ok just a little peek

Is that the current DB rather than the one with the PAINT annotations?

Is that the current DB rather than the one with the PAINT annotations?

It's the one with PAINT annotations.  There are definitely more annotations.  For example the slim categories have more genes:

https://www.pombase.org/browse-curation/fission-yeast-bp-go-slim-terms
http://paint.pombase.kmr.nz/browse-curation/fission-yeast-bp-go-slim-terms

ok thanks, not looking now

OK let's go for it.
Include the PAIN annotation with the current precedent  for evidence codes (We might bump IBA up a bit later)
I will follow up with an e-mail to crowd-source the final QC. Then nobody can complain if they are wrong, they know that they just need to let us know...

PINT, NOT PAIN!

arggh

Great.  I've added the PAINT annotations to tonight's load.  The main site will update itself at 6am-ish.

oooh , excitiing!

Done!  It's on the dev site: http://dev.pombase.kmr.nz/

The main site will update itself at 6am-ish.

I've disabled that for today.  I'll update it manually when you're happy with the dev site.

I'm happy, there are still problems, but I am happy to crowdsource the QC!

OK, it's done.  The main site is updated.

Whoop whoop!

I guess this can be closed now?

yes!


Question about matrix power algo

I am implementing randomized SVD in BidMach/BidMat, which I would love to contribute to BidMach later if possible :-).
One of the steps of my algorithm involves, for a large dense matrix A, computing (AA')qA
I was wondering if there was an operator or function in BidMat for the exponentiation part (a fast Mq)? I checked  the wiki pages Scientific Functions and Matrix Algebra and could not find anything. There is a pow function but that seems to be an element-wise power between two matrices. It might already exist in BidMat but I couldn't find it in the documentation.
I thought there could be some method to this with exponentiation by squaring, or even just a pre-written method that would remove the need to write a for loop every time. I can implement this if you would like.
Cheers,
Amédée

I'm not clear on what you want from A^q. The element-wise operator is exposed as A ^ q.
But if you want a matrix power, you have to compute an eigendecomposition of A (assuming it exists) and then power the diagonal eigenvalues element-wise by q. Normally this requires A to be positive definite.


Backend script for Lido staking TryLSD bot

Transfered to @rootedbox with https://github.com/VolumeFi/paloma/issues/1306


Incorrect scrollbar styling when swapping to dark mode

Steps to Reproduce

Navigate to the website
Swap to dark mode

Expected Behavior

The scrollbar styling should swap to dark mode.

Actual Behavior

The scrollbar styling remains light.

Affected Environments

Browsers:

Chrome
Edge

Screenshots

I would like to take it on me please


Add support for SLE Micro

QA test, see if can identify any issues. Does SELinux work when enforcing?
Test with SLE Micro 5.0

This is to remain in the backlog for now. Perhaps later we'll want to QA test and certify SLE Micro 5.0, 5.1 or later version down the road.

This has been mostly validated on v1.22.3+k3s1, v1.21.6+k3s1, and v1.20.12+k3s1 following our New OS Support Matrix (installing rancher as local cluster, running sonobuoy conformance checks, using docker cri, and upgrades via SUC). I have not run some automated kubernetes checks through rancher yet, which is the final validation we like to do.
One thing I'd like to call out is that in all of these cases, I did this through VirtualBox VMs, which was taxing on my machine so I was only able to run a single server and single agent (although did see another server able to join in one case before I ran OOM). For the final check on all versions, I will upload the SLE Micro ISO to an internal server and use that to install it on 3 servers, 1 agent, and perform the final check with that configuration.
This is all done with SLE Micro 5.1

sle-micro 5.1 should at least work now via #4331, #4398, and #4402

Validated all versions according to our support matrix. Confirmed it is working correctly with selinux as well.


TODO support ChatGLM-6B

It seems my Raspberry Pi can't run ChatGLM-6B

yes, m1 I checked the issue seems ok


Do not fire the delegate method for the selected item after a rotate

Fixes #123
I removed the call in the graph view controller that manually hit the delegate method to indicate an item was selected. I'm not really certain why this was here in the first place, possibly as a workaround for a different bug that was solved.
Wil need to make sure we test this one with backgrounding the app, rotating, then foregrounding it. Also test on iPad and iPhone devices. Make sure to include iOS 7 with at least one device as application lifecycle is slightly different between the OSs.

Going to merge this and let people test internally.


add rocm into build info flags

This is a bug fix from JIZHI, the AI platform in Tencent.
@deven-amd
Below bug is caused by build_config_info changed from "--build_config cuda" to "--is_config_cuda True", but miss the file tensorflow/contrib/cmake/CMakeLists.txt
ERROR: /tensorflow-rep/tensorflow/python/BUILD:199:1: Executing genrule //tensorflow/python:py_build_info_gen failed (Exit 2): bash failed: error executing command
(cd /xxxxxxxxxx/execroot/org_tensorflow &&
exec env -
LD_LIBRARY_PATH=/usr/local/cuda/extras/CUPTI/lib64/:/usr/local/cuda/lib64:/usr/local/nccl_2.4.7-1+cuda10.0_x86_64/lib:/usr/local/lib64
PATH=/usr/local/cuda/bin:/usr/local/cuda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/opt/ibutils/bin:/root/.ft:/root/bin:/root/.ft
/bin/bash -c 'source external/bazel_tools/tools/genrule/genrule-setup.sh; bazel-out/host/bin/tensorflow/tools/build_info/gen_build_info --raw_generate "bazel-out/host/bin/tensorflow/python/platform/build_info.py"  --is_config_cuda True --is_config_rocm False --key_value  cuda_version_number=${TF_CUDA_VERSION:-} cudnn_version_number=${TF_CUDNN_VERSION:-} ')
Execution platform: @bazel_tools//platforms:host_platform
usage: gen_build_info.py [-h] [--build_config BUILD_CONFIG]
[--raw_generate RAW_GENERATE]
[--key_value [KEY_VALUE [KEY_VALUE ...]]]
gen_build_info.py: error: unrecognized arguments: --is_config_cuda True --is_config_rocm False
Target //tensorflow/tools/pip_package:build_pip_package failed to build

closing this PR as contrib folder will be depricated in 2.0, thank you.
CC @mihaimaruseac

Should I submit the PR in r1.15 again?
@mihaimaruseac and @rthadur

Please make it against master, without anymore contrib (contrib is removed anyway).
The window for cherry-picks for 1.15 is ended


Update container image for v1.1.1

Resolve part of #1321
/cc @terrytangyuan @PatrickXYS
This image comes from latest master commit and it is built from CI
commit 47a74b738920edbf4207160cec7e1dff9cdab3f2 (upstream/master, master)
Author: jazzsir<EMAIL_ADDRESS>Date:   Tue Jul 20 16:10:15 2021 +0900

    add a specific version of tensorflow_datasets (#1305)

    re-push with signed email

@terrytangyuan Can you help leave a /lgtm? :D


Default logger does not support event listeners

Please tell us about your environment:

_winston 3.1.0
_node -v 8.9.3
_Operating System? macOS
_Language? ES6

What is the problem?
const winston = require('winston');
winston.error('Something went wrong');
winston.on('finish', () => {
   console.log('Finished writing');
});
winston.end();

TypeError: winston.on is not a function
What do you expect to happen instead?
Per the documentation, Any method that you could call on an instance of a logger is available on the default logger , so I was expecting that .on would be supported

I'm also having this problem. Have you found any workaround for this, @TomRomanowski?

Also ran into this issue. Does anyone have a workaround? There doesn't appear to be a way to access the defaultLogger either.

Guys please do something about the default logger.
It doesn't have half the features of the regular logger because you are picking them manually and attaching them to the winston exports.
The least would be to actually expose the defaultLogger object in the exports.


domain req for: vamika.is-local.org

Requirements

[x] You have completed your website.
[x] The website is reachable.
[x] The CNAME record doesn't contain https:// or /.
[x] There is sufficient information at the owner field.
[x] Your website is not hosting on the following due to SSL issues: Vercel, Netlify

Description

Link to Website

https://real-yash.github.io/vamika/

heyy maintainers, im new here, i have no idea if i mad any mistake please fix it for me!! T_T

@DEV-DIBSTER i have  changed file name


[WIP] Add essential boundary support in ex16 [ex16-add-dirichlet-bc]

Setting essential boundary values in time-dependent laplace problem is
not totally trivial. We need a definitive example to show how to apply
the boundary condition in this situation. This patch adds dirichlet
value support to example 16.

Add --boundary-type option to select either natural (0) or dirichlet
(1) boundary type.
Add --dirichlet option to define the constant coefficient boundary
value
Use K->FullMult() to actually apply diffusion involving the essential
boundary DoF

Signed-off-by: Francis Giraldeau<EMAIL_ADDRESS>

Thanks for the comments. Setting the boundary dofs in the rhs is somewhat hacky, but is working with non-conforming meshes, as this example shows:
./ex16 -o 1 -r 0 -m ../mfem/data/amr-quad.mesh -visit --kappa 0.05 --boundary-type 1 --dirichlet -1

Hi @giraldeau, is this PR ready for review from your perspective? If so, can you please remove the draft status and add the ready-for-review label?
Thank you for your contribution!

Hello! I think we still have to settle on the proper way to address the Dirichlet BC in this case. Because we want to support both implicit and explicit integration scheme, and also cache the matrices when possible, I was not sure how to best handle the situation.
I would set the boundary value on the r.h.s, because it is more general, but @jandrej suggested instead to rather overwriting the solution after the solve. This yield the same result when du_dt is zero, but not if the time derivative is different than zero.
I can rework the patch according to what is best. Thanks!


CONDA_PREFIX issue

Hello,
I am CMS PhD student testing PocketCoffea, and I was following the documentation in PocketCoffea on lxplus, and after I created the singularity by:
apptainer shell --bind /afs -B /cvmfs/cms.cern.ch \
                --bind /tmp  --bind /eos/cms/ \
    --env KRB5CCNAME=$KRB5CCNAME --bind /etc/sysconfig/ngbauth-submit  \
    /cvmfs/unpacked.cern.ch/gitlab-registry.cern.ch/cms-analysis/general/pocketcoffea:lxplus-cc7-latest

and clone with: git clone https://github.com/PocketCoffea/PocketCoffea.git and when I use
runner.py --cfg example_config.py  --full --test -lf 1 -lc  2 -o output_v1

I have to mention that I was working with it last week and it worked completely, but this week
for running it I constantly got this error:
File "/usr/local/bin/runner.py", line 146, in <module>
    f'conda activate {os.environ["CONDA_PREFIX"]}',

when we checked the runner file had been changed recently. (link)

This is from my changes. I think it will work for you if you just move the condor_extra = [ ] block back under the elif run_env == "conda" block. So that it is not executed for you, since you do not use conda.

@Mehrnoosh-Moallemi sorry for the inconvenience.  We are working on a refactoring of runner.py to avoid this kind of environment problems.

Many thanks for fixing the issue.


znc --makeconf username does not correctly allow alphanumeric

znc --makeconf
username validation does not correctly allow all alphanumerics.
e.g try "77abc" this will be rejected, then try "abc77" this will be accepted. Both should be valid alphanumeric.

I think the IRC RFC forbids usernames from starting with numbers and I didn't check, but I think ZNC uses username as the default nickname, so I don't think this is an issue.

Ah yes
nickname = ( letter / special ) *8( letter / digit / special / "-" )
From section 2.3.1
Thanks!


allPass currying fix

I realized in my implementation that the currying would behave unexpectedly if a falsy value was supplied, so I made the condition in the ternary expression explicitly check for the argument to be undefined.

@kightlingerh good catch! Thanks for spotting this, I missed it in the review.
This PR though has a few issues, I've opened #25 instead

adding a type-level test is not really testing the execution of the function (only the type signature!). I added a test that actually fails on current master for 0
In general, I would say it is best to always call our FR.function implemented in fp-ts-ramda in the curried form in tests, in order to catch possible similar issues


Security Incident resolution - revert deployment template

Deployable artifacts with SA SAS token within Azure Deploy Button ARM template - expose security vulnerability and must be disabled.

Reverted SAS URLs in ARM template code and disabled SAS token in current deployable artifacts.
Note: this moved us step back to undeployable fnapp code issue. Will have to change ARM config adding new yaml pipeline to run fnapp deployment via github action workflow


filter does not seem to work on Linux.

Verify canary release

[X] I verified that the issue exists in the latest Turborepo canary release.

Link to code that reproduces this issue

What package manager are you using / does the bug impact?
pnpm
What operating system are you using?
Linux
Which canary version will you have in your reproduction?
2.0.9
Describe the Bug
The local machine is Mac, CI/CD uses Linux. The same command has different --filter=@scope/*[HEAD^1] results:
Mac

Linux

``
Expected Behavior
The results are consistent with Mac.
To Reproduce
The most recent git record is invalid.
Additional context
No response

Can you try adding enclosing quotes around your filters e.g. --filter="@scope/*[HEAD^1]"? Many shells expand * as a wild card and this happens before turbo receives the command line arguments.
If this doesn't work could you:

Provide the raw text of the command you're running. It's hard to tell exactly what the command is from your screenshots
What shell is being used in each environment

Thank you for your reply. I roughly know the cause of the problem. It is estimated that the pnpm-lock.yaml file has changed due to the execution of pnpm i on the deployment server.


RM Report-template field "IndexIsotope" (in Custom Report Builder) does not update

Re the new (Squid3 version 1.9.2) RM Report-fields: "PrimaryDaughterParentRatio" and "SecondaryDaughterParentCalculation" are both fundamental directives controlled by the form of the selected Task.
However, "IndexIsotope" is controlled by radio-button within the Project, and (linked) within the Reference Material Interpretation. That radio-button needs to be polled every single time an RM Report is generated:

Really, the radio-buttons controlling all three fields should be polled every time, regardless.
When I switch the radio-button, I can generate a new RM Summary report which understands the change, but nothing I do is capable of changing the outdated contents of the IndexIsotope field in the RM report-template.

Then I switched the Project to a Perm2-style Task (i.e. direct calibrations for both Pb/U and Pb/Th), and all three of the new RM Report-template fields ("IndexIsotope", "PrimaryDaughterParentRatio" and "SecondaryDaughterParentCalculation") returned "not found" in my RM Report.

I cannot replicate - please send .squid file.

Here is my RM Report super-template:
SQ2.50 StandardData ALL Report-template.zip
Here are the two Tasks I have used in this Project at different times:
10peak_zircon_Tasks.zip
Here is the Project (I don't remember which Task is actually loaded at present):
170111_GA6357_Sq3-192.zip

The new metadata fields do not appear in these files, so I added them and saved the report and they behave properly.  Can you send the same files with the mis-performing metadata fields present?  Maybe we should schedule an online demo of the problem if I still can't replicate it after that?

Followup - I see where the fields are present in the group "Prelims", so no need to send anything, but they still behave correctly for me so maybe an online demo of the problem is in order?

I can see them in the version I sent, when I use my Custom RM report-template, as follows:

In the process of generating this screenshot and pressing Create CSV, I have discovered that the new fields come out fine in the CSV, as long as you Peek at them first (as per my screenshot). But if you don't Peek at them individually, you get "not found" in the CSV, which is not great.

I can replicate and fix that!

In addition, if I change the Project Index Isotope (e.g. from 204Pb to 207Pb) using the radio-button and then quit Squid3 without saving, that also fools the IndexIsotope field in the Custom Report Builder. It "remembers" the change (even though I didn't Save),
So when I restart Squid3 and open that Project, the Project Index Isotope setting is 204Pb (because the change to 207Pb was not Saved), but when I go to CustomReport Builder and press View CSV (without Peeking), the RM Report-field IndexIsotope still returns 207Pb in the CSV. Which is wrong.

Yeah that is related to the previous problem.


Update expired Microsoft tokens to fix test failures

Connector Name
other (None Listed Above)
What happened?
Microsoft connector tests are failing due to expired tokens.
Relevant log output
No response

Since we cannot use the existing App for the Microsoft connectors, the Infra team has created a new Azure subscription for connectors. We have created a new App for these connectors, But the API fails with the error The tenant does not have a valid SharePoint license., and we could not find a proper solution, so we have raised a support ticket to Azure support team. Support request ID -<PHONE_NUMBER>001697


Add code for Install packages if not already installed in render_variant_matrix_qc.R

Add code for Install packages if not already installed in render_variant_matrix_qc.R


findOneAndUpdate() seems to not return result if no updates to apply

Send the following commands to jsonapi and you'll see that findOneAndUpdate() returns no results, even though there's a document that matches.
{
  "deleteMany": {
    "filter": {}
  }
}

{
  "insertMany": {
    "documents": [
      {
        "username": "a"
      }
    ]
  }
}

{
  "findOneAndUpdate": {
    "filter": {},
    "update": {
      "$set": {
        "username": "a"
      }
    },
    "options": {
      "returnDocument": "before"
    },
    "sort": {
      "username": 1
    }
  }
}

Change the last command to the following and a document is returned.
{
  "findOneAndUpdate": {
    "filter": {},
    "update": {
      "$set": {
        "username": "aaa"
      }
    },
    "options": {
      "returnDocument": "before"
    },
    "sort": {
      "username": 1
    }
  }
}

@vkarpov15 If there is no update to the document, the api currently doesn't return document. Will make the change to return document in this scenario too.

@vkarpov15 I believe this behavior is required for findOneAndReplace() api too?

@maheshrajamani yes, findOneAndReplace() as well. Although it looks like findOneAndReplace() isn't affected - the following series of commands seems to result in a document being returned from findOneAndReplace():
{
  "deleteMany": {
    "filter": {}
  }
}

{
  "insertMany": {
    "documents": [
      {
        "username": "a"
      }
    ]
  }
}

{
  "findOneAndReplace": {
    "filter": {},
    "replacement": {
      "$set": {
        "username": "a"
      }
    },
    "options": {
      "returnDocument": "before"
    },
    "sort": {
      "username": 1
    }
  }
}


updated Readme

I have added the HTML tags and updated the appearance . Please merge it 🤩

Thanks Ishita for making your valuable contribution :) Happy Hacking


Dockerize ontop service

We won't use Ontop in our system. Ontop requires a separate query for each database column; automatic joining of identical columns is not straightforward.


steps for hosoya triangle

fix #3984

@sairish2001 I think that this can come under level 2 ....Just a sugggestion ... Thank you


Clarify minimum jQuery version

in bower.json it asks for jquery ^2.0.0
in the Readme is says it works with jQuery 1.7+   // ie8+

Oh, Sorry, That's my fault. I'll fixed it
Thanks


Support HTTP '409 Conflict' Errors when updating a work item link type (#1311)

Modified the design file to add the 'Conflict' response type and added a test
to verify the output when the version does not match the expectation.
Signed-off-by: Xavier Coulon<EMAIL_ADDRESS>

[test]

[test]

Codecov Report

Merging #1314 into master will increase coverage by 0.14%.
The diff coverage is n/a.

@@            Coverage Diff             @@
##           master    #1314      +/-   ##
==========================================
+ Coverage   60.06%   60.21%   +0.14%
==========================================
  Files         118      118
  Lines       10690    10690
==========================================
+ Hits         6421     6437      +16
+ Misses       3636     3622      -14
+ Partials      633      631       -2

Impacted Files
Coverage Δ

workitem/link/type_repository.go
69.04% <0%> (+1.58%)
:arrow_up:

remoteworkitem/scheduler.go
63.41% <0%> (+9.75%)
:arrow_up:

models/transaction.go
70% <0%> (+20%)
:arrow_up:

remoteworkitem/github.go
100% <0%> (+22.85%)
:arrow_up:

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update d3ce286...8a30871. Read the comment docs.

thanks for the review and approval, @aslakknutsen !


Coala auto run after reset / power loss

I am trying to use coala within code composer studio. Running it trough the debug option with a simple self made app works well, but after pressing reset or unplugging and replugging the MSP430FR5969 it won't start up again.
Additionally i can't find the line in the Linker Script which is mentioned in the readme to be edited. The one closest matching it is
"FRAM (rx)        : ORIGIN = 0x4400, LENGTH = 0xBB80 /* END=0xFF7F, size 48000 */"

Dear @GrueneNeun - Thanks a lot for posting this issue and glad to see your interest in our project. We will be getting back to you with an answer shortly.

Dear @GrueneNeun - Thanks a lot for posting this issue and glad to see your interest in our project. We will be getting back to you with an answer shortly.

Hi @GrueneNeun
Thanks for your interest and question.

You do not need to build Coala with CCS. You can go to the app folder and type make and it will build it. Then, you can flash it to your MCU with a different tool.
Coala requires GCC or Clang. Set your environment in this file https://github.com/TUDSSL/Coala/blob/master/maker/envCom.mk
Modifications in the linker file https://github.com/TUDSSL/Coala/blob/c0f9be03ebda4301b217dd991b83065f910fffdb/coala/linkerScripts/8KB_pages/msp430fr5969.ld#L49 and the 2 lines below it.  Also https://github.com/amjadmajid/CoalaRepo/blob/3269951255782e10ffa5bb8ad779610525a78041/apps/sort/msp430fr5969.ld#L236 and the 21 lines below it.

Using CCS
I have built this app with CCS https://github.com/amjadmajid/CoalaRepo/tree/master/apps/sort. If you want to follow what I have done, please make sure that

you direct CCS to use the linker script in this app folder, and
you link Coala and the needed libraries properly (https://www.youtube.com/watch?v=FzHtq51IjDM).
For further assistance, we need to know more about the problem (more details).

Hi @GrueneNeun
Thanks for your interest and question.

You do not need to build Coala with CCS. You can go to the app folder and type make and it will build it. Then, you can flash it to your MCU with a different tool.
Coala requires GCC or Clang. Set your environment in this file https://github.com/TUDSSL/Coala/blob/master/maker/envCom.mk
Modifications in the linker file https://github.com/TUDSSL/Coala/blob/c0f9be03ebda4301b217dd991b83065f910fffdb/coala/linkerScripts/8KB_pages/msp430fr5969.ld#L49 and the 2 lines below it.  Also https://github.com/amjadmajid/CoalaRepo/blob/3269951255782e10ffa5bb8ad779610525a78041/apps/sort/msp430fr5969.ld#L236 and the 21 lines below it.

Using CCS
I have built this app with CCS https://github.com/amjadmajid/CoalaRepo/tree/master/apps/sort. If you want to follow what I have done, please make sure that

you direct CCS to use the linker script in this app folder, and
you link Coala and the needed libraries properly (https://www.youtube.com/watch?v=FzHtq51IjDM).
For further assistance, we need to know more about the problem (more details).

Sorry for responding so late.
Using the Youtube Video and your hint about the linker script i have been successfully able to get a Coala up and running inside a CCS Project.
Thank you very much for your help.


feat Add Redirect REST Call

This modification adds the ability to request Redirect data from the
Shopify REST API.

@tres we run a few checks on code you can find it all here: https://github.com/pixelunion/elixir-shopifyapi/blob/master/.github/workflows/push.yml#L33-L49
You can also click through the "details" link on the failing Action here and drill down to find out what it is complaining about.


dotnet test --blame is creating sequence.xml(attachment file) in "location-dotnet\sdk\version-folder\ResultsDirectory"

Description

dotnet test --blame is creating sequence.xml(attachment file) in "location-dotnet\sdk\version-folder\ResultsDirectory"

Steps to reproduce

create a test project with a test which will crash ( A test method with stackOverFlowException)
run dotnet test --blame

Expected behavior

it should create attachment(Sequence.xml) in current working directory

Actual behavior

it tries to create file in dotnet folder

Work Around

Pass ResultsDirectory in commandLine or in runsettings

Work Around
Pass ResultsDirectory in commandLine or in runsettings

Fix : https://github.com/Microsoft/vstest/pull/1208


Vietnamese translation

I add the Vietnamese doc's link to other docs. Please check if it is accessible. Thank you 😃

Thanks, LGTM


Resolving port placeholders in Marathon labels

Adds a feature of port placeholders in Marathon labels that are resolved in consul tags when registering a service.
Placeholders format: {port:<port name>}, where <port name> should be a name of an existing port definitions. Such placeholder will be replaced by related port number when mapping Marathon labels into Consul tags.

Coverage increased (+0.1%) to 90.718% when pulling 958f0a757195bbc1d788996156299365d7d9181e on pbetkier:port_placeholders_in_labels into 149a59e4e26d44cbaa7d28c6792107a919d26a51 on allegro:master.


[Bug?? Maybe Not???] Audio gets louder as time progresses

(I haven't made an issue in forever so I don't know what I'm doing)
I'm not on the latest build of OutFox (and I should be to be honest. I'm highly sure updating will fix this issue even though I've never had this happen before [I think I'm on 4.9]).
The audio gets louder as time goes on, but when I switch songs it gets quiet and then does the same thing??
Attached are 2 videos (through Google Drive, because they are way bigger than 10MB. Thanks, phone camera!) For some reason, it's not noticeable in the first video but it's very very noticeable in person, and it's slightly noticeable in the second video...?
First Video (not very noticeable)
Second Video (more noticeable, but still not that much)

Can you test again on the latest build (4.9.7GG)?

Yup! Will do later today, and then I'll report back.

Tested a few days ago (sorry for keeping you waiting!), and it turns out it's just an issue with my TV... nice.


[FEATURE] Add date of birth and driving licence

Can you please add an input for date of birth and driving licences in basics information section (under address for exemple)?

Any specific reason to add date of birth within a resume? I've read multiple articles and seen cases to dispute that age shouldn't be a deciding factor when applying for a job. As explained in articles like these.
As for driving license, could you provide me with an example screenshot of some other resumes that show these type of extra information? I could implement another section to add extra info, which can just be key value pairs. But I'm curious to know how to display it in the resume.

This can be helpful: https://www.indeed.com/career-advice/resumes-cover-letters/drivers-license-on-resume

Hi @AmruthPillai. Things a little different here in China.  As a fresh graduate of this year, it would be very helpful if you could make the “date of birth” field optional or disabled by default.
Thank you!

I've added Date of Birth as a field in basics now, as of v3.4.0 :)


Add acceptExpression to host

Adding acceptExpression to Go. See #1264.
PR checklist:

[ ] Added changelog entry.

Hi @joshrotenberg, thanks for the contribution! Do you need any help from us on pushing this forward? Would love to get it into the next release (~November 10th)

Hi @joshrotenberg, thanks for the contribution! Do you need any help from us on pushing this forward? Would love to get it into the next release (~November 10th)

I think I did the easy part, looking at polar.go now to see what's next.

Haha I feel like I just made more work for @samscott89


undefined is not an ovject (evaluating '_react.PropTypes.string')

I get this error and it points to this node module in src/Scene.js
I looked at the file and it's still using React.PropTypes and not import PropTypes from prop-types.  That might be part of the problem.

Please check 4.0.0-beta.7, I don't see usage of React.PropTypes

I am facing same issue and don't have any Idea how I can resolve it, could you please explain me why it's happening ?


fix: exclude COMMENTED PRs from affecting label status

There's a flaw in this GitHub action where it removes the +2 or +1 labels from pull requests that have an APPROVED status. This happens because comments are counted as PR reviews, and the action only considers the most recent review by each reviewer. This means if a reviewer approves a pull request but later comments on it, their latest "review" is now just a comment, and the approval is ignored.
Review states for pull requests include:

APPROVED: The pull request can merge.
CHANGES_REQUESTED: Prevents merging.
COMMENTED: Just informational.
DISMISSED: Negates an earlier review.
PENDING: Review is incomplete.

To address this, we should ignore reviews that are solely comments. Our focus is on the most recent review. A pull request should only lose its +1 or +2 status if a subsequent review either requests changes, dismisses the earlier approval, or is still pending. Comments alone should not strip away an APPROVED status.

@zhubert, I opened this PR before testing these changes. I hoped some GitHub action on this repo would give me instructions on how to test it. I didn't get that, so now I suspect I can target a branch and will look into that next.

I found another issue: if you have an approval but it's dismissed, the approval is still counted in the calculation. I am closing this PR to work on it to avoid notifications.

@wassimk oh this is funny, I didn't realize I was the code owner for this. Let me know if you need any help digging into this code.


Release

New approach, direct from dev to main

Codecov Report

Merging #226 (fe9dacb) into main (2bb7d97) will increase coverage by 2.13%.
The diff coverage is 88.11%.

:exclamation: Current head fe9dacb differs from pull request most recent head 6dd73cc. Consider uploading reports for the commit 6dd73cc to get more accurate results

@@            Coverage Diff             @@
##             main     #226      +/-   ##
==========================================
+ Coverage   53.58%   55.71%   +2.13%
==========================================
  Files          57       59       +2
  Lines        4130     4284     +154
==========================================
+ Hits         2213     2387     +174
+ Misses       1917     1897      -20

Impacted Files
Coverage Δ

sample_metadata/parser/generic_metadata_parser.py
76.21% <74.28%> (+4.11%)
:arrow_up:

scripts/parse_ont_sheet.py
78.43% <78.43%> (ø)

sample_metadata/parser/generic_parser.py
75.19% <85.71%> (+1.37%)
:arrow_up:

models/enums/analysis.py
100.00% <100.00%> (ø)

models/enums/sequencing.py
100.00% <100.00%> (ø)

sample_metadata/parser/sample_file_map_parser.py
72.50% <100.00%> (+4.07%)
:arrow_up:

test/test_parse_file_map.py
100.00% <100.00%> (+64.00%)
:arrow_up:

test/test_parse_generic_metadata.py
100.00% <100.00%> (ø)

test/test_parse_ont_sheet.py
100.00% <100.00%> (ø)

... and 3 more

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update 2bb7d97...6dd73cc. Read the comment docs.


Drop control message Scala wrapper - UnregisterShuffle/UnregisterShuffleResponse

What changes were proposed in this pull request?
Why are the changes needed?

What are the items that need reviewer attention?
Related issues.
Related pull requests.
How was this patch tested?
/cc @related-reviewer
/assign @main-reviewer

ping @waitinfuture


Tooltip labels adds a 0 before each tooltip

When you hover a 0 is added to the front of the label text.

weird. cant replicate now.

Sounds really odd!


Add -Region option to Get-GceManagedInstanceGroup

This change is

@ILMTitan That's a good point. PTAL.

LGTM

Thanks!


There is no styling on disabled selects showing that they are disabled

I noticed this during development. I think I ended up not having to disable any of them (they are simply hidden instead), but I thought this is worth noting.
Issue transferred from https://github.com/mattermost/mattermost-plugin-ee-jira/issues/28

Closing issues due to inactivity. This issue can be re-opened with more interest from our community.


Avances Primera Semana (Gonzalo)

General changes and commentaries

Numpy and Scipy adoption
Internally all the procedures that use arrays are implemented using Numpy Arrays.

Implementations

The class ActiveContour is defined and it's constructor is documented (but missing a brief description)
The following methods where implemented inside ActiveContour class

laplacian
edgeMap
calcGGVF

Queda pendiente la documentacion de los metodos implementados


Plugin does not include all dependencies

Please include ejs with the plugin.
ERROR Plugin load failed: hexo-generator-amp
Error: Cannot find module 'ejs'

@matthewsanders
Thank you for teaching me. The issue has been fixed.

Thanks for adding :)


Instruction for cross-compilation

Hi there,
I'm trying to cross-compile from linux with OSX as target but I get the following error
building for OS darwin ARCH amd64
# github.com/keybase/go-keychain
../../../go/pkg/mod/github.com/keybase/go-keychain@v0.0.0-20190712205309-48d3d31d256d/corefoundation_1.10.go:9:10: fatal error: 'CoreFoundation/CoreFoundation.h' file not found
#include <CoreFoundation/CoreFoundation.h>
         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1 error generated.
# net
/usr/local/go/src/net/cgo_bsd.go:15:72: could not determine kind of name for C.AI_MASK
# os/user
/usr/local/go/src/os/user/getgrouplist_darwin.go:16:11: warning: implicit declaration of function 'getgrouplist' is invalid in C99 [-Wimplicit-function-declaration]

I saw the issue #23 but I don't understand how the PR #20 could fix this issue, that PR "just" add cgo build tag
What I have tried
I've tried the following build commands:

GOOS=darwin GOARCH=amd64 go build works without building keychain
GOOS=darwin GOARCH=amd64 CGO_ENABLED=1 go build doesn't work, fail withe the above error
CC=clang-11 GOOS=darwin GOARCH=amd64 CGO_ENABLED=1 go build doesn't work, fails with the above error
CC=clang-11 CXX=clang++-11 GOOS=darwin GOARCH=amd64 CGO_ENABLED=1 go build doesn't work, faisl with the above error

Build environment
go version:
go version go1.15.3 linux/amd64

keyring module version
github.com/99designs/keyring v1.1.6

clang-11 --version:
Ubuntu clang version 11.0.0-++20201008094836+176249bd673-1~exp1~20201008080315.114
Target: x86_64-pc-linux-gnu
Thread model: posix
InstalledDir: /usr/bin

clang++-11 --version:
Ubuntu clang version 11.0.0-++20201008094836+176249bd673-1~exp1~20201008080315.114
Target: x86_64-pc-linux-gnu
Thread model: posix
InstalledDir: /usr/bin

OS version (lsb_release -a):
No LSB modules are available.
Distributor ID:	Ubuntu
Description:	Ubuntu 18.04.5 LTS
Release:	18.04
Codename:	bionic

I have part of this solved for you, but I'm here in the issues section to comment on a compile error which could be related to my environment setup.  None the less this will get you further along.  That error is because golang cannot find the xcode libraries with swift.  So you need to install swift then tell go where the libraries and header files are.
so you need
apt-get install -yq wget git build-essential
apt-get install -yq libpython2.7 libpython2.7-dev
apt-get install -yq llvm libicu-dev clang

wget -c https://swift.org/builds/swift-5.4.2-release/ubuntu2004/swift-5.4.2-RELEASE/swift-5.4.2-RELEASE-ubuntu20.04.tar.gz
tar -xvf swift-5.4.2-RELEASE-ubuntu20.04.tar.gz
mv swift-5.4.2-RELEASE-ubuntu20.04 /usr/share/swift
export PATH=/usr/local/go/bin:/usr/share/swift/usr/bin:$PATH

GOARCH=amd64
CGO_ENABLED=1
GOOS=darwin
CXX=clang++
CC=clang
CGO_CFLAGS=-I/usr/share/swift/usr/lib/swift


Sometimes the runtime fails to continue after hitting a breakpoint in a handler

Describe the bug
Sometimes the runtime fails to continue after hitting a breakpoint in a handler
To Reproduce
Steps to reproduce the behavior:

Go to https://makecode.com/_W9dC8zAjAK2x
Go into debug mode
Place a breakpoint inside the on button pressed block
Press the button in the sim
Try to continue after the breakpoint is hit. Sometimes it's successful, sometimes it isn't

5. Try to continue after the breakpoint is hit. Sometimes it's successful, sometimes it isn't
We need to keep investigating to find out why this is happening.

This was fixed by https://github.com/Microsoft/pxt/pull/5420.


Wrong order for multipart/alternative children

We create multipart/alternative parts with a text/html part as first child and text/plain as second child. This isn't what other clients do. And it seems to confuse Thunderbird which then only displays the text/plain part.
Affected version: 5.111

Relevant RFC here is RFC1341 (key part bolded):

7.2.3 The Multipart/alternative subtype

The multipart/alternative type is syntactically identical to multipart/mixed, but the semantics are different. In particular, each of the parts is an "alternative" version of the same information. User agents should recognize that the content of the various parts are interchangeable. The user agent should either choose the "best" type based on the user's environment and preferences, or offer the user the available alternatives. In general, choosing the best type means displaying only the LAST part that can be displayed. This may be used, for example, to send mail in a fancy text format in such a way that it can easily be displayed anywhere: