Unable to Install eukdetect

(eukdetect) [mchege@crcfe01 tests]$ python test_eukdetect.py
.FFF.
FAIL: test_class (main._02_RunRunall)
Traceback (most recent call last):
File "test_eukdetect.py", line 26, in test_class
self.assertTrue(code==0, msg=stderr)
AssertionError: False is not true : b'01/20/2023 14:54:14:  Parsing config file ...\nTraceback (most recent call last):\n  File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/bin/eukdetect", line 33, in \n    sys.exit(load_entry_point('EukDetect==1.0.1', 'console_scripts', 'eukdetect')())\n  File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/EukDetect-1.0.1-py3.6.egg/eukdetect/runall.py", line 88, in main\nFileNotFoundError: [Errno 2] No such file or directory: 'tests/configfile_for_tests.yml'\n'
======================================================================
FAIL: test_class (main._03_RunAlnCmd)
Traceback (most recent call last):
File "test_eukdetect.py", line 33, in test_class
self.assertTrue(code ==0, msg=stderr)
AssertionError: False is not true : b'01/20/2023 14:54:14:  Parsing config file ...\nTraceback (most recent call last):\n  File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/bin/eukdetect", line 33, in \n    sys.exit(load_entry_point('EukDetect==1.0.1', 'console_scripts', 'eukdetect')())\n  File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/EukDetect-1.0.1-py3.6.egg/eukdetect/runall.py", line 88, in main\nFileNotFoundError: [Errno 2] No such file or directory: 'tests/configfile_for_tests.yml'\n'
======================================================================
FAIL: test_class (main._04_RunAln_and_filter)
Traceback (most recent call last):
File "test_eukdetect.py", line 44, in test_class
self.assertTrue(alncode==0 and filtercode == 0, msg=alnstderr + filterstderr)
AssertionError: False is not true : b'01/20/2023 14:54:14:  Parsing config file ...\nTraceback (most recent call last):\n  File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/bin/eukdetect", line 33, in \n    sys.exit(load_entry_point('EukDetect==1.0.1', 'console_scripts', 'eukdetect')())\n  File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/EukDetect-1.0.1-py3.6.egg/eukdetect/runall.py", line 88, in main\nFileNotFoundError: [Errno 2] No such file or directory: 'tests/configfile_for_tests.yml'\n01/20/2023 14:54:14:  Parsing config file ...\nTraceback (most recent call last):\n  File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/bin/eukdetect", line 33, in \n    sys.exit(load_entry_point('EukDetect==1.0.1', 'console_scripts', 'eukdetect')())\n  File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/EukDetect-1.0.1-py3.6.egg/eukdetect/runall.py", line 88, in main\nFileNotFoundError: [Errno 2] No such file or directory: 'tests/configfile_for_tests.yml'\n'

Ran 5 tests in 2.852s
FAILED (failures=3)
(eukdetect) [mchege@crcfe01 tests]$

Thanks for reaching out. The error you're getting is that there isn't a file in the 'tests' directory named 'configfile_for_tests.yml'. This is included in the eukdetect repo so should be present unless you've moved or renamed it. Can you check it's still there (and that you've edited it to add the directory where you've put the database)?

Hey Allind,
I am still getting an error with my installation:
(eukdetect) [mchege@crcfe01 EukDetect]$ ls
build                   dist             eukdb      EukDetect.egg-info                LICENSE    rules     tests
default_configfile.yml  environment.yml  eukdetect  eukdetect_pipeline_schematic.pdf  README.md setup.py
(eukdetect) [mchege@crcfe01 EukDetect]$ cd tests/
(eukdetect) [mchege@crcfe01 tests]$ nano configfile_for_tests.yml
(eukdetect) [mchege@crcfe01 tests]$ cd ..
(eukdetect) [mchege@crcfe01 EukDetect]$ python tests/test_eukdetect.py
.FFF.
FAIL: test_class (main._02_RunRunall)
Traceback (most recent call last):
File "tests/test_eukdetect.py", line 26, in test_class
self.assertTrue(code==0, msg=stderr)
AssertionError: False is not true : b'01/25/2023 02:42:33:  Parsing config file ...\nTraceback (most recent call last):\n  File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/bin/eukdetect", line 33, in \n    sys.exit(load_entry_point('EukDetect==1.0.1', 'console_scripts', 'eukdetect')())\n  File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/EukDetect-1.0.1-py3.6.egg/eukdetect/runall.py", line 89, in main\n  File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/yaml/init.py", line 114, in load\n    return loader.get_single_data()\n  File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/yaml/constructor.py", line 49, in get_single_data\n    node = self.get_single_node()\n  File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/yaml/composer.py", line 39, in get_single_node\n    if not self.check_event(StreamEndEvent):\n  File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/yaml/parser.py", line 98, in check_event\n    self.current_event = self.state()\n  File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/yaml/parser.py", line 174, in parse_document_start\n    self.peek_token().start_mark)\nyaml.parser.ParserError: expected '', but found ''\n  in "tests/configfile_for_tests.yml", line 6, column 1\n'
======================================================================
FAIL: test_class (main._03_RunAlnCmd)
Traceback (most recent call last):
File "tests/test_eukdetect.py", line 33, in test_class
self.assertTrue(code ==0, msg=stderr)
AssertionError: False is not true : b'01/25/2023 02:42:33:  Parsing config file ...\nTraceback (most recent call last):\n  File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/bin/eukdetect", line 33, in \n    sys.exit(load_entry_point('EukDetect==1.0.1', 'console_scripts', 'eukdetect')())\n  File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/EukDetect-1.0.1-py3.6.egg/eukdetect/runall.py", line 89, in main\n  File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/yaml/init.py", line 114, in load\n    return loader.get_single_data()\n  File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/yaml/constructor.py", line 49, in get_single_data\n    node = self.get_single_node()\n  File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/yaml/composer.py", line 39, in get_single_node\n    if not self.check_event(StreamEndEvent):\n  File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/yaml/parser.py", line 98, in check_event\n    self.current_event = self.state()\n  File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/yaml/parser.py", line 174, in parse_document_start\n    self.peek_token().start_mark)\nyaml.parser.ParserError: expected '', but found ''\n  in "tests/configfile_for_tests.yml", line 6, column 1\n'
======================================================================
FAIL: test_class (main._04_RunAln_and_filter)
Traceback (most recent call last):
File "tests/test_eukdetect.py", line 44, in test_class
self.assertTrue(alncode==0 and filtercode == 0, msg=alnstderr + filterstderr)
AssertionError: False is not true : b'01/25/2023 02:42:34:  Parsing config file ...\nTraceback (most recent call last):\n  File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/bin/eukdetect", line 33, in \n    sys.exit(load_entry_point('EukDetect==1.0.1', 'console_scripts', 'eukdetect')())\n  File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/EukDetect-1.0.1-py3.6.egg/eukdetect/runall.py", line 89, in main\n  File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/yaml/init.py", line 114, in load\n    return loader.get_single_data()\n  File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/yaml/constructor.py", line 49, in get_single_data\n    node = self.get_single_node()\n  File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/yaml/composer.py", line 39, in get_single_node\n    if not self.check_event(StreamEndEvent):\n  File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/yaml/parser.py", line 98, in check_event\n    self.current_event = self.state()\n  File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/yaml/parser.py", line 174, in parse_document_start\n    self.peek_token().start_mark)\nyaml.parser.ParserError: expected '', but found ''\n  in "tests/configfile_for_tests.yml", line 6, column 1\n01/25/2023 02:42:34:  Parsing config file ...\nTraceback (most recent call last):\n  File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/bin/eukdetect", line 33, in \n    sys.exit(load_entry_point('EukDetect==1.0.1', 'console_scripts', 'eukdetect')())\n  File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/EukDetect-1.0.1-py3.6.egg/eukdetect/runall.py", line 89, in main\n  File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/yaml/init.py", line 114, in load\n    return loader.get_single_data()\n  File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/yaml/constructor.py", line 49, in get_single_data\n    node = self.get_single_node()\n  File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/yaml/composer.py", line 39, in get_single_node\n    if not self.check_event(StreamEndEvent):\n  File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/yaml/parser.py", line 98, in check_event\n    self.current_event = self.state()\n  File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/yaml/parser.py", line 174, in parse_document_start\n    self.peek_token().start_mark)\nyaml.parser.ParserError: expected '', but found ''\n  in "tests/configfile_for_tests.yml", line 6, column 1\n'

Ran 5 tests in 1.197s
FAILED (failures=3)
(eukdetect) [mchege@crcfe01 EukDetect]$ cd tests/
(eukdetect) [mchege@crcfe01 tests]$ nano configfile_for_tests.yml
(eukdetect) [mchege@crcfe01 tests]$ cd ..
(eukdetect) [mchege@crcfe01 EukDetect]$ python tests/test_eukdetect.py
.FFF.
FAIL: test_class (main._02_RunRunall)
Traceback (most recent call last):
File "tests/test_eukdetect.py", line 26, in test_class
self.assertTrue(code==0, msg=stderr)
AssertionError: False is not true : b'01/25/2023 02:47:21:  Parsing config file ...\nTraceback (most recent call last):\n  File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/bin/eukdetect", line 33, in \n    sys.exit(load_entry_point('EukDetect==1.0.1', 'console_scripts', 'eukdetect')())\n  File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/EukDetect-1.0.1-py3.6.egg/eukdetect/runall.py", line 89, in main\n  File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/yaml/init.py", line 114, in load\n    return loader.get_single_data()\n  File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/yaml/constructor.py", line 49, in get_single_data\n    node = self.get_single_node()\n  File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/yaml/composer.py", line 39, in get_single_node\n    if not self.check_event(StreamEndEvent):\n  File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/yaml/parser.py", line 98, in check_event\n    self.current_event = self.state()\n  File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/yaml/parser.py", line 174, in parse_document_start\n    self.peek_token().start_mark)\nyaml.parser.ParserError: expected '', but found ''\n  in "tests/configfile_for_tests.yml", line 6, column 1\n'
======================================================================
FAIL: test_class (main._03_RunAlnCmd)
Traceback (most recent call last):
File "tests/test_eukdetect.py", line 33, in test_class
self.assertTrue(code ==0, msg=stderr)
AssertionError: False is not true : b'01/25/2023 02:47:21:  Parsing config file ...\nTraceback (most recent call last):\n  File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/bin/eukdetect", line 33, in \n    sys.exit(load_entry_point('EukDetect==1.0.1', 'console_scripts', 'eukdetect')())\n  File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/EukDetect-1.0.1-py3.6.egg/eukdetect/runall.py", line 89, in main\n  File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/yaml/init.py", line 114, in load\n    return loader.get_single_data()\n  File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/yaml/constructor.py", line 49, in get_single_data\n    node = self.get_single_node()\n  File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/yaml/composer.py", line 39, in get_single_node\n    if not self.check_event(StreamEndEvent):\n  File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/yaml/parser.py", line 98, in check_event\n    self.current_event = self.state()\n  File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/yaml/parser.py", line 174, in parse_document_start\n    self.peek_token().start_mark)\nyaml.parser.ParserError: expected '', but found ''\n  in "tests/configfile_for_tests.yml", line 6, column 1\n'
======================================================================
FAIL: test_class (main._04_RunAln_and_filter)
Traceback (most recent call last):
File "tests/test_eukdetect.py", line 44, in test_class
self.assertTrue(alncode==0 and filtercode == 0, msg=alnstderr + filterstderr)
AssertionError: False is not true : b'01/25/2023 02:47:21:  Parsing config file ...\nTraceback (most recent call last):\n  File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/bin/eukdetect", line 33, in \n    sys.exit(load_entry_point('EukDetect==1.0.1', 'console_scripts', 'eukdetect')())\n  File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/EukDetect-1.0.1-py3.6.egg/eukdetect/runall.py", line 89, in main\n  File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/yaml/init.py", line 114, in load\n    return loader.get_single_data()\n  File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/yaml/constructor.py", line 49, in get_single_data\n    node = self.get_single_node()\n  File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/yaml/composer.py", line 39, in get_single_node\n    if not self.check_event(StreamEndEvent):\n  File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/yaml/parser.py", line 98, in check_event\n    self.current_event = self.state()\n  File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/yaml/parser.py", line 174, in parse_document_start\n    self.peek_token().start_mark)\nyaml.parser.ParserError: expected '', but found ''\n  in "tests/configfile_for_tests.yml", line 6, column 1\n01/25/2023 02:47:21:  Parsing config file ...\nTraceback (most recent call last):\n  File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/bin/eukdetect", line 33, in \n    sys.exit(load_entry_point('EukDetect==1.0.1', 'console_scripts', 'eukdetect')())\n  File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/EukDetect-1.0.1-py3.6.egg/eukdetect/runall.py", line 89, in main\n  File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/yaml/init.py", line 114, in load\n    return loader.get_single_data()\n  File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/yaml/constructor.py", line 49, in get_single_data\n    node = self.get_single_node()\n  File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/yaml/composer.py", line 39, in get_single_node\n    if not self.check_event(StreamEndEvent):\n  File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/yaml/parser.py", line 98, in check_event\n    self.current_event = self.state()\n  File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/yaml/parser.py", line 174, in parse_document_start\n    self.peek_token().start_mark)\nyaml.parser.ParserError: expected '', but found ''\n  in "tests/configfile_for_tests.yml", line 6, column 1\n'

Ran 5 tests in 1.077s
FAILED (failures=3)
(eukdetect) [mchege@crcfe01 EukDetect]$ ls
build                   dist             eukdb      EukDetect.egg-info                LICENSE    rules     tests
default_configfile.yml  environment.yml  eukdetect  eukdetect_pipeline_schematic.pdf  README.md setup.py
(eukdetect) [mchege@crcfe01 EukDetect]$ cd eukdb
(eukdetect) [mchege@crcfe01 eukdb]$ ls
busco_taxid_link.txt                     ncbi_eukprot_met_arch_markers.fna.3.bt2       taxa.sqlite
marker_genes_per_species.csv             ncbi_eukprot_met_arch_markers.fna.4.bt2       taxa.sqlite.traverse.pkl
ncbi_eukprot_met_arch_markers.fna        ncbi_eukprot_met_arch_markers.fna.rev.1.bt2   taxdump_1_14_2020.tar.gz
ncbi_eukprot_met_arch_markers.fna.1.bt2  ncbi_eukprot_met_arch_markers.fna.rev.2.bt2
ncbi_eukprot_met_arch_markers.fna.2.bt2  specific_and_inherited_markers_per_taxid.txt
(eukdetect) [mchege@crcfe01 eukdb]$ cd ..
(eukdetect) [mchege@crcfe01 EukDetect]$ cd tests/
(eukdetect) [mchege@crcfe01 tests]$ ls
configfile_for_tests.yml  test_eukdetect.py  test_R1.fastq.gz  test_R2.fastq.gz
(eukdetect) [mchege@crcfe01 tests]$ nano configfile_for_tests.yml
(eukdetect) [mchege@crcfe01 tests]$ ls
configfile_for_tests.yml  test_eukdetect.py  test_R1.fastq.gz  test_R2.fastq.gz

EukDetect_Troubleshoot.txt

(base) [mchege@crcfe01 eukdb]$ cd ..
(base) [mchege@crcfe01 EukDetect]$ conda activate eukdetect
(eukdetect) [mchege@crcfe01 EukDetect]$ ls
build                   dist             eukdb      EukDetect.egg-info                LICENSE    rules     tests
default_configfile.yml  environment.yml  eukdetect  eukdetect_pipeline_schematic.pdf  README.md setup.py
(eukdetect) [mchege@crcfe01 EukDetect]$ pwd
/afs/crc.nd.edu/group/ArchieLab/Mary/EukDetect
(eukdetect) [mchege@crcfe01 EukDetect]$ cd tests/
(eukdetect) [mchege@crcfe01 tests]$ ls
configfile_for_tests.yml  test_eukdetect.py  test_R1.fastq.gz  test_R2.fastq.gz
(eukdetect) [mchege@crcfe01 tests]$ nano configfile_for_tests.yml
(eukdetect) [mchege@crcfe01 tests]$ cd ..
(eukdetect) [mchege@crcfe01 EukDetect]$ python tests/test_eukdetect.py
.....
Ran 5 tests in 61.068s
OK

Hey Allind,
It has finally worked and onto the next steps !!

Hey Allind/Eukdetect,
I am kindly getting this when I run my samples. what could be the problem?
Empty read count file. Likely no aligned reads in the sample.
SRR1747042_filtered_hits_eukfrac.txt (END)
Kind regards,
On Wed, Jan 25, 2023 at 12:35 AM Abigail Lind @.***>
wrote:

Thanks for reaching out. The error you're getting is that there isn't a
file in the 'tests' directory named 'configfile_for_tests.yml'. This is
included in the eukdetect repo so should be present unless you've moved or
renamed it. Can you check it's still there (and that you've edited it to
add the directory where you've put the database)?
—
Reply to this email directly, view it on GitHub
https://github.com/allind/EukDetect/issues/35#issuecomment-1402717249,
or unsubscribe
https://github.com/notifications/unsubscribe-auth/AUPGWQBRVNBKJPSMRWDBRJTWUBDI5ANCNFSM6AAAAAAUB56EVI
.
You are receiving this because you authored the thread.Message ID:
@.***>

--
Mary Chege
(MSc. Bioinformatics and Molecular biology )
One Health Centre,
Institute of Primate Research,
Karen, Nairobi.

Hi Mary, thanks for your patience. That's not an error message - that means that there were no detected eukaryotic reads in your sequencing.

Awesome, thanks!
On Wed, Feb 8, 2023 at 12:58 AM Abigail Lind @.***>
wrote:

Hi Mary, thanks for your patience. That's not an error message - that
means that there were no detected eukaryotic reads in your sequencing.
—
Reply to this email directly, view it on GitHub
https://github.com/allind/EukDetect/issues/35#issuecomment-1421514117,
or unsubscribe
https://github.com/notifications/unsubscribe-auth/AUPGWQD3X65CKYIDVDGV23LWWLAPXANCNFSM6AAAAAAUB56EVI
.
You are receiving this because you modified the open/close state.Message
ID: @.***>

--
Mary Chege
(MSc. Bioinformatics and Molecular biology )
One Health Centre,
Institute of Primate Research,
Karen, Nairobi.

Hey Abigail,
I hope that you are well.
I just finished running my samples on the pipeline, out of the 48 samples
(about 1.4 billion reads), only 14 samples aligned with about 1 taxon in
each sample. The rest of the samples either indicated "No taxa passing
filter requirement" and the rest indicated "Empty reads". I couldn't
understand these considering it is a high read depth.
I have checked on the pre-filtering intermediate files, and I can see that
some samples that ticked for "No taxa passing filter requirement", have a
reasonable number of hits, yet they did not pass for alignment.
Kindly advise me on this.
Kind regards,
On Wed, Feb 8, 2023 at 11:01 AM Mary Chege @.***> wrote:

Awesome, thanks!
On Wed, Feb 8, 2023 at 12:58 AM Abigail Lind @.***>
wrote:

Hi Mary, thanks for your patience. That's not an error message - that
means that there were no detected eukaryotic reads in your sequencing.
—
Reply to this email directly, view it on GitHub
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or unsubscribe
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.
You are receiving this because you modified the open/close state.Message
ID: @.***>

--
Mary Chege
(MSc. Bioinformatics and Molecular biology )
One Health Centre,
Institute of Primate Research,
Karen, Nairobi.

--
Mary Chege
(MSc. Bioinformatics and Molecular biology )
One Health Centre,
Institute of Primate Research,
Karen, Nairobi.

Hi Mary,
Would you be open to sharing all of the output from eukdetect with me? I can look through everything and see if there might be something going on. You can compress the folder and email it to me at<EMAIL_ADDRESS>Best,
Abigail


A Working Project Without Google Play Services

I've successfully remove the google play service from alkitab project. I've found that the google play service library is used mainly for Tracking and Sync. If I remove the tracking, should we change to another library? And for sync, I found that it use gcm key as the id. How can we change the id without using gcm at all?
Thank you for your wonderful project.
Related issue: #39 #43
God bless you.

I've forked the project and clean up the google play service. Still waiting confirmation about the Tracking and Sync features.
https://github.com/joielechong/androidbible

Yes, the Google services are used for tracking and receiving push
notifications.
You can remove the tracking, but in order for the app to always have the
latest update of the bookmarks etc, the GCM is needed. Otherwise, the app
will only check for updates each time it is started. If you are okay with
this,you can remove GCM as well.
On Mar 14, 2017 14:40, "Joielechong"<EMAIL_ADDRESS>wrote:

I've successfully remove the google play service from alkitab project.
I've found that the google play service library is used mainly for Tracking
and Sync. If I remove the tracking, should we change to another library?
And for sync, I found that it use gcm key as the id. How can we change the
id without using gcm at all?
Thank you for your wonderful project.
God bless you.
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Cut v1.21.5+k3s1

Summary:
Task covering patch release work.
Dev Complete: 09/08/2021
List of required releases:
To release as soon as able for QA:

v1.21.5-rc1+k3s1

To release once have approval from QA:

v1.21.5+k3s1 (Never release on a Friday unless specified otherwise)

Prep work:

[x] PM: Dev and QA team to be notified of the incoming releases - add event to team calendar
[x] PM: Dev and QA team to be notified of the date we will mark the latest release as stable - add event to team calendar [ONLY APPLICABLE FOR LATEST MINOR RELEASE]
[x] QA: Review changes and understand testing efforts
[x] Release Captain: Prepare release notes in our private release-notes repo (submit PR for changes taking care to carefully check links and the components, once merged, create the release in GitHub and mark as a draft and check the pre-release box, fill in title, set target release branch, leave tag version blank for now until we are ready to release)
[x] QA: Validate and close out all issues in the release milestone.

Vendor and release work:

[x] Release Captain: Vendor in the new patch version and release rancher/kubernetes
[x] Release Captain: Tag and release any necessary RCs for QA to test K3s and KDM on the Rancher side
[x] Release Captain: Tag and release when have QA approval

Post-Release work:

[x] Release Captain: Once release is fully complete (CI is all green and all release artifacts exist), edit the release, uncheck "Pre-release", and save.
[x] Release Captain: Prepare PRs as needed to update KDM in the appropriate dev branches.
[x] PM: Close the milestone in GitHub.

Closing this out as Chris has done the KDM PR


Make feature selection specific to feature sets

With nkululeko, you can

combine feature sets
select specific features by name

Now what's missing is a way to say:

i want all features from set a (e.g. embeddings)
and these two special features from set b (e.g. Praat)

done with 0.48.0


Gyfcat 403 Errors

When doing anything involving a large number of Gfycat urls, you will eventually get 403 errors that persist until your IP changes. This occurs even when only extracting urls, and only using one download thread. I'm not sure how to fix it, but maybe a timeout between option downloads would work?

This could be it: https://old.reddit.com/r/gfycat/comments/e61gw0/latency_issues_investigating/?st=k3xd64zz&sh=f89fea7f

This could be it: https://old.reddit.com/r/gfycat/comments/e61gw0/latency_issues_investigating/?st=k3xd64zz&sh=f89fea7f

That's probably it, though in my experience it's still a problem regardless, albeit much less severe & in many fewer scenarios

I'm still having this issue...

anyone find a fix?

This problem still exists. After few requests gfycat sends 403, stopping download and waiting a bit resets DDOS protecion.  As there is no way to add delays between requests ripme gets stuck in 403.


184 mops csv to json scripts

Hi, could you please look at the code? Thanks!

I have had a look. All of the proposed commits are self-contained and should be fine except for one. There is a change in the CompChemParser to do with getting elements' molecular weight by their symbol. I remember an issue with this arising from multiple letter symbols. I believe Aleks and I implemented a temporary fix several months back, but Daniel subsequently fixed it on develop. Daniel, could you confirm this? If so, I would not change the parser. Otherwise, we will need to double check if we want to accept the changes from Aleks' branch.

I have just had a look, and indeed that issue was fixed by you Angiras :) and is already on develop. I have suggested changes that Aleks needs to make to the "thermo/CoMoCompChemParser/compchemparser/helpers/elements_data.py" file. Once that is done I am happy for his code to be merged.


WIP: Bumped Mesos package to 1.7.0-rc2 for testing.

High-level description
This PR is being used to aid in testing of the 1.7.0-rc2 release of Mesos. This PR will be closed when testing is complete.

@mesosphere-mergebot bump-ee


Consider a virtual DOM approach

https://github.com/Matt-Esch/virtual-dom
https://github.com/tmpvar/jsdom

Dupe


Feature bookstore styling

In this milestone, I did the following task:
Added any missing JSX elements to my project (without adding extra functionality)
My final design  matches zeplin's design (this includes all elements + the same styling)
I used the CSS rules detailed in Zeplin to style the website.
Fix Linter issues
Update readme

@ShadyShawkat  I want to thank you for recognizing all my efforts  cheers and Happy code


Books page, replace JS alert with modal

Describe the task
Currently, when we click on delete button for a book, a JS alert appears for confirmation. We would like to replace it with a modal, that would ask users for deletion in the same manner, with a Yes and Cancel button. The background of Yes button should be red and text should be white in color. For the Cancel button, it should be gray background with white text

This issue is completed. Closing it.


Start building Calico API repo

This PR is the first step to build Calico API repo

I would have expected the full structures to be defined in pkg/apis/projectcalico/v3 and no need for the pkg/apis/projectcalico/v3/calico/ sub-backage. Is there a reason for that?

Yeah, I don't think I've got any reason why the package should be split up

I'm going to close this PR and open it again to trigger CI

Make sure to squash before merging @song-jiang !


Nginx 1.10 does not support OpenTracing. Nginx tracing need to be migrated to OpenTelemetry

Issue description
nginx ingress controller v1.10 breaks current Opentracing configuration:
nginx controller does not start with the following message:
-------------------------------------------------------------------------------
  Warning  RELOAD  117s  nginx-ingress-controller  Error reloading NGINX:
-------------------------------------------------------------------------------
Error: exit status 1
2024/03/02 09:56:48 [emerg] 27#27: unknown "opentracing_context_x_b3_traceid" variable
nginx: [emerg] unknown "opentracing_context_x_b3_traceid" variable
nginx: configuration file /tmp/nginx/nginx-cfg3140476767 test failed

According to 1.10 release notes

This version dropped Opentracing and zipkin modules, just Opentelemetry is supported as of this release

Testing nginx OpenTelemetry configuration
The following helm values can be used to activate nginx OpenTelemetry configuration
controller:
  podAnnotations:
    linkerd.io/inject: enabled

  # Allow snpippet anotations
  # From v1.9 default value has chaged to false.
  # allow-snippet-annotations: Enables Ingress to parse and add -snippet annotations/directives created by the user.
  # linkerd-viz ingress uses this annotations
  allowSnippetAnnotations: true

  config:
    # Open Telemetry
    enable-opentelemetry: "true"
    otlp-collector-host: tempo-distributor.tempo.svc.cluster.local
    otlp-service-name: nginx-internal
    # Print access log to file instead of stdout
    # Separating acces logs from the rest
    access-log-path: "/data/access.log"
    log-format-escape-json: "true"
    log-format-upstream: '{"source": "nginx", "time": $msec, "resp_body_size": $body_bytes_sent, "request_host": "$http_host", "request_address": "$remote_addr", "request_length": $request_length, "request_method": "$request_method", "uri": "$request_uri", "status": $status,  "user_agent": "$http_user_agent", "resp_time": $request_time, "upstream_addr": "$upstream_addr", "trace_id": "$opentelemetry_trace_id", "span_id": "$opentelemetry_span_id"}'
  # controller extra Volume
  extraVolumeMounts:
    - name: data
      mountPath: /data
  extraVolumes:
    - name: data
      emptyDir: {}
  extraContainers:
    - name: stream-accesslog
      image: busybox
      args:
      - /bin/sh
      - -c
      - tail -n+1 -F /data/access.log
      imagePullPolicy: Always
      resources: {}
      terminationMessagePath: /dev/termination-log
      terminationMessagePolicy: File
      volumeMounts:
      - mountPath: /data
        name: data

With this configuration access log entries contain trace_id and span_id.
{"source": "nginx", "time":<PHONE_NUMBER>.521, "resp_body_size": 560, "request_host": "emojivoto", "request_address": "<IP_ADDRESS>", "request_length": 512, "request_method": "GET", "uri": "/", "status": 200,  "user_agent": "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/<IP_ADDRESS> Safari/537.36", "resp_time": 0.009, "upstream_addr": "<IP_ADDRESS>:8080", "trace_id": "0739b6b5dac6d6bae83b0d9534eeed19", "span_id": "2a495451e6da1118"}
{"source": "nginx", "time":<PHONE_NUMBER>.620, "resp_body_size": 1785688, "request_host": "emojivoto", "request_address": "<IP_ADDRESS>", "request_length": 354, "request_method": "GET", "uri": "/js", "status": 200,  "user_agent": "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/<IP_ADDRESS> Safari/537.36", "resp_time": 0.080, "upstream_addr": "<IP_ADDRESS>:8080", "trace_id": "1f9bd4362d7207de85e9b13f191f2bc9", "span_id": "339547188e45c00d"}

With this changes the e2e test using linkerd, and emojivoto test application does not work.
E2E Trace context propagation is not working (nginx -> linkerd -> emojivoto application):

Propagation is only working between nginx and linkerd.

Ingress Nginx only supports w3c context propagation. B3 context propagation is not supported. See open issue https://github.com/kubernetes/ingress-nginx/issues/10324. B3 context propagation was used by emojivoto application and linkerd.

linkerd included support to w3c context in release 2.13. See https://github.com/linkerd/linkerd2/issues/5416. So if linkerd receives w3c headers it will be use that in the context.

Default emojivoto application is using opencensus and not opentelemety. It needs to be updated to support it. linkerd's developer for testing w3c propagation feature refactored emojivoto app to support opentelemetry. See https://github.com/linkerd/linkerd2-proxy/pull/2179#issuecomment-1402266875. That changes never were pushed to the  main branch of emojivoto app.

Pull Request #389 will fixed the issue, enabling the upgrade to 1.10.
New issue created to replace emojivoto application by other application supporting opentelemetry: #390


Add package nodesnim

E: nodesnim: a package by that name already exists.

You need to pick another name for your package.

It is already be added to packages+
https://github.com/nim-lang/packages/blob/80087047926e084dee35dc097c495be3c5827e8f/packages.json#L18795


Java_buildpack failed

Hi,
When I start pcfdev using "cf dev start -s scs" I get the following error:
←[31;1mFAILED←[0m
Error: failed to provision VM: Process exited with: 1. Reason was:  ().
in the provision.log file i see "Java_buildpack download failed".
I can still do the cf login, but do not see spring services like eureka or config server.
If I cf push a java application I get the same "Downloading java_buildpack failed" error.  But instead if I use "-b java_buildpack" option, application gets deployed successfully. That means getting a java buildpack doesn't seem to be issue.
I want to use spring services for my java project which I am not able to use.
I am using pcfdev-v0.26.0 windows version.
Thanks.

Can you provide the full output of cf dev start -s scs?

The output of the command is as follows.  Also attaching provision.log file.
PS C:\temp> cf dev start -s scs
Using existing image.
Allocating 8161 MB out of 16323 MB total system memory (9389 MB free).
Importing VM...
Starting VM...
Provisioning VM...
Waiting for services to start...
7 out of 52 running
7 out of 52 running
7 out of 52 running
35 out of 52 running
52 out of 52 running
?[31;1mFAILED?[0m
Error: failed to provision VM: Process exited with: 1. Reason was:  ().
PS C:\temp>
provision.txt

Hi @phduser, apologies for the delay.
Can you try starting the VM with more memory?
cf dev start -s scs -m 10000

You may have to free up some memory on your machine before you do this:
 (9389 MB free)

Closing due to inactivity.


Typo for FE_ALLEXCEPT

FE_ALLEXCEPT should be FE_ALL_EXCEPT

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

ID: f53f5e72-861c-7526-d1af-fae8f3402edc
Version Independent ID: 7b13b46e-33ba-5426-023e-d7a340ecf046
Content: feclearexcept1
Content Source: docs/c-runtime-library/reference/feclearexcept1.md
Product: visual-cpp
GitHub Login: @corob-msft
Microsoft Alias: corob

Thanks. This is a great issue to test your GitHub pull request skills on, too. :)

Good work! Thanks for driving higher quality into our docs.


Bundle size analysis

Would be nice to do some analysis of resulting bundle size in a real world application, considering basic case (1 page) and how it evolves as more pages are added.

This has been done, blog post in https://www.javierchavarri.com/js_of_ocaml-bundle-size-study/.


Improvement/sentry errors

Description
Stop reporting non-actionable errors on Sentry
Fixes #20443
Type of change

Chore (housekeeping or task changes that don't impact user perception)

How Has This Been Tested?

Manual

Test Plan

Add Testsmith test cases links that relate to this PR

Issues raised during DP testing

Link issues raised during DP testing for better visiblity and tracking (copy link from comments dropped on this PR)

Checklist:
Dev activity

[ ] My code follows the style guidelines of this project
[ ] I have performed a self-review of my own code
[ ] I have commented my code, particularly in hard-to-understand areas
[ ] I have made corresponding changes to the documentation
[ ] My changes generate no new warnings
[ ] I have added tests that prove my fix is effective or that my feature works
[ ] New and existing unit tests pass locally with my changes
[ ] PR is being merged under a feature flag

QA activity:

[ ] Test plan has been approved by relevant developers
[ ] Test plan has been peer reviewed by QA
[ ] Cypress test cases have been added and approved by either SDET or manual QA
[ ] Organized project review call with relevant stakeholders after Round 1/2 of QA
[ ] Added Test Plan Approved label after reveiwing all Cypress test

/ok-to-test sha=8da6c13

@Rishabh-Rathod It's a bit tough to reproduce some of the errors reported on the card. So I put checks to ensure there is no errors. We want to ensure user errors are also not picked up. So I tried to reproduce them but it seems we are already not picking up these errors -
api response error
query response error
Data source connection
Lint
Only time we were passing the errors to sentry was for the Cyclic dependency error which I removed.


Unix socket: add switch to disable adding the instance name to path

Feature Description
When creating a unix socket (-u), the name of the instance is concatenated to the path given by -u. This can cause an issue even if -u is very short: when using a long instance name, creating a UNIX socket can fail due to the length restriction.
(See also https://github.com/GoogleCloudPlatform/cloud-sql-proxy/issues/970)
This can be avoided if cloud-sql-proxy would allow the user to disable adding the instance name as an extra directory, which is done here:
https://github.com/GoogleCloudPlatform/cloud-sql-proxy/blob/c6830422a5b098871836e509e8c06c7972f49625/internal/proxy/proxy.go#L892
I was able to workaround my local issues by building a custom version with address = dir at that line.
It would be great if there would be a switch to control this.
If this is acceptable to you, I'll be happy to contribute a PR to implement this.
Sample code
No response
Alternatives Considered
No response
Additional Details
Related issue: https://github.com/GoogleCloudPlatform/cloud-sql-proxy/issues/970
With this simple change I can work with very long instance names:
https://github.com/eldad/cloud-sql-proxy/commit/950bb2a8e0502bd73dc0963fb1c6ed9e9eb78281
(obviously this behavior would need to be feature-flag controlled)

Hi, you are going to want to use the unix-socket-path parameter. This allows you to override the default socket path with your own, absolute path to the socket.
From the docs:
When necessary, you may specify the full path to a Unix socket. Set the
unix-socket-path query parameter to the absolute path of the Unix socket for
the database instance. The parent directory of the unix-socket-path must
exist when the Proxy starts or else socket creation will fail. For Postgres
instances, the Proxy will ensure that the last path element is
'.s.PGSQL.5432' appending it if necessary. For example,
      ./cloud-sql-proxy \
        'my-project:us-central1:my-db-server?unix-socket-path=/path/to/socket'

Thanks, I was not aware of this option!
It would be great if it would be at mentioned in the --help text.

It would be great if it would be at mentioned in the --help text

@eldad It is mentioned in the --help text, albeit somewhat hidden in the text.
https://github.com/GoogleCloudPlatform/cloud-sql-proxy/blob/c6830422a5b098871836e509e8c06c7972f49625/cmd/root.go#L160-L169

Hidden in plain sight :smile: My bad, I didn't even notice the whole text before the command line switches. Thanks again!


Add entry for University of Technology, Katowice, Poland --> wst.com.pl

The University of Technology in Katowice offers  3.5 year long IT related course at first university grade (according to Polish law). The course website in English can be found here: http://www.en.wst.com.pl/education_offer/computer_science.

@pansamolot Pull request merged. Thank you!

It is me who should thank you! :>


Ruby warnings ⚠

I was very much surprised to see tons of Ruby warnings when I run rubocop with RUBYOPT="-w".
So here's a fix for all of them that I see.

Nice work. I looked into some of this a few weeks back and only got around to making a couple of small tweaks.

This PR looks great and I'll merge it soon. There's something else to consider, though - seems we're missing some lint checks ourselves. RuboCop has always tried to emulate all built-in MRI lint checks and we haven't really checked what was added to recent Rubies. Ideally someone should figure this out and file some tickets to track the progress of implementing those missing checks.

@bbatsov Thank you for merging!
I don't see which ones you actually mean by "what was added to recent Rubies".
AFAIK we didn't add any new important warning in 2.4.
I only could find some trivial ones like
StringIO.new { } https://github.com/ruby/ruby/commit/7a5b56677a075677439fbfc61025ddf93ca708f8
or
using Module.new do end https://github.com/ruby/ruby/commit/b6b1038c6bc487b0b8f7d1675d02a22a4ee8f4b8
but I don't think RuboCop has to care about them.


Can't install nuget package from LiGet server

I'm running LiGet server and I've pushed one package to it which was generated by vcpkg.
When I try to install it (from VS2017 or with nuget.exe) I get following error:

An error occurred while retrieving package metadata for 'cc-license-manager_x86-windows-static_20190<IP_ADDRESS>' from source 'My Feed'.
Unable to cast object of type 'Newtonsoft.Json.Linq.JValue' to type 'Newtonsoft.Json.Linq.JArray'.

LiGet server can be found at https://nuget.cc-api.com/.
I'm not sure if problem is caused by nuget package itself or by LiGet.

Hi tomzo,
I just set up your LiGet server on CoreOS.
I've been evaluating BaGet and LiGet, and yours seems to be the way to go -thanks for all the effort (especially docker) you put into it.
I created (via Paket)/pushed/retrieved 3 packages:
A: XYZ.2.0.1.nupkg
B: XYZ.2.0.2.nupkg
C: XYZ.4.7.0.nupkg

Here are the results:
BaGet: had no issues (from what I'm recalling -this was about 2 month ago.  If it had an issue with (A), I don't recall it, sorry).
LiGet: I was able to push all 3 packages to your server, but when I attempted to retrieve them, I had errors for package (A).  The other 2 (B, C) had no issues when retrieving them.
The error (below output from Visual Studio 2015) is the same as was previously reported:
Error		An error occurred while retrieving package metadata for 'XYZ.2.0.1' from source 'CoreOS (.Net Core: NuGet server)'.
Unable to cast object of type 'Newtonsoft.Json.Linq.JValue' to type 'Newtonsoft.Json.Linq.JArray'.			0

I unzipped/diffed (A) with a "good" package (B -which is similar to C), and I see this difference:
(A):

XYZ
2.0.1
George H.
A 30 day logging utility.

(B):

XYZ
2.0.2
George H.
A 30 day logging utility.

Notice there is no  tag in (A), but there is one in (B) -also in (C).
Could this be causing the issue -I assume you must be parsing this tag to store dependencies in your SQLite DB, and the upload works fine, but not the download...?
Thanks,
George H.
02/07/2019 1:45pm ET

Hmmm.. looks like my XML embedded in my previous comment was deleted...?
It should have looked like this:
(A):
`

XYZ
2.0.1
George H.
A 30 day logging utility.

`
(B):
<?xml version="1.0" encoding="utf-8" standalone="yes"?> <package xmlns="http://schemas.microsoft.com/packaging/2011/10/nuspec.xsd">   <metadata>     <id>XYZ</id>     <version>2.0.2</version>     <authors>George H.</authors>     <description>A 30 day logging utility.</description>     <dependencies>       <group targetFramework="net35" />     </dependencies>   </metadata> </package>

Hi tomzo,
I just set up your LiGet server on CoreOS.
I've been evaluating BaGet and LiGet, and yours seems to be the way to go -thanks for all the effort (especially docker) you put into it.
I created (via Paket)/pushed/retrieved 3 packages:
A: XYZ.2.0.1.nupkg
B: XYZ.2.0.2.nupkg
C: XYZ.4.7.0.nupkg

Here are the results:
BaGet: had no issues (from what I'm recalling -this was about 2 month ago.  If it had an issue with (A), I don't recall it, sorry).
LiGet: I was able to push all 3 packages to your server, but when I attempted to retrieve them, I had errors for package (A).  The other 2 (B, C) had no issues when retrieving them.
The error (below output from Visual Studio 2015) is the same as was previously reported:
Error		An error occurred while retrieving package metadata for 'XYZ.2.0.1' from source 'CoreOS (.Net Core: NuGet server)'.
Unable to cast object of type 'Newtonsoft.Json.Linq.JValue' to type 'Newtonsoft.Json.Linq.JArray'.			0

I unzipped/diffed (A) with a "good" package (B -which is similar to C), and I see this difference (there isn't actually 3 blank lines in (A), I just did this to illustrate):
(A):
<?xml version="1.0" encoding="utf-8" standalone="yes"?>
<package xmlns="http://schemas.microsoft.com/packaging/2011/10/nuspec.xsd">
  <metadata>
    <id>XYZ</id>
    <version>2.0.1</version>
    <authors>George H.</authors>
    <description>A 30 day logging utility.</description>

  </metadata>
</package>

(B):
<?xml version="1.0" encoding="utf-8" standalone="yes"?>
<package xmlns="http://schemas.microsoft.com/packaging/2011/10/nuspec.xsd">
  <metadata>
    <id>XYZ</id>
    <version>2.0.2</version>
    <authors>George H.</authors>
    <description>A 30 day logging utility.</description>
    <dependencies>
      <group targetFramework="net35" />
    </dependencies>
  </metadata>
</package>

Notice there is no <dependencies> tag in (A), but there is one in (B) -also in (C).
Could this be causing the issue -I assume you must be parsing this tag to store dependencies in your SQLite DB, and the upload works fine, but not the download...?
Thanks,
George H.
02/07/2019 1:59pm ET

Hi,
Thanks for posting the xml details, this is something to work with. I will have to reproduce it in tests and see if that is the issue.
Do you that that error only in visual studio or is any other client is also failing?

Hi tomzo,
from the command line (DOS prompt), I just tried:

Paket (Paket version 5.196.2):
.paket\paket.exe install
-and it worked fine for both (A: 2.0.1) and (C: 4.7.0)

NuGet (NuGet Version: <IP_ADDRESS>93):
nuget install XYZ -version 2.0.1
An error occurred while retrieving package metadata for 'XYZ.2.0.1' from source 'CoreOS (.Net Core: NuGet server)'.
Unable to cast object of type 'Newtonsoft.Json.Linq.JValue' to type 'Newtonsoft.Json.Linq.JArray'.
nuget install XYZ -version 4.7.0
Successfully installed 'XYZ 4.7.0' to C:\PROJECTS\MISC\NUGET_PACKET_TEST\201902072_LiGet_TEST\NUGET
Executing nuget actions took 124.57 ms

Hmmmm.... this seems to be a NuGet issue, or Paket is creating packages (the packages were originally created via Paket) not fully compatible with NuGet spec...?
Thanks,
George H.
02/07/2019 3:33pm ET

This is fixed now in 1.0.1.
Packages which did not have dependencies had invalid response returned by server.
@gggggeorge thanks for detailed feedback.
@mersadk your case most likely works now.

Hi @tomzo ,
I just tested your fix, and my problem has been resolved -many thanks!
Thanks,
George H.
02/15/2019 11:40am ET


update LICENSE with info about mixed licensing

@jodok here's a first stab at updating our LICENSE file to talk properly about how CrateDB is a mixed license software bundle
we still need to fix NOTICE so it follows proper ASF standards, and move all the appropriate license texts into the LICENSE file. but I figure we can do that as a separate piece of work

@jodok I've updated this a bit based on our recent convos
it's not entirely finish
for the time being, ignore LICENSE. that's a work in progress
I want to direct your attention to the NOTICE file. which I have written/edited by hand
https://github.com/crate/crate/blob/e8c888de8021b139cb31b5ebf7581b208e73daa7/NOTICE

note for self:

see to enterprise/jmx-monitoring and others

@jodok @mxm @m-kharbat I gone through LICENSE and from what I can tell, everything except es/upstream is a build time inclusion/dependency (including admin UI code)
I have tagged each of you on different FIXME lines in the LICENSE. can you check the things I have tagged you in and let me know if my guess is correct / provide info
thanks!!

@mxm thanks for the feedback! I have left some replies!

@jodok @mxm I believe this PR is now ready to merge

@mxm rebased and pushed. ty

@jodok @mxm okay I split this into two separate commits. ready to review again
please also view my commit message (which is detailed now)


a confusing issue

cos, sin = self.rotary_emb(value_states, seq_len=kv_seq_len)
ValueError: too many values to unpack (expected 2)
I follow the instructions in the Full inference code,bu then I encounter this issue.
How can I fix this?

This error is usually caused by calling  replace_with_chunkllama() after  model.from_pretrained().  If it cannot solve the error, please provide more details.

from transformers import AutoTokenizer, LlamaTokenizer, LlamaForCausalLM, AutoModelForCausalLM
from chunkllama_attn_replace import replace_with_chunkllama
import torch

replace_with_chunkllama(pretraining_length=4096)

tokenizer = LlamaTokenizer.from_pretrained("path_to_Llama-2-7b-hf", trust_remote_code=True)
model = LlamaForCausalLM.from_pretrained("path_to_Llama-2-7b-hf", trust_remote_code=True, torch_dtype=torch.bfloat16)
inputs = tokenizer("Long...docs\n Q: How to extend the context window of LLMs? ", return_tensors="pt")

output_ids = model.generate(**inputs, max_length=128)[0]
print(tokenizer.decode(output_ids))

I just precisely followde the inference instructions,but the issue remained...

Hey guys, the code works in my environment.  My transformer version is 4.37.2
from transformers import AutoTokenizer, LlamaTokenizer, LlamaForCausalLM, AutoModelForCausalLM
from chunkllama_github import replace_with_chunkllama
import torch

model_path = "path/to/llama2"

replace_with_chunkllama(pretraining_length=4096)

tokenizer = LlamaTokenizer.from_pretrained(model_path, trust_remote_code=True)
model = LlamaForCausalLM.from_pretrained(model_path, trust_remote_code=True, torch_dtype=torch.bfloat16).to("cuda:0")
inputs = tokenizer("Long...docs\n Q: How to extend the context window of LLMs? ", return_tensors="pt").to("cuda:0")

output_ids = model.generate(**inputs, max_length=128)[0]
print(tokenizer.decode(output_ids))

Please use Flash Attention for processing longer input:
model = LlamaForCausalLM.from_pretrained(model_path, attn_implementation="flash_attention_2", trust_remote_code=True, torch_dtype=torch.bfloat16).to(device)

thank you all guys !!!😄
finally get success
It is my torch version that caused the issue, previous version is 2.2.1+cu118
success environment:
 torch_version:2.0.1+cu118
transformers_version:4.37.2

If there are no further questions or follow-up discussions, I will close this issue shortly. Thank you all for your contributions and participation.

infer is corret, but when finetune, it comes out again


fix gateio derivative position error

Before submitting this PR, please make sure:

[x] Your code builds clean without any errors or warnings
[x] You are using approved title ("feat/", "fix/", "docs/", "refactor/")

A description of the changes proposed in the pull request:
link to https://github.com/hummingbot/hummingbot/issues/6539
https://github.com/hummingbot/hummingbot/issues/6510
Tests performed by the developer:
dev-1.19, tested with perpetual_market_making strategy
Tips for QA testing:

@yancong001 Could you please fix failing tests?

PR update:

Test latest commit 5de82f82547fea
Successfully opened a position
Stop/exit the client and check if position will be retrieved when started again ✅
Open a position manually and start perp-mm on client ✅
When a position is open with take-profit order created, run exit -f:

Relaunch client and run the strategy again, able to retrieve the position and cancel the existing order that was left due to force exit

Build docker image and ran same tests ✅

Note: PR good to be approved, thank you 🙇🏼

Github workflow failed due to:


Update dependency module, LESS to v2.

Less API was changed in v2, so please update this module.

We have deprecated the use of less.Parser and toCss to generate the css. Instead we require you to use the less.render shorthand. See Programmatic Usage for more information.

http://lesscss.org/usage/#v2-upgrade-guide

Published v4.2.2


Dropdown menu selection with items and childs items

Hi,
Is there a way to create a Semantic UI dropdown selection box with items and childs items ?
I try to mix Menu Selection and Menu Direction here : http://jsfiddle.net/vjn1hx7m/
But it does not work :(
Thanks !

Hi @J2BB, your JSFiddle is empty. Can you please give an example of such an implementation?

Oops ! Sorry : http://jsfiddle.net/vjn1hx7m/

@J2BB I see, it seems to be a duplicate of #3101; no, it’s not possible, and the enhancement was declined.

Sad news ! But thanks for your answer ;)


custom ORM model manager

Two issues when working with a custom entity manager:
In:  aws-ses-monitor-bundle/Command/SnsSetupCommandAbstract.php
line 90 needs to be changed from:
$this->getContainer()->get('doctrine.orm.default_entity_manager')->flush();
to:
$this->getContainer()->get('aws_ses_monitor.entity_manager')->flush();
and line 181 from:
$this->getContainer()->get('doctrine.orm.default_entity_manager')->persist($topic);
to:
$this->getContainer()->get('aws_ses_monitor.entity_manager')->persist($topic);
Thanks!

Can you send a PR for this?


Whenever someone hits 100 days, tweet out a congratulations

@amandeepmittal thank you very much. I am looking into it. I'll keep posted.

solved by PR #8


Coordinating Julia version with system image version?

Thanks for a very interesting package! I am just exploring how it works, and was wondering if there was a way to ensure that the system image installed matches the Julia version. Consider:
$ julia +1.7
               _
   _       _ _(_)_     |  Documentation: https://docs.julialang.org
  (_)     | (_) (_)    |
   _ _   _| |_  __ _   |  Type "?" for help, "]?" for Pkg help.
  | | | | | | |/ _` |  |
  | | |_| | | | (_| |  |  Version 1.7.3 (2022-05-06)
 _/ |\__'_|_|_|\__'_|  |  Official https://julialang.org/ release
|__/                   |

(@v1.7) pkg> add https://github.com/MichaelHatherly/CuratedSystemImages.jl

julia> using CuratedSystemImages

julia> CuratedSystemImages.install()
Pick the system images you would like to install.
[press: d=done, a=all, n=none]
   [ ] AlgebraOfGraphics
 > [X] DataFrames
   [ ] JuliaFormatter
   [ ] JuliaSyntax
[ Info: installing `DataFrames` system image.
  Downloaded artifact: DataFrames
  Downloaded artifact: DataFrames
[ Info: finished installing `DataFrames` system image.

Add short names for selected images.
[press: d=done, a=all, n=none]
 > [X] DataFrames
[ Info: `juliaup` channel `1.7.3` already added, skipping.

julia> exit()

$ julia +DataFrames
ERROR: could not load library "/Users/jack/.julia/artifacts/caf82f4d14d28fb959b803f7823ce4731f93feea/environments/DataFrames/DataFrames.dylib"
dlopen(/Users/jack/.julia/artifacts/caf82f4d14d28fb959b803f7823ce4731f93feea/environments/DataFrames/DataFrames.dylib, 6): Symbol not found: _ijl_apply_generic
  Referenced from: /Users/jack/.julia/artifacts/caf82f4d14d28fb959b803f7823ce4731f93feea/environments/DataFrames/DataFrames.dylib
  Expected in: /Users/jack/.julia/juliaup/julia-1.7.3+0.x64/lib/julia/libjulia-internal.1.dylib
 in /Users/jack/.julia/artifacts/caf82f4d14d28fb959b803f7823ce4731f93feea/environments/DataFrames/DataFrames.dylib

As I understand how the package works, this is because the DataFrames sysimage was built for 1.8.1, but I was in 1.7.3 when I ran the install method, so it installed the image with that Julia channel.
In the artifacts file it looks like there is no reference to the Julia version, other than the fact that the URLs correspond to 1.8-latest. (as an aside I wonder there is a potential for a problem if the -latest version drifts between juliaup and the generated system images?)
I am wondering what the best way to ensure compatibility between the versions might be. Some possible options:

specify the version in the artifact somehow and only install the system image if there exists a matching artifact for the current Julia version used to run the install
install the system image for the Julia version corresponding to the system image, not the Julia version used to run the install (one drawback is that the long name of the channel might be hard to discover if you don't know the version of julia the system image was made with)
prompt the user to select the system image to install, and then offer a choice of Julia versions for which there exist system images (defaulting to the current version being used if compatible)

Keen to hear your thoughts!

Hi Jack, thanks for taking interest.

and was wondering if there was a way to ensure that the system image installed matches the Julia version

Would be great if Julia itself would give a nicer error message when you try to do that rather than just saying ERROR: could not load library, which isn't great for new users.
If Pkg.add for git repo URLs handled compat then https://github.com/MichaelHatherly/CuratedSystemImages.jl/blob/main/Project.toml#L11 should solve the issue of only installing for the expected versions, but I'm pretty sure that requires the package to actually be registered to work correctly.
The simplest way to properly detect the used version and ensure that we have a usable Julia version is to check what the Manifest.toml associated with a particular system image has as it's julia_version field and then make sure to use that version for the --julia= flag to system-image-loader.

https://github.com/MichaelHatherly/SystemImageLoader.jl/pull/23 should improve the handling of this somewhat.

Thanks for your thoughts, I think #23 is a good solution for this. Looking forward to playing around with things a bit more!


Yarn build fails

I'm trying to follow the minting tutorial from  https://docs.near.org/tutorials/nfts/minting. I followed the guide exactly the same. However, after making all the mentioned changes when I run yarn build I get following errors.

remove this file https://github.com/near-examples/nft-tutorial/blob/main/rust-toolchain and dont forget to add the wasm32 toolchain: rustup target add wasm32-unknown-unknown.


webhooks/stripe: Handle invoice and payout events explicitly.

I have added the support payout events. The changes in the view.py and tests.py file is in a separate commit and the new fixtures files are in a separate commit.
Please review and let me know what you think.
@eeshangarg @timabbott
Thanks
Sameer

@eeshangarg There is already a list there on line 169 like this, if category in ['payment_intent', 'payout', 'plan', 'product', 'recipient',                     'reporting', 'review', 'sigma', 'sku', 'source', 'subscription_schedule',                     'topup', 'transfer']:  # nocoverage         # Not implemented. In theory doing something like         #   body = default_body()         # may not be hard for some of these         raise NotImplementedEventType()
Still, there are certain places where we have raised SupressedEvent or NotImplementEvent. Do you want me to make edit it with the others events and move it to the top, right?


Android target

Is there any way to set targetSdkVersion to 29 or 30
When I try to change the target to 30, application gets crashed

There's an issue with trying to get permission when you set the target SDK version of your app to 30. It was reported here https://issuetracker.google.com/issues/145082934 and you can find some investigations around that in here: https://github.com/saki4510t/UVCPermissionTest


Can we provide the page as official app?

@falkben
Thank you for creating the app.
I'm the author of the datamodel-code-generator
I wanted to run datamodel-code-generator with pyscript.
But, I met dependency problems.
I checked your repository. you have resolved the problems.
I have some questions.

Do you have the plan to support all CLI options and another input file type?

I would support all CLI options in the app.

May I create a new page based on your pyscript?

I don't want to block your business. But I need the page as official.

If you have any plans for the project then could you please tell me?

Wow, you found this fast! I'm glad you like it!
I'd love to work together. I have no big future plans for this, aside from doing a little cleanup.
I don't know if you've seen this, but @brokenloop created https://github.com/brokenloop/jsontopydantic. I need to update this project's README.md and the deployed page to make that more clear. The way that page works is it sends the JSON input to a server, which I wanted to avoid, thus the pyscript implementation.
The only thing I really added was the pyscript deployment.
Regarding getting the dependencies working in pyscript/pyodide, datamodel-code-generator requires a lot of them. Some of which are difficult to compile to webm. I found that for a simple JSON -> pydantic converter, only a few were actually needed. My solution was to install datamodel-code-generator using micropip with the option to avoid installing any dependencies. Any additional features (e.g. yaml) likely will require more dependencies, but we can figure out how to solve those as needed.

Wow, you found this fast! I'm glad you like it!

Recently, GitHub tell me about the project's user and use case on the project's top page. 😄

The way that page works is it sends the JSON input to a server, which I wanted to avoid, thus the pyscript implementation.

I knew the project and had stared the project ⭐ .
I agree with you . I wanted to create the page by pyscript when I know pyscript last year.

My solution was to install datamodel-code-generator using micropip with the option to avoid installing any dependencies.

It's great 👍 I didn't know the solution.

I'd love to work together. I have no big future plans for this, aside from doing a little cleanup.

OK, What should we do?
If you have the time to do tasks for the project, then I prefer to collaborate with you.
Because I have a bunch of tasks for datamodel-code-generator  and other OSS projects 😅
https://github.com/koxudaxi/datamodel-code-generator/issues/1042
We should decide task for the project as a start point.

Where should we provide the project on? I think the current repository name focused only json to pydantic
Where should we distribute to the site? same reason.


Fixed missing font-awesome class.

Added "fa" to the subchart toggle link to fix the font-awesome icons.

Coverage remained the same when pulling 6477dc82d9fddd909388d8338f3a238160e04e5d on mattlucas121:class-fix into d6517ad9ff8942786843d7e7bb4f530e51f74f73 on maxklenk:develop.

@mattlucas121 thank you for the pull request


[typescript] tintColor type does not exist on Image but working

https://snack.expo.dev/@acidcoder/tintcolor-type

Resolved in NativeBase 3.2.2. Let us know if you face any issue.


Improve ReplaceAll

According to heaptrack this improves memory consumption for this module's unittest in release mode by a couple of megabytes.

Instead of ReplaceAll(args...) how about keeping it as ReplaceAll(alias T, alias U, TList...)? Since DMD 2.087.0: Template alias parameters now match basic types as a conversion that should work without either needing four declarations of ReplaceAll or using the varargs template parameter trick for mixing types and aliases.

Instead of ReplaceAll(args...) how about keeping it as ReplaceAll(alias T, alias U, TList...)? Since DMD 2.087.0: Template alias parameters now match basic types as a conversion that should work without either needing four declarations of ReplaceAll or using the varargs template parameter trick for mixing types and aliases.

Would love to, but there are still bugs, see forum discussion titled "What's the deal with..."


Don't include IL aggregate in a beacon block

I made some changes assuming each attesters derive IL aggregate from block B. It seems the decision to not include IL_agg to beacon block is a big one. It's impact is widespread in the EIP.
Here are some questions and comments that are not reflected on the modification.

If IL aggregate is not added to a beacon block. it doesn't have to be (from_address, gas_limit, bitlist). It could be a set of (transsaction, bitlist), if it's more useful.

I think we need to add something like Derive to "Main FOCIL Functions" section. It will be used by attesters when validating a block.

I'm not sure how FOCIL can still address concerns around IL equivocations in EIP-7547. I wonder if liveness and safety are guaranteed respectively when some committee members, let's say, (256 - 1) / 3 = 85 so that the honest majority assumption holds, equivocate IL. Is there any analysis on this? (I left that part blank.)

This will be replaced with the upcoming PR based on the latest discussion.


stacks broken due to clobbered frame pointer (fix: support DWARF/LBR)

bpftrace version: bpftrace v0.9.2-139-g873d
kernel: Linux 4.19
I modified offwake.bt to print userspace stacks, in order to get more information about what's causing the program in question (neovim) to go to sleep.
NOTE: I recompiled it with -fno-omit-frame-pointer to be sure frame-pointer based stack walking would work.
I've made a simplified bpftrace program to debug this issue:
profile:hz:99 /comm == "nvim"/ {
	@samplestacks[ustack(perf, 10)] = count();
	printf("99hz: %s\n", ustack(perf, 10));
}

kprobe:finish_task_switch /comm == "nvim"/ {
	@switchstacks[ustack(perf, 10)] = count();
	printf("finish_task_switch: %s\n", ustack(perf, 10));
}

Usually I get stacks like:
finish_task_switch:
        7fa2516d1f4e epoll_pwait+110 (/lib/x86_64-linux-gnu/libc-2.28.so)
finish_task_switch:
        7fa2516cc869 syscall+25 (/lib/x86_64-linux-gnu/libc-2.28.so)
finish_task_switch:
        7fa252347f0c __lll_lock_wait+28 (/lib/x86_64-linux-gnu/libpthread-2.28.so)
        558c66768c78 uv__async_io.part.0+280 (/home/aktau/neovim/bin/nvim)
        4 0x4 ([unknown])
        4 0x4 ([unknown])
        4 0x4 ([unknown])
        4 0x4 ([unknown])
        4 0x4 ([unknown])
        4 0x4 ([unknown])
        4 0x4 ([unknown])
        4 0x4 ([unknown])

The syscall is the xstat system call, verified by checking the kstack counterpart of the wake-up). I'm not sure what those 0x4 instructions are for, or how it's even stack walking this, it may be a a hint as to what's going wrong.
Sometimes I do get complete stacks in finish_task_switch, but it is rare:
finish_task_switch:
        7fa252347f0c __lll_lock_wait+28 (/lib/x86_64-linux-gnu/libpthread-2.28.so)
        558c66534b7f tui_scheduler+54 (/home/aktau/neovim/bin/nvim)
        558c66528583 ui_bridge_flush+109 (/home/aktau/neovim/bin/nvim)
        558c6652a80e ui_call_flush+51 (/home/aktau/neovim/bin/nvim)
        558c6653473c ui_flush+80 (/home/aktau/neovim/bin/nvim)
        558c665fba8e normal_execute.lto_priv.220+1311 (/home/aktau/neovim/bin/nvim)
        558c6655264d state_enter+71 (/home/aktau/neovim/bin/nvim)
        558c665f87c5 normal_enter+136 (/home/aktau/neovim/bin/nvim)
        558c6664b605 main+2252 (/home/aktau/neovim/bin/nvim)
        7fa2515fc52b __libc_start_main+235 (/lib/x86_64-linux-gnu/libc-2.28.so)

This is likely because these wakeup events are rarer, epoll_pwait is by far the most frequent (neovim uses it to wait for user input). But why is the stack truncated? How can I debug this?
By contrast, @samplestacks are usually full stacks. There are a couple of truncated ones though:
99hz:
        7fa25165cc89 __GI___libc_malloc+345 (/lib/x86_64-linux-gnu/libc-2.28.so)

99hz:
        558c667740e0 uv_write2+464 (/home/aktau/neovim/bin/nvim)
        3 0x3 ([unknown])

99hz:
        558c66777f67 uv__hrtime+71 (/home/aktau/neovim/bin/nvim)

99hz:
        7fa25165cb89 __GI___libc_malloc+89 (/lib/x86_64-linux-gnu/libc-2.28.so)

I don't know why these are broken either. I've once even observed a stack inside the 99hz sampler which looked the same as the most frequent one in finish_task_switch: 7fa2516d1f4e epoll_pwait+110 (/lib/x86_64-linux-gnu/libc-2.28.so) . Though this is hard to reproduce.
I thought maybe this was related to some incomplete process state inside of finish_task_switch. But changing to a kretprobe didn't fix it and then I noticed that every so often I get similar broken stacks from the 99hz profiler.
It seems like a wakeup from a select number of syscalls provokes these broken stacks. I've
Also very curious, in the aggregated stacks, I get two keys in the same map which look identical to me, but apparently aren't to bpftrace.
@switchstacks[
        7fa2516d1f4e epoll_pwait+110 (/lib/x86_64-linux-gnu/libc-2.28.so)
]: 565
@switchstacks[
        7fa2516d1f4e epoll_pwait+110 (/lib/x86_64-linux-gnu/libc-2.28.so)
]: 3446

What gives?

I just had a thought that this may be due to frame pointers being omitted in libraries, like glibc (see https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=767756, I'm on Debian).
What about the glibc function that was walkable (__GI_chdir)?
00000000000ea610 <chdir@@GLIBC_2.2.5>:
   ea610:       b8 50 00 00 00          mov    $0x50,%eax
   ea615:       0f 05                   syscall
   ea617:       48 3d 01 f0 ff ff       cmp    $0xfffffffffffff001,%rax  <----- instruction pointer
   ea61d:       73 01                   jae    ea620 <chdir@@GLIBC_2.2.5+0x10>
   ...

So it seems like the essential difference is that chdir is simple enough that it didn't clobber the frame pointer.
Since recompiling all libraries with frame pointers would be a very arduous task, it's probably best to wait for the resolution of https://github.com/iovisor/bcc/issues/1234 (which seems like an old issue).

Will take a closer look at your writeup soon, but I can comment about LBR stuff.
I've spent some time hacking on lbr+bpf in the kernel (have a patch on lkml pending) and I think it would be quite tricky to get lbr based stacks into bpf progs. You'd have to save + restore lbr data on every context switch for complete stacks. That'd involve quite a bit of arch specific hackery not to mention the constant overhead of saving + restoring lbr data because you can never know when someone will read the data. My guess is even if someone managed to upstream this code, few distros would enable this option b/c of the perf hit.
DWARF based unwinding won't happen for the kernel -- they tried that and went with something custom instead (ORC). Not sure we have a good answer for stacks without frame pointers at the moment.

Also very curious, in the aggregated stacks, I get two keys in the same map which look identical to me, but apparently aren't to bpftrace.

ustack stores both the pid and the stackid as the pid is needed to translate addresses to symbols, so they're unique entries which just get printed the same way :)

ustack stores both the pid and the stackid as the pid is needed to translate addresses to symbols, so they're unique entries which just get printed the same way :)

I had no idea. Thanks! For now, I think this should be documented.
Isn't the only thing required the mappings (/proc/$PID/maps), which (if saved) would also allow resolving symbols after the process as exited. It's reasonably annoying that quiting bpftrace after the target process has exited yields unsymbolized stacks.
This makes me think about what it would take to normalize stacks so that one could decide whether two stacks are essentially identical (imagine the same binary with different mapping offsets which when subtracted yield the same stack). I would prefer using this ustacknorm.
In my case, it even seems like different pids have the same address layout (mapping), so one wouldn't even have to normalize. Just save a single /proc/$PID/maps and save the stack as <mapsref, stack> instead of <pid, stack>. But I have to admit I have no idea how common it is that multiple processes launched in the same way have the same mapping.

I've spent some time hacking on lbr+bpf in the kernel (have a patch on lkml pending) and I think it would be quite tricky to get lbr based stacks into bpf progs. You'd have to save + restore lbr data on every context switch for complete stacks.

Ouch. That sounds expensive.

DWARF based unwinding won't happen for the kernel -- they tried that and went with something custom instead (ORC). Not sure we have a good answer for stacks without frame pointers at the moment.

Does it need to happen in the kernel though? If we have the stack and the mapping it would be possible to symbolize user-space stacks in user-space. Of course, you would need to actually know which process to get mappings for. Since aggregation happens in the kernel, bpftrace may be notified long after the process is dead. Some thoughts:

Register a hidden tracepoint/probe that saves maps whenever a new process is created. (I realize this is extremely hacky and expensive, as I suspect the maps aren't even loaded when exec(2) is done.) Likely won't work.
Some stub code whenever ustack is called that saves the important part of the process address space to some hidden map if it's not present yet. (I don't know how to deal with PID re-use here, but that seems like a minor problem given all the others.)

Does it need to happen in the kernel though? If we have the stack and the mapping it would be possible to symbolize user-space stacks in user-space

Right, so symbolization always happens in userspace. And we could definitely save /proc/pid/maps and figure out base addrs and stuff to enabled symbolization after process exit. I'm planning on adding that to bcc soon.
But getting the raw addrs has to be in kernel b/c that's where the bpf prog runs. And without frame pointers enabled, the kernel can't walk the stack to give us the raw addrs. Theoretically, the kernel could parse DWARF info to figure out where the top of the frame is given current PC, but Linus really hates the DWARF state machines.

Does it need to happen in the kernel though? If we have the stack and the mapping it would be possible to symbolize user-space stacks in user-space.

For dwarf we would have to copy the  stack so we can walk through it. bpf won't know which stacks are the same either, so none of the aggregation will work. Instead every single stack will have to be copied to us. I think you're better of using perf in that case.

Isn't the only thing required the mappings (/proc/$PID/maps), which (if saved) would also allow resolving symbols after the process as exited

Yes this pid is used to find the relevant maps in prod/pid/maps.

Just save a single /proc/$PID/maps and save the stack as <mapsref, stack> instead of <pid, stack>

What would mapsref be in this case? Afaik there is no mapsref in bpf,  which is why we use the pid.

For dwarf we would have to copy the stack so we can walk through it. bpf won't know which stacks are the same either, so none of the aggregation will work. Instead every single stack will have to be copied to us. I think you're better of using perf in that case.

You're right. Throughout this entire thread I've made a mess of symbolization and stack walking. The former can indeed be improved in bpftrace, but as you state, stack-walking must be done by the kernel to be able to reap the advantages of in-kernel aggregation. Alas.
Thinking on it, it would have helped me during my investigation to get full stack traces whenever I chose to do per-event output (without aggregation). I'm not sure how feasible such a thing is in the bpftrace model.

Thinking on it, it would have helped me during my investigation to get full stack traces whenever I chose to do per-event output (without aggregation). I'm not sure how feasible such a thing is in the bpftrace model.

You can printf individual stacks, like: bpftrace -e 'p:hz:1 { printf("%s\n", ustack()); }'

You can printf individual stacks, like: bpftrace -e 'p:hz:1 { printf("%s\n", ustack()); }'

Yes, I can. But what I was trying to say is that this uses the same kernel stack walking which is limited to "only when the frame pointer is used as a frame pointer". It can't/doesn't use DWARF, which is more likely to be available in user space. What caused me to write about this is the realization that I was missing important information because the application I'm tracing is using glibc which is not compiled with -fno-omit-frame-pointer on my workstation, making many syscall-terminated traces' ustacks useless.
Something like perf(1), which also does per-event tracing, is able to use DWARF. I'm not sure how this process works, as I'd assume the target thread needs to be stopped and its stack walked which could be slow.

I am trying to get user space stack traces without frame pointers. My initial approach was to compile the .eh_frame section to bpf based on [0] and the corresponding c++ code in [1]. For this I ported it to rust, as I couldn't get the code to compile and I happen to be a rust guy. Anyway, the issue that came up was that for some reason clang thinks that the stack size of 512 bytes is exceeded. I'm not sure if that is really the case or if it just makes sure that pointer offsets are smaller than 512, even if those offsets are into code and not the stack.
However I think that this tool could easily be extended to support generating orc sections. If someone kernel savy would like to collaborate, that would be cool.

[0] https://hal.inria.fr/hal-02297690/document
[1] https://github.com/frdwarf/dwarf-assembly
[2] https://github.com/dvc94ch/ehframe-bpf-compiler

I am trying to get user space stack traces without frame pointers. My initial approach was to compile the .eh_frame section to bpf based on [0] and the corresponding c++ code in [1]. For this I ported it to rust, as I couldn't get the code to compile and I happen to be a rust guy. Anyway, the issue that came up was that for some reason clang thinks that the stack size of 512 bytes is exceeded. I'm not sure if that is really the case or if it just makes sure that pointer offsets are smaller than 512, even if those offsets are into code and not the stack.
However I think that this tool could easily be extended to support generating orc sections. If someone kernel savy would like to collaborate, that would be cool.

[0] https://hal.inria.fr/hal-02297690/document
[1] https://github.com/frdwarf/dwarf-assembly
[2] https://github.com/dvc94ch/ehframe-bpf-compiler


MdDialog cannot display AngularJS content upgraded via UpgradeModule

Bug:
Content upgraded via the UpgradeModule cannot be displayed in a modal.
What is the expected behavior?
Dialog displays with the upgraded component.
What is the current behavior?
Error: No provider for $scope!
at NoProviderError.BaseError [as constructor] (VM444 core.umd.js:1244)
at NoProviderError.AbstractProviderError [as constructor] (VM444 core.umd.js:1365)
at new NoProviderError (VM444 core.umd.js:1405)
at ReflectiveInjector_.throwOrNull (VM444 core.umd.js:2937)
at ReflectiveInjector.getByKeyDefault (VM444 core.umd.js:2976)
at ReflectiveInjector.getByKey (VM444 core.umd.js:2908)
at ReflectiveInjector.get (VM444 core.umd.js:2777)
at PlunkerAppModuleInjector.NgModuleInjector.get (VM444 core.umd.js:8491)
at View_DialogExample1.AppView.injectorGet (VM444 core.umd.js:11935)
at View_DialogExample1.DebugAppView.injectorGet (VM444 core.umd.js:12315)
What are the steps to reproduce?
https://plnkr.co/edit/fbEavuu5Va78MgdTwLhy?p=preview
Clicking "Show Upgraded Component" works, but showing the same component in a dialog via the "Show Dialog" button does not.
What is the use-case or motivation for changing an existing behavior?
We have rewritten our app in Angular, but still rely on a few AngularJS components.  They work everywhere else in our app except for inside of a modal.
Which versions of Angular, Material, OS, browsers are affected?
Tested with both Angular 2.4.7 and 4.0 beta 5.  Material 2.0 beta 2.  Chrome, IE, Firefox on Windows 8.

So of course, after fighting with this for a day and a half, I figure it out a solution 30 minutes after posting an issue.  It's using an undocumented config option (well, the option is listed on the docs page: https://material.angular.io/components/component/dialog, it just has no description) to pass the viewContainerRef of the component that's showing the dialog.  If anyone from the material team would like to comment on whether that is the correct use of that option, or to update the documentation with more info, that would be great, but I think this issue can be closed.
Here is the updated plunk:
https://plnkr.co/edit/WrdhYrNQ4UAL6dmQYiGi?p=preview

Thanks for the report- I've filed #3651 to track the missing docs.


[ENTESB-18654] wrong XSD url generated with XML initialiser

Issue: https://issues.redhat.com/browse/ENTESB-18654

Please open a PR upstream too.

@apupier I'll modify this PR. Thanks.


Pass along realtime-js options

What kind of change does this PR introduce?
Feature
What is the new behavior?
Passes along constructor options to realtime-js
Depends on https://github.com/supabase/realtime-js/pull/95 before merge.

Should be good to go

@quicksnap yep, let me do a release of realtime-js, version bump it here, and then we can merge this

Should be good to go now

:tada: This PR is included in version 1.19.0 :tada:
The release is available on:

npm package (@latest dist-tag)
GitHub release

Your semantic-release bot :package::rocket:


SM2: add ec_algo_set param to choose which EC algos to use

This is based on the commits in #6386 new change is 2bc8ea9
I investigated adding an SM2 PKEY (and have most of the change saved in a branch if this is useful) but I got hung up the fact that (AIUI) the PKEY is chosen based on the OID in the key, but with SM2 the standard ECC OID is used so an SM2 key is basically indistinguishable from an ECDSA or ECDH key (modulo probably using the sm2p256v1 curve instead of secpxxxr1, which is how we currently decide when to use SM2). So it doesn't seem there is any way to make a distinct SM2 PKEY work. So I looked at what GmSSL does here, which is have a  EVP_PKEY_CTX_ctrl hook to let application switch between algorithms. So I did that. (None of the code is copied from GmSSL, I just reimplemented the same idea.)
@mattcaswell does this seem ok? If not I can try the PKEY approach but I'll need some hints on how to approach it.

There is a distinction between an EVP_PKEY_ASN1_METHOD, and an EVP_PKEY_METHOD. The former is where we worry about the OIDs etc, but it is the latter that we are concerned about with regards to SM2.
In theory I think we can create an SM2 specific EVP_PKEY_METHOD and retain the existing (common) EVP_PKEY_ASN1_METHOD. I can think of a couple of ways to do this.
Option 1: Handle it when creating the EVP_PKEY_CTX
So, if you want "standard" EDSA/ECDH etc then just do:
ctx = EVP_PKEY_CTX_new(mykey, NULL);

But if you want SM2 algos then you do:
ctx = EVP_PKEY_CTX_new_id(EVP_PKEY_SM2, NULL);
EVP_PKEY_CTX_set_pkey(ctx, mykey);

Note, I just made up the EVP_PKEY_CTX_set_pkey() function - it doesn't exist yet. But it would just have to: confirm that the EVP_PKEY is consistent with the id for the EVP_PKEY_CTX; up-ref the EVP_PKEY; and call the pmeth->init() function. Or (possibly) better would be to have:
ctx = EVP_PKEY_CTX_new_with_pkey(mykey, EVP_PKEY_SM2, NULL);

Option 2: Create an EVP_PKEY alias
We already have the concept of "aliases" for variants of an EVP_PKEY. For SM2 this might look like:
const EVP_PKEY_ASN1_METHOD sm2_asn1_meth = {
     EVP_PKEY_SM2,
     EVP_PKEY_EC,
     ASN1_PKEY_ALIAS}
};

Normally this idea is used where we have multiple OIDs for the same thing - which is almost the situation we have here. We (effectively) have one OID for "standard" EC and an "undefined" OID for SM2. This means that when you first create the EVP_PKEY it will initially have the type of EVP_PKEY_EC (because there is no SM2 specific OID). Then you would have to call some function to "convert" it into one of its alias types, e.g.
EVP_PKEY_set_alias_type(mykey, EVP_PKEY_SM2);

Again, I made up the function EVP_PKEY_set_alias_type(). It would have to verify that the specified nid really was an alias of the base type (e.g. its not valid to convert an RSA key into a DSA key).
Finally we just need to associate the EVP_PKEY_SM2 nid with a new EVP_PKEY_METHOD for SM2 and everything should "just work". At least in theory :-)
The more I think about it, the more I prefer option 2.

One other thing I just thought about with Option 2. We might need to do something clever with the encoding. Otherwise if you have an EVP_PKEY of type EVP_PKEY_SM2 and try and encode it, it might fall over because there is no OID associated with it...

@mattcaswell Thanks for your guidance here, I will try implementing Option 2 this week.

Closing in favor of #6443 which splits SM2 into its own PMETH and uses API suggested here to toggle using SM2 algos vs NIST algos.


⚠ Samsung has degraded performance

In de3aacd, Samsung (https://samsung.com) experienced degraded performance:

HTTP code: 200
Response time: 2338 ms

Resolved: Samsung performance has improved in 69c77b0.


Release 0.1

This is the release-0.1 pull request. I have made a ton of changes and tried to make the functions look consistent. Could you please check thoroughly and make sure that compulsory elements for this release are included?
I look forward to your comments and suggestions.

The install script is missing a file called viziphant/VERSION, which is a text file with the version number 0.1.


Polygon with zero-height shape hangs PyFerret

Reported by ansley b manke on 16 Jun 2017 18:46 UTC
This data and the plot command are set up by the bar_chart_3.jnl script
yes? use bar_chart_data.nc
yes? POLY/LINE/NOLABEL/FILL/lev=12/coord_ax=Z  BCHx4,BCHy4 ,wt_plt

The data has a polygon with zero height. PyFerret seems to hang, but I can get this message when in the debugger,
grdelWindowDelete: error when calling the Python binding's deleteWindow method:
**ERROR <type 'exceptions.ValueError'>: height of the rectangle (0.0) in not positive

It's a simple enough matter to check that the polygon coordinates vary in the routine FILLPOL before making the graphics call.
Migrated-From: http://dunkel.pmel.noaa.gov/trac/ferret/ticket/2542

Comment by ansley.b.manke on 16 Jun 2017 22:19 UTC
I've fixed this in ppl/tmapadds/fillpol.F
It's checked in both on the trunk and the PyFerret branch.

Attachment from ansley.b.manke on 16 Jun 2017 18:47 UTC
REPLACE THIS TEXT WITH UPLOADED FILE ./attachments/TRAC_2542_GIT_1814/bar_chart_data.nc

Attachment from ansley.b.manke on 16 Jun 2017 18:48 UTC
REPLACE THIS TEXT WITH UPLOADED FILE ./attachments/TRAC_2542_GIT_1814/polygon_bug.png


Issues with physics on larger ships

Hello, I've been toying with the BoatAlignNormal.cs file on trying to figure out how to tweak the properties to fit heavier, larger ships. I can't seem to get realistic buoyancy physics despite any changes I make to the properties, and including modifying mass and drag on the Rigidbody.

Hi @FuriousChad , thanks for getting in touch.
I'll start off with the huge disclaimer - the buoyancy stuff in BoatAlignNormal is rough and unrealistic - it tries to approximate floating dynamics by sampling the normal at the position of the boat and aligning the boat to the water surface using forces. This is not how buoyancy works. There is an article https://www.gamasutra.com/view/news/237528/Water_interaction_model_for_boats_in_video_games.php that covers the physics and a potential implementation, or there are Asset Store plugins which do floating physics. I'm not sure if I'm likely to work on a proper buoyancy simulation any time soon.
However having said all of the above, there are some things that will help the simplistic physics approximate a larger ship:

Give the Boat Width parameter an accurate value, or go larger with it. The physics will ignore wavelengths that are small compared to this width, which will effectively filter them out, so if you pick a large value for this it will only take into account the long waves (not the sharp/small ones).
Scale down Buoyancy Torque - this is the rotational force applied to the boat and is independent of mass (which is why modifying mass did not help)
Engine Power and Turn Power probably want to be reduced - these are also mass independent

There are other params that could help but i think the above are the main ones. Let me know if you have any luck?

@FuriousChad If you are interested to use the model in the gamasutra article, there is a unity tutorial here : https://www.habrador.com/tutorials/unity-boat-tutorial/. I currently trying to use it with crest. I just need to found how to implement a custom WaterController that can get the y pos of water from a world position and timeSinceStart...

Oh thats cool thanks for the note. I'm pretty sure we can get the WaterController stood up. I'll take a look some point soon but if you have specific questions about how to get at the height queries in Crest let me know..
(Spoiler: it is accessible through OceanRenderer.Instance.CollisionProvider , and best to set OceanRenderer._cachedCpuOceanQueries on the script to make the hieight queries fast).

Cool!!! This is very good news.
My bad about the cache, must have broke it during a refactor :( i just pushed a fix to master which should sort it, let me know.

I reached out to Erik Nordeus and he graciously gave the thumbs up to port an implementation of his floating physics to Crest 👍 . I will probably make a number of modifications to it before its ready to merge into the master branch, but in the meantime I've pushed a commit with the basic stuff ported across and a cube floating in the boat.unity scene - see the referenced commit above.

I'm voting for also keeping the existing buoyancy around.  Realistic is often not the best gameplay, depends on the game.  Like if you look at some of the best ocean ship games such as sea of thieves, not at all realistic.  Aligning to surface normals is I think a great starting point for non realistic buoyancy.

Thanks for the notes! The align to normal script is quite simple and can indeed be kept around.
After posting my last comment above, I grabbed the build from Erik's website and the ship buoyancy acts quite strange, the boats seem to spin on the spot for me. Also, as I hinted in my comment above the code needs a fair bit of work. This needs some focus and love, and has not turned out to be the slam dunk or quick win i initially hoped.
I've decided now to shift course - I'm going to spend time polishing the rendering (partly driven by issue 85, but things generally need a bit of TLC, guided by a strong visual target), and consolidating the existing Crest features. We've been adding features at a rate of knots and we now need to settle and document them, and look at making better example content that showcases the features.
I'll close for now but I'm keen to pick this up when the other parts of crest are in better shape in the future. If you guys push it forward in the meantime please do post!

@huwb Thanks is a good idea to be more focused on polishing the rendering part before all.
If I have some time to optimize the buoyancy part, I will post progress here.

@FuriousChad - while looking into something I found the Boat Width parameter (on the BoatAlignNormal script) that i described above to be broken, and has probably been broken for a while :/. I've pushed a fix to master now in the above referenced commit - if you get latest now you should clearly see how this parameter. Sorry for the confusion this no doubt caused :(, I should have double checked it at the time..

Would there also be a good way to apply a particle effect at the peak of a certain wave spectrum?  My guess  it would be similar to when foam is created, wondering if there is some way to get access to that on the cpu side in some manor.  Do not need all of them just would create a nice visual effect.

Man, when i try to put BoatPhysics i catch a bug, it pretty weird when put more boats in a line, the first boat act normally but the rest slowly stand up. I try to dig deeper and it seem something relate to buoyancy force.

Hi @DEKAGATO - does it change when you move the camera closer? I'm working heavily on the collision system right now - evolving in PR #100 . I can emit a warning if the boat is off the edge of the LOD data which would have this effect.
If its indepdent of camera, yes stepping through the BoatAlignNormal FixedUpdate() function with a debugger should shed light.

https://drive.google.com/open?id=1cfsOlGLpE23eRr4RA_0TPkDny3Dw74TX
it's not relate with camera position or LOD.

Sorry i havent been able to help more @DEKAGATO . I'm not sure what would cause that to happen.

Just a note, since BoatAlignNormal seems to be finding way more use than i initially planned, I have just done a big tidy up of the params and added some tooltips.
I also added an optional Boat Length alongside the Boat Width param. This is demo'd in the main.unity example scene - note the rowboat will now roll at a higher frequency than it will pitch, due to the dimensions of the boat.
ec895c0b406cb668dd539371ca1cb2a1716ea1f5