Problem of T1078 example

I follow the tutorial of  README file like this.
$./run_pipeline.sh example/T1078.fa example/T1078
Running HHblits
Running PSIPRED
Running hhsearch
cat: /home/test/Downloads/trRosetta2/example/T1078/t000_.msa0.a3m: No such file or directory
Generating TAPE features
Running sequence-based trRosetta
Folding trRosetta models
Running trRefine
Running DeepAccNet-msa on trRefine models
touch: cannot touch '/home/test/Downloads/trRosetta2/example/T1078/pdb-trRefine/DONE_DAN': No such file or directory
Picking final models
Final models saved in: example/T1078/model
Done

Terminal shows Done but there is no result in example folder.
trRosetta2/example/T1078 on via 🅒 casp14-baker took 5s
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.
├── DONE_iter0
├── DONE_iter1
├── hhblits
├── log
│   ├── dan-msa.stderr
│   ├── dan-msa.stdout
│   ├── folding.stderr
│   ├── folding.stdout
│   ├── hhsearch.stderr
│   ├── hhsearch.stdout
│   ├── make_msa.stderr
│   ├── make_msa.stdout
│   ├── make_ss.stderr
│   ├── make_ss.stdout
│   ├── msa-net.stderr
│   ├── msa-net.stdout
│   ├── pick.stderr
│   ├── pick.stdout
│   ├── tbm-net.stderr
│   ├── tbm-net.stdout
│   ├── trRefine.stderr
│   └── trRefine.stdout
├── parallel.list
├── pdb-msa
├── pdb-tbm
├── t000_.msa0.ss2.a3m
├── t000_.ss2
└── t000_.tape.npy

4 directories, 24 files

I open the trRefine.stderr and find out  sklearn package not installed.
Traceback (most recent call last):
  File "/home/test/Downloads/trRosetta2/trRefine/run_trRefine_DAN.py", line 7, in <module>
    from sklearn.cluster import AgglomerativeClustering
ModuleNotFoundError: No module named 'sklearn'

Therefore, I install scikit-learn.
conda install scikit-learn -y

But still got a error
Traceback (most recent call last):
  File "/home/test/Downloads/trRosetta2/trRefine/run_trRefine_DAN.py", line 220, in <module>
    main()
  File "/home/test/Downloads/trRosetta2/trRefine/run_trRefine_DAN.py", line 195, in main
    rep_s = pick_rep(args.msa_npz, args.tbm_npz, args.pdb_dir_s, args.n_core, rescore=args.rescore)
  File "/home/test/Downloads/trRosetta2/trRefine/run_trRefine_DAN.py", line 91, in pick_rep
    sys.stdout.write("INFO: Pick 10 lowest E conformations from %s, Emin=%.3f / Emax=%.3f\n"%(pdb_dir, score_s[-1][0], score_s[-1][-1]))
IndexError: index 0 is out of bounds for axis 0 with size 0

Please help me out.

in hhsearch.stderr
- 13:08:50.103 ERROR: In /home/test/Downloads/trRosetta2/hh-suite/src/hhalignment.cpp:223: Read:

- 13:08:50.103 ERROR: 	sequence ss_pred contains no residues.

in hhsearch.stderr
- 13:08:50.103 ERROR: In /home/test/Downloads/trRosetta2/hh-suite/src/hhalignment.cpp:223: Read:

- 13:08:50.103 ERROR: 	sequence ss_pred contains no residues.

I got the same error.

Could you also check the log/make_msa.stderr file? Based on the info you provided it looks like the first step of building an MSA was not successful.

Could you also check the log/make_msa.stderr file? Based on the info you provided it looks like the first step of building an MSA was not successful.

This is make_msa.stderr file

- 16:08:45.211 INFO: Output file = /home/test/Downloads/trRosetta2/example/T1078/hhblits/t000_.1e-30.id90cov75.a3m

- 16:08:45.215 INFO: Input file = /home/test/Downloads/trRosetta2/example/T1078/hhblits/t000_.1e-30.a3m

- 16:08:45.215 INFO: Output file = /home/test/Downloads/trRosetta2/example/T1078/hhblits/t000_.1e-30.id90cov50.a3m

- 16:09:47.137 INFO: Input file = /home/test/Downloads/trRosetta2/example/T1078/hhblits/t000_.1e-10.a3m

- 16:09:47.137 INFO: Output file = /home/test/Downloads/trRosetta2/example/T1078/hhblits/t000_.1e-10.id90cov75.a3m

- 16:09:47.144 INFO: Input file = /home/test/Downloads/trRosetta2/example/T1078/hhblits/t000_.1e-10.a3m

- 16:09:47.144 INFO: Output file = /home/test/Downloads/trRosetta2/example/T1078/hhblits/t000_.1e-10.id90cov50.a3m

- 16:10:48.960 INFO: Input file = /home/test/Downloads/trRosetta2/example/T1078/hhblits/t000_.1e-6.a3m

- 16:10:48.960 INFO: Output file = /home/test/Downloads/trRosetta2/example/T1078/hhblits/t000_.1e-6.id90cov75.a3m

- 16:10:48.969 INFO: Input file = /home/test/Downloads/trRosetta2/example/T1078/hhblits/t000_.1e-6.a3m

- 16:10:48.969 INFO: Output file = /home/test/Downloads/trRosetta2/example/T1078/hhblits/t000_.1e-6.id90cov50.a3m

- 16:11:35.944 INFO: Input file = /home/test/Downloads/trRosetta2/example/T1078/hhblits/t000_.1e-3.a3m

- 16:11:35.944 INFO: Output file = /home/test/Downloads/trRosetta2/example/T1078/hhblits/t000_.1e-3.id90cov75.a3m

- 16:11:35.953 INFO: Input file = /home/test/Downloads/trRosetta2/example/T1078/hhblits/t000_.1e-3.a3m

- 16:11:35.953 INFO: Output file = /home/test/Downloads/trRosetta2/example/T1078/hhblits/t000_.1e-3.id90cov50.a3m

but in the  make_ss.stderr

ERROR: Unable to read input file '/home/test/Downloads/trRosetta2/example/T1078/t000_.msa0.a3m'!
head: cannot open '/home/test/Downloads/trRosetta2/example/T1078/t000_.msa0.a3m' for reading: No such file or directory
[makemat] FATAL ERROR: Unable to open file t000_.msa0.tmp.chk

Bad psipred pass1 file format!
rm: cannot remove '/home/test/Downloads/trRosetta2/example/T1078/t000_.msa0.a3m.csb.hhblits.ss2': No such file or directory

It seems that the HHblits step did generate alignments but for some reason the final alignment was not copied over to t000_.msa0.a3m (i.e. line #54 cp $tmp_dir/t000_.1e-3.id90cov50.a3m ${out_prefix}.msa0.a3m in scripts/make_msa.sh).  I have made a few bugfixes to the code and changed the installation process a bit to hopefully make it more portable - you may check it out.

still stuck in a problems.
#trRefind.stderr
2021-06-16 19:39:49.705834: I tensorflow/core/platform/cpu_feature_guard.cc:142] Your CPU supports instructions that this TensorFlow binary was not compiled to use: SSE4.1 SSE4.2 AVX AVX2 FMA
2021-06-16 19:39:49.728703: I tensorflow/core/platform/profile_utils/cpu_utils.cc:94] CPU Frequency:<PHONE_NUMBER> Hz
2021-06-16 19:39:49.729664: I tensorflow/compiler/xla/service/service.cc:168] XLA service 0x56085832c490 executing computations on platform Host. Devices:
2021-06-16 19:39:49.729689: I tensorflow/compiler/xla/service/service.cc:175]   StreamExecutor device (0): <undefined>, <undefined>
2021-06-16 19:39:49.730407: I tensorflow/stream_executor/platform/default/dso_loader.cc:42] Successfully opened dynamic library libcuda.so.1
2021-06-16 19:39:49.746456: I tensorflow/stream_executor/cuda/cuda_gpu_executor.cc:1005] successful NUMA node read from SysFS had negative value (-1), but there must be at least one NUMA node, so returning NUMA node zero
2021-06-16 19:39:49.746701: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1640] Found device 0 with properties:
name: GeForce GTX 1660 SUPER major: 7 minor: 5 memoryClockRate(GHz): 1.785
pciBusID: 0000:2b:00.0
2021-06-16 19:39:49.746805: I tensorflow/stream_executor/platform/default/dso_loader.cc:42] Successfully opened dynamic library libcudart.so.10.1
2021-06-16 19:39:49.747719: I tensorflow/stream_executor/platform/default/dso_loader.cc:42] Successfully opened dynamic library libcublas.so.10
2021-06-16 19:39:49.748673: I tensorflow/stream_executor/platform/default/dso_loader.cc:42] Successfully opened dynamic library libcufft.so.10
2021-06-16 19:39:49.748810: I tensorflow/stream_executor/platform/default/dso_loader.cc:42] Successfully opened dynamic library libcurand.so.10
2021-06-16 19:39:49.749692: I tensorflow/stream_executor/platform/default/dso_loader.cc:42] Successfully opened dynamic library libcusolver.so.10
2021-06-16 19:39:49.750111: I tensorflow/stream_executor/platform/default/dso_loader.cc:42] Successfully opened dynamic library libcusparse.so.10
2021-06-16 19:39:49.752039: I tensorflow/stream_executor/platform/default/dso_loader.cc:42] Successfully opened dynamic library libcudnn.so.7
2021-06-16 19:39:49.752103: I tensorflow/stream_executor/cuda/cuda_gpu_executor.cc:1005] successful NUMA node read from SysFS had negative value (-1), but there must be at least one NUMA node, so returning NUMA node zero
2021-06-16 19:39:49.752361: I tensorflow/stream_executor/cuda/cuda_gpu_executor.cc:1005] successful NUMA node read from SysFS had negative value (-1), but there must be at least one NUMA node, so returning NUMA node zero
2021-06-16 19:39:49.752587: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1763] Adding visible gpu devices: 0
2021-06-16 19:39:49.752604: I tensorflow/stream_executor/platform/default/dso_loader.cc:42] Successfully opened dynamic library libcudart.so.10.1
2021-06-16 19:39:49.796646: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1181] Device interconnect StreamExecutor with strength 1 edge matrix:
2021-06-16 19:39:49.796661: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1187]      0
2021-06-16 19:39:49.796664: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1200] 0:   N
2021-06-16 19:39:49.796756: I tensorflow/stream_executor/cuda/cuda_gpu_executor.cc:1005] successful NUMA node read from SysFS had negative value (-1), but there must be at least one NUMA node, so returning NUMA node zero
2021-06-16 19:39:49.797008: I tensorflow/stream_executor/cuda/cuda_gpu_executor.cc:1005] successful NUMA node read from SysFS had negative value (-1), but there must be at least one NUMA node, so returning NUMA node zero
2021-06-16 19:39:49.797245: I tensorflow/stream_executor/cuda/cuda_gpu_executor.cc:1005] successful NUMA node read from SysFS had negative value (-1), but there must be at least one NUMA node, so returning NUMA node zero
2021-06-16 19:39:49.797467: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1326] Created TensorFlow device (/job:localhost/replica:0/task:0/device:GPU:0 with 5329 MB memory) -> physical GPU (device: 0, name: GeForce GTX 1660 SUPER, pci bus id: 0000:2b:00.0, compute capability: 7.5)
2021-06-16 19:39:49.798420: I tensorflow/compiler/xla/service/service.cc:168] XLA service 0x56085832ccf0 executing computations on platform CUDA. Devices:
2021-06-16 19:39:49.798429: I tensorflow/compiler/xla/service/service.cc:175]   StreamExecutor device (0): GeForce GTX 1660 SUPER, Compute Capability 7.5
2021-06-16 19:39:57.788377: F tensorflow/core/kernels/split_lib_gpu.cu.cc:207] Non-OK-status: CudaLaunchKernel(SplitOpKernel<T>, config.block_count, config.thread_per_block, 0, d.stream(), input, prefix_dim_size, split_dim_size, suffix_dim_size, output_ptr_data) status: Internal: out of memory
Aborted (core dumped)
Traceback (most recent call last):
  File "/home/simon/Downloads/trRosetta2/trRefine/run_trRefine_DAN.py", line 220, in <module>
    main()
  File "/home/simon/Downloads/trRosetta2/trRefine/run_trRefine_DAN.py", line 210, in main
    tor_s.append(np.load("rep_s/rep_%d_SS.npz"%i)['tor'].astype(np.float32)+1e-9)
  File "/home/simon/anaconda3/envs/casp14-baker/lib/python3.6/site-packages/numpy/lib/npyio.py", line 416, in load
    fid = stack.enter_context(open(os_fspath(file), "rb"))
FileNotFoundError: [Errno 2] No such file or directory: 'rep_s/rep_0_SS.npz'

# trRefine_fold.stderr
Traceback (most recent call last):
  File "/home/simon/Downloads/trRosetta2/folding/RosettaTR.py", line 340, in <module>
    main()
  File "/home/simon/Downloads/trRosetta2/folding/RosettaTR.py", line 44, in main
    rst = gen_rst(params)
  File "/home/simon/Downloads/trRosetta2/folding/utils.py", line 14, in gen_rst
    npz = np.load(params['NPZ'])
  File "/home/simon/anaconda3/envs/casp14-baker/lib/python3.6/site-packages/numpy/lib/npyio.py", line 416, in load
    fid = stack.enter_context(open(os_fspath(file), "rb"))
FileNotFoundError: [Errno 2] No such file or directory: '/home/simon/Downloads/trRosetta2/example/T1078/t000_.trRefine.npz'
Traceback (most recent call last):
  File "/home/simon/Downloads/trRosetta2/folding/RosettaTR.py", line 340, in <module>
    main()
  File "/home/simon/Downloads/trRosetta2/folding/RosettaTR.py", line 44, in main
    rst = gen_rst(params)
  File "/home/simon/Downloads/trRosetta2/folding/utils.py", line 14, in gen_rst
    npz = np.load(params['NPZ'])
  File "/home/simon/anaconda3/envs/casp14-baker/lib/python3.6/site-packages/numpy/lib/npyio.py", line 416, in load
    fid = stack.enter_context(open(os_fspath(file), "rb"))
FileNotFoundError: [Errno 2] No such file or directory: '/home/simon/Downloads/trRosetta2/example/T1078/t000_.trRefine.npz'
Traceback (most recent call last):
  File "/home/simon/Downloads/trRosetta2/folding/RosettaTR.py", line 340, in <module>
    main()
  File "/home/simon/Downloads/trRosetta2/folding/RosettaTR.py", line 44, in main
    rst = gen_rst(params)
  File "/home/simon/Downloads/trRosetta2/folding/utils.py", line 14, in gen_rst
    npz = np.load(params['NPZ'])
  File "/home/simon/anaconda3/envs/casp14-baker/lib/python3.6/site-packages/numpy/lib/npyio.py", line 416, in load
    fid = stack.enter_context(open(os_fspath(file), "rb"))
FileNotFoundError: [Errno 2] No such file or directory: '/home/simon/Downloads/trRosetta2/example/T1078/t000_.trRefine.npz'
Traceback (most recent call last):
  File "/home/simon/Downloads/trRosetta2/folding/RosettaTR.py", line 340, in <module>
    main()
  File "/home/simon/Downloads/trRosetta2/folding/RosettaTR.py", line 44, in main
    rst = gen_rst(params)
  File "/home/simon/Downloads/trRosetta2/folding/utils.py", line 14, in gen_rst
    npz = np.load(params['NPZ'])
  File "/home/simon/anaconda3/envs/casp14-baker/lib/python3.6/site-packages/numpy/lib/npyio.py", line 416, in load
    fid = stack.enter_context(open(os_fspath(file), "rb"))
FileNotFoundError: [Errno 2] No such file or directory: '/home/simon/Downloads/trRosetta2/example/T1078/t000_.trRefine.npz'
Traceback (most recent call last):
  File "/home/simon/Downloads/trRosetta2/folding/RosettaTR.py", line 340, in <module>
    main()
  File "/home/simon/Downloads/trRosetta2/folding/RosettaTR.py", line 44, in main
    rst = gen_rst(params)
  File "/home/simon/Downloads/trRosetta2/folding/utils.py", line 14, in gen_rst
    npz = np.load(params['NPZ'])
  File "/home/simon/anaconda3/envs/casp14-baker/lib/python3.6/site-packages/numpy/lib/npyio.py", line 416, in load
    fid = stack.enter_context(open(os_fspath(file), "rb"))
FileNotFoundError: [Errno 2] No such file or directory: '/home/simon/Downloads/trRosetta2/example/T1078/t000_.trRefine.npz'
Traceback (most recent call last):
  File "/home/simon/Downloads/trRosetta2/folding/RosettaTR.py", line 340, in <module>
    main()
  File "/home/simon/Downloads/trRosetta2/folding/RosettaTR.py", line 44, in main
    rst = gen_rst(params)
  File "/home/simon/Downloads/trRosetta2/folding/utils.py", line 14, in gen_rst
    npz = np.load(params['NPZ'])
  File "/home/simon/anaconda3/envs/casp14-baker/lib/python3.6/site-packages/numpy/lib/npyio.py", line 416, in load
    fid = stack.enter_context(open(os_fspath(file), "rb"))
FileNotFoundError: [Errno 2] No such file or directory: '/home/simon/Downloads/trRosetta2/example/T1078/t000_.trRefine.npz'
Traceback (most recent call last):
  File "/home/simon/Downloads/trRosetta2/folding/RosettaTR.py", line 340, in <module>
    main()
  File "/home/simon/Downloads/trRosetta2/folding/RosettaTR.py", line 44, in main
    rst = gen_rst(params)
  File "/home/simon/Downloads/trRosetta2/folding/utils.py", line 14, in gen_rst
    npz = np.load(params['NPZ'])
  File "/home/simon/anaconda3/envs/casp14-baker/lib/python3.6/site-packages/numpy/lib/npyio.py", line 416, in load
    fid = stack.enter_context(open(os_fspath(file), "rb"))
FileNotFoundError: [Errno 2] No such file or directory: '/home/simon/Downloads/trRosetta2/example/T1078/t000_.trRefine.npz'
Traceback (most recent call last):
  File "/home/simon/Downloads/trRosetta2/folding/RosettaTR.py", line 340, in <module>
    main()
  File "/home/simon/Downloads/trRosetta2/folding/RosettaTR.py", line 44, in main
    rst = gen_rst(params)
  File "/home/simon/Downloads/trRosetta2/folding/utils.py", line 14, in gen_rst
    npz = np.load(params['NPZ'])
  File "/home/simon/anaconda3/envs/casp14-baker/lib/python3.6/site-packages/numpy/lib/npyio.py", line 416, in load
    fid = stack.enter_context(open(os_fspath(file), "rb"))
FileNotFoundError: [Errno 2] No such file or directory: '/home/simon/Downloads/trRosetta2/example/T1078/t000_.trRefine.npz'
Traceback (most recent call last):
  File "/home/simon/Downloads/trRosetta2/folding/RosettaTR.py", line 340, in <module>
    main()
  File "/home/simon/Downloads/trRosetta2/folding/RosettaTR.py", line 44, in main
    rst = gen_rst(params)
  File "/home/simon/Downloads/trRosetta2/folding/utils.py", line 14, in gen_rst
    npz = np.load(params['NPZ'])
  File "/home/simon/anaconda3/envs/casp14-baker/lib/python3.6/site-packages/numpy/lib/npyio.py", line 416, in load
    fid = stack.enter_context(open(os_fspath(file), "rb"))
FileNotFoundError: [Errno 2] No such file or directory: '/home/simon/Downloads/trRosetta2/example/T1078/t000_.trRefine.npz'
Traceback (most recent call last):
  File "/home/simon/Downloads/trRosetta2/folding/RosettaTR.py", line 340, in <module>
    main()
  File "/home/simon/Downloads/trRosetta2/folding/RosettaTR.py", line 44, in main
    rst = gen_rst(params)
  File "/home/simon/Downloads/trRosetta2/folding/utils.py", line 14, in gen_rst
    npz = np.load(params['NPZ'])
  File "/home/simon/anaconda3/envs/casp14-baker/lib/python3.6/site-packages/numpy/lib/npyio.py", line 416, in load
    fid = stack.enter_context(open(os_fspath(file), "rb"))
FileNotFoundError: [Errno 2] No such file or directory: '/home/simon/Downloads/trRosetta2/example/T1078/t000_.trRefine.npz'
Traceback (most recent call last):
  File "/home/simon/Downloads/trRosetta2/folding/RosettaTR.py", line 340, in <module>
    main()
  File "/home/simon/Downloads/trRosetta2/folding/RosettaTR.py", line 44, in main
    rst = gen_rst(params)
  File "/home/simon/Downloads/trRosetta2/folding/utils.py", line 14, in gen_rst
    npz = np.load(params['NPZ'])
  File "/home/simon/anaconda3/envs/casp14-baker/lib/python3.6/site-packages/numpy/lib/npyio.py", line 416, in load
    fid = stack.enter_context(open(os_fspath(file), "rb"))
FileNotFoundError: [Errno 2] No such file or directory: '/home/simon/Downloads/trRosetta2/example/T1078/t000_.trRefine.npz'
Traceback (most recent call last):
  File "/home/simon/Downloads/trRosetta2/folding/RosettaTR.py", line 340, in <module>
    main()
  File "/home/simon/Downloads/trRosetta2/folding/RosettaTR.py", line 44, in main
    rst = gen_rst(params)
  File "/home/simon/Downloads/trRosetta2/folding/utils.py", line 14, in gen_rst
    npz = np.load(params['NPZ'])
  File "/home/simon/anaconda3/envs/casp14-baker/lib/python3.6/site-packages/numpy/lib/npyio.py", line 416, in load
    fid = stack.enter_context(open(os_fspath(file), "rb"))
FileNotFoundError: [Errno 2] No such file or directory: '/home/simon/Downloads/trRosetta2/example/T1078/t000_.trRefine.npz'
Traceback (most recent call last):
  File "/home/simon/Downloads/trRosetta2/folding/RosettaTR.py", line 340, in <module>
    main()
  File "/home/simon/Downloads/trRosetta2/folding/RosettaTR.py", line 44, in main
    rst = gen_rst(params)
  File "/home/simon/Downloads/trRosetta2/folding/utils.py", line 14, in gen_rst
    npz = np.load(params['NPZ'])
  File "/home/simon/anaconda3/envs/casp14-baker/lib/python3.6/site-packages/numpy/lib/npyio.py", line 416, in load
    fid = stack.enter_context(open(os_fspath(file), "rb"))
FileNotFoundError: [Errno 2] No such file or directory: '/home/simon/Downloads/trRosetta2/example/T1078/t000_.trRefine.npz'
Traceback (most recent call last):
  File "/home/simon/Downloads/trRosetta2/folding/RosettaTR.py", line 340, in <module>
    main()
  File "/home/simon/Downloads/trRosetta2/folding/RosettaTR.py", line 44, in main
    rst = gen_rst(params)
  File "/home/simon/Downloads/trRosetta2/folding/utils.py", line 14, in gen_rst
    npz = np.load(params['NPZ'])
  File "/home/simon/anaconda3/envs/casp14-baker/lib/python3.6/site-packages/numpy/lib/npyio.py", line 416, in load
    fid = stack.enter_context(open(os_fspath(file), "rb"))
FileNotFoundError: [Errno 2] No such file or directory: '/home/simon/Downloads/trRosetta2/example/T1078/t000_.trRefine.npz'
Traceback (most recent call last):
  File "/home/simon/Downloads/trRosetta2/folding/RosettaTR.py", line 340, in <module>
    main()
  File "/home/simon/Downloads/trRosetta2/folding/RosettaTR.py", line 44, in main
    rst = gen_rst(params)
  File "/home/simon/Downloads/trRosetta2/folding/utils.py", line 14, in gen_rst
    npz = np.load(params['NPZ'])
  File "/home/simon/anaconda3/envs/casp14-baker/lib/python3.6/site-packages/numpy/lib/npyio.py", line 416, in load
    fid = stack.enter_context(open(os_fspath(file), "rb"))
FileNotFoundError: [Errno 2] No such file or directory: '/home/simon/Downloads/trRosetta2/example/T1078/t000_.trRefine.npz'

I experience the same problem.

I'm not sure why run_trRefine_DAN.py which requires the input -n_core $CPU when my env is in gpu setting.
2021-06-18 17:40:51.844471: I tensorflow/core/platform/cpu_feature_guard.cc:142] Your CPU supports instructions that this TensorFlow binary was not compiled to use: SSE4.1 SSE4.2 AVX AVX2 FMA
2021-06-18 17:40:51.866726: I tensorflow/core/platform/profile_utils/cpu_utils.cc:94] CPU Frequency:<PHONE_NUMBER> Hz
2021-06-18 17:40:51.867855: I tensorflow/compiler/xla/service/service.cc:168] XLA service 0x55f3d8d03bf0 executing computations on platform Host. Devices:
2021-06-18 17:40:51.867891: I tensorflow/compiler/xla/service/service.cc:175]   StreamExecutor device (0): ,
2021-06-18 17:40:51.868916: I tensorflow/stream_executor/platform/default/dso_loader.cc:42] Successfully opened dynamic library libcuda.so.1
2021-06-18 17:40:51.881368: I tensorflow/stream_executor/cuda/cuda_gpu_executor.cc:1005] successful NUMA node read from SysFS had negative value (-1), but there must be at least one NUMA node, so returning NUMA node zero
2021-06-18 17:40:51.881630: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1640] Found device 0 with properties:
name: GeForce RTX 3080 major: 8 minor: 6 memoryClockRate(GHz): 1.71

I had the same problem. It works for me when I changed from gpu run to cpu run using the suggestion from @gjoni by editing #131 of the run_pipeline.sh script to:
CUDA_VISIBLE_DEVICES="" python $PIPEDIR/trRefine/run_trRefine_DAN.py -msa_npz $WDIR/t000_.msa.npz \

I had the same problem. It works for me when I changed from gpu run to cpu run using the suggestion from @gjoni by editing #131 of the run_pipeline.sh script to:
CUDA_VISIBLE_DEVICES="" python $PIPEDIR/trRefine/run_trRefine_DAN.py -msa_npz $WDIR/t000_.msa.npz \

I've tried but same problem.
OMP: Info #155: KMP_AFFINITY: Initial OS proc set respected: 0-31
OMP: Info #216: KMP_AFFINITY: decoding x2APIC ids.
OMP: Info #157: KMP_AFFINITY: 32 available OS procs
OMP: Info #158: KMP_AFFINITY: Uniform topology
OMP: Info #287: KMP_AFFINITY: topology layer "LL cache" is equivalent to "socket".
OMP: Info #192: KMP_AFFINITY: 1 socket x 16 cores/socket x 2 threads/core (16 total cores)
OMP: Info #218: KMP_AFFINITY: OS proc to physical thread map:
OMP: Info #172: KMP_AFFINITY: OS proc 0 maps to socket 0 core 0 thread 0
OMP: Info #172: KMP_AFFINITY: OS proc 16 maps to socket 0 core 0 thread 1
OMP: Info #172: KMP_AFFINITY: OS proc 1 maps to socket 0 core 1 thread 0
OMP: Info #172: KMP_AFFINITY: OS proc 17 maps to socket 0 core 1 thread 1
OMP: Info #172: KMP_AFFINITY: OS proc 2 maps to socket 0 core 2 thread 0
OMP: Info #172: KMP_AFFINITY: OS proc 18 maps to socket 0 core 2 thread 1
OMP: Info #172: KMP_AFFINITY: OS proc 3 maps to socket 0 core 3 thread 0
OMP: Info #172: KMP_AFFINITY: OS proc 19 maps to socket 0 core 3 thread 1
OMP: Info #172: KMP_AFFINITY: OS proc 4 maps to socket 0 core 4 thread 0
OMP: Info #172: KMP_AFFINITY: OS proc 20 maps to socket 0 core 4 thread 1
OMP: Info #172: KMP_AFFINITY: OS proc 5 maps to socket 0 core 5 thread 0
OMP: Info #172: KMP_AFFINITY: OS proc 21 maps to socket 0 core 5 thread 1
OMP: Info #172: KMP_AFFINITY: OS proc 6 maps to socket 0 core 6 thread 0
OMP: Info #172: KMP_AFFINITY: OS proc 22 maps to socket 0 core 6 thread 1
OMP: Info #172: KMP_AFFINITY: OS proc 7 maps to socket 0 core 7 thread 0
OMP: Info #172: KMP_AFFINITY: OS proc 23 maps to socket 0 core 7 thread 1
OMP: Info #172: KMP_AFFINITY: OS proc 8 maps to socket 0 core 8 thread 0
OMP: Info #172: KMP_AFFINITY: OS proc 24 maps to socket 0 core 8 thread 1
OMP: Info #172: KMP_AFFINITY: OS proc 9 maps to socket 0 core 9 thread 0
OMP: Info #172: KMP_AFFINITY: OS proc 25 maps to socket 0 core 9 thread 1
OMP: Info #172: KMP_AFFINITY: OS proc 10 maps to socket 0 core 10 thread 0
OMP: Info #172: KMP_AFFINITY: OS proc 26 maps to socket 0 core 10 thread 1
OMP: Info #172: KMP_AFFINITY: OS proc 11 maps to socket 0 core 11 thread 0
OMP: Info #172: KMP_AFFINITY: OS proc 27 maps to socket 0 core 11 thread 1
OMP: Info #172: KMP_AFFINITY: OS proc 12 maps to socket 0 core 12 thread 0
OMP: Info #172: KMP_AFFINITY: OS proc 28 maps to socket 0 core 12 thread 1
OMP: Info #172: KMP_AFFINITY: OS proc 13 maps to socket 0 core 13 thread 0
OMP: Info #172: KMP_AFFINITY: OS proc 29 maps to socket 0 core 13 thread 1
OMP: Info #172: KMP_AFFINITY: OS proc 14 maps to socket 0 core 14 thread 0
OMP: Info #172: KMP_AFFINITY: OS proc 30 maps to socket 0 core 14 thread 1
OMP: Info #172: KMP_AFFINITY: OS proc 15 maps to socket 0 core 15 thread 0
OMP: Info #172: KMP_AFFINITY: OS proc 31 maps to socket 0 core 15 thread 1
OMP: Info #254: KMP_AFFINITY: pid 96884 tid 96884 thread 0 bound to OS proc set 0
OMP: Info #254: KMP_AFFINITY: pid 96884 tid 96906 thread 1 bound to OS proc set 1
OMP: Info #254: KMP_AFFINITY: pid 96884 tid 96913 thread 2 bound to OS proc set 2
OMP: Info #254: KMP_AFFINITY: pid 96884 tid 96914 thread 3 bound to OS proc set 3
OMP: Info #254: KMP_AFFINITY: pid 96884 tid 96916 thread 5 bound to OS proc set 5
OMP: Info #254: KMP_AFFINITY: pid 96884 tid 96920 thread 9 bound to OS proc set 9
OMP: Info #254: KMP_AFFINITY: pid 96884 tid 96921 thread 10 bound to OS proc set 10
OMP: Info #254: KMP_AFFINITY: pid 96884 tid 96917 thread 6 bound to OS proc set 6
OMP: Info #254: KMP_AFFINITY: pid 96884 tid 96922 thread 11 bound to OS proc set 11
OMP: Info #254: KMP_AFFINITY: pid 96884 tid 96919 thread 8 bound to OS proc set 8
OMP: Info #254: KMP_AFFINITY: pid 96884 tid 96918 thread 7 bound to OS proc set 7
OMP: Info #254: KMP_AFFINITY: pid 96884 tid 96923 thread 12 bound to OS proc set 12
OMP: Info #254: KMP_AFFINITY: pid 96884 tid 96915 thread 4 bound to OS proc set 4
OMP: Info #254: KMP_AFFINITY: pid 96884 tid 96924 thread 13 bound to OS proc set 13
OMP: Info #254: KMP_AFFINITY: pid 96884 tid 96925 thread 14 bound to OS proc set 14
OMP: Info #254: KMP_AFFINITY: pid 96884 tid 96926 thread 15 bound to OS proc set 15
OMP: Info #254: KMP_AFFINITY: pid 96884 tid 96927 thread 16 bound to OS proc set 16
OMP: Info #254: KMP_AFFINITY: pid 96884 tid 96928 thread 17 bound to OS proc set 17
OMP: Info #254: KMP_AFFINITY: pid 96884 tid 96929 thread 18 bound to OS proc set 18
OMP: Info #254: KMP_AFFINITY: pid 96884 tid 96930 thread 19 bound to OS proc set 19
OMP: Info #254: KMP_AFFINITY: pid 96884 tid 96931 thread 20 bound to OS proc set 20
OMP: Info #254: KMP_AFFINITY: pid 96884 tid 96932 thread 21 bound to OS proc set 21
OMP: Info #254: KMP_AFFINITY: pid 96884 tid 96933 thread 22 bound to OS proc set 22
OMP: Info #254: KMP_AFFINITY: pid 96884 tid 96934 thread 23 bound to OS proc set 23
OMP: Info #254: KMP_AFFINITY: pid 96884 tid 96935 thread 24 bound to OS proc set 24
OMP: Info #254: KMP_AFFINITY: pid 96884 tid 96936 thread 25 bound to OS proc set 25
OMP: Info #254: KMP_AFFINITY: pid 96884 tid 96937 thread 26 bound to OS proc set 26
OMP: Info #254: KMP_AFFINITY: pid 96884 tid 96939 thread 28 bound to OS proc set 28
OMP: Info #254: KMP_AFFINITY: pid 96884 tid 96938 thread 27 bound to OS proc set 27
OMP: Info #254: KMP_AFFINITY: pid 96884 tid 96940 thread 29 bound to OS proc set 29
OMP: Info #254: KMP_AFFINITY: pid 96884 tid 96941 thread 30 bound to OS proc set 30
OMP: Info #254: KMP_AFFINITY: pid 96884 tid 96942 thread 31 bound to OS proc set 31
OMP: Info #254: KMP_AFFINITY: pid 96884 tid 96943 thread 32 bound to OS proc set 0
OMP: Info #254: KMP_AFFINITY: pid 96884 tid 96905 thread 33 bound to OS proc set 1
OMP: Info #254: KMP_AFFINITY: pid 96884 tid 96945 thread 35 bound to OS proc set 3
OMP: Info #254: KMP_AFFINITY: pid 96884 tid 96944 thread 34 bound to OS proc set 2
OMP: Info #254: KMP_AFFINITY: pid 96884 tid 96946 thread 36 bound to OS proc set 4
OMP: Info #254: KMP_AFFINITY: pid 96884 tid 96948 thread 38 bound to OS proc set 6
OMP: Info #254: KMP_AFFINITY: pid 96884 tid 96947 thread 37 bound to OS proc set 5
OMP: Info #254: KMP_AFFINITY: pid 96884 tid 96949 thread 39 bound to OS proc set 7
OMP: Info #254: KMP_AFFINITY: pid 96884 tid 96950 thread 40 bound to OS proc set 8
OMP: Info #254: KMP_AFFINITY: pid 96884 tid 96951 thread 41 bound to OS proc set 9
OMP: Info #254: KMP_AFFINITY: pid 96884 tid 96952 thread 42 bound to OS proc set 10
OMP: Info #254: KMP_AFFINITY: pid 96884 tid 96953 thread 43 bound to OS proc set 11
OMP: Info #254: KMP_AFFINITY: pid 96884 tid 96954 thread 44 bound to OS proc set 12
OMP: Info #254: KMP_AFFINITY: pid 96884 tid 96955 thread 45 bound to OS proc set 13
OMP: Info #254: KMP_AFFINITY: pid 96884 tid 96956 thread 46 bound to OS proc set 14
OMP: Info #254: KMP_AFFINITY: pid 96884 tid 96957 thread 47 bound to OS proc set 15
OMP: Info #254: KMP_AFFINITY: pid 96884 tid 96958 thread 48 bound to OS proc set 16
OMP: Info #254: KMP_AFFINITY: pid 96884 tid 96959 thread 49 bound to OS proc set 17
OMP: Info #254: KMP_AFFINITY: pid 96884 tid 96960 thread 50 bound to OS proc set 18
OMP: Info #254: KMP_AFFINITY: pid 96884 tid 96961 thread 51 bound to OS proc set 19
OMP: Info #254: KMP_AFFINITY: pid 96884 tid 96962 thread 52 bound to OS proc set 20
OMP: Info #254: KMP_AFFINITY: pid 96884 tid 96963 thread 53 bound to OS proc set 21
OMP: Info #254: KMP_AFFINITY: pid 96884 tid 96964 thread 54 bound to OS proc set 22
OMP: Info #254: KMP_AFFINITY: pid 96884 tid 96965 thread 55 bound to OS proc set 23
OMP: Info #254: KMP_AFFINITY: pid 96884 tid 96966 thread 56 bound to OS proc set 24
OMP: Info #254: KMP_AFFINITY: pid 96884 tid 96967 thread 57 bound to OS proc set 25
OMP: Info #254: KMP_AFFINITY: pid 96884 tid 96968 thread 58 bound to OS proc set 26
OMP: Info #254: KMP_AFFINITY: pid 96884 tid 96969 thread 59 bound to OS proc set 27
OMP: Info #254: KMP_AFFINITY: pid 96884 tid 96970 thread 60 bound to OS proc set 28
OMP: Info #254: KMP_AFFINITY: pid 96884 tid 96971 thread 61 bound to OS proc set 29
OMP: Info #254: KMP_AFFINITY: pid 96884 tid 96972 thread 62 bound to OS proc set 30
OMP: Info #254: KMP_AFFINITY: pid 96884 tid 96974 thread 64 bound to OS proc set 0
OMP: Info #254: KMP_AFFINITY: pid 96884 tid 96973 thread 63 bound to OS proc set 31
OMP: Info #155: KMP_AFFINITY: Initial OS proc set respected: 0-31
OMP: Info #216: KMP_AFFINITY: decoding x2APIC ids.
OMP: Info #157: KMP_AFFINITY: 32 available OS procs
OMP: Info #158: KMP_AFFINITY: Uniform topology
OMP: Info #287: KMP_AFFINITY: topology layer "LL cache" is equivalent to "socket".
OMP: Info #192: KMP_AFFINITY: 1 socket x 16 cores/socket x 2 threads/core (16 total cores)
OMP: Info #218: KMP_AFFINITY: OS proc to physical thread map:
OMP: Info #172: KMP_AFFINITY: OS proc 0 maps to socket 0 core 0 thread 0
OMP: Info #172: KMP_AFFINITY: OS proc 16 maps to socket 0 core 0 thread 1
OMP: Info #172: KMP_AFFINITY: OS proc 1 maps to socket 0 core 1 thread 0
OMP: Info #172: KMP_AFFINITY: OS proc 17 maps to socket 0 core 1 thread 1
OMP: Info #172: KMP_AFFINITY: OS proc 2 maps to socket 0 core 2 thread 0
OMP: Info #172: KMP_AFFINITY: OS proc 18 maps to socket 0 core 2 thread 1
OMP: Info #172: KMP_AFFINITY: OS proc 3 maps to socket 0 core 3 thread 0
OMP: Info #172: KMP_AFFINITY: OS proc 19 maps to socket 0 core 3 thread 1
OMP: Info #172: KMP_AFFINITY: OS proc 4 maps to socket 0 core 4 thread 0
OMP: Info #172: KMP_AFFINITY: OS proc 20 maps to socket 0 core 4 thread 1
OMP: Info #172: KMP_AFFINITY: OS proc 5 maps to socket 0 core 5 thread 0
OMP: Info #172: KMP_AFFINITY: OS proc 21 maps to socket 0 core 5 thread 1
OMP: Info #172: KMP_AFFINITY: OS proc 6 maps to socket 0 core 6 thread 0
OMP: Info #172: KMP_AFFINITY: OS proc 22 maps to socket 0 core 6 thread 1
OMP: Info #172: KMP_AFFINITY: OS proc 7 maps to socket 0 core 7 thread 0
OMP: Info #172: KMP_AFFINITY: OS proc 23 maps to socket 0 core 7 thread 1
OMP: Info #172: KMP_AFFINITY: OS proc 8 maps to socket 0 core 8 thread 0
OMP: Info #172: KMP_AFFINITY: OS proc 24 maps to socket 0 core 8 thread 1
OMP: Info #172: KMP_AFFINITY: OS proc 9 maps to socket 0 core 9 thread 0
OMP: Info #172: KMP_AFFINITY: OS proc 25 maps to socket 0 core 9 thread 1
OMP: Info #172: KMP_AFFINITY: OS proc 10 maps to socket 0 core 10 thread 0
OMP: Info #172: KMP_AFFINITY: OS proc 26 maps to socket 0 core 10 thread 1
OMP: Info #172: KMP_AFFINITY: OS proc 11 maps to socket 0 core 11 thread 0
OMP: Info #172: KMP_AFFINITY: OS proc 27 maps to socket 0 core 11 thread 1
OMP: Info #172: KMP_AFFINITY: OS proc 12 maps to socket 0 core 12 thread 0
OMP: Info #172: KMP_AFFINITY: OS proc 28 maps to socket 0 core 12 thread 1
OMP: Info #172: KMP_AFFINITY: OS proc 13 maps to socket 0 core 13 thread 0
OMP: Info #172: KMP_AFFINITY: OS proc 29 maps to socket 0 core 13 thread 1
OMP: Info #172: KMP_AFFINITY: OS proc 14 maps to socket 0 core 14 thread 0
OMP: Info #172: KMP_AFFINITY: OS proc 30 maps to socket 0 core 14 thread 1
OMP: Info #172: KMP_AFFINITY: OS proc 15 maps to socket 0 core 15 thread 0
OMP: Info #172: KMP_AFFINITY: OS proc 31 maps to socket 0 core 15 thread 1
OMP: Info #254: KMP_AFFINITY: pid 98053 tid 98053 thread 0 bound to OS proc set 0
2021-06-28 12:33:08.710889: I tensorflow/core/platform/cpu_feature_guard.cc:145] This TensorFlow binary is optimized with Intel(R) MKL-DNN to use the following CPU instructions in performance critical operations:  SSE4.1 SSE4.2 AVX AVX2 FMA
To enable them in non-MKL-DNN operations, rebuild TensorFlow with the appropriate compiler flags.
2021-06-28 12:33:08.732313: I tensorflow/core/platform/profile_utils/cpu_utils.cc:94] CPU Frequency:<PHONE_NUMBER> Hz
2021-06-28 12:33:08.732415: I tensorflow/compiler/xla/service/service.cc:168] XLA service 0x55d835c411d0 executing computations on platform Host. Devices:
2021-06-28 12:33:08.732429: I tensorflow/compiler/xla/service/service.cc:175]   StreamExecutor device (0): <undefined>, <undefined>
2021-06-28 12:33:08.732498: I tensorflow/core/common_runtime/process_util.cc:115] Creating new thread pool with default inter op setting: 2. Tune using inter_op_parallelism_threads for best performance.
Traceback (most recent call last):
  File "/home/simon/anaconda3/envs/casp14-baker/lib/python3.6/site-packages/tensorflow/python/client/session.py", line 1356, in _do_call
    return fn(*args)
  File "/home/simon/anaconda3/envs/casp14-baker/lib/python3.6/site-packages/tensorflow/python/client/session.py", line 1339, in _run_fn
    self._extend_graph()
  File "/home/simon/anaconda3/envs/casp14-baker/lib/python3.6/site-packages/tensorflow/python/client/session.py", line 1374, in _extend_graph
    tf_session.ExtendSession(self._session)
tensorflow.python.framework.errors_impl.InvalidArgumentError: No OpKernel was registered to support Op 'CudnnRNNCanonicalToParams' used by {{node SStorPred/AttBiLSTM/cudnn_lstm/cudnn_lstm/CudnnRNNCanonicalToParams}}with these attrs: [dropout=0, seed=0, num_params=48, input_mode="linear_input", T=DT_FLOAT, direction="bidirectional", rnn_mode="lstm", seed2=0]
Registered devices: [CPU, XLA_CPU]
Registered kernels:
  <no registered kernels>

	 [[SStorPred/AttBiLSTM/cudnn_lstm/cudnn_lstm/CudnnRNNCanonicalToParams]]

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/simon/anaconda3/envs/casp14-baker/lib/python3.6/site-packages/tensorflow/python/training/saver.py", line 1286, in restore
    {self.saver_def.filename_tensor_name: save_path})
  File "/home/simon/anaconda3/envs/casp14-baker/lib/python3.6/site-packages/tensorflow/python/client/session.py", line 950, in run
    run_metadata_ptr)
  File "/home/simon/anaconda3/envs/casp14-baker/lib/python3.6/site-packages/tensorflow/python/client/session.py", line 1173, in _run
    feed_dict_tensor, options, run_metadata)
  File "/home/simon/anaconda3/envs/casp14-baker/lib/python3.6/site-packages/tensorflow/python/client/session.py", line 1350, in _do_run
    run_metadata)
  File "/home/simon/anaconda3/envs/casp14-baker/lib/python3.6/site-packages/tensorflow/python/client/session.py", line 1370, in _do_call
    raise type(e)(node_def, op, message)
tensorflow.python.framework.errors_impl.InvalidArgumentError: No OpKernel was registered to support Op 'CudnnRNNCanonicalToParams' used by node SStorPred/AttBiLSTM/cudnn_lstm/cudnn_lstm/CudnnRNNCanonicalToParams (defined at /Downloads/trRosetta2/trRefine/SStor_pred/model.py:296) with these attrs: [dropout=0, seed=0, num_params=48, input_mode="linear_input", T=DT_FLOAT, direction="bidirectional", rnn_mode="lstm", seed2=0]
Registered devices: [CPU, XLA_CPU]
Registered kernels:
  <no registered kernels>

	 [[SStorPred/AttBiLSTM/cudnn_lstm/cudnn_lstm/CudnnRNNCanonicalToParams]]

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/simon/Downloads/trRosetta2/trRefine/SStor_pred/main_multi.py", line 83, in <module>
    main()
  File "/home/simon/Downloads/trRosetta2/trRefine/SStor_pred/main_multi.py", line 80, in main
    ML_model.predict_multi(FLAGS, a3m_s, pdb_s, hhr_s, out_s)
  File "/home/simon/Downloads/trRosetta2/trRefine/SStor_pred/model.py", line 566, in predict_multi
    self.load(config.model_dir, 'model')
  File "/home/simon/Downloads/trRosetta2/trRefine/SStor_pred/model.py", line 379, in load
    self.saver.restore(self.sess, folder+"/%s.ckpt"%prefix)
  File "/home/simon/anaconda3/envs/casp14-baker/lib/python3.6/site-packages/tensorflow/python/training/saver.py", line 1322, in restore
    err, "a mismatch between the current graph and the graph")
tensorflow.python.framework.errors_impl.InvalidArgumentError: Restoring from checkpoint failed. This is most likely due to a mismatch between the current graph and the graph from the checkpoint. Please ensure that you have not altered the graph expected based on the checkpoint. Original error:

No OpKernel was registered to support Op 'CudnnRNNCanonicalToParams' used by node SStorPred/AttBiLSTM/cudnn_lstm/cudnn_lstm/CudnnRNNCanonicalToParams (defined at /Downloads/trRosetta2/trRefine/SStor_pred/model.py:296) with these attrs: [dropout=0, seed=0, num_params=48, input_mode="linear_input", T=DT_FLOAT, direction="bidirectional", rnn_mode="lstm", seed2=0]
Registered devices: [CPU, XLA_CPU]
Registered kernels:
  <no registered kernels>

	 [[SStorPred/AttBiLSTM/cudnn_lstm/cudnn_lstm/CudnnRNNCanonicalToParams]]
Traceback (most recent call last):
  File "/home/simon/Downloads/trRosetta2/trRefine/run_trRefine_DAN.py", line 220, in <module>
    main()
  File "/home/simon/Downloads/trRosetta2/trRefine/run_trRefine_DAN.py", line 210, in main
    tor_s.append(np.load("rep_s/rep_%d_SS.npz"%i)['tor'].astype(np.float32)+1e-9)
  File "/home/simon/anaconda3/envs/casp14-baker/lib/python3.6/site-packages/numpy/lib/npyio.py", line 416, in load
    fid = stack.enter_context(open(os_fspath(file), "rb"))
FileNotFoundError: [Errno 2] No such file or directory: 'rep_s/rep_0_SS.npz'

@johnny-rodriguez wrote /mnt/d/trRosetta2/example/T1078/t000_.msa0.a3m: No such file or directory
Look like your run failed to produce the msa file therefore subsequent steps failed.  Please try to run make_msa.sh alone based on the run_pipeline.sh input to see if you could get t000_.msa0.a3m file.  Hope this helps. Jen

Hello everyone,
After struggling with the same issue myself, and eventually running everything manually and parsing through the python scripts, I've found a solution to this particular problem.
The "run_trRefine_DAN.py" script, by default uses GPUS.  To make it use ONLY CPUs, apart from the CUDA_VISIBLE_DEVICES="" solution presented (which I'm not yet sure how or if it works, it didn't work for me), you also need to add the option "--use_cpu" in the python line.
In other words, the code below (from run_pipeline.sh):
if [ ! -s $WDIR/t000_.trRefine.npz ] then     echo "Running trRefine"     cd $WDIR     python $PIPEDIR/trRefine/run_trRefine_DAN.py -msa_npz $WDIR/t000_.msa.npz \         -tbm_npz $WDIR/t000_.tbm.npz -pdb_dir_s $WDIR/pdb-msa $WDIR/pdb-tbm \         -a3m_fn $WDIR/t000_.msa0.a3m -hhr_fn $WDIR/t000_.hhr \         -n_core $CPU > $WDIR/log/trRefine.stdout 2> $WDIR/log/trRefine.stderr     cd - fi
needs to be changed to this:
if [ ! -s $WDIR/t000_.trRefine.npz ] then     echo "Running trRefine"     cd $WDIR     CUDA_VISIBLE_DEVICES="" python $PIPEDIR/trRefine/run_trRefine_DAN.py -msa_npz $WDIR/t000_.msa.npz \         -tbm_npz $WDIR/t000_.tbm.npz -pdb_dir_s $WDIR/pdb-msa $WDIR/pdb-tbm \         -a3m_fn $WDIR/t000_.msa0.a3m -hhr_fn $WDIR/t000_.hhr \         --use_cpu -n_core $CPU > $WDIR/log/trRefine.stdout 2> $WDIR/log/trRefine.stderr     cd - fi
The above change worked for me, as the script now only worked with my CPUs and didn't even search for a graphics card.


ENH: more stringent version checking

Propose adding a new, mandatory argument to ExperimentController called expyfun_version (or maybe just version?), that accepts a string (7-character GitHub commit hash) or None.  This argument would have no default, so users would be required to provide it, thus making the change non-backwards-compatible.  On init, the existing expyfun.assert_version() would be used to check the version string; specifying None would simply not run the check.  The ability to use assert_version outside of an ExperimentController instance would remain, so that it could be used in scripts that only do stimulus generation, plotting, etc.
@rkmaddox and I just discussed this, want to run it by you @Eric89GXL before we start hacking.

That's reasonable, but in order not to break argument order I'd just put it at the end with version='' by default. If version=None then don't check.

(it's another way of requiring people to set it explicitly while breaking backward compat less)

That makes sense. Or even make the default string 'must_set' or something.


Server side: keep connection open when client incorrectly disconnects

In the docs there are ample examples showing how a client can reopen a connection after loosing it, but what about the other way around? I am writing a server that should allow for clients to reconnect after a websockets.ConnectionClosedError has been thrown. This seems like it should be a common use case. Is it possible? If so, how? My server code looks something like this:
class MyServer:
    async def _ws_handler(self, ws):
            try:
                async for data in ws:
                    pass # TODO: do something

            except websockets.ConnectionClosedOK:
                pass

            except websockets.ConnectionClosedError as e:
                pass # TODO: reconnect?

    def serve(self):
        return websockets.serve(self._ws_handler, MY_HOST, MY_PORT)

I tried to simpy wrap the try ... catch inside the handler in a while loop but that does not work since an asyncio.exceptions.InvalidStateError will be thrown once the client reconnects.

You need to preserve session state somewhere, authenticate the client when it reconnects, and pick up where you left off. I'm afraid the details are going to be quite specific to each application.
As soon as you have more than one websockets process, you need to rebuild the whole state in the memory of a new process, so the kind of pseudocode you provided doesn't make sense.
If you want that kind of behavior, it would probably be easier to structure it it as:

a component that maintains connections with clients and routes messages from / to them; this component should be stateless so that disconnections and reconnections are transparent;
some kind of central process that handles incoming messages and sends outgoing messages; this component can be stateful; this is how you get the "pick up where you left off" behavior.


Creating HTML report with CLI

Hello ,
I am using the following code to produce html report :
Archi -application com.archimatetool.commandline.app -consoleLog -nosplash  --modelrepository.cloneModel https://xxxx/kurumsal_mimari_modeli.git --modelrepository.loadModel /model/  --modelrepository.userName  xxxx --modelrepository.passFile c:\dosya\dosya.txt --html.createReport c:\archi4\ -p
if elements have property then command gives an error :
context [/modelreport /expandFolder /_sub1 /expandFolder /_sub1 /expandFolder /_sub2 /classesFromProperties /sub3] 1:25 no such template: /IGNORE_ERROR
[HTMLReport] Report generated!
After this error index.html file size is 0 so I cant see report.
can you help me ?
Thanks

This can happen if there is a blank property (no value) in the model. The report should still work, though.

thank you very much for fast reply.


Animation trigger when "active" prop is updated

Tried to update the 'active' prop without pressing the hamburger. The animate function does not trigger.
This PR fix this.
I think it resolve issue https://github.com/GeekyAnts/react-native-hamburger/issues/1 too

@sankhadeeproy007 are you planning on merging this at some point?

Thank you @Nyl000


Installation issues

We're trying to replicate the results from the FFCV paper, and are having difficulty setting up a working environment. The suggested conda install command appears to hang (no progress after 2 hours, 100% CPU usage) using a fresh conda installation (as suggested by #85). The suggested troubleshooting tips for a conda install made no apparent change.
We were able to build and run the provided conda-less dockerfile, however we're still unable to use FFCV, as seen below.
root@ac2fad055eeb:/workspace# python
Python 3.8.10 (default, May 26 2023, 14:05:08)
[GCC 9.4.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import ffcv
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/usr/local/lib/python3.8/dist-packages/ffcv/__init__.py", line 1, in <module>
    from .loader import Loader
  File "/usr/local/lib/python3.8/dist-packages/ffcv/loader/__init__.py", line 1, in <module>
    from .loader import Loader, OrderOption
  File "/usr/local/lib/python3.8/dist-packages/ffcv/loader/loader.py", line 14, in <module>
    from ffcv.fields.base import Field
  File "/usr/local/lib/python3.8/dist-packages/ffcv/fields/__init__.py", line 3, in <module>
    from .rgb_image import RGBImageField
  File "/usr/local/lib/python3.8/dist-packages/ffcv/fields/rgb_image.py", line 5, in <module>
    import cv2
  File "/usr/local/lib/python3.8/dist-packages/cv2/__init__.py", line 181, in <module>
    bootstrap()
  File "/usr/local/lib/python3.8/dist-packages/cv2/__init__.py", line 175, in bootstrap
    if __load_extra_py_code_for_module("cv2", submodule, DEBUG):
  File "/usr/local/lib/python3.8/dist-packages/cv2/__init__.py", line 28, in __load_extra_py_code_for_module
    py_module = importlib.import_module(module_name)
  File "/usr/lib/python3.8/importlib/__init__.py", line 127, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "/usr/local/lib/python3.8/dist-packages/cv2/typing/__init__.py", line 169, in <module>
    LayerId = cv2.dnn.DictValue
AttributeError: module 'cv2.dnn' has no attribute 'DictValue'

System details:

Ubuntu 20.04
kernel 5.4.0-91-generic
conda 23.7.2
Intel Xeon Gold 6126 CPU @ 2.60GHz (2 sockets)
Nvidia RTX6000 (CUDA 11.2)
192GB RAM

Any suggestions?

Hi @gustrain ! What conda command are you using to install (the one that hangs?)

Hi @andrewilyas -- thanks for the quick reply!
I'm running conda create -y -n ffcv python=3.9 cupy pkg-config libjpeg-turbo opencv pytorch torchvision cudatoolkit=11.3 numba -c pytorch -c conda-forge as suggested in the FFCV readme.

Interesting, that command seems to work for me, with the difference being that I am on CUDA 11.6. I'm not 100% sure but  there might be a compatibility issue between PyTorch 2.0 and CUDA 11.2 - can you try updating CUDA to 11.6 and see if the issue persists?

I updated CUDA, but this unfortunately did not seem to make any difference. I'll see if it just needs a bit more time, but as of right now it just seems to be spinning on "Solving environment," as it was doing before.
How long should the installation take when successful?

So it should terminate in like a day or so, this is something we experienced a few versions ago but should have been fixed a while back now. What version of CUDA are you on now?  If it's not too much trouble, can you try separating out the steps? So first installing pytorch using the instructions from pytorch.org, and then running conda install cupy pkg-config libjpeg-turbo opencv numba -c conda-forge?

Hi @andrewilyas, I followed your suggestions and find that it is the libjpeg-turbo package that is halting my installation. Specifically, i was able to create a conda environment and install all other requirements (other than libjpeg-turbo). For the last step, I was running:
conda install -c conda-forge libjpeg-turbo

I get the following results, which keeps hanging:

any suggestions on how to solve this.

@andrewilyas thanks for the package! I was wondering if ffcv is now compatible with newer versions of python (3.11) and torch 2.0?


Added SharpDX Direct2D sample

Hi @SamuelEnglard, I'm your friendly neighborhood Microsoft Pull Request Bot (You can call me MSBOT). Thanks for your contribution!

In order for us to evaluate and accept your PR, we ask that you sign a contribution license agreement. It's all electronic and will take just minutes. I promise there's no faxing. https://cla.microsoft.com.

TTYL, MSBOT;

@SamuelEnglard, Thanks for signing the contribution license agreement so quickly! Actual humans will now validate the agreement and then evaluate the PR.
Thanks, MSBOT;

Can we have a readme, or the like, so people understand the requirements (compile time, run time on a user machine, etc...) to run the sample?

Added the spaces and a README


egg

I agree

egg

...no

https://user-images.githubusercontent.com/116702642/198414879-657c5d53-487d-47c6-ba1b-ab4aa690f93b.mp4

lolwhy

...no

what are you doing with ur life

...no

First.of.all.Your.Jordan.s.are.Fake-.onlinevideoconverter.com.mp4

...no

First.of.all.Your.Jordan.s.are.Fake-.onlinevideoconverter.com.mp4

just close this bruh

He ain’t gonna do it
so we have to wait for shadow Mario to do the move

just close this bruh

He ain’t gonna do it so we have to wait for shadowmario to do the move

We do a little


Adds support for overriding the new cf color variables coming to cf-buttons.

:+1:

Thanks for the review! :smile:


exception name consistency

I see 2 different exception strings but the meaning is the same
"invalid excess blob gas" : "Error in field: excessBlobGas",
      "invalid excessBlobGas" : "Error in field: excessBlobGas",

Nice - should be changed here:
https://github.com/ethereum/execution-spec-tests/blob/main/tests/cancun/eip4844_blobs/test_excess_blob_gas.py#L518

also the names are too general like this one:
invalid transaction  referes actually to an invalid blob transaction. and within inside the transaction could be much more exceptions. I suggest using exception codes like INVALID_TR_1  that will refer to particular exception  string

also here you put an expected exception, but the returned exception is actually different
Error: insufficient_account_balance Not found in client response to postmine block tweak!
Import result of postmine block:
'Error importing raw rlp block: max priority fee per gas higher than max fee per gas: address 0xa94f5374Fce5edBC8E2a8697C15331677e6EbF0B, maxPriorityFeePerGas: 8, maxFeePerGas: 7',
 Test Expected:
'insufficient funds for gas * price'
 (cancun/eip4844_blobs/001-fork=Cancun--exact_balance_minus_1-tx_max_fee_per_blob_gas=1-no_calldata-tx_value=0-tx_max_priority_fee_per_gas=8, fork: Cancun, block: 1)

Error: Invalid params Not found in client response to postmine block tweak!
Import result of postmine block:
'Error importing raw rlp block: blob transaction with zero blobs',
 Test Expected:
'unknown block type'
 (cancun/eip4844_blobs/000-fork=ShanghaiToCancunAtTime15k-no_blob_tx, fork: ShanghaiToCancunAtTime15k, block: 1)

Can be that Invalid params in the produced test stands for multiple different exceptions. such as invalid block encoding and tx with 0 blobs.

fixed now with the PR


Make sure formatting is applied to std-bits projects

[ci no changelog needed]
Pull Request Description
@radeusgd discovered that no formatting was being applied to std-bits projects.
This was caused by the fact that enso project didn't aggregate them. Compilation and
packaging still worked because one relied on the output of some tasks but
sbt> javafmtAll

didn't apply it to std-bits.
Important Notes
Apart from build.sbt no manual changes were made.
Checklist
Please include the following checklist in your PR:

[ ] The documentation has been updated if necessary.
[x] All code conforms to the
Scala,
Java,
and
Rust
style guides.
All code has been tested:

[ ] Unit tests have been written where possible.
[ ] If GUI codebase was changed: Enso GUI was tested when built using BOTH
./run.sh ide dist and ./run.sh ide watch.

@4e6 Thanks for noticing those


Too colourful?

I'm finding these templates a bit too colourful if we compare them to the original ones. Cycling through the various templates I noticed that neutral colours such as white are not very commonly used.
Take base16-nord for example:
In http://chriskempson.com/projects/base16/

In vim with vim-base16:

In nvim  with nvim-base16 with treesitter turned off:

In nvim  with nvim-base16 with treesitter turned on:

And this is pretty much the same with all the schemes

There's a few things going on here.
First for the regular non-treesitter highlights, most of the highlight groups are the same, but there was a few places where I diverged from vim-base16 such as the string in your screenshot (I would argue green strings is more correct than red based on styling guidelines), line number column, and a few other places. That being said, when I get the chance I'll go back through the normal highlight groups since I may have diverged a bit too much since I focused on following the styling guidelines than following the other base16 repos.
Second, the treesitter highlights had no guide so again I focused on styling guidelines which is quite vague. For example, the html tag in vim-base16 uses base05 while I use base0A for TSTag, it's not clear which colour should be used (it could also be base08). Again, when i get the chance I'll take a look through to see if I can get things closer to the guidelines.
Third, you won't see much normal colour when using treesitter, everything is a node in the syntax tree.


Fix precedence of attrs on assignment expr in stmt position

Heya, we think this may have caused a breakage due to a differing AST for attributes preceding a assignment expression. Is this expected / WAI?
https://github.com/twitchyliquid64/usbd-hid/issues/32


fix SharedMemory on Win32 platforms

don't close the mapped file handle cause the mapped file can not be opened from another process. This fixes the sharing of memory needed to synchronize realm file access between windows processes

good point will fix


Standardizing new content type names across the CMS fields

Hi @teddybradford:
I made a list of all the instances that I could find of fields that are titled with the older content type names that I would really love to get changed to match the new content type names. My apologies for the length of this, but it seemed to make more sense to keep these items together. Thanks SO much, and please just let me know if anything is unclear:

In Universal - Calendar Items, can you please change the names of these two fields: "Pages (Important Dates)" to "Universal - Pages" and "Date Group" to "Universal - Calendar Item Group":

In Universal - Orientation Program items, can you please change the name of the field "Pages(Programs)" to "Universal - Pages"

In Universal - Post-Enrollment Info items, can you please delete the "Pages(Important Dates)" field, since we have the "Universal - Pages" field

In Universal - Providence General Info items, can you please delete the "Pages(Programs)" field, since we have the "Universal - Pages" field

In Universal - Providence Specifics items, can you please change the name of the field "Pages(Transportation" to "Universal - Pages"

In Universal - RISD Resources/Offices items, can you please delete the "Pages(Programs)" field, since we have the "Universal - Pages" field

In Universal - Stories, can you please change the name of the field "Pages" to "Universal - Pages"

For Phase 1 - Secondary Nav items and Phase 2 - Secondary Nav items, can we just have the following fields:

"Name"
"Universal - Pages"
"Phase 1 Navigation"
"Phase 2 Navigation"
and with the "Phase 1 Navigation" field can we say something like "type "Main Nav" in this field for this page(s) to display in this section of the Phase 1 Navigation"
and with the "Phase 2 Navigation" field can we say something like "type "Main Nav" in this field for this page(s) to display in this section of the Phase 2 Navigation"

A little backstory: Right now I need Universal - Post-Enrollment Info items to still have the "Date Group" field - because I have three of these items still sitting on http://congratulations.risd.edu/next-steps/next-steps-to-enroll under the "More Info" header. Soon, though, we will have a page with additional (non date-based general planning info for students) that I'm working on here: https://risd-undergraduate-welcome.risd.systems/_wh_previews/pages/e0da5ab9-d75c-ccd8-9179-2bad8880f218/ and once this is live I will take the "More Info" items off of this page: http://congratulations.risd.edu/next-steps/next-steps-to-enroll/ and we'll be able to remove the "Date Group" field from the Universal -
Post-Enrollment Info items (since Post-Enrollment items aren't date based). Given these future events, can we possibly add a field for Universal - Post-Enrollment items that will allow for them to fall under a given header?  Right now, on https://risd-undergraduate-welcome.risd.systems/_wh_previews/pages/e0da5ab9-d75c-ccd8-9179-2bad8880f218/ the items fall under the "More Info" header (because I have the 3 "More Info" items on that page - that are also on http://congratulations.risd.edu/next-steps/next-steps-to-enroll/ but I'll be taking those three items off of the next steps to enroll page and it would be great to be able to choose a header for all the items on https://risd-undergraduate-welcome.risd.systems/_wh_previews/pages/e0da5ab9-d75c-ccd8-9179-2bad8880f218/ And when we do take those 3 items off of the next steps to enroll page we can then also delete "More Info" as a Universal - Calendar Item Group. Phew! hope that wasn't too confusing, but please just let me know if it was. So I guess the first step here would be enabling a header to be added to Universal - Post-Enrollment Info items.

For Universal - Pages items, can you take the following fields and change their names:

"Stories" to "Universal - Stories"
"Programs" to "Universal - Orientation Programs"
"RISD Resources/Offices" to "Universal - RISD Resources/Offices"
"Providence General Info" to "Universal - Providence General Info"
"Resources" to "Universal - Images Gallery"
"Alumni Bios" to "Universal - Alumni Bios"
"Lists" to "Universal - Graphic Alumni Lists"
"Important Dates" to "Universal - Calendar Items"
"Information Snippets" to "Universal - Providence Specifics"
"Post-Enrollment Info" to "Universal - Post-Enrollment Info"

and these three, which are at the very bottom of the page, can be deleted

Universal - Post-Enrollment Info (Pages (Important Dates))
Universal - RISD Resources/Offices (Pages (Programs))
Universal - Providence General Info (Pages (Programs))

THANK YOU SO SO MUCH!

@cmiller02 I've tackled 1-8, and 10. There were a few tricky things that had to happen due to limitations of Webhook CMS, but I think I was able to get everything working properly with the updated naming scheme.
We should revisit 9 next week. I'm a little unclear as to what exactly you want, so we can go over that together.

Hey @teddybradford - sorry for the confusion on #9.
Let me see if I can make this clearer with some images:
So right now we have this page: http://congratulations.risd.edu/next-steps/next-steps-to-enroll/#early-decision which looks like this:

We want to change this page to take the More Info stuff at the bottom off of it. I have already put these items on another page, that I just haven't published yet and that looks like this:

Before I publish this page, though, I'm wondering if you can do two things for me:

(per my other Github issue) can you please make it so the audience filter can work for this page:
 (more info in the other Github issue)
This page is made up of Universal - Post-Enrollment Info items, and the "Date Group" field:
 for these items doesn't make sense anymore. (If you recall we pulled the Universal - Post-Enrollment Info items out from being within Calendar Items, so for them to still have the "Date Group" field (which stems from the Universal Calendar Item Groups) doesn't make sense (basically Universal - Post-Enrollment Info items are NOT date based). So, I'm wondering if you can remove the "Date Group" field from Universal - Post-Enrollment Items. But, once you do that, I'll still need a way to make a header appear on this page:
 (We'll want to just have the text read something other than More Info at the top) So, I'm wondering if you can create a field that enables a header so that we can make whatever text we want, instead of More Info, appear at the top. Does this make sense?

Also, was wondering if you could look back to 1. in my first comment - I put the second part of the request in bold. (Not sure if you saw that that one had two parts to it).
THANKS SO SO MUCH FOR ALL THESE DETAILS and if you want to talk over the phone at some point, if this still is too crazy to follow, please just let me know.

@cmiller02 Thanks for clarifying that. I've gone ahead and updated the systems site. I've enabled the audience filter for post-enrollment info as per #17. There's also now a field in the pages content type that let's you specify a post-enrollment info title. If no title is entered there, it will default to "More Info" on the page.

Also, was wondering if you could look back to 1. in my first comment - I put the second part of the request in bold. (Not sure if you saw that that one had two parts to it).

The first item you listed in this issue? I don't see any bold text. Can you copy+paste the bit that I missed?

Hey @teddybradford - I just got out of a meeting and am so excited about all the progress you've made! Thank you! Sorry, I must have forgotten to save the bold. Here's what I think you might have missed:
In Universal - Calendar Items, can you please change the name of the field called "Date Group" to instead be "Universal - Calendar Item Group"
The audience filter and header look great!

Finished! 🏁


[tool_crash] FileSystemException: Failed to decode data using encoding 'utf-8', null

Command
flutter pub get

Steps to Reproduce

flutter pub get
Console display:

Failed to send crash report due to a network error: SocketException: OS Error: 信号灯超时时间已到
, errno = 121, address = clients2.google.com, port = 53398
Oops; flutter has exited unexpectedly: "FileSystemException: Failed to decode data using encoding 'utf-8', path =
'C:\flutter\.pub-cache\hosted\pub.flutter-io.cn\path_provider_android-2.0.14\android\src\main\java\io\flutter\plugins\pa
thprovider\PathProviderPlugin.java'".

Deleting the corresponding dependency will work normally

Several dependent individual files will be prompted like this
Logs
FileSystemException: Failed to decode data using encoding 'utf-8', null
#0      _File._tryDecode (dart:io/file_impl.dart:564:7)
#1      _File.readAsStringSync (dart:io/file_impl.dart:584:7)
#2      ForwardingFile.readAsStringSync (package:file/src/forwarding/forwarding_file.dart:96:16)
#3      AndroidPlugin._getSupportedEmbeddings (package:flutter_tools/src/platform_plugins.dart:186:53)
#4      AndroidPlugin._supportedEmbeddings (package:flutter_tools/src/platform_plugins.dart:133:49)
#5      AndroidPlugin._supportedEmbeddings (package:flutter_tools/src/platform_plugins.dart)
#6      AndroidPlugin.toMap (package:flutter_tools/src/platform_plugins.dart:127:30)
#7      _extractPlatformMaps (package:flutter_tools/src/flutter_plugins.dart:341:40)
#8      _writeAndroidPluginRegistrant (package:flutter_tools/src/flutter_plugins.dart:357:5)
#9      injectPlugins (package:flutter_tools/src/flutter_plugins.dart:1082:11)
<asynchronous suspension>
#10     FlutterProject.ensureReadyForPlatformSpecificTooling (package:flutter_tools/src/project.dart:335:5)
<asynchronous suspension>
#11     PackagesGetCommand.runCommand (package:flutter_tools/src/commands/packages.dart:177:5)
<asynchronous suspension>
#12     FlutterCommand.run.<anonymous closure> (package:flutter_tools/src/runner/flutter_command.dart:1140:27)
<asynchronous suspension>
#13     AppContext.run.<anonymous closure> (package:flutter_tools/src/base/context.dart:150:19)
<asynchronous suspension>
#14     CommandRunner.runCommand (package:args/command_runner.dart:209:13)
<asynchronous suspension>
#15     FlutterCommandRunner.runCommand.<anonymous closure> (package:flutter_tools/src/runner/flutter_command_runner.dart:288:9)
<asynchronous suspension>
#16     AppContext.run.<anonymous closure> (package:flutter_tools/src/base/context.dart:150:19)
<asynchronous suspension>

[✓] Flutter (Channel stable, 2.8.1, on Microsoft Windows [Version 10.0.19042.1526], locale zh-CN)
    • Flutter version 2.8.1 at C:\flutter
    • Upstream repository https://github.com/flutter/flutter.git
    • Framework revision 77d935af4d (5 months ago), 2021-12-16 08:37:33 -0800
    • Engine revision 890a5fca2e
    • Dart version 2.15.1
    • Pub download mirror https://pub.flutter-io.cn
    • Flutter download mirror https://storage.flutter-io.cn

[!] Android toolchain - develop for Android devices (Android SDK version 30.0.2)
    • Android SDK at E:\workApps\android-sdk-windows-new
    ✗ cmdline-tools component is missing
      Run `path/to/sdkmanager --install "cmdline-tools;latest"`
      See https://developer.android.com/studio/command-line for more details.
    ✗ Android license status unknown.
      Run `flutter doctor --android-licenses` to accept the SDK licenses.
      See https://flutter.dev/docs/get-started/install/windows#android-setup for more details.

[✓] Chrome - develop for the web
    • Chrome at C:\Program Files\Google\Chrome\Application\chrome.exe

[✓] Visual Studio - develop for Windows (Visual Studio Community 2022 17.1.4)
    • Visual Studio at E:\workApps\Visual-studio-m
    • Visual Studio Community 2022 version 17.1.32407.343
    • Windows 10 SDK version 10.0.19041.0

[✓] Android Studio (version 4.1)
    • Android Studio at E:\workApps\android studio
    • Flutter plugin can be installed from:
      🔨 https://plugins.jetbrains.com/plugin/9212-flutter
    • Dart plugin can be installed from:
      🔨 https://plugins.jetbrains.com/plugin/6351-dart
    • Java version OpenJDK Runtime Environment (build 1.8.0_242-release-1644-b01)

[✓] IntelliJ IDEA Ultimate Edition (version 2021.1)
    • IntelliJ at E:\workApps\IntelliJ IDEA 2021.1.2
    • Flutter plugin version 65.2.2
    • Dart plugin version 211.7798

[✓] VS Code (version 1.67.2)
    • VS Code at C:\Users\Administrator\AppData\Local\Programs\Microsoft VS Code
    • Flutter extension version 3.40.0

[✓] Connected device (4 available)
    • YAL AL10 (mobile) • ERLDU20423010578 • android-arm64  • Android 10 (API 29)
    • Windows (desktop) • windows          • windows-x64    • Microsoft Windows [Version 10.0.19042.1526]
    • Chrome (web)      • chrome           • web-javascript • Google Chrome 101.0.4951.67
    • Edge (web)        • edge             • web-javascript • Microsoft Edge 98.0.1108.56
    ! Device <IP_ADDRESS>:5555 is not authorized.
      You might need to check your device for an authorization dialog.

! Doctor found issues in 1 category.

Flutter Application Metadata
Type: malformed
Version: 1.0.0+1
Material: true
Android X: true
Module: true
Plugin: false
Android package: com.example.flutter_module
iOS bundle identifier: com.example.flutterModule
Creation channel: null
Creation framework version: null
Plugins
path_provider-2.0.10
path_provider_android-2.0.14
path_provider_ios-2.0.9
path_provider_linux-2.1.6
path_provider_macos-2.0.6
path_provider_windows-2.0.6
permission_handler-8.3.0
vibration-1.7.4-nullsafety.0
vibration_web-1.6.3-nullsafety.0
webview_flutter-3.0.4
webview_flutter_android-2.8.8
webview_flutter_wkwebview-2.7.5

Closing this as duplicate of https://github.com/flutter/flutter/issues/65021

Closing this as duplicate of #65021

I tried deleting Flutter plugins file, but it seems useless.
I don't know how to deal with it now.
Failed to send crash report due to a network error: SocketException: OS Error: 信号灯超时时间已到
, errno = 121, address = clients2.google.com, port = 51638
Oops; flutter has exited unexpectedly: "FileSystemException: Failed to decode data using encoding 'utf-8', path =
'C:\flutter\.pub-cache\hosted\pub.flutter-io.cn\shared_preferences_android-2.0.12\android\src\main\java\io\flutter\plugi
ns\sharedpreferences\SharedPreferencesPlugin.java'".


App crashes when given no input for Server URL

The app crashes when the user has not entered a Server URL (Text Field for the Server URL input is empty) and pressed enter button. Which should not happen. Instead an error message should be shown. I would like to work on this issue.

Good catch!
The intended behavior is that the button is disabled.
Feel free to work on this!

@borisyankov I will send a PR in some time.
And I just wanted to know the procedure for sending proposal for GSOC 2018 for this project? Thanks.

According to the timeline here https://developers.google.com/open-source/gsoc/timeline you have about a month before you can send a proposal.
The most successful students in the past did contribute several PRs before doing the proposal.
Not only was their proposal on-point, but we also were assured the student is motivated and skilled.

@borisyankov Thanks.

@zulipbot claim

@zulipbot claim

@zulipbot abandon

@zulipbot claim --force

Hello @sd1998 are you still working on it? If not, please abandon it so that I can pick this up.

This is fixed. Closing the issue.


Add a note about a known issue.

Mention https://github.com/apache/beam/issues/28318  in release notes.

R: @liferoad or @damccorm


The deprecation of the YouTube JavaScript Player API

The deprecation of the YouTube JavaScript Player API was announced on January 27, 2015. YouTube Flash  embeds have also been deprecated. See the deprecation policy for more information. Please migrate your applications to the IFrame API, which can intelligently use whichever embedded player – HTML () or Flash () – the client supports.

Source: https://developers.google.com/youtube/js_api_reference

Good thing we already use IFrame API :+1:

\e/


User interface has trouble loading upon auto-opening UI in Firefox

When running the binary the user interface is opened in the default browser at localhost:8000.
The UI does open up, but for Firefox the user interface is (most of the times) not fully loaded but looks like this:

The user interface actually shows up before turning completely white. But not the complete interface, only the outer parts without the trade and history components.
Upon refresh everything loads correctly.
With Chrome I never had this problem, only Firefox.
I checked the rocket triggers and on_ignite should be correct for our use-case. But somehow it seems the user-interface may not be fully served directly after the launch.

This was fixed with https://github.com/itchysats/itchysats/pull/2273


[RESOLVED] High ICMP ping response time

Problem started at 11:02:16 on 2023.08.14
Problem name: High ICMP ping response time
Host: ST-FG
Severity: Warning
Operational data: Value: 491ms
Original problem ID: 36135
Event details in Zabbix: http://<IP_ADDRESS>/tr_events.php?triggerid=23135&eventid=36135

Problem has been resolved in 6m 0s at 11:08:16 on 2023.08.14
Problem name: High ICMP ping response time
Host: ST-FG
Severity: Warning
Original problem ID: 36135


Update to Commanders Act version 5

As a member of the analytics team I want results to be gathered with the new Commanders Act platform requiring version 5 of the SDKs to be running in mobile applications.
Acceptance criteria

The Commanders Act SDK has been updated.
Integration documentation has been updated if needed.
The SDK is available on GitHub.
Integrators have been notified about the change and the deadline.

Remark: Server-side tags need to be migrated as well for the whole integration to work. Handled by the GD.
Hints

Migration to V5 is documented. In particular the events are now not anonymous data dictionaries but are specifically defined with their associated data.
The list of available events is documented.

Tasks

[x] Update SDK.
[x] Gather examples to be able to discuss how each use case we support (page view, hidden event, streaming event) must be sent with v5.
[x] Ask for source key to use.
[x] Update instantiation.
[x] Update request interceptor.
[x] Update hidden event implementation.
[x] Update page view implementation.
[x] Update stream tracking implementation.
[x] Profile app launch time.
[x] Update integration documentation.
[x] Replace references to Tag Commander with Commanders Act.
[x] Remove prod / preprod environment flag. Callers must provide source keys for debug / production instead (and pick the correct one at initialization time).
[x] Use debug key in SRG Analytics demo.
[ ] Build and send fields which were previously built server-side, e.g. page_unique_name (if the feature is not provided by the new Commanders Act platform).
[x] Generate test data for Commanders Act (Play app with v5) sent to debug source keys.
[ ] If SRG SSR debug / production source keys are known to be fixed provide constants for them.
[ ] Related to TCCore 5.x versions, update documentation to provide information about NSBluetoothPeripheralUsageDescription and NSBluetoothAlwaysUsageDescription keys in application Info.plist. Example: "The application should not use Bluetooth. Please don’t allow.".
[ ] Archive SRGSSR "Tag Commander" repositories.
[ ] Update to version 5.3.0+ and figure out a new name for the event title, conflicting with the reserved event_name from the SDK. Have a look at potential related decisions.

Some questions to Tag Commander:
About the initialization

Where can the source key be found in our case?
Will we need one source key per app or will each BU (or maybe the entire SRG SSR) only need one key for all apps?

General questions

Looking at the Android implementation it seems that any custom event parameter set might accidentally override existing official parameters like event_name, for example. This is something that was possible with version 4 of the SDK but can you confirm this is intended v5 behavior as well?
We assume that the same answer holds for the iOS / tvOS SDK. Correct?

Page views
We have looked at TCPageViewEvent and we think it should match our needs for page view measurements, as follows:

The page titles are sent under the content_title key with v4 and are technical non-localized page identifiers (e.g. home or player). We therefore think we should send them in page_type with v5. Is it a good idea?
We are currently not sending any pretty page title, thus we think we should leave page_name empty. Correct?
We are currently sending other values under other keys and we will send them to v5 in the same way. Some of them are currently processed server-side (e.g. navigation levels which are concatenated together to produce a new identifier) and we assume these rules will be migrated to the new platform as is. Correct?

Hidden events
Hidden events are any kind of other tracked events we are currently sending (e.g. the user clicked on some button related to some feature). For those we think we should use TCCustomEvent:

The event_name should be set to hidden_event. Is it a good idea?
We are currently sending other values but the keys we are using conflict with official Commanders Act SDK keys (e.g. event_name and event_id). For those we probably need new keys (e.g. hidden_event_name and hidden_event_id) and it is likely that the mapping to Mapp will need to be updated accordingly. Alternatively, we could use page_type to convey the event name (e.g. favorite_add for a tracked button used to add some item to user favorites) instead of introducing a custom parameter name. Which approach would be preferrable?

Streaming events
For those we think we should use TCCustomEvent:

The kind of streaming event (e.g. play, pause, etc.) could be sent in event_name. Is it a good idea?
The rest of the values would be sent in other parameters, as we do today.

We'll define a production / test source key pair for the SRG account, which must be supplied when configuring the tracker.

I had a look at our tracker configuration to see whether we could hide the source key internally (release / test). But I am not sure this is a good idea, we should likely treat it like we did with the container. The API is namely already complicated enough (we have prod / preprod flag, source keys are not known for some BUs yet, and we also have a unit test flag).
I am also not sure having a test source key built with SRG Analytics would be helpful (except for us during the initial validation). So adding it would only add confusion IMHO.
If we obtain one key per BU we could harcode them but otherwise we should likely still ask them at startup time. This is similar to what we were doing with the container until now anyway.

I had to avoid using _attribute((constructor)) in unit tests since the new Commander Act SDK would otherwise deadlock if initialized from such a function.

As discussed with Commanders Act we currently filter and map some fields server-side (e.g. page_unique_name or fields which are nullable). This feature is not available yet but might be delivered next month. If missing we must be prepared to implement some logic client-side.

@defagos neither Letterbox Web nor TP have ever sent the media_embedding_environment property to TagCommander.

I tried to switch to the official SPM repository with version 5.2.1.
https://github.com/CommandersAct/iOSV5/releases/tag/5.2.1
TCCore is still linked to <CoreBluetooth/CoreBluetooth.h>:
TCCore.xcframework/tvos-arm64/TCCore.framework/Headers/TCNetworkManager.h:#import <CoreBluetooth/CoreBluetooth.h>
TCCore.xcframework/tvos-arm64_x86_64-simulator/TCCore.framework/Headers/TCNetworkManager.h:#import <CoreBluetooth/CoreBluetooth.h>
TCCore.xcframework/ios-arm64_x86_64-simulator/TCCore.framework/Headers/TCNetworkManager.h:#import <CoreBluetooth/CoreBluetooth.h>
TCCore.xcframework/ios-arm64/TCCore.framework/Headers/TCNetworkManager.h:#import <CoreBluetooth/CoreBluetooth.h>

So applications needs to add NSBluetoothPeripheralUsageDescription and NSBluetoothAlwaysUsageDescription NSBluetoothAlwaysUsageDescription to the Info.plist to avoid "ITMS-90683: Missing purpose string in Info.plist".
But this official SPM repository has TCCore by default, which use IDFA and linked to `AdSupport! (see #51).

Update to Commanders Act 5.2.2.
https://github.com/CommandersAct/iOSV5/releases/tag/5.2.2
✅ TCServerSide_noIDFA product is used. The library is not linked to AdSupport anymore.
⚠ TCCore is still linked to <CoreBluetooth/CoreBluetooth.h>.
Checking unit tests, global default labels are now fixed: used internally with SRGIdentity logged account.

@defagos @StaehliJ I've updated to TG 5.3.1 versions (SPM issue again with 5.2.2), and apply the event_title renamed for hidden event "name", before to the flatten payload and the conflict with the reserved event_name from the SDK.
When change validated, we should change on both platforms (Apple and Android), maybe on the third one too, the web JS.  I could be involve if needed. https://github.com/SRGSSR/pillarbox-documentation/issues/26

Meeting with Julius, Mario and @StaehliJ and @waliid to clarify and update specifications:
1. PageView event
- event_name : page_view (TC predefined key)
- SDK: TCPageViewEvent
- In TC server, for MAPP Page View destination filter: event_name is page_view

2. Media events
- event_name : play, pause , stop, pos, uptime, seek, eof
- SDK: TCCustomEvent
- In TC server, for MAPP Media destination filter: media_urn exists

3. Custom events
- event_name : Event name example (ScrollTo, ButtonClicked, favorite_add, …)
- SDK: TCCustomEvent
- In TC server, for MAPP Event destination filter: event_name is not page_view AND media_urn doesn't exit

For iOS, we'll:

remove "hidden_event"
remove "event_title"
Set event_name as the custom event name.

During a mapping review in TagCommander server V2, the content_title replaced by page_type is an issue. I fixed 2 times.
After a meeting with Julius, Mario, 2 MAPP consultants, 1 Commander Act consultant, they all spoke about page_name and page_type.
Like the TC example, type and name for a page a common convention.
From documentation in confluence and SRF News iOS app code, and regarding mapping:
| SRG current property | SDK TCPageView property | mandatory |
| ------ | ------ | ------ | ------ |
| content_title | page_name | pageName | true |
| content_page_type | page_type | pageType | false |
For sure, type ≠ title/name
We could add the page_type in the public API as pageType (String). Or ignore and set pageType to null.
Example from SRF News (UDP):

content_page_type= "Artikel"
content_title = "feuerwehren-kaempfen-weiter-braende- halten-griechenland-und-tuerkei-weiter-in-atem"

Example from SRF News (Webtrekk):

content_page_type= "Landingpage"
content_title = "uebersicht"

Update after a meeting with Julius and Mario:

Page views
We have looked at TCPageViewEvent and we think it should match our needs for page view measurements, as follows:

The page titles are sent under the content_title key with v4 and are technical non-localized page identifiers (e.g. home or player). We therefore think we should send them in page_type with v5. Is it a good idea?
We are currently not sending any pretty page title, thus we think we should leave page_name empty. Correct?
We are currently sending other values under other keys and we will send them to v5 in the same way. Some of them are currently processed server-side (e.g. navigation levels which are concatenated together to produce a new identifier) and we assume these rules will be migrated to the new platform as is. Correct?

Answers for ADI DG team

No. Leave null for now. But Mario will check to set is as Mandatory: As it's described in the SRG specification. maybe content_page_type property.
No, content_title has to move to page_name. Still Mandary, String.
All transformations do server side V1 has been be done now also server side V2.

Page view title is set to page_name property.
ADI teams asked to set page_type as mandatory.
Should we add it in the global send page view method?

I tried to switch to the official SPM repository with version 5.2.1. https://github.com/CommandersAct/iOSV5/releases/tag/5.2.1
TCCore is linked to <CoreBluetooth/CoreBluetooth.h>:
grep -r CoreBluetooth/CoreBluetooth.h TCCore.xcframework
[…]
So applications needs to add NSBluetoothPeripheralUsageDescription and NSBluetoothAlwaysUsageDescription to the Info.plist to avoid "ITMS-90683: Missing purpose string in Info.plist".
[…]
UPDATE: TagCommander team is working on an improvement for TCServerSide-noIDFA and SPM.

iOSV5 Commanders Act version for SPM makes dependency to TCore with a different version value.

CA v 5.2.1: TCCore 5.2.0: https://github.com/CommandersAct/iOSV5/blob/5.2.1/TCCore/5/2/0/TCCore.zip Issue.
CA v 5.2.2: TCCore 5.2.1: https://github.com/CommandersAct/iOSV5/blob/5.2.2/TCCore/5/2/1/TCCore.zip No more issue.

So not need anymore to add Bluetooth descriptions in info plist.


Add UIView+Swizzle file

UIApplication receives all the events from the app and therefore is notified when you remove your finger from the screen after a responder object is removed from the hierarchy.
TODO: Have to properly understand how UIApplication dispatches events to UIWindow. [ will do it at the end of the week when I have finished other important tasks ] ✅
Video
https://github.com/bandlab/TouchVisualizer/assets/84300828/3165c454-9b18-4392-ae32-61734bd2b550

@kolyasev Please do help me merge the changes once review is done because I do not have access 🙈

@Aranoledur can you please help to merge the changes.


[homeassistant.components.http.ban] Login attempt or request with invalid authentication from ...

Hi,
I'm using python3 version Python 3.5.2 and HAS 0.48.0.
I read somewhere that this issue should have been fixed in version 1.45.1 but unfortunately it still seems to exist. Only when using an api password.
Any ideas how to fix this?
Regards,
Peter

Closing this issue because the issue template has not been used.


Add ok to JSON result

Codecov Report

Merging #28 (77ccbc2) into main (4bdd3b0) will increase coverage by 0.18%.
The diff coverage is 100.00%.

@@            Coverage Diff             @@
##             main      #28      +/-   ##
==========================================
+ Coverage   86.37%   86.56%   +0.18%
==========================================
  Files           9        9
  Lines         499      506       +7
==========================================
+ Hits          431      438       +7
  Misses         56       56
  Partials       12       12

Impacted Files
Coverage Δ

internal/workspace/process/result.go
93.26% <100.00%> (+0.48%)
:arrow_up:

Help us with your feedback. Take ten seconds to tell us how you rate us. Have a feature suggestion? Share it here.


Add git stash

In Telescope we have git_stash command to look for available stashes. It would be nice to have something like this here too.

Thank you!

https://github.com/ibhagwan/fzf-lua/commit/23034bb022b28fb26e07532ad99ecdd6681095f6 - added a new command git_stash.
Default commands:
<CR> - git stash apply (requires confirmation with y)
<C-x> - drop a stash

Multi-select is disabled since dropping multiple stashes messes up the numbering of stashes (due to pop) and therefore can cause unintended consequences, same goes for applying multiple patches.

 - drop a stash

Maybe we could have a shortcut for pop?

drop a stash

Maybe we could have a shortcut for pop?

Added a new action git_stash_pop, defaults stay the same, you can either define a new keybind or change the default action (to pop instead of apply):
require'fzf-lua'.setup{
  git = {
    stash = {
      actions = {
        ["default"] = require'fzf-lua'.actions.git_stash_pop,
      },
    },
  }
}

Thanks!


RFC: lookup prebuilt releases by commit hash rather than tag

I'm experimenting with the prebuilt release feature and it's really great. There's only one issue: I'd like to create a binary archive for every commit, but this means that every commit also needs a corresponding tag. Would it be possible to look up releases by commit instead of by tag?
Looking at the Github API, this is maybe not straightforward: they provide a way to get the release corresponding to a tag, but not to a commit. We could query all the releases and filter them, but that's not nice either.

Is it really worthwhile to have a prebuilt release for every commit? I would suggest building nightlies and using a scheduled GitHub action to generate a tag and release every night for the latest commit.

Since Lean dependency management is based on commit hashes atm, it would be nice to guarantee that the specific commit used by a dependent project has a prebuilt release. But mathlib now uses a different mechanism to cache build artifacts, including dependencies, so this is even less urgent than before.

The Lake repository is being deprecated and its issues transferred to leanprover/lean4. As this issue is stale and while likely be addressed in more broad-scoped fashion via a Lake-based successor to lake exe cache, I am closing it instead of transferring it. Feel free to reopen a similar issue over on leanprover/lean4.


Add basic backend support

Is this functional enough to try out with a custom portal, or should I instead look to making my own helpers on top of zbus?

We have diverged quite a lot in main and simplified the whole process, it should be much simpler to add new portals backend support. Regarding the demo, I think we should keep it as simple as possible, so bringing gtk is a bit too much.
Thanks for starting this initiative though, closing.


active player's PlayerInfo on top

This will help players to stay focus on their info.
Bewteen player's info and the rest we could add the turn order. Something like :
nevlas, baltaks, terrans(passed)

That was almost what I did, but then I wanted to insert the turn order in between the first player's info and the others, but I wasn't able


@alloy - Various QA for ArtworkFilter

Thanks for the detailed issues!
Also closes #155

Awesome ✨


add laCymNodo2

Assembly review request

ToLID: laCymNodo2
Species: Cymodocea nodosa
Project: ERGA-BGE
Affiliation: Genoscope

Ok

Yes

Hi @bistace,
I have looked through laCymNodo2 and here's what I think:
SUPER_2
746-768 Kbp possible small retained haplotype
I think your SUPER_2_unloc_1 can join in the gap @ 18.3Mb in -ve orientation
SUPER_3
26.63 - end belongs on RH end of SUPER_5 in other orientation
SUPER_7
9.408-9.424Mb, possible small retained haplotype
Break in gap @ 19.97Mb and join this piece to LH end of SUPER_7
SUPER_10
4.55-4.59Mb approx, looks like retained haplotype
SUPER_12
10.891-10.907Mb, possible small retained haplotype
SUPER_13
5.35-5.37Mb, possible small retained haplotype
SUPER_15
Looks like incorrect join @ 3.28Mb, flip from 0-3.28Mb and join to RH end
scaffold_31 can be placed on SUPER_15, and potentially goes in the gap created from the above break. This isn’t 100% certain though as it could go in at either gap at 2.69, or 2.63 so might be better left as unlocalised.
SUPER_16
Break @ 6.22Mb, flip 0-6.22 and rejoin
SUPER_17
0-236Kb approx looks like it should move to SUPER_17 @ approx 2.79Mb
3.976Mb - I think this looks like the telomeres are joined so needs breaking here, and 3.97 to end moving to start (there is affinity at this point to other telos)
10-4-10.6 approx looks like it needs to be flipped
SUPER_18
I think this needs a bit more investigation:
If the telomeric sequence at the start of SUPER_18 is definitely correct, then the hic mappings indicate that there is also potentially telomeric sequence @ 1.428Mb (hic mapping indicates they may join)
I would suggest to break @ 1.428Mb, and then flip from 1.428 to end and rejoin. The resulting new join looks to have a similar amount of hic data mapping to it in the map to the current one @ 1.428Mb.
Thanks,
Sarah

Hi @bistace,
Please take a careful look at the excellent review from @SarahPelan. Related to SUPER_18, hopefully regenerating the plot after the flipping will fix the Telo signal.
A few things I wanted to point out:
. Why the QV and Kmer completeness in the pre-curation assembly are showing such a low values?
. It is nice to have the unloc at the end on begginign of each chromosome
Just a heads-up. We updated the make_EAR and yaml files, now is easier to enter the Assembly and Curation tools used :)

Hello and thank you for your review!
I agree with all your suggestions and have made the changes. The Pretext map and the EAR are being generated and should be ready tomorrow.
@diegomics It seems that I gave the wrong input directory for the pre-curation stats, this will be fixed in the next iteration of the EAR report. I agree with the unlocs needing to be at the end of chromosomes, the 'preserve order' checkbox was apparently not enabled when I generated the AGP and this will also be fixed with the corrected map. Thank you for updating the make_EAR script and yaml, I will need to integrate it into our pipeline so this will be a bit slower than the rest!

Hello and sorry for the delay!
I did the modifications on the SUPER_18 scaffold but the telomeric signal did not appear and the contacts seem to indicate that the region is flipped. The updated Pretext map includes this modification but I think that it would look better by flipping back the region.

Thanks for generating the EAR PDF with the new script @bistace !!
I think the super 15 looks better like this:

Let's wait for @SarahPelan feedback :)

Hi @bistace
Apologies for the delay in re-looking at this one - I was off last week.
I think:
SUPER_3
Still think the rh end looks incorrect  and 26.63 - end of SUPER_3 belongs on RH end of SUPER_5 in other orientation
SUPER_10
4.55-4.59Mb approx, looks like retained haplotype still - if you’d prefer to leave as is then that’s fine
SUPER_15
10.26-13.53Mb (end of chr) needs flipping as @diegomics  says
SUPER_16
Still need to break @ ~6.2Mb, flip 0-6.22Mb and rejoin
SUPER_18
I agree that the region at the start looks like it should be flipped back.
Also, I noticed there is scaffold_31_unloc_1 - It belongs in SUPER_15 - possibly a scaffold painting issue in pretext - I frequently do this!!
Thanks,
Sarah

Hi @SarahPelan, thank you again for your review and no worries for the delay, I hope that you had a great time!
@diegomics nice catch for the SUPER_15, I did not see it!
I've updated the EAR and Pretext map to include your modifications. For the SUPER_3, I've moved only a portion of the region to the end of SUPER_5 because I think that, even though it shows some contacts, moving the entire region does not make a nice diagonal appear like at the end of SUPER_3.

Hi @bistace please check the link, I think the pretext file is not updated

Hi, I reuploaded the map so the link should work correctly now!

Hi @bistace
I have rechecked, I think you missed off some unloc tags?
SUPER_2
27.4-end of chr, either needs to be broken and tagged as unloc, or joined in @ ~18.3Mb
SUPER_5
25.5-chr end, needs to be in other orientation.  Then, the addition of the remaining  small piece from the end of SUPER_3  looks good across the diagonal

SUPER_7
24.1-end of chr,needs to be broken off and tagged as unloc
SUPER_10
18.9-end of chr,needs to be broken off and tagged as unloc
SUPER_17
Looks like there is some retained hap between 6.4-6.6Mb
Also, SUPER_18
This now has a telo tag @ ~1.4Mb, sequence from ~1.4Mb onwards appears to have contacts to other telomeres so I think it is probably telomere here.
I think that there is probably telomere on both sides of the gap, and the piece from 0-1.4Mb actually belongs on the other end (same orientation).  Would you be able to check?  This doesn’t look great on the hic map when it’s moved, but there could be data missing from this new resulting join between ~10.37Mb and 0Mb.
If moved, I think the overall patterning of the contacts across SUPER_18 then looks more consistent with the other chromosomes, I've added a screenshot and circled the patterning I mean - I hope it makes sense

SUPER_19 painted by mistake as a chromosome?
Thanks,
Sarah

Hi @SarahPelan,
I checked the SUPER_18 situation and I agree with you that moving the start to the end makes the contacts look a bit more like other chromosomes.
I searched for telomeric repeats and they appear to be located before the gap (I found only three TTTAGGG repetitions 6kb after the gap). Do you think that the region before the gap should still be moved at the end of the chromosome?

Hi @bistace
Yes, I think that whole section 0-1.4ish of SUPER_18 should move to the end.
Even though there are telo repeats only before the gap, the hic contacts suggest that the sequence after the gap is also telo.  We quite often see these mis-joins around the telomere with it looking as though the join should be where the assembler has placed it, but due to the telo tags, we can be confident that these in fact are the ends.
I hope that make sense..
I think it's likely that there is data missing across the new join which is why you aren't getting the nice diagonal mappings.
Thanks,
Sarah

Ok, I will move this section then and I will regenerate the EAR and Pretext map! Thank you again for your review and very helpful comments.

no problem :)

Hello,
I applied the requested changes and updated the EAR report and Pretext map. After moving the part at the end of SUPER_3 to SUPER_5, the end of SUPER_3 now shows contact with the end of several other chromosomes so I moved the part you indicated @SarahPelan and did not apply any further modifications to  the SUPER_3 scaffold.

Thanks @bistace for another nice Genoscope assembly! I want to take a moment to point out the extraordinary review by @SarahPelan 🙌


paperless-ngx: re-add xdist

Without it the tests run in ~12 1/2 minutes. With it and max 8 cores they only take 2 1/2 minutes but sometimes fail. Lets max at 4 which takes 3 1/2 minutes. Upstream maxes at 16 by default which doesn't work for us.

Things done

Built on platform(s)

[x] x86_64-linux
[ ] aarch64-linux
[ ] x86_64-darwin
[ ] aarch64-darwin

For non-Linux: Is sandboxing enabled in nix.conf? (See Nix manual)

[ ] sandbox = relaxed
[ ] sandbox = true

[x] Tested, as applicable:

NixOS test(s) (look inside nixos/tests)
and/or package tests
or, for functions and "core" functionality, tests in lib/tests or pkgs/test
made sure NixOS tests are linked to the relevant packages

[ ] Tested compilation of all packages that depend on this change using nix-shell -p nixpkgs-review --run "nixpkgs-review rev HEAD". Note: all changes have to be committed, also see nixpkgs-review usage
[ ] Tested basic functionality of all binary files (usually in ./result/bin/)
25.05 Release Notes (or backporting 24.11 and 25.05 Release notes)

[ ] (Package updates) Added a release notes entry if the change is major or breaking
[ ] (Module updates) Added a release notes entry if the change is significant
[ ] (Module addition) Added a release notes entry if adding a new NixOS module

[x] Fits CONTRIBUTING.md.

Add a :+1: reaction to pull requests you find important.

@ofborg build paperless-ngx


Sometimes mute doesn't work

Describe the bug
Sometimes when using /mute the player does not become muted
To Reproduce
Steps to reproduce the behavior:

Have someone load in
Try to mute them, sometimes it works and sometimes it doesn't

Expected behavior
The player is expected to be muted
Server Info:

Server Version: 4278
Client Version: canary
Client Build: b2372

Additional context
Happens randomly, no absolute reproducible steps

Doubt there's a real fix for this unless a server side native is added to mute players

Damn that's unlucky :/