Cannot get rdkit-rs to compile with RDKit on ARM64 Mac

I successfully built RDKit using the instructions in this repo's README:
git clone --depth 1 https://github.com/rdkit/rdkit
cd rdkit
mkdir build
cd build
cmake .. -DRDK_BUILD_INCHI_SUPPORT=ON
make

but I get an error when I try cargo test or cargo build in rdkit-rs. It seems like a problem is that RDKit was built for x86_64, and the rust binary (and libshim) for arm64.
Here is file information for the rdkit files:
my_username@computer lib % file libRDKitRDGeneral.1.dylib
libRDKitRDGeneral.1.dylib: Mach-O 64-bit dynamically linked shared library x86_64
my_username@computer lib % file libRDKitRDGeneral.2024.03.1pre.dylib
libRDKitRDGeneral.2024.03.1pre.dylib: Mach-O 64-bit dynamically linked shared library x86_64
my_username@computer lib % file libRDKitRDGeneral.dylib
libRDKitRDGeneral.dylib: Mach-O 64-bit dynamically linked shared library x86_64

And for the rust outputs:
my_username@computer deps % file rdkit_rs-322809f945b58704
rdkit_rs-322809f945b58704: Mach-O 64-bit executable arm64
my_username@computer deps % file rdkit_rs-322809f945b58704.1ippcslhdowi4g30.rcgu.o
rdkit_rs-322809f945b58704.1ippcslhdowi4g30.rcgu.o: Mach-O 64-bit object arm64

I tried to force rust to target x86_64 by putting in my Cargo.toml:
[package]
target = "x86_64-apple-darwin"

but still get the same error  ld: symbol(s) not found for architecture x86_64
my_username@computer rdkit-rs % DYLD_LIBRARY_PATH=/Users/my_username/Projects/rdkit-build4/build/lib LDFLAGS='-undefined dynamic_lookup' CXX='clang++ -v' RDROOT=/Users/my_username/Projects/rdkit-build4 cargo test --locked --all-features --target x86_64-apple-darwin

   Compiling rdkit-rs v0.1.0 (/Users/my_username/Projects/rdkit-rs)

error: linking with `cc` failed: exit status: 1

  = note: ld: warning: ignoring file '/Users/my_username/Projects/rdkit-rs/target/x86_64-apple-darwin/debug/build/rdkit-sys-7ee35bed4ca4fed8/out/libshim.so': found architecture 'arm64', required architecture 'x86_64'
          Undefined symbols for architecture x86_64:
            "_RDKit_MolToInchiKey", referenced from:
                rdkit_rs::ROMol::to_inchi_key::h5172cd82370ef807 in rdkit_rs-e2a4e46d956ccc68.28o1si5g1c9cz2gk.rcgu.o
            "_RDKit_MolToSmiles", referenced from:
                rdkit_rs::ROMol::to_smiles::h7713d3c3f54d59e4 in rdkit_rs-e2a4e46d956ccc68.28o1si5g1c9cz2gk.rcgu.o
            "_RDKit_ROMol_copy", referenced from:
                _$LT$rdkit_rs..ROMol$u20$as$u20$core..clone..Clone$GT$::clone::h28647307f8ff299d in rdkit_rs-e2a4e46d956ccc68.28o1si5g1c9cz2gk.rcgu.o
            "_RDKit_ROMol_delete", referenced from:
                _$LT$rdkit_rs..ROMol$u20$as$u20$core..ops..drop..Drop$GT$::drop::hc264690e13ba42c0 in rdkit_rs-e2a4e46d956ccc68.3k3fy8uhmxfe4loy.rcgu.o
            "_RDKit_ROMol_getNumAtoms", referenced from:
                rdkit_rs::ROMol::num_atoms::h304c369f182c51ae in rdkit_rs-e2a4e46d956ccc68.28o1si5g1c9cz2gk.rcgu.o
            "_RDKit_RunReactants", referenced from:
                rdkit_rs::fragment::ChemicalReaction::run_reactants::h9847ee103a6b48e0 in rdkit_rs-e2a4e46d956ccc68.18ph80dy2z5e5khk.rcgu.o
            "_RDKit_RxnSmartsToChemicalReaction", referenced from:
                rdkit_rs::fragment::ChemicalReaction::from_smarts::ha643d2ce11b283d7 in rdkit_rs-e2a4e46d956ccc68.18ph80dy2z5e5khk.rcgu.o
            "_RDKit_SanitizeMol", referenced from:
                rdkit_rs::ROMol::sanitize::h20a2c2852434aae5 in rdkit_rs-e2a4e46d956ccc68.28o1si5g1c9cz2gk.rcgu.o
            "_RDKit_SmilesToMol", referenced from:
                rdkit_rs::ROMol::from_smiles_full::h70e14b47ed6df605 in rdkit_rs-e2a4e46d956ccc68.28o1si5g1c9cz2gk.rcgu.o
          ld: symbol(s) not found for architecture x86_64
          clang: error: linker command failed with exit code 1 (use -v to see invocation)
error: could not compile `rdkit-rs` (lib test) due to 1 previous error

Ah this is actually a helpful error message! Those symbols look like they're actually from my C wrapper, not RDKit itself. Can you try find . -name libshim.so -exec file {} \; in your rdkit-rs directory? I'm guessing that my make recipe/clang is compiling the wrapper shared library from rdkit-sys for the wrong architecture. Hopefully this is a good sign!

my_username@computer rdkit-rs % find . -name libshim.so -exec file {} \;
./target/x86_64-apple-darwin/debug/build/rdkit-sys-7ee35bed4ca4fed8/out/libshim.so: Mach-O 64-bit dynamically linked shared library arm64
./target/debug/build/rdkit-sys-d14b2b3ea9597d35/out/libshim.so: Mach-O 64-bit dynamically linked shared library arm64

Those are compiled for the arm64 architecture.

There are three separate files/sets of files involved here:

RDKit shared libraries
libshim.so
Final Rust binary

From these steps, it looks like your RDKit is compiled for x86_64, but the other two are compiled for ARM? This may not be the final problem, but it at least makes sense to me for them not to get along if they are compiled for different architectures.
Since the other two are ARM, it seems potentially easiest to see if RDKit can be compiled for ARM. On the other hand, I assume that some additional CXX flag should tell clang to compile for a specific architecture, which should "fix" libshim. I don't know the specific flags to make either Rust or clang compile for a particular architecture, but I think this is a good approach to pursue at least.

it seems potentially easiest to see if RDKit can be compiled for ARM

Pursuing that option, I tried make CC=clang CXX=clang++ to get target compilation to ARM64. It gave errors, here's a partial log:
(base) my_username@MacBook-Air Projects % git clone --depth 1 https://github.com/rdkit/rdkit rdkit-build7
Cloning into 'rdkit-build7'...
remote: Enumerating objects: 5576, done.
remote: Counting objects: 100% (5576/5576), done.
remote: Compressing objects: 100% (3995/3995), done.
remote: Total 5576 (delta 1638), reused 3435 (delta 1406), pack-reused 0
Receiving objects: 100% (5576/5576), 76.17 MiB | 8.49 MiB/s, done.
Resolving deltas: 100% (1638/1638), done.
(base) my_username@MacBook-Air Projects % cd rdkit-build7
(base) my_username@MacBook-Air rdkit-build7 % mkdir build
(base) my_username@MacBook-Air rdkit-build7 % cd build
(base) my_username@MacBook-Air build % cmake .. -DRDK_BUILD_INCHI_SUPPORT=ON
-- The C compiler identification is AppleClang <IP_ADDRESS>00309
-- The CXX compiler identification is AppleClang <IP_ADDRESS>00309
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /Library/Developer/CommandLineTools/usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /Library/Developer/CommandLineTools/usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
RDK_OPTIMIZE_POPCNT is not available on aarch64 or arm64
Disabling boost::stacktrace on non-linux platform
CMake Warning at CMakeLists.txt:152 (find_package):
  By not providing "FindCatch2.cmake" in CMAKE_MODULE_PATH this project has
  asked CMake to find a package configuration file provided by "Catch2", but
  CMake did not find one.

  Could not find a package configuration file provided by "Catch2" (requested
  version 3) with any of the following names:

    Catch2Config.cmake
    catch2-config.cmake

  Add the installation prefix of "Catch2" to CMAKE_PREFIX_PATH or set
  "Catch2_DIR" to a directory containing one of the above files.  If "Catch2"
  provides a separate development package or SDK, be sure it has been
  installed.

-- Performing Test HAVE_FLAG__ffile_prefix_map__Users_my_username_Projects_rdkit_build7_build__deps_catch2_src__
-- Performing Test HAVE_FLAG__ffile_prefix_map__Users_my_username_Projects_rdkit_build7_build__deps_catch2_src__ - Success
-- Could NOT find InChI in system locations (missing: INCHI_LIBRARY INCHI_INCLUDE_DIR)
Downloading https://rdkit.org/downloads/INCHI-1-SRC.zip...
-- Found PythonInterp: /opt/miniconda3/bin/python (found version "3.12.1")
-- Found PythonLibs: /opt/miniconda3/lib/libpython3.12.dylib (found version "3.12.1")
PYTHON Py_ENABLE_SHARED: 0
PYTHON USING LINK LINE: -bundle -undefined dynamic_lookup -Wl,-rpath,/opt/miniconda3/lib -L/opt/miniconda3/lib -Wl,-rpath,/opt/miniconda3/lib -L/opt/miniconda3/lib
nbval not found, disabling the jupyter tests
-- Found Eigen3: /usr/local/include/eigen3 (Required is at least version "2.91.0")
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success
-- Found Threads: TRUE
-- Found Boost: /opt/miniconda3/lib/cmake/Boost-1.82.0/BoostConfig.cmake (found suitable version "1.82.0", minimum required is "1.58.0") found components: system serialization iostreams
-- Found Boost: /opt/miniconda3/lib/cmake/Boost-1.82.0/BoostConfig.cmake (found suitable version "1.82.0", minimum required is "1.58.0") found components: system iostreams
== Using strict rotor definition
-- maeparser include dir set as 'maeparser_INCLUDE_DIRS-NOTFOUND'
-- maeparser libraries set as 'maeparser_LIBRARIES-NOTFOUND'
-- Could NOT find maeparser (missing: maeparser_INCLUDE_DIRS maeparser_LIBRARIES)
Downloading https://github.com/schrodinger/maeparser/archive/v1.3.1.tar.gz...
-- coordgen include dir set as coordgen_INCLUDE_DIRS-NOTFOUND
-- coordgen libraries set as 'coordgen_LIBRARIES-NOTFOUND'
-- Could NOT find coordgen (missing: coordgen_INCLUDE_DIRS coordgen_LIBRARIES)
Downloading https://github.com/schrodinger/coordgenlibs/archive/v3.0.2.tar.gz...
Downloading https://github.com/rareylab/RingDecomposerLib/archive/v1.1.3_rdkit.tar.gz...
== Updating Filters.cpp from pains file
== Done updating pains files
Downloading https://github.com/google/fonts/raw/main/ofl/comicneue/ComicNeue-Regular.ttf...
Downloading https://github.com/google/fonts/raw/main/ofl/comicneue/OFL.txt...
-- Found Freetype: /usr/local/lib/libfreetype.dylib (found version "2.13.2")
-- Found Boost: /opt/miniconda3/lib/cmake/Boost-1.82.0/BoostConfig.cmake (found suitable version "1.82.0", minimum required is "1.58.0") found components: program_options
Downloading https://github.com/Tencent/rapidjson/archive/v1.1.0.tar.gz...
-- Configuring done (12.8s)
-- Generating done (1.0s)
-- Build files have been written to: /Users/my_username/Projects/rdkit-build7/build
(base) my_username@MacBook-Air build % make CC=clang CXX=clang++
...
 From what you pasted here, it looks like the cmake .. step completed successfully, but building with make failed. From the very end of the output, it looks like there could be an issue with your boost library or the standard library (!), but the first error is usually the most informative. If there is an issue with one of these libraries, it's probably due to them being installed for a different architecture from what you're compiling for. This might be a question for the RDKit maintainers. I found these two threads:
https://github.com/conda-forge/rdkit-feedstock/issues/63
https://github.com/conda-forge/rdkit-feedstock/pull/54
But I don't see anything in the main installation docs about targeting ARM.
Maybe the other option (building the Rust code and libshim for x86) is the better approach then. I'm just throwing out ideas because there's no real way for me to debug this locally.


@stimulus/polyfills: Polyfill Reflect.construct

When calling blessDefinition from the @stimulus/core/definition
package, the private extend function relies on Reflect.construct,
which is unsupported in Internet Explorer 11.
This commit imports Reflect.construct from the core-js alongside the
other polyfills.

Reflect.construct is only used in browsers that support it and there's a fallback implementation for those that don't: https://github.com/stimulusjs/stimulus/blob/7f58b5597292e88423c3fa9ccd0e6f25ffc83192/packages/%40stimulus/core/src/definition.ts#L45-L50
Are you seeing related errors in IE 11?

Are you seeing related errors in IE 11?

Yup! I discovered the need for a Reflect.construct polyfill in our application when troubleshooting in IE11.
I didn't notice the fallback conditional toward the bottom of this file.
From what I saw while troubleshooting, without the polyfill, the fallback doesn't seem to be effective.
What sort of information would be helpful for me to provide?

What sort of information would be helpful for me to provide?

Can you create a bare bones Stimulus app on glitch (or elsewhere) that fails in IE 11?

@javan I've created https://amethyst-piano.glitch.me/ .
To keep things simple, I've included Stimulus through a <script src="https://unpkg.com..."> tag, along with a babel-standalone tag.
I'm not sure how to add the polyfills with unpkg.com, since they don't include a dist version.
If you don't know of a simple way to consume the polyfills in the same style, I'll do my best to create a repro repo.

Here's one that includes @stimulus/polyfills: https://glitch.com/~atom-theory
I'm not seeing any errors in IE 11:

Thanks for creating that Glitch @javan!
I attempted my own (https://glitch.com/edit/#!/distinct-cyclone), but had some trouble integrating the polyfills.

I'm not seeing any errors in IE 11:

That's interesting. I'm not seeing any when visiting that Glitch either.
The application that this issue arose in includes some other polyfills to make use of Custom Elements, so the two sets of polyfills might've clobbered one another or not integrated properly.
I'm going to close this.
Thank you!


Set exit code to non-zero value on error, fix #42

@jere1862 please rebase with master to bring the version fixes.

@bobisjan please rebase with master to bring the fixes for the versions.

@rtfpessoa done.

Will be released as version 2.1.0


How do I decode low quality image

I have images in low quality like this. Could anyone help me to decode such images?

This image is shot in dark environment but the main content is still good i think.
I have tried to light it up and change the contrast but cannot decode it.

I was able to scan it once, you know what the code should be for the image you posted?
I am getting this:
CR114761X9E0T3XAC
Gimp has a tool for color curves. Screenshot below shows the curve I used to get the result (with app on my phone)

If you find a way to do that in OpenCV you should be able to scan the codes.

Thanks dude. Maybe color curves is a good solution to this problem. Thank you.


Uncomment pytensor.config.compute_test_value = "raise"

PyMC 5.9.2 has been released with a fix, so this no longer crashes test_marginal. Fixes #93.

Thanks! Do you know why the tests are failing?
Should we add a lower bound here too:
https://github.com/exoplanet-dev/celerite2/blob/7feb2e3366ab6a015cf8c62ec65db911faceeafe/setup.py#L43

I updated the lower bound!
I don't know why the tests are failing. They run fine locally, but there is some compilation error on the Github test environment. I ran them locally on Linux with venv, openblas, and I tried Python 3.10 and 3.11.
FAILED python/test/pymc/test_pymc_celerite2.py::test_consistency[10.5-RotationTerm-args6] - ImportError: /home/runner/.pytensor/compiledir_Linux-6.2--azure-x86_64-with-glibc2.35-x86_64-3.10.13-64/tmp5a7fpkjc/me5764f3d0dadd4197faacbf8742b57837127a6f6bbd36ab7bacfb70bd48fd2b0.so: undefined symbol: dgemm_

I'll try installing with mamba to see if the issue still happens (suggestion from @bmorris3)

Looks like using a conda/mamba env does the trick, but this also points to a bug introduced in the most recent PyMC/Pytensor release (classic!) since it worked previously with pip!
I don't like using mamba for this cause it's still far slower than the pip version, but we do what we need to these days :/

Thanks again for all your work on this, @vandalt!


[5.7.x] Thumbnails generated with wrong size

There is a little Thumbnail resizing Problem when working with responsive Images as described here in 5.7.13.
In v8.2.1 this seems to be fixed already.
When using a Thumbnail Type with a maximum width and no(auto) Height i would expect to get a Thumbnail that has the defined Width and a calculated height, so the aspect Ratio is kept the same.
As long as the Image is in a landscape format (width > height), this works fine.
Width portrait format(width < height) images however, wierd things happen:
The resulting Thumbnail has the height of what i've defined as maximum width and the width is smaller, according to the Images aspect ratio. - Quite the oppiste from what's intended.

There will be no more 5.7 feature releases. While we may do major bug or security updates to 5.7 the best idea would be to upgrade to the latest stable version of concrete5.


[Feature] Support configure rocksdb meta column family options.

What type of PR is this：

[ ] BugFix
[x] Feature
[ ] Enhancement
[ ] Refactor
[ ] UT
[ ] Doc
[ ] Tool

Which issues of this PR fixes ：

Fixes #14395
Problem Summary(Required) ：

Checklist:

[ ] I have added test cases for my bug fix or my new feature
[ ] This pr will affect users' behaviors
[ ] This pr needs user documentation (for new or modified features or behaviors)

[ ] I have added documentation for my new feature or new function

Bugfix cherry-pick branch check:

[x] I have checked the version labels which the pr will be auto backported to target branch

[x] 2.5
[x] 2.4
[x] 2.3
[x] 2.2

run starrocks_be_unittest

run starrocks_admit_test

run starrocks_be_unittest

run starrocks_admit_test

run starrocks_admit_test

run starrocks_admit_test

run starrocks_admit_test

@Mergifyio backport branch-2.5

@Mergifyio backport branch-2.4

@Mergifyio backport branch-2.3

@Mergifyio backport branch-2.2


Improve suggestions for location terms

Use better suggestions for location-based terms (fixes #11, see issue for details).

top -> beginning / start / first
bottom -> end / last
above -> previous
below -> following

Merging as these substitutions seem decent (see https://github.com/frankharkins/qiskit-ibm-runtime/pull/3 for examples).


Seek back to beginning before reading file

In the LoadExternalFile function the stream needs to seek back to the beginning before the file is read.

BEFORE this gets merged, we need to decide if it is OK to take a change to TinyGltf.

Any update on this?


feat(sqllab): Replace FilterableTable by AgGrid Table

SUMMARY
Following up #27645, This commit includes the migration of the component used for SQLLab results from the ant-table component to the ag-grid component.
During this process, the existing logic(getWidthsForColumns) that measured column size to adjust the width was removed because it was not only performance-intensive but also unnecessary, as the resizable column option in ag-grid allows users to adjust the width as needed.
Additionally, other property options were modified to ensure compatibility with ag-grid. Moreover, a column menu feature was added, enabling users to pin specific columns and apply filters.
BEFORE/AFTER SCREENSHOTS OR ANIMATED GIF
Before:

After:

Header menu (Actions):

TESTING INSTRUCTIONS
Go to SQL Lab and run a query to explore the data
ADDITIONAL INFORMATION

[ ] Has associated issue:
[ ] Required feature flags:
[x] Changes UI
[ ] Includes DB Migration (follow approval process in SIP-59)

[ ] Migration is atomic, supports rollback & is backwards-compatible
[ ] Confirm DB migration upgrade and downgrade tested
[ ] Runtime estimates and downtime expectations provided

[x] Introduces new feature or API
[ ] Removes existing feature or API

@justinpark this looks great! I think I might have asked this question before, so apologies if I did, but for how long custom table settings are kept - just for session and just for this specific query?

/testenv up

how long custom table settings are kept - just for session and just for this specific query?

This will only apply to the current query in the current session. I considered saving it, but I thought it might be better not to, as revisiting the query later when the memory has faded could cause confusion with different items being displayed in the query results.

when is the release target date  and release version ?

when is the release target date and release version ?

@Hokwang this will most likely be released in 5.0 around April 2025.

/testenv up

@eschutho Thanks for your comment, but I can't find 5.0 project. Please add this item.

@eschutho Thanks for your comment, but I can't find at 5.0 project. Please add this item.

@Hokwang The 5.0 project board contain only breaking changes that need consensus which is not the case for this PR. That does not mean that only what's in the board will be released. On February 3rd, we'll cut from master branch and all PRs merged by then will be included in the release. Check our Release Process for more details.

@michael-s-molina Oh, I see. Thanks for more detail information.


upgraded to iText 2.1.7 and flying saucer 9.0.3

nvm.  Config directory structure change for Grails v3/4+


Install Kibana + security failing

Chart version:
7.1.1
Kubernetes version:
1.13.0
Kubernetes provider: E.g. GKE (Google Kubernetes Engine)
Kubespray
Helm Version:
2.13
helm get release output:
	$ helm get helm-kibana-security
	REVISION: 1
	RELEASED: Fri Jun 28 21:02:23 2019
	CHART: kibana-7.1.1
	USER-SUPPLIED VALUES:
	elasticsearchHosts: https://security-master:9200
	extraEnvs:
	- name: ELASTICSEARCH_USERNAME
	  valueFrom:
	    secretKeyRef:
	      key: username
	      name: elastic-credentials
	- name: ELASTICSEARCH_PASSWORD
	  valueFrom:
	    secretKeyRef:
	      key: password
	      name: elastic-credentials
	kibanaConfig:
	  kibana.yml: |
	    server.ssl:
	      enabled: true
	      key: /usr/share/kibana/config/certs/kibana/kibana.key
	      certificate: /usr/share/kibana/config/certs/kibana/kibana.crt
	    xpack.security.encryptionKey: something_at_least_32_characters
	    elasticsearch.ssl:
	      certificateAuthorities: /usr/share/kibana/config/certs/elastic-certificate.pem
	      verificationMode: certificate
	protocol: https
	secretMounts:
	- name: elastic-certificate-pem
	  path: /usr/share/kibana/config/certs
	  secretName: elastic-certificate-pem
	- name: kibana-certificates
	  path: /usr/share/kibana/config/certs/kibana
	  secretName: kibana-certificates

	COMPUTED VALUES:
	affinity: {}
	antiAffinity: hard
	antiAffinityTopologyKey: kubernetes.io/hostname
	elasticsearchHosts: https://security-master:9200
	elasticsearchURL: ""
	extraEnvs:
	- name: ELASTICSEARCH_USERNAME
	  valueFrom:
	    secretKeyRef:
	      key: username
	      name: elastic-credentials
	- name: ELASTICSEARCH_PASSWORD
	  valueFrom:
	    secretKeyRef:
	      key: password
	      name: elastic-credentials
	fullnameOverride: ""
	healthCheckPath: /app/kibana
	httpPort: 5601
	image: docker.elastic.co/kibana/kibana
	imagePullPolicy: IfNotPresent
	imagePullSecrets: []
	imageTag: 7.1.1
	ingress:
	  annotations: {}
	  enabled: false
	  hosts:
	  - chart-example.local
	  path: /
	  tls: []
	kibanaConfig:
	  kibana.yml: |
	    server.ssl:
	      enabled: true
	      key: /usr/share/kibana/config/certs/kibana/kibana.key
	      certificate: /usr/share/kibana/config/certs/kibana/kibana.crt
	    xpack.security.encryptionKey: something_at_least_32_characters
	    elasticsearch.ssl:
	      certificateAuthorities: /usr/share/kibana/config/certs/elastic-certificate.pem
	      verificationMode: certificate
	maxUnavailable: 1
	nameOverride: ""
	nodeSelector: {}
	podSecurityContext:
	  fsGroup: 1000
	priorityClassName: ""
	protocol: https
	readinessProbe:
	  failureThreshold: 3
	  initialDelaySeconds: 10
	  periodSeconds: 10
	  successThreshold: 3
	  timeoutSeconds: 5
	replicas: 1
	resources:
	  limits:
	    cpu: 1000m
	    memory: 1Gi
	  requests:
	    cpu: 300m
	    memory: 500m
	secretMounts:
	- name: elastic-certificate-pem
	  path: /usr/share/kibana/config/certs
	  secretName: elastic-certificate-pem
	- name: kibana-certificates
	  path: /usr/share/kibana/config/certs/kibana
	  secretName: kibana-certificates
	securityContext:
	  capabilities:
	    drop:
	    - ALL
	  runAsNonRoot: true
	  runAsUser: 1000
	serverHost: <IP_ADDRESS>
	service:
	  annotations: {}
	  nodePort: 30999
	  port: 5601
	  type: NodePort
	serviceAccount: ""
	tolerations: []
	updateStrategy:
	  type: Recreate

	HOOKS:
	MANIFEST:

	---
	# Source: kibana/templates/configmap.yaml
	apiVersion: v1
	kind: ConfigMap
	metadata:
	  name: helm-kibana-security-kibana-config
	  labels:
	    app: kibana
	    release: "helm-kibana-security"
	data:
	  kibana.yml: |
	    server.ssl:
	      enabled: true
	      key: /usr/share/kibana/config/certs/kibana/kibana.key
	      certificate: /usr/share/kibana/config/certs/kibana/kibana.crt
	    xpack.security.encryptionKey: something_at_least_32_characters
	    elasticsearch.ssl:
	      certificateAuthorities: /usr/share/kibana/config/certs/elastic-certificate.pem
	      verificationMode: certificate
	---
	# Source: kibana/templates/service.yaml
	apiVersion: v1
	kind: Service
	metadata:
	  name: helm-kibana-security-kibana
	  labels:
	    app: kibana
	    release: "helm-kibana-security"
	    heritage: Tiller
	spec:
	  type: NodePort
	  ports:
	    - port: 5601
	      nodePort: 30999
	      protocol: TCP
	      name: http
	      targetPort: 5601
	  selector:
	    app: kibana
	    release: "helm-kibana-security"
	---
	# Source: kibana/templates/deployment.yaml
	apiVersion: apps/v1
	kind: Deployment
	metadata:
	  name: helm-kibana-security-kibana
	  labels:
	    app: kibana
	    release: "helm-kibana-security"
	spec:
	  replicas: 1
	  strategy:
	    type: Recreate
	  selector:
	    matchLabels:
	      app: kibana
	      release: "helm-kibana-security"
	  template:
	    metadata:
	      labels:
	        app: kibana
	        release: "helm-kibana-security"
	      annotations:
	        configchecksum: 267bd33171fad555b70bea0a84d9966ffe76ea9eddb4f89885f3e3fb5ca76e9
	    spec:
	      securityContext:
	        fsGroup: 1000
	      volumes:
	        - name: elastic-certificate-pem
	          secret:
	            secretName: elastic-certificate-pem
	        - name: kibana-certificates
	          secret:
	            secretName: kibana-certificates
	        - name: kibanaconfig
	          configMap:
	            name: helm-kibana-security-kibana-config
	      containers:
	      - name: kibana
	        securityContext:
	          capabilities:
	            drop:
	            - ALL
	          runAsNonRoot: true
	          runAsUser: 1000
	        image: "docker.elastic.co/kibana/kibana:7.1.1"
	        env:
	          - name: ELASTICSEARCH_HOSTS
	            value: "https://security-master:9200"
	          - name: SERVER_HOST
	            value: "<IP_ADDRESS>"
	          - name: ELASTICSEARCH_USERNAME
	            valueFrom:
	              secretKeyRef:
	                key: username
	                name: elastic-credentials
	          - name: ELASTICSEARCH_PASSWORD
	            valueFrom:
	              secretKeyRef:
	                key: password
	                name: elastic-credentials
	        readinessProbe:
	          failureThreshold: 3
	          initialDelaySeconds: 10
	          periodSeconds: 10
	          successThreshold: 3
	          timeoutSeconds: 5
	          exec:
	            command:
	              - sh
	              - -c
	              - |
	                #!/usr/bin/env bash -e
	                http () {
	                    local path="${1}"
	                    set -- -XGET -s --fail

	                    if [ -n "${ELASTIC_USERNAME}" ] && [ -n "${ELASTIC_PASSWORD}" ]; then
	                      set -- "$@" -u "${ELASTIC_USERNAME}:${ELASTIC_PASSWORD}"
	                    fi

	                    curl -k "$@" "https://localhost:5601${path}"
	                }
	                http "/app/kibana"
	        ports:
	        - containerPort: 5601
	        resources:
	          limits:
	            cpu: 1000m
	            memory: 1Gi
	          requests:
	            cpu: 300m
	            memory: 500m
	        volumeMounts:
	          - name: elastic-certificate-pem
	            mountPath: /usr/share/kibana/config/certs
	          - name: kibana-certificates
	            mountPath: /usr/share/kibana/config/certs/kibana
	          - name: kibanaconfig
	            mountPath: /usr/share/kibana/config/kibana.yml
	            subPath: kibana.yml

Describe the bug:
Deploy kibana from examples/security result in error
Error: release helm-kibana-security failed: timed out waiting for the condition
make: *** [install] Error 1
Steps to reproduce:

Deployed elasticsearch + security

Deploy kibana + security from examples/security

Run the command 'make'

Error:
 $ make
 kubectl delete secret kibana-certificates || true
 Error from server (NotFound): secrets "kibana-certificates" not found
 vault read -field=kibana.crt secret/devops-ci/helm-charts/kibana/security/certificates | base64 --decode > kibana.crt
 /bin/sh: vault: command not found
 vault read -field=kibana.key secret/devops-ci/helm-charts/kibana/security/certificates | base64 --decode > kibana.key
 /bin/sh: vault: command not found
 kubectl create secret generic kibana-certificates --from-file=kibana.crt --from-file=kibana.key && \
 rm -f kibana.crt kibana.key
 secret/kibana-certificates created
 helm upgrade --wait --timeout=600 --install --values ./security.yml helm-kibana-security ../../ ; \

 Release "helm-kibana-security" does not exist. Installing it now.
 Error: release helm-kibana-security failed: timed out waiting for the condition
 make: *** [install] Error 1

The helm-kibana-security pod stuck in 'ContainerCreating'

Expected behavior:
Provide logs and/or server output (if relevant):
Any additional context:

This makefile target is also used for the automated testing. The issue here is that it is trying to pull secrets from our secret service (which you don't have access too). I'm working on a PR now to fixup the docs. But in the meantime can you try just doing helm upgrade --wait --timeout=600 --install --values ./security.yml kibana ../../ ; \ instead of running make.

@Crazybus Run the helm upgrade as you suggested,
  $ helm upgrade --wait --timeout=600 --install --values ./security.yml kibana ../../ ;
  Release "kibana" does not exist. Installing it now.
  Error: release kibana failed: timed out waiting for the condition'

having the same issue :
$ helm upgrade --wait --timeout=600 --install --values ./security.yml kibana ../../ ;
  Release "kibana" does not exist. Installing it now.
  Error: release kibana failed: timed out waiting for the condition

https://github.com/elastic/helm-charts/pull/205 is an overhaul of the the security bootstrapping process and docs. If you checkout the alright_keep_your_secrets you can give it a go to see if this works better for you.

I am checking it right now

@mounaBoo @Crazybus Hi, What is the status of the testing? Is it ready to be install?

@Crazybus I was able to deployed (elasticsearch + security) and (kibana + security) from the branch %alright_keep_your_secrets%

The kibana deployment has a minor error during the pod testing first attempt:

That's totally fine and expected. The testing tool has retries built in since Kibana may not be fully ready yet when it starts running. Glad you got it working!

@Crazybus When will you merge the branch 'alright_keep_your_secrets' to master? and thanks for the fixed.

@Crazybus When will you merge the branch 'alright_keep_your_secrets' to master? and thanks for the fixed.

It's already in master, it was merged in a few hours before your previous comment.

  How does the elastic-certificate.pem file get into the /usr/share/kibana/config/certs/ directory on the pod?  with the elastic helm, executing this: kubectl create secret generic elastic-certificates --from-file=elastic-certificates.p12 places the cert where it needs to go in the pod.


Wandering Witch Hexes apply to the user as long as they're selected.

I don't currently have any screenshots of it (cause the playthrough I had with a Witch ended, DLC3 with Last Azlanti mode), but I noticed it because I had a random -4 on my attack rolls. Turns out, switching from Evil Eye to Fortune made it go away. Not sure on the exact causes, but it's very odd.

I cannot find how I would cause this bug. I don't understand how AbilityApplyFact works. I doubt I can bug fix this.


Sorting Images

Currently, I'm only able to sort images by their image names. I would like to be able to sort on other things, mostly just on the age of the image. It would be nice to be able to sort and get the oldest / newest images.
Thanks!

There is no way to sort images by creation date/age. Because the registry itself is badly designed and does not provide any efficient way to get this information w/o making extra calls. This is an expensive operation.


add slurm id logging

Codecov Report
Attention: Patch coverage is 25.00000% with 3 lines in your changes are missing coverage. Please review.

Project coverage is 30.93%. Comparing base (a15db84) to head (02f03d5).

Files
Patch %
Lines

crabs/detection_tracking/train_model.py
25.00%
3 Missing :warning:

Additional details and impacted files
@@            Coverage Diff             @@
##             main     #153      +/-   ##
==========================================
- Coverage   30.95%   30.93%   -0.02%
==========================================
  Files          19       19
  Lines        1263     1267       +4
==========================================
+ Hits          391      392       +1
- Misses        872      875       +3

:umbrella: View full report in Codecov by Sentry.
:loudspeaker: Have feedback on the report? Share it here.


[WIP] Removed code taken from core, using those features instead

Tracking issues:

maybe_uninit_slice https://github.com/rust-lang/rust/issues/63569
maybe_uninit_uninit_array (no tracking issue)
maybe_uninit_array_assume_init https://github.com/rust-lang/rust/issues/80908

Going to move this to #536


Add individual file upload on Windows and Linux

Fixes issue #341.

👍
tests would be helpful for this, did you test the behavior manually?  We can mock the fs calls using rewire, mocking SiaAPI is as simple as defining a global.SiaAPI in the test script.

I tested the behavior on Windows/Mac up until it sends the post call to the api. I might setup a test net to confirm the uploads are working as expected. I think we might be able to just get ride of the folder upload button all together, as long as people can select multiple files/drag and drop. I'll work on tests in the mean time.

You don't need to test the entire upload process, only that this component has the expected behaviour (it calls uploadFolder with the selected folder(s) (if it's a folder), uploadFile with the selected file(s), dispatches the expected actions, etc)

LGTM


Enable Continuous Delivery of the preview website from the "master" branch + Bulk cleanup

Just quality of life improvement. Full continuous deployment automation is coming later, but at least we will have a preview site where we could verify the status. I do not want to put too much effort, because ultimately I'd like Jekyll to be replaced by Docusaurus or, as @tomakehurst prefers, Hugo. FTR #24 for the migration.
Preview: https://wiremock.github.io/wiremock.org-sources/
Chore

[x] Add CD to GitHub Pages: https://wiremock.github.io/wiremock.org-sources/
[x] Dependency updates so that it builds on latest Ruby 2.x, Jekyll and Bundler
[x] Switch from base_path to modern abolute_url filter to fix non-root-URL deployments
[x] Fix main.css documentation generation which was (most likely) broken in the recent versions
[x] Fix Gemlock that breaks on Setup Ruby (currently a hackaround instead of proper setup_ruby GitHub Action use)

Content

[x] Fix OpenGraph and other metadata which was broken in the recent site versions - #26
[x] Fix many broken absolute and subsection links (but not all of them)


Make ext2 the default FS for recovery on disks

Confirmed in test logs that the disk was build with ext2
INFO[2024-03-07T10:40:47Z] Creating image /build/build/recovery/recovery.img from rootDir /build/build/recovery.img.root
DEBU[2024-03-07T10:40:47Z] Image size 891M
DEBU[2024-03-07T10:40:47Z] Running cmd: 'mkfs.ext2 -L COS_SYSTEM -d /build/build/recovery.img.root /build/build/recovery/recovery.img'

Nice! Looks like you need to update the tests as well, approving anyways 👍

Yes, gonna force merge. Then make v2 available and then update tests to actually use v1.1.4 for upgrade tests and v2.0.0 for downgrade and recovery tests. So they will be green again and testing actual tags.

Nice! Looks like you need to update the tests as well, approving anyways 👍

Yes, gonna force merge. Then make v2 available and then update tests to actually use v1.1.4 for upgrade tests and v2.0.0 for downgrade and recovery tests. So they will be green again and testing actual tags.

Ah, I was thinking of the cli unit-tests which expect "mksquashfs" to be called.


Error 403 Forbidden

my IFTTT recipes were turned off automatically because of unknown problem. followed link to discover 403 from pinterest or heroku app? see for yourself: https://pinfeed.herokuapp.com/attilaolah Does visting this link come up with a 403 for you? Is it just me? Everything was working perfectly fine  (sucessful posting dailyfrom Pinterest to Twitter, Tumblr, Facebook, and Blogger) until October 15th. That's when my IFTTT recipes sent me a notice telling me that my recipes have been automatically deactivated.
Is this because pinterest is having issues for the past few days, or maybe heroku is being blocked?

I have the same issue. Either it is a problem with the cache server or something you describe, but yet i am not that skilled to find out what it is and how to solve it. Maybe the creator will know what's wrong. @attilaolah ?

+1, having the same issue (Varnish Cache Server 403)

+1 I'm having the same issue. My Heroku deployment has the same 403 error and as a result my IFTTT feed has been deactiveated. Can anyone find the actual code in the github repository to see if it is a tweak made by Pinterest in their feed format maybe?

Any update on this, or is this abandoned?

Obviously abandoned. :)

I went through all forks and it seems no one even tried to fix it.

doesn't work... is that really all we need to do, press the deploy and use update the URLs?? getting 403 forbidden as well

I was one of the users of this repo. Not sure why it no longer works, but I managed to build my own app. Not very elegant, but it works for now. Feel free to use/improve it.
Here is mine:
https://github.com/pinLarge/pinLarge


requesting package libjpeg

@Liumkattan There is no Debian package called libjpeg, and libjpeg62-turbo is already installed.
Do you need the development headers for it, rather?  (libjpeg62-turbo-dev)

i meant libjpeg-dev but it is solved now python cherrypy pack required that lib but i found a way around so if there is no one else need the lib it's not required

OK, I'm glad to hear that.


Updated New/Set-HostedOutboundSpamFilterPolicy

Added AutoForwardingMode param per Issue #6365

Docs Build status updates of commit 1f95105:
:clock10: Full build: the average full build time is 17 min(s) 37 sec(s), this is based on the last 1000 build(s) for this repository.

Docs Build status updates of commit 1f95105:
:white_check_mark: Validation status: passed

File
Status
Preview URL
Details

exchange/exchange-ps/exchange/New-HostedOutboundSpamFilterPolicy.md
:white_check_mark:Succeeded
View (exchange-ps)

exchange/exchange-ps/exchange/Set-HostedOutboundSpamFilterPolicy.md
:white_check_mark:Succeeded
View (exchange-ps)

For more details, please refer to the build report.
Note: Broken links written as relative paths are included in the above build report. For broken links written as absolute paths or external URLs, see the broken link report.
For any questions, please:Try searching in the Docs contributor and Admin GuideSee the frequently asked questionsPost your question in the Docs support channel


WFLY-14497 HttpSessionActivationListener.sessionWillPassivate method is not triggered on shutdown for local, passivating caches.

https://issues.redhat.com/browse/WFLY-14497
Requires https://github.com/wildfly/wildfly/pull/14106 Merged.

@rhusar Please review.


Last commit time is not returned correctly

local.branch.current.lastCommitTime key value misses timeparts after hour
Expected: 2015-12-01 13:33:33 +0200
Actual: 2015-12-01 13
The same problem exists for remote.origin.url
Expected<EMAIL_ADDRESS>Actual: http
most probably because ":" symbol is used to join the result lines

Actually this problem seems to exist in version 0.0.5 which appears to be the last one available from official npm registry.


Documentation confusion

https://github.com/docusign/docusign-csharp-client/blob/37e3edf4af9099695f8129fb126b46ee5977698d/sdk/src/DocuSign.eSign/Client/ApiClient.cs#L1135
The name and the description are using different units. Just a bit confusing.

Thank you for the report. The parameter is being interpreted as hours.
By the way, the correct value for this parameter is always 1 (1 hour). Note that this parameter is setting how long the JWT will be valid, not the validity time for the access token that is returned.
-- The returned access tokens are generally valid for 8 hours. (See the expires attribute in the returned object.
I will file a documentation bug.

This is resolved with https://www.nuget.org/packages/DocuSign.eSign.dll/4.0.3-rc


Use GlobalID for all Jobs

Rails provides GlobalID serialization for all activerecord objects, so there's no need to pass just the id and then find the record inside the job.

Pull Request Test Coverage Report for Build<PHONE_NUMBER>

6 of 6 (100.0%)  changed or added relevant lines in 6 files are covered.
No unchanged relevant lines lost coverage.
Overall coverage decreased (-0.01%) to 96.91%

Totals

Change from base Build<PHONE_NUMBER>:
-0.01%

Covered Lines:
690

Relevant Lines:
712

💛  - Coveralls

Thanks!


Adding a dropdown menu options to the 'Help' button

Adding a dropdown menu options to the 'Help' button so that there can be multiple help documents under the main Help option.

@ThiashaV you moved this to In Progress 11 days ago. It should be up to @Fanevanjanahary to put it there when she's actually working on it otherwise it appears she's been workign on it for nearly two weeks.
Hopefully @Fanevanjanahary #368 you made today fixes this? It's high priority, please get it deployed asap.

Drop down is implemented and in a user friendly order:


Remove moment dependency

Moment.js was used to build new Date objects even though we could use native Date object directly. Saves around 51 kB in the final JS bundle when building the React Native app.
Closes #125

Great! Thank you anqqa! Merged.

Landed in v5.0.0


Update for MS.Azure.Management.Automation

Converting Automation to .netCore.
Tests are still .net45 (still have issues with Hydra Framework and Common Dependecy as well as ServiceManagement Clients)
All .net 45 test works and are passing.
Automation nugget is VS2017 compliant.
Moving existing legacy code base under Legacy directory.
Reusing test project

Will reopen once Hyak binaries are published.


styling aanpassen popup naar huisstijl

'The :popover-open CSS pseudo-class represents a popover element (i.e. one with a popover attribute) that is in the showing state. You can use this to apply style to popover elements only when they are shown.' --https://developer.mozilla.org/en-US/docs/Web/CSS/:popover-open
Kan je hiermee de css veranderen?

Originally posted by @Shannafdnd in #15

@annelinderaadsheer


synology-drive-client:  error while loading shared libraries: libxcb.so.1

Describe the bug
Synology dirve client is not longer working. Not sure since which version it broken to be honest.
Steps To Reproduce
Steps to reproduce the behavior:

Add  pkgs.synology-drive-client to home.packages
Run synology-drive in terminal
Will produce following errors:

❯ synology-drive
qt.qpa.plugin: Could not find the Qt platform plugin "wayland" in ""
debug.message: Cannot find path by key "user_cloud_station_app_path"
debug.message: Cannot find path by key "user_cloud_station_data_path"
debug.message: Cannot find path by key "user_cloud_station_working_dir_path"
debug.message: Cannot find path by key "user_cloud_station_drive_ui_path"
~/nix-config on main !3 ?2 ❯ /home/deividas/.SynologyDrive/SynologyDrive.app/bin/cloud-drive-ui: error while loading shared libraries: libxcb.so.1: cannot open shared object file: No such file or directory             ≡ at 16:58:32

Expected behavior
Should launch synology client UI.
Notify maintainers
@jcouyang, @MoritzBoehme

Metadata
Please run nix-shell -p nix-info --run "nix-info -m" and paste the result.
❯ nix-shell -p nix-info --run "nix-info -m"
 - system: `"x86_64-linux"`
 - host os: `Linux 6.9.4, NixOS, 24.11 (Vicuna), 24.11.20240701.00d80d1`
 - multi-user?: `yes`
 - sandbox: `yes`
 - version: `nix-env (Nix) 2.18.4`
 - channels(root): `"nixos, nixos-hardware"`
 - nixpkgs: `/nix/store/j4jzjbr302cw5bl0n3pch5j9bh5qwmaj-source`

Add a :+1: reaction to issues you find important.

Removing .SynologyDrive in home directory fixed issue and allowed to start application. Note that previous app settings were lost by doing so.


Add StyleCop for a more consistent code base.

The current way of coding is a bit inconsistent on the formatting part. An analyzer like StyleCop could help us with that. I added a simple Ruleset file containing a few rules that will guide contributers in writing code in a similar manner.
Actual implementation has not changed. Not sure if we should merge this. Maybe the first thing to do is defining a good ruleset for this repository, if we want to do this at all.

Looks good.
Can you push this to a branch in this repository? That way, I can rebase/merge for you.
Or, can you rebase onto develop?

Sure, I created the following branch in this repository: https://github.com/qmlnet/qmlnet/tree/feature/add-stylecop


Make definitions of forms more obvious

Move definitions of various forms into a bullet list
(so they are more obvious), and tweak some surrounding text.
Signed-off-by: David A. Wheeler<EMAIL_ADDRESS>

I believe this addresses issue #128

Looks good to me.


modelcard.md now lives in hub-docs

new permanent link is https://github.com/huggingface/hub-docs/blob/main/modelcard.md?plain=1

The docs for this PR live here. All of your documentation changes will be reflected on that endpoint.


Hygieia-Jenkins plugin question

Hi all,
I had a question about the Hygieia-Jenkins plugin. During setup on the Jenkins machine you provide it with a Hygieia API url so the plugin knows where to push the data. I have multiple teams on a single jenkins machine and they each want to  stand up their own instance of the Hygieia Dashboard. Is there a way to provide multiple Hygieia API urls on one jenkins machine?
thanks!

@kavalpatel15 : what do you mean by own instance of Hygieia Dashboard. Do you mean own dashboard or own instance of Hygieia stack (api, DB, and UI).

They would like their own instance of the ygieia stack.

It will not be possible to send data to multiple Hygieia instances from same jenkins server.
Hygieia-Jenkins plugin is configured at Jenkins server level and it can send data only to one Hygieia instance.


FAILED: (99) Cannot assign requested address: unicast bind  : Cannot assign requested address

Ping -C "aeron:udp?endpoint=<IP_ADDRESS>:40124" -c "aeron:udp?endpoint=<IP_ADDRESS>:40123"
the err happened , while do it;  please help!

Please provide more details and a repeatable example.

while  communicating  in the tow host, one is pub,  another is sub, this err happened.
i  find sub channel bind socket, while  reading the code,  and why bind remote address?

FAILED: (99) Cannot assign requested address: unicast bind [<IP_ADDRESS>:40124] : Cannot assign requested address : std::shared_ptraeron::Subscription aeron::ClientConductor::findSubscription(int64_t) : /home/tangminghong/msg-bus/aeron-src/aeron/aeron-client/src/main/cpp/ClientConductor.cpp : 273

please help me;  why Subscription  need to bind  remote address ?  the only locale address band socket

Try setting the BasicPublisher and BasicSubscriber channels to communicate in each direction, then try transposing those addresses into Ping and Pong channels.


Add support for material preset in furniture definition

furniture items with alternative Materials can have preset materials in their sceneStructure definition.
support for this allows for more furniture variety within a-frame

if I'm not mistaken, it works when setting the attribute accordingly in
HTML
Am 10.09.2017 5:57 nachm. schrieb "Frederic Schwarz" <
<EMAIL_ADDRESS>
Closed #47 https://github.com/archilogic-com/3dio-js/issues/47 via
ef0daec
https://github.com/archilogic-com/3dio-js/commit/ef0daec10f8e564de268ac505940eb55d805bb9a
.
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Deprecate the default signed cookie algorithm

Deprecate the default value for the signed_cookie.hash_algo configuration value (currently "sha256") in preparation for a change in 4.0.
Relates to #324.

Thanks


build(deps): monthly upgrade

:tada: This PR is included in version 1.7.1 :tada:
The release is available on GitHub release
Your semantic-release bot :package::rocket:


added the final project proposal pdf

This is the actually submitted project proposal.

@RustyRaptor I just merged in the .tex code an this PDF.

Is this commit incorrect?https://github.com/JiveyGuy/Meteorite_Data_Mine/pull/18/commits/a662bbca34acd7c3133b220cbb833c3154e20da2

Closing as I checked and I pushed the latest one already.