text:
Map does not work anymore

No map is shown at http://smeijer.github.io/GeoSearch/ anymore, what could be the cause?

FWIW, the call to cloudmade.com returns a 403.

I get this error when trying to load the example using OpenStreetMap. This is the default example. I can get the example to work when using Google.
l.control.geosearch.js:153 XMLHttpRequest cannot load file://nominatim.openstreetmap.org/search?q=12%20galloway%20cres%20ontario&format=json. Cross origin requests are only supported for protocol schemes: http, data, chrome, chrome-extension, https, chrome-extension-resource.L.Control.GeoSearch.L.Control.extend.sendRequest @ l.control.geosearch.js:153L.Control.GeoSearch.L.Control.extend.geosearch @ l.control.geosearch.js:103L.Control.GeoSearch.L.Control.extend._onKeyUp @ l.control.geosearch.js:233t.(anonymous function).a @ leaflet.js:7

FWIW, the body of a 403 page (example) says “Forbidden, wrong apikey”.

Duplicate with #41

authors: Mithgol asymmetric leolux penproductions smeijer


text:
Fix compiling to wasm

Fixes #50
I dont really know if this is correct since I didnt dig too deep into the issue but it does compile and work for me

Looks alright to me.

Thanks for having a look. :+1:

I would add a check for WASM to the CI if it's supported by this crate.

Good point. I'll add that in a separate PR.

source: gharchive/pull-request

authors: kuviman zeenix

repo: smol-rs/async-broadcast

license_type: permissive

license_source: github-api


text:
Retransmission bug?

I'm testing the latest merge from @Dirbaio  that brings Medium::Ethernet/IP support. Code that before worked before on the sketch of the now merged code isn't working. now
A simple tcp connect isn't working. Even though the tcp server on the other side responds with SYN + ACK, smoltcp decides to retransmit the connection packet again (SYN).
---------------------------------------------------------------
[2021-06-19T23:33:28Z DEBUG async_smoltcp::async_smoltcp] >>>>>>> on_virtual_tun_write for buffer with len 52
[2021-06-19T23:33:28Z DEBUG async_smoltcp::async_smoltcp] ip: Some(Version4(Ipv4Header { ihl: 5, differentiated_services_code_point: 0, explicit_congestion_notification: 0, payload_len: 32, identification: 0, dont_fragment: true, more_fragments: false, fragments_offset: 0, time_to_live: 64, protocol: 6, header_checksum: 59874, source: [192, 168, 69, 2], destination: [54, 207, 20, 104], options: [] }))
[2021-06-19T23:33:28Z DEBUG async_smoltcp::async_smoltcp] transport: Some(Tcp(TcpHeader { source_port: 47675, destination_port: 80, sequence_number: 42, acknowledgment_number: 0, data_offset: 8, ns: false, fin: false, syn: true, rst: false, psh: false, ack: false, urg: false, ece: false, cwr: false, window_size: 65000, checksum: 27031, urgent_pointer: 0 }))
[2021-06-19T23:33:28Z DEBUG async_smoltcp::async_smoltcp] payload: ""
---------------------------------------------------------------
[2021-06-19T23:33:29Z DEBUG async_smoltcp::async_smoltcp] <<<<<<< on_virtual_tun_read for buffer with len 52
[2021-06-19T23:33:29Z DEBUG async_smoltcp::async_smoltcp] ip: Some(Version4(Ipv4Header { ihl: 5, differentiated_services_code_point: 0, explicit_congestion_notification: 0, payload_len: 32, identification: 0, dont_fragment: true, more_fragments: false, fragments_offset: 0, time_to_live: 240, protocol: 6, header_checksum: 14819, source: [54, 207, 20, 104], destination: [192, 168, 69, 1], options: [] }))
[2021-06-19T23:33:29Z DEBUG async_smoltcp::async_smoltcp] transport: Some(Tcp(TcpHeader { source_port: 80, destination_port: 47675, sequence_number: 3339187062, acknowledgment_number: 43, data_offset: 8, ns: false, fin: false, syn: true, rst: false, psh: false, ack: true, urg: false, ece: false, cwr: false, window_size: 26883, checksum: 16459, urgent_pointer: 0 }))
[2021-06-19T23:33:29Z DEBUG async_smoltcp::async_smoltcp] payload: ""
---------------------------------------------------------------
[2021-06-19T23:33:29Z DEBUG smoltcp::socket::tcp] #0:0.0.0.0:47675:54.207.20.104:80: retransmitting at t+0.709s
---------------------------------------------------------------
[2021-06-19T23:33:29Z DEBUG async_smoltcp::async_smoltcp] >>>>>>> on_virtual_tun_write for buffer with len 52
[2021-06-19T23:33:29Z DEBUG async_smoltcp::async_smoltcp] ip: Some(Version4(Ipv4Header { ihl: 5, differentiated_services_code_point: 0, explicit_congestion_notification: 0, payload_len: 32, identification: 0, dont_fragment: true, more_fragments: false, fragments_offset: 0, time_to_live: 64, protocol: 6, header_checksum: 59874, source: [192, 168, 69, 2], destination: [54, 207, 20, 104], options: [] }))
[2021-06-19T23:33:29Z DEBUG async_smoltcp::async_smoltcp] transport: Some(Tcp(TcpHeader { source_port: 47675, destination_port: 80, sequence_number: 42, acknowledgment_number: 0, data_offset: 8, ns: false, fin: false, syn: true, rst: false, psh: false, ack: false, urg: false, ece: false, cwr: false, window_size: 65000, checksum: 27031, urgent_pointer: 0 }))
[2021-06-19T23:33:29Z DEBUG async_smoltcp::async_smoltcp] payload: ""

You can see at the line
[2021-06-19T23:33:29Z DEBUG smoltcp::socket::tcp] #0:0.0.0.0:47675:54.207.20.104:80: retransmitting at t+0.709s
It tires to retransmit very fast. I tried socket.set_timeout(Some(smoltcp::time::Duration::from_millis(10000))); but even with this, it still retransmit in less than 1 second.
Is master a work in progress? I tried the latest release but it does not have the TunTapInterface and etc.

TCP connecting should definitely work, even in master. Can you post the full trace-level logs?

@Dirbaio it looks like it was a problem on my side but anyways the set_timeout looks like it has no effect. It tried to retransmit after 0.7s, don't have an idea why. At least for tcp connect it does this.

set_timeout sets the time after which the socket will time out (close), not the retransmit timeout. That one is automatically set based on the RTT estimation, and that estimation starts at the ~0.7s you're seeing.

source: gharchive/issue

authors: Dirbaio lucaszanella

repo: smoltcp-rs/smoltcp


text:
fix: Support dynamic WS endpoint by using browserURL

Summary
see https://github.com/smooth-code/jest-puppeteer/issues/210

hi @shayke
I am not sure it can fix your problem. could you please help us to test your case?

repo: smooth-code/jest-puppeteer

license: MIT


text:
Will not download mseed files

Hi,
I am having trouble downloading the mseed files and I can't figure out where I am going wrong.
I successfully am able to make the stations list, and I checked the json files and it looks good.
NET = "7F" STA = "A01,A02,A03,A04" CHA ="GHZ" STIME="2020-01-15 15:00:00.00" ETIME="2020-01-15 16:00:00.00" MINLAT= 22.881267 MAXLAT= 22.881167 MINLON= 58.70056 MAXLON= 58.700606
import os json_basepath = os.path.join(os.getcwd(),"json/station_list.json") makeStationList(json_path=json_basepath,                   client_list=["IRIS"],                   min_lat=None, max_lat=None, min_lon=None, max_lon=None,                    network=NET,                   station=STA,                   channel=CHA,                                         start_time=STIME,                    end_time=ETIME,                   filter_network=[])
It gives me the output I expect:
7F--A01 7F--A02 7F--A03 7F--A04
However, when I go to download the appropriate mseed files using:
downloadMseeds(client_list=["IRIS"],            stations_json=json_basepath,            output_dir="downloads_mseeds",            start_time=STIME,            end_time=ETIME,            min_lat=MINLAT,            max_lat=MAXLAT,            min_lon=MINLON,            max_lon=MAXLON,           chunk_size=1,           channel_list=[],           n_processor=2)
It starts the process, and doesn't throw me any errors, but it doesn't download anything. It just initializes the process.

[2022-09-13 11:23:24,429] - obspy.clients.fdsn.mass_downloader - INFO: Initializing FDSN client(s) for IRIS.
[2022-09-13 11:23:24,433] - obspy.clients.fdsn.mass_downloader - INFO: Successfully initialized 1 client(s): IRIS.
####### There are 4 stations in the list. #######
======= Working on A01 station.
======= Working on A02 station.
======= Working on A03 station.
======= Working on A04 station.

Any idea what could be happening?

@sbrent88 have you tried Obspy directly? EqT uses Obspy under the hood and sometimes there are issues with network APIs.

license: mit

license_source: bigquery


text: 메인화면 포토샵

repo: smu-nity/SMU-Petition


text:
Add solution to Adjacent Bit Counts

Problem  - Adjacent bit counts
Language used will be C++

/assign


text:
snakemake cannot run multithreading scripts

Hi,
I have a script that uses multithreading, but the scripts cannot recgonize snakemake and caused an error "NameError: name 'snakemake' is not defined" when running with Snakemake. Not sure it was caused by snakemake itself or the script itself. Here is the related issue:
https://github.com/aertslab/pySCENIC/issues/523

It's like user "ghulp" commented in your issue to pyscenic: You could call your script via the shell directive as any no-snakemake script (along with flags and parameters) or show your code.

Are you still interested in getting help? This is not a bug. Snakemake can run multithreaded scripts, as Snakemake scripts or as from the shell.
BTW: the folks at Stack Overflow are really helpful when it comes to Snakemake.

Hi, I am on Chinese spring festival now. I'll try to call the script from shell because It doesn't work as snakemake scripts
script:
    scripts/pyscenic.py

In order to work as a "Snakemake script", it has to adhere to a set of requirements, see the docs, here. Without knowing the code, there is little anyone can do.

Hi,
I still cannot run pyscenic.py script, but I can run all other scripts. Here is all code I used:
rule pyscenic_module:
    input:
        adata ="scvi_integration/integration.h5ad"
    output:
        df_motifs = "pyscenic_module/df_motifs.csv",
        regulon_pkl = "pyscenic_module/integration_regulons.p",
        regulon_df = "pyscenic_module/integration_regulons.xlsx",
        auc_mtx = "pyscenic_module/integration_auc_mtx.csv",
        regulons_umap = "pyscenic_module/umap_integration_regulons.pdf",
        adata = "pyscenic_module/integration.h5ad",
        rss = "pyscenic_module/integration_rss/rss.csv",
        clustermap = "pyscenic_module/integration_clustermap.pdf",
        cluster_rows = "pyscenic_module/integration_clustermap_rows.csv",
        cluster_columns = "pyscenic_module/integration_clustermap_columns.csv"
    params:
        sc_plot = "pyscenic_module",
        rss_plot = "pyscenic_module/integration_rss/"
    threads: 10
    script:
        "scripts/pyscenic_module.py"

And this is the scripts:
import os
import pickle
import pandas as pd
import scanpy as sc

from arboreto.utils import load_tf_names
from arboreto.algo import grnboost2

from ctxcore.rnkdb import FeatherRankingDatabase as RankingDatabase
from pyscenic.utils import modules_from_adjacencies, load_motifs
from pyscenic.prune import prune2df, df2regulons
from pyscenic.aucell import aucell

from pyscenic.export import add_scenic_metadata
from pyscenic.rss import regulon_specificity_scores
from pyscenic.plotting import plot_rss

import matplotlib
import seaborn as sns
from matplotlib import pyplot as plt
matplotlib.use('Agg')
sc.settings.figdir = snakemake.params.sc_plot

# Generate expression matrix from anndata object
adata = sc.read_h5ad(snakemake.input.adata)
ex_matrix = pd.DataFrame(adata.layers['counts'].A,index=adata.obs_names,columns=adata.var_names)
# Load Transcription Factors
tf_names = load_tf_names(snakemake.config["scenic"]["TFs"])
# Load motif annotataions
motifs = snakemake.config["scenic"]["motifs"]
# Load ranking databases
db_fnames = snakemake.config["scenic"]["databases"].split(",")
def name(fname):
    return os.path.splitext(os.path.basename(fname))[0]
dbs = [RankingDatabase(fname=fname, name=name(fname)) for fname in db_fnames]
# Infer co-expression
adjacencies = grnboost2(ex_matrix, tf_names=tf_names, verbose=True)
# Add TF to the module and remove modules that have less than 20 genes
modules = list(modules_from_adjacencies(adjacencies, ex_matrix))
# Calculate a list of enriched motif and the corresponding target genes for all modules
df_motifs = prune2df(dbs, modules, motifs, num_workers=snakemake.threads)
# Save motifs and load again becuase of the bug reported in https://github.com/aertslab/pySCENIC/issues/509
df_motifs.to_csv(snakemake.output.df_motifs)
df_motifs = load_motifs(snakemake.output.df_motifs)
# Create regulons from this table of enriched motifs
regulons = df2regulons(df)

# Save the enriched motifs and discovered regulons to disk
with open(snakemake.output.regulon_pkl, "wb") as f:
    pickle.dump(regulons, f)
# Export regulons as a table
regulon_df =  pd.DataFrame(columns = ["regulon_name", "transcription_factor", "genes","weights", "score", "context"])
for i in range(len(regulons)):
    regulon = regulons[i]
    regulon_dict = dict({"regulon_name": regulon.name,"transcription_factor": regulon.transcription_factor,"genes":list(regulon.genes),
                    "weights":list(regulon.weights),"score":regulon.score,"context":list(regulon.context)})
    regulon_df = pd.concat([regulon_df, pd.DataFrame.from_dict(regulon_dict,orient="index").T], ignore_index=True)

regulon_df.genes = regulon_df.genes.apply(lambda x: ", ".join(x))
regulon_df.weights = regulon_df.weights.apply(lambda x: str(x))
regulon_df.weights = regulon_df.weights.apply(lambda x: x.replace('[', ''))
regulon_df.weights = regulon_df.weights.apply(lambda x: x.replace(']', ''))
regulon_df.context = regulon_df.context.apply(lambda x: ", ".join(x))
regulon_df.to_excel(snakemake.output.regulon_df,index=False) # Some strings are too long to save as csv

# Enrichment of a regulon is measured as the Area Under the recovery curve (AUC)
auc_mtx = aucell(ex_matrix, regulons, num_workers=snakemake.threads)
auc_mtx = auc_mtx[auc_mtx.columns[auc_mtx.sum(axis=0)!=0]] # Some columns are all zeros and need to be removed to run sns.clustermap
auc_mtx.to_csv(snakemake.output.auc_mtx)
# Integration with scanpy
add_scenic_metadata(adata, auc_mtx, regulons)
top6 = ["Regulon("+i+")" for i in auc_mtx.columns[0:6]]
sc.pl.umap(adata, color=top6, ncols=3, save="_integration_regulons.pdf")

Then I run snakemake using snakemake -j 30 -s multiSC.smk pyscenic_module/df_motifs.csv, the same error still occurred:

And by the way, I can run python version of pySCENIC inside snakemake rule successfully using run

Can you post full traceback as well as the wrapper script generated by snakemake? I wonder if this is a pickling issue

I doubt it's something related to dask.
"pySCENIC can be run on a single desktop machine but easily scales to multi-core clusters to analyze thousands of cells in no time. The latter is achieved via the dask framework for distributed computing"
But in fact, pySCENIC has a poor compatibility with dask:
https://github.com/aertslab/pySCENIC/issues/22
https://github.com/aertslab/pySCENIC/issues/524

The full traceback is too verbose so I copied the first 300 lines here and you can find the full one in the attachment.
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 30
Rules claiming more threads will be scaled down.
Job stats:
job                count

pyscenic_module        1
total                  1
Select jobs to execute...
[Fri Feb 23 09:28:46 2024]
rule pyscenic_module:
input: scvi_integration/integration.h5ad
output: pyscenic_module/df_motifs.csv, pyscenic_module/integration_regulons.p, pyscenic_module/integration_regulons.xlsx, pyscenic_module/integration_auc_mtx.csv, pyscenic_module/umap_integration_regulons.pdf, pyscenic_module/integration.h5ad, pyscenic_module/integration_rss/rss.csv, pyscenic_module/integration_clustermap.pdf, pyscenic_module/integration_clustermap_rows.csv, pyscenic_module/integration_clustermap_columns.csv
jobid: 0
reason: Missing output files: pyscenic_module/integration_rss/rss.csv
threads: 10
resources: tmpdir=/home/wangjw/data/temp
/home/wangjw/programs/miniconda3/envs/py311/lib/python3.11/site-packages/loompy/bus_file.py:67: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
@jit
/home/wangjw/programs/miniconda3/envs/py311/lib/python3.11/site-packages/loompy/bus_file.py:84: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
@jit
/home/wangjw/programs/miniconda3/envs/py311/lib/python3.11/site-packages/loompy/bus_file.py:101: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
@jit
/home/wangjw/programs/miniconda3/envs/py311/lib/python3.11/site-packages/distributed/node.py:182: UserWarning: Port 8787 is already in use.
Perhaps you already have a cluster running?
Hosting the HTTP server on port 37737 instead
warnings.warn(
preparing dask client
/home/wangjw/programs/miniconda3/envs/py311/lib/python3.11/site-packages/loompy/bus_file.py:67: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
@jit
/home/wangjw/programs/miniconda3/envs/py311/lib/python3.11/site-packages/loompy/bus_file.py:84: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
@jit
/home/wangjw/programs/miniconda3/envs/py311/lib/python3.11/site-packages/loompy/bus_file.py:101: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
@jit
/home/wangjw/programs/miniconda3/envs/py311/lib/python3.11/site-packages/loompy/bus_file.py:67: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
@jit
/home/wangjw/programs/miniconda3/envs/py311/lib/python3.11/site-packages/loompy/bus_file.py:84: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
@jit
/home/wangjw/programs/miniconda3/envs/py311/lib/python3.11/site-packages/loompy/bus_file.py:101: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
@jit
/home/wangjw/programs/miniconda3/envs/py311/lib/python3.11/site-packages/loompy/bus_file.py:67: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
@jit
/home/wangjw/programs/miniconda3/envs/py311/lib/python3.11/site-packages/loompy/bus_file.py:84: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
@jit
/home/wangjw/programs/miniconda3/envs/py311/lib/python3.11/site-packages/loompy/bus_file.py:101: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
@jit
/home/wangjw/programs/miniconda3/envs/py311/lib/python3.11/site-packages/loompy/bus_file.py:67: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
@jit
/home/wangjw/programs/miniconda3/envs/py311/lib/python3.11/site-packages/loompy/bus_file.py:84: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
@jit
/home/wangjw/programs/miniconda3/envs/py311/lib/python3.11/site-packages/loompy/bus_file.py:101: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
@jit
/home/wangjw/programs/miniconda3/envs/py311/lib/python3.11/site-packages/loompy/bus_file.py:67: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
@jit
/home/wangjw/programs/miniconda3/envs/py311/lib/python3.11/site-packages/loompy/bus_file.py:84: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
@jit
/home/wangjw/programs/miniconda3/envs/py311/lib/python3.11/site-packages/loompy/bus_file.py:101: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
@jit
/home/wangjw/programs/miniconda3/envs/py311/lib/python3.11/site-packages/loompy/bus_file.py:67: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
@jit
/home/wangjw/programs/miniconda3/envs/py311/lib/python3.11/site-packages/loompy/bus_file.py:84: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
@jit
/home/wangjw/programs/miniconda3/envs/py311/lib/python3.11/site-packages/loompy/bus_file.py:101: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
@jit
/home/wangjw/programs/miniconda3/envs/py311/lib/python3.11/site-packages/loompy/bus_file.py:67: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
@jit
/home/wangjw/programs/miniconda3/envs/py311/lib/python3.11/site-packages/loompy/bus_file.py:84: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
@jit
/home/wangjw/programs/miniconda3/envs/py311/lib/python3.11/site-packages/loompy/bus_file.py:101: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
@jit
/home/wangjw/programs/miniconda3/envs/py311/lib/python3.11/site-packages/loompy/bus_file.py:67: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
@jit
/home/wangjw/programs/miniconda3/envs/py311/lib/python3.11/site-packages/loompy/bus_file.py:84: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
@jit
/home/wangjw/programs/miniconda3/envs/py311/lib/python3.11/site-packages/loompy/bus_file.py:101: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
@jit
Traceback (most recent call last):
File "", line 1, in
File "/home/wangjw/programs/miniconda3/envs/py311/lib/python3.11/multiprocessing/spawn.py", line 122, in spawn_main
exitcode = _main(fd, parent_sentinel)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/wangjw/programs/miniconda3/envs/py311/lib/python3.11/multiprocessing/spawn.py", line 131, in _main
prepare(preparation_data)
File "/home/wangjw/programs/miniconda3/envs/py311/lib/python3.11/multiprocessing/spawn.py", line 246, in prepare
_fixup_main_from_path(data['init_main_from_path'])
File "/home/wangjw/programs/miniconda3/envs/py311/lib/python3.11/multiprocessing/spawn.py", line 297, in _fixup_main_from_path
main_content = runpy.run_path(main_path,
^^^^^^^^^^^^^^^^^^^^^^^^^
File "", line 291, in run_path
File "", line 98, in _run_module_code
File "", line 88, in _run_code
File "/data/wjw/test/singlecell/multiple/scripts/pyscenic_module.py", line 22, in
sc.settings.figdir = snakemake.params.sc_plot
^^^^^^^^^
NameError: name 'snakemake' is not defined
Traceback (most recent call last):
File "", line 1, in
File "/home/wangjw/programs/miniconda3/envs/py311/lib/python3.11/multiprocessing/spawn.py", line 122, in spawn_main
exitcode = _main(fd, parent_sentinel)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/wangjw/programs/miniconda3/envs/py311/lib/python3.11/multiprocessing/spawn.py", line 131, in _main
prepare(preparation_data)
File "/home/wangjw/programs/miniconda3/envs/py311/lib/python3.11/multiprocessing/spawn.py", line 246, in prepare
_fixup_main_from_path(data['init_main_from_path'])
File "/home/wangjw/programs/miniconda3/envs/py311/lib/python3.11/multiprocessing/spawn.py", line 297, in _fixup_main_from_path
main_content = runpy.run_path(main_path,
^^^^^^^^^^^^^^^^^^^^^^^^^
File "", line 291, in run_path
File "", line 98, in _run_module_code
File "", line 88, in _run_code
File "/data/wjw/test/singlecell/multiple/scripts/pyscenic_module.py", line 22, in
sc.settings.figdir = snakemake.params.sc_plot
^^^^^^^^^
NameError: name 'snakemake' is not defined
/home/wangjw/programs/miniconda3/envs/py311/lib/python3.11/site-packages/loompy/bus_file.py:67: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
@jit
/home/wangjw/programs/miniconda3/envs/py311/lib/python3.11/site-packages/loompy/bus_file.py:84: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
@jit
/home/wangjw/programs/miniconda3/envs/py311/lib/python3.11/site-packages/loompy/bus_file.py:101: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
@jit
/home/wangjw/programs/miniconda3/envs/py311/lib/python3.11/site-packages/loompy/bus_file.py:67: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
@jit
/home/wangjw/programs/miniconda3/envs/py311/lib/python3.11/site-packages/loompy/bus_file.py:84: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
@jit
/home/wangjw/programs/miniconda3/envs/py311/lib/python3.11/site-packages/loompy/bus_file.py:101: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
@jit
/home/wangjw/programs/miniconda3/envs/py311/lib/python3.11/site-packages/loompy/bus_file.py:67: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
@jit
/home/wangjw/programs/miniconda3/envs/py311/lib/python3.11/site-packages/loompy/bus_file.py:84: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
@jit
/home/wangjw/programs/miniconda3/envs/py311/lib/python3.11/site-packages/loompy/bus_file.py:101: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
@jit
/home/wangjw/programs/miniconda3/envs/py311/lib/python3.11/site-packages/loompy/bus_file.py:67: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
@jit
/home/wangjw/programs/miniconda3/envs/py311/lib/python3.11/site-packages/loompy/bus_file.py:84: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
@jit
/home/wangjw/programs/miniconda3/envs/py311/lib/python3.11/site-packages/loompy/bus_file.py:101: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
@jit
/home/wangjw/programs/miniconda3/envs/py311/lib/python3.11/site-packages/loompy/bus_file.py:67: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
@jit
/home/wangjw/programs/miniconda3/envs/py311/lib/python3.11/site-packages/loompy/bus_file.py:84: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
@jit
/home/wangjw/programs/miniconda3/envs/py311/lib/python3.11/site-packages/loompy/bus_file.py:101: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
@jit
/home/wangjw/programs/miniconda3/envs/py311/lib/python3.11/site-packages/loompy/bus_file.py:67: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
@jit
/home/wangjw/programs/miniconda3/envs/py311/lib/python3.11/site-packages/loompy/bus_file.py:84: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
@jit
/home/wangjw/programs/miniconda3/envs/py311/lib/python3.11/site-packages/loompy/bus_file.py:101: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
@jit
/home/wangjw/programs/miniconda3/envs/py311/lib/python3.11/site-packages/loompy/bus_file.py:67: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
@jit
/home/wangjw/programs/miniconda3/envs/py311/lib/python3.11/site-packages/loompy/bus_file.py:84: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
@jit
/home/wangjw/programs/miniconda3/envs/py311/lib/python3.11/site-packages/loompy/bus_file.py:101: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
@jit
Traceback (most recent call last):
File "", line 1, in
File "/home/wangjw/programs/miniconda3/envs/py311/lib/python3.11/multiprocessing/spawn.py", line 122, in spawn_main
exitcode = _main(fd, parent_sentinel)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/wangjw/programs/miniconda3/envs/py311/lib/python3.11/multiprocessing/spawn.py", line 131, in _main
prepare(preparation_data)
File "/home/wangjw/programs/miniconda3/envs/py311/lib/python3.11/multiprocessing/spawn.py", line 246, in prepare
_fixup_main_from_path(data['init_main_from_path'])
File "/home/wangjw/programs/miniconda3/envs/py311/lib/python3.11/multiprocessing/spawn.py", line 297, in _fixup_main_from_path
main_content = runpy.run_path(main_path,
^^^^^^^^^^^^^^^^^^^^^^^^^
File "", line 291, in run_path
File "", line 98, in _run_module_code
File "", line 88, in _run_code
File "/data/wjw/test/singlecell/multiple/scripts/pyscenic_module.py", line 22, in
sc.settings.figdir = snakemake.params.sc_plot
^^^^^^^^^
NameError: name 'snakemake' is not defined
/home/wangjw/programs/miniconda3/envs/py311/lib/python3.11/site-packages/loompy/bus_file.py:67: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
@jit
/home/wangjw/programs/miniconda3/envs/py311/lib/python3.11/site-packages/loompy/bus_file.py:84: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
@jit
/home/wangjw/programs/miniconda3/envs/py311/lib/python3.11/site-packages/loompy/bus_file.py:101: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
@jit
Traceback (most recent call last):
File "", line 1, in
File "/home/wangjw/programs/miniconda3/envs/py311/lib/python3.11/multiprocessing/spawn.py", line 122, in spawn_main
exitcode = _main(fd, parent_sentinel)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/wangjw/programs/miniconda3/envs/py311/lib/python3.11/multiprocessing/spawn.py", line 131, in _main
prepare(preparation_data)
File "/home/wangjw/programs/miniconda3/envs/py311/lib/python3.11/multiprocessing/spawn.py", line 246, in prepare
_fixup_main_from_path(data['init_main_from_path'])
File "/home/wangjw/programs/miniconda3/envs/py311/lib/python3.11/multiprocessing/spawn.py", line 297, in _fixup_main_from_path
main_content = runpy.run_path(main_path,
^^^^^^^^^^^^^^^^^^^^^^^^^
File "", line 291, in run_path
File "", line 98, in _run_module_code
File "", line 88, in _run_code
File "/data/wjw/test/singlecell/multiple/scripts/pyscenic_module.py", line 22, in
sc.settings.figdir = snakemake.params.sc_plot
^^^^^^^^^
NameError: name 'snakemake' is not defined
Traceback (most recent call last):
File "", line 1, in
File "/home/wangjw/programs/miniconda3/envs/py311/lib/python3.11/multiprocessing/spawn.py", line 122, in spawn_main
exitcode = _main(fd, parent_sentinel)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/wangjw/programs/miniconda3/envs/py311/lib/python3.11/multiprocessing/spawn.py", line 131, in _main
prepare(preparation_data)
File "/home/wangjw/programs/miniconda3/envs/py311/lib/python3.11/multiprocessing/spawn.py", line 246, in prepare
_fixup_main_from_path(data['init_main_from_path'])
File "/home/wangjw/programs/miniconda3/envs/py311/lib/python3.11/multiprocessing/spawn.py", line 297, in _fixup_main_from_path
main_content = runpy.run_path(main_path,
^^^^^^^^^^^^^^^^^^^^^^^^^
File "", line 291, in run_path
File "", line 98, in _run_module_code
File "", line 88, in _run_code
File "/data/wjw/test/singlecell/multiple/scripts/pyscenic_module.py", line 22, in
sc.settings.figdir = snakemake.params.sc_plot
^^^^^^^^^
NameError: name 'snakemake' is not defined
Traceback (most recent call last):
File "", line 1, in
File "/home/wangjw/programs/miniconda3/envs/py311/lib/python3.11/multiprocessing/spawn.py", line 122, in spawn_main
exitcode = _main(fd, parent_sentinel)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/wangjw/programs/miniconda3/envs/py311/lib/python3.11/multiprocessing/spawn.py", line 131, in _main
prepare(preparation_data)
File "/home/wangjw/programs/miniconda3/envs/py311/lib/python3.11/multiprocessing/spawn.py", line 246, in prepare
_fixup_main_from_path(data['init_main_from_path'])
File "/home/wangjw/programs/miniconda3/envs/py311/lib/python3.11/multiprocessing/spawn.py", line 297, in _fixup_main_from_path
main_content = runpy.run_path(main_path,
^^^^^^^^^^^^^^^^^^^^^^^^^
File "", line 291, in run_path
File "", line 98, in _run_module_code
File "", line 88, in _run_code
File "/data/wjw/test/singlecell/multiple/scripts/pyscenic_module.py", line 22, in
sc.settings.figdir = snakemake.params.sc_plot
^^^^^^^^^
NameError: name 'snakemake' is not defined
Traceback (most recent call last):
File "", line 1, in
File "/home/wangjw/programs/miniconda3/envs/py311/lib/python3.11/multiprocessing/spawn.py", line 122, in spawn_main
exitcode = _main(fd, parent_sentinel)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/wangjw/programs/miniconda3/envs/py311/lib/python3.11/multiprocessing/spawn.py", line 131, in _main
prepare(preparation_data)
File "/home/wangjw/programs/miniconda3/envs/py311/lib/python3.11/multiprocessing/spawn.py", line 246, in prepare
_fixup_main_from_path(data['init_main_from_path'])
File "/home/wangjw/programs/miniconda3/envs/py311/lib/python3.11/multiprocessing/spawn.py", line 297, in _fixup_main_from_path
main_content = runpy.run_path(main_path,
^^^^^^^^^^^^^^^^^^^^^^^^^
File "", line 291, in run_path
File "", line 98, in _run_module_code
File "", line 88, in _run_code
File "/data/wjw/test/singlecell/multiple/scripts/pyscenic_module.py", line 22, in
sc.settings.figdir = snakemake.params.sc_plot
^^^^^^^^^
NameError: name 'snakemake' is not defined
Traceback (most recent call last):
File "", line 1, in
File "/home/wangjw/programs/miniconda3/envs/py311/lib/python3.11/multiprocessing/spawn.py", line 122, in spawn_main
exitcode = _main(fd, parent_sentinel)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/wangjw/programs/miniconda3/envs/py311/lib/python3.11/multiprocessing/spawn.py", line 131, in _main
prepare(preparation_data)
File "/home/wangjw/programs/miniconda3/envs/py311/lib/python3.11/multiprocessing/spawn.py", line 246, in prepare
_fixup_main_from_path(data['init_main_from_path'])
File "/home/wangjw/programs/miniconda3/envs/py311/lib/python3.11/multiprocessing/spawn.py", line 297, in _fixup_main_from_path
main_content = runpy.run_path(main_path,
^^^^^^^^^^^^^^^^^^^^^^^^^
File "", line 291, in run_path
File "", line 98, in _run_module_code
File "", line 88, in _run_code
File "/data/wjw/test/singlecell/multiple/scripts/pyscenic_module.py", line 22, in
sc.settings.figdir = snakemake.params.sc_plot
^^^^^^^^^
NameError: name 'snakemake' is not defined
Traceback (most recent call last):
File "", line 1, in
File "/home/wangjw/programs/miniconda3/envs/py311/lib/python3.11/multiprocessing/spawn.py", line 122, in spawn_main
exitcode = _main(fd, parent_sentinel)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/wangjw/programs/miniconda3/envs/py311/lib/python3.11/multiprocessing/spawn.py", line 131, in _main
prepare(preparation_data)
File "/home/wangjw/programs/miniconda3/envs/py311/lib/python3.11/multiprocessing/spawn.py", line 246, in prepare
_fixup_main_from_path(data['init_main_from_path'])
File "/home/wangjw/programs/miniconda3/envs/py311/lib/python3.11/multiprocessing/spawn.py", line 297, in _fixup_main_from_path
main_content = runpy.run_path(main_path,
^^^^^^^^^^^^^^^^^^^^^^^^^
File "", line 291, in run_path
File "", line 98, in _run_module_code
File "", line 88, in _run_code
File "/data/wjw/test/singlecell/multiple/scripts/pyscenic_module.py", line 22, in
sc.settings.figdir = snakemake.params.sc_plot
^^^^^^^^^
NameError: name 'snakemake' is not defined
Traceback (most recent call last):
Uploading nohup.out.txt…

My best guess is that when pysenic/dask spawns child processes, snakemake object is not properly serialized and passed on. I don't know how Dask handles multiprocessing but you can try the following:

Use only a single thread in your script and see if the error goes away
Wrap your code in a function and pass snakemake in as an argument
Modify your script to work as a cli python script and call it from shell directive instead of script directive

I finally call pyscenic_module.py from script directive by enclose the code in a if name == 'main': construct.
This is a known case but it didn't work before (about two years before), but now it works. I don't know why, however, it can solve my problem now !

authors: SichongP cmeesters wangjiawen2013

repo: snakemake/snakemake


text:
remote prefix for input and output files separately?

The google life sciences option is wonderful and very easy to use. However, I don't seem to have figured out a way to specify input and output buckets separately.
I would like to store the output of the workflow in a different bucket from the input bucket. It seems that --default-remote-prefix needs to be specified (otherwise I get an error) and cannot be an empty string (I tried "" and '').
I would like to either have an option to specify an empty string so that I can set the buckets for each input and output in the workflow; or have an option to specify input and output buckets separately, would that be possible?

Hi @shukwong,
My understanding is that the default remote prefix won't be applied to inputs that are marked as remote files via GS.remote(). I'm not sure if this approach also works for outputs, though.
If you'd like to request a new feature related to the Google Life Sciences backend, you should put it in #457.

Thanks @aryarm! Your suggestion works very well indeed!

authors: aryarm shukwong


text:
make lightgbm_link_baseline memory efficient

there is a join operation going on here
# Include src and dst entity table features for `test_df`
test_df = pd.merge(
    test_df,
    src_entity_df,
    how="left",
    left_on=left_entity,
    right_on=src_entity_table.pkey_col,
)
test_df = test_df.explode(right_entity)
test_df = pd.merge(
    test_df,
    dst_entity_df,
    how="left",
    left_on=right_entity,
    right_on=dst_entity_table.pkey_col,
)

this step is basically making a really massive df
instead of a row having (src, list_of_dst) it will make a row for each src, dst for dst in  list_of_dst
this leads to memory issues (e.g. rel-amazon/user-item-rate takes ~200G memory, most runs just fail with memory error)
i think this can be solved with negative sampling of the rows, but will need some thought. please look into it, thanks!

I think one way to resolve this is to instead of sample only on the src entities, we could sample on both src and dst entities instead, since we expand the train table into a list of src entity dst entity pairs during training.

Additionally, it is likely we need to sample validation table as well to further reduce memory usage.

I would think of constructing the table like this:

use all (src, dst) pairs for which there is a link (positive pairs)
use sampling for (src, dst) pairs without link (negative sampling)
I think negative sampling is used in other parts of the codebase too, so you can look at the implementation. The sampling strategy can possibly be a commandline arg to the script.

@weihua916 what do you think?

@rishabh-ranjan I think we are already doing that in the lightgbm implementation https://github.com/snap-stanford/relbench/blob/main/examples/lightgbm_link_baseline.py#L131

ah, i see!

authors: XinweiHe rishabh-ranjan

repo: snap-stanford/relbench


text:
optgroup with bootsrap 5

Hello,
I faced below unexpected behavior in bootstrap-select v1.14.0-beta2 with bootstrap 5.0 beta-3.

If optgroup is used, selected option will be repeated multiple times (same count of optgroups).
If option is used with optgroup, for example to show default selected option, then list will disappear.

I've created sample codepen to illustrate the issue:
bootstrap-select optgroup issue
Thanks

Can confirm, I have this issue as well on bootstrap 5.0.0-beta3 and bootstrap-select 1.14.0-beta2.

Same as #2607 (which will be resolved in the next release).

I am unable to find anything newer than mentioned 1.14.0 beta 2 on jsdelivr, am I missing something?

This issue seems to be resolved in 1.14.0-beta3
you can upgrade the package to https://cdn.jsdelivr.net/npm/bootstrap-select@1.14.0-beta3/dist/js/bootstrap-select.min.js
and it should work fine

repo: snapappointments/bootstrap-select


text:
Add support for API key

We should introduce API key to help monitor number of request that the API receive and prevent someone to spam the hub.

Pitch details here 🙏

Closing as the there is another API Keys issue active in #541

authors: bonustrack zzuziak

repo: snapshot-labs/snapshot-hub


text:
[multidelegation] feat: multidelegation strategy

Changes proposed in this pull request:

Added support for users to delegate to multiple addresses

Hey guys, i feel like this is too heavy for us, we stopped adding new strategies that depend on other voters https://github.com/snapshot-labs/snapshot-strategies#code do you think of any other alternatives? maybe you can run this on our side and use api strategy to return the voting power?

authors: ChaituVR ncomerci

repo: snapshot-labs/snapshot-strategies


text:
published/updated not always populating (HTML to Atom)

I'm using a granary Atom feed of https://gregorlove.com/stream/ and some posts don't seem to convert the published or updated date. It appears to happen with RSVPs, bookmarks, and likes.
https://gregorlove.com/2023/01/im-probably-attending-homebrew-website-club/
<entry>
  <author>
    <activity:object-type>http://activitystrea.ms/schema/1.0/person</activity:object-type>
    <uri>https://gregorlove.com/</uri>
    <name>gRegor Morrill</name>
  </author>
  <activity:object-type>http://activitystrea.ms/schema/1.0/event</activity:object-type>
  <id>https://gregorlove.com/2023/01/im-probably-attending-homebrew-website-club/</id>
  <title>Iâ€™m probably attending </title>
  <content type="xhtml">

Iâ€™m <data class="p-rsvp" value="maybe">probably</data> attending Homebrew Website Club - Pacific tonight at 6PM Pacific.

  </content>
  <link rel="alternate" type="text/html" href="https://gregorlove.com/2023/01/im-probably-attending-homebrew-website-club/" />
  <link rel="ostatus:conversation" href="https://gregorlove.com/2023/01/im-probably-attending-homebrew-website-club/" />
  <activity:verb>http://activitystrea.ms/schema/1.0/rsvp-maybe</activity:verb>
  <activity:object>https://events.indieweb.org/2023/01/homebrew-website-club-pacific-MKOZpT2yDqpU</activity:object>
  <published></published>
  <updated></updated>
  <link rel="self" type="application/atom+xml" href="https://gregorlove.com/2023/01/im-probably-attending-homebrew-website-club/" />
</entry>

Other posts currently in the stream this happens with:

Like: https://gregorlove.com/2023/01/star-dave-millar/
Bookmark: https://gregorlove.com/2023/01/bookmarked-make-your-own/
Like: https://gregorlove.com/2023/01/star-taking-a-break/

Hmm! Thanks for reporting, will look.

Fixed, thanks again!

@snarfed Thanks! This bookmark is still showing blank, but the others are working now. Is it cached?

Argh, true, thanks for following up. Reopening.

Fixed!

authors: gRegorLove snarfed

repo: snarfed/granary


text:
BC break with SncRedisBundle >=4.0 when calling multi()

I had code which was working just fine with SncRedisBundle 3.* branch:
        $redis = $this->redisClient->multi();
        foreach ($items as $item) {
            $redis->zAdd(self::QUEUE_KEY, $item->getAuditDefinitionId(), $this->serialize($item));
        }
        $result = $redis->exec();

After upgrading to 4.0 it started to cause multiple errors in tests:

NOTE; the offending line 31 is the one which starts multi transaction
This can be solved by setting mode value manually when calling multi:
        $redis = $this->redisClient->multi(\Redis::MULTI);
        foreach ($items as $item) {
            $redis->zAdd(self::QUEUE_KEY, $item->getAuditDefinitionId(), $this->serialize($item));
        }
        $result = $redis->exec();

NOTE; I am explicitly using value which is supposed to be used by default according to phpredis documentation
When I lock this bundle to version below <4.0 everything runs as before.
Configuration details:
PHP version:

PHP Redis extension:

Bundle configuration in Symfony:

Symfony version: 5.4.1

I've created https://github.com/phpredis/phpredis/issues/2044 as issue should be solved there.

authors: noofaq ostrolucky

repo: snc/SncRedisBundle


text:
Require future.annotations for all files with type annotations, not just for forward references

TC100 helpfully warns me when files contain annotations that cannot be resolved at runtime because they were imported inside a T.TYPE_CHECKING block. What about files that contain annotations using builtin types (or coincidentally runtime-also types) that don't need an import?
There are two advantages of future annotations:

it avoids the runtime cost of evaluating them
it avoids the runtime fatal error of evaluating them when they cannot be evaluated

I want both. flake8-type-checking currently helps me do the latter.
The former can kind of be done via isort --add-imports or ruff missing-required-import except that both of those are based around the notion that all files must have some arbitrary import. This causes it to demand that every empty __init__.py file receives that import. Also, there are sometimes files that contain pure data with trivially deducible types and don't need annotations. I figured a specialized check designed for validating annotations in the first place, might be a better place to implement such a feature.

I don't think we should make that the default behavior for TC100, but I would be open to adding an additional setting for that. Just like we have a strictness setting for TC001/TC002/TC003.
It should be very straightforward to implement, PRs welcome.

Yup, I'd be happy to request it in .flake8 as a separate error code (and actually kinda assumed that would be preferred).
I may find time to look into implementing this myself but I cannot predict that in advance. Anyone else interested in this shouldn't bother waiting on me. :)

I'd actually prefer a setting over a separate error code, since the error message would be the same for both error codes, you're just changing the condition for when you emit the code.

authors: Daverball eli-schwartz


text:
为什么我文章列表页的每篇文章下面都会渲染出评论框？

我看插件是执行的过滤器after_post_render，那么在我首页文章列表页上，每篇文章渲染后也会渲染出评论框？？？

暂时没有找到比较好的方法,希望大佬能提供pr,附图说明更加简单直观哟

是否能够选择某些文章不需要评论？

authors: Veitor hanjie-chen snowdreams1006


text:
Feature: Kafka as input type

With Kafka as input type it would be possible to set up a snowplow stack on-premise for smaller setups.

You can show me how you do it. Thanks

Hi, you'd need to add kafka there.
But ideally this repo would need some refactoring to have several modules (e.g. like here) so that each app brings only the libraries of the message queue it is using, See how each techno gets its own app.

@benjben please, is there a chance the Kafka input will be implemented?
I have tried to deal with it, but im not skilled in scala.

Hi @lukas-pastva , this is not on our radar to implement this, sorry. As stated in the docs Postgres loader is not recommended for production use. Our development effort focuses on fully-fledged data warehouses (e.g. Databricks, Snowflake, BigQuery) and more recently on data lakes (e.g. Delta, Iceberg). /cc @stanch

authors: benjben dinhphu2k1-gif korpa lukas-pastva


text:
Adds network type and technology to mobile context

First attempt to solve #179. Haven't tested this yet.

Thanks @bernardosrulzon ! Josh, Bernardo has signed the CLA.

authors: alexanderdean bernardosrulzon

repo: snowplow/snowplow-android-tracker


text:
Bump to Snowplow.Tracker.PlatformExtensions.Dotnet to 4.8

The last supported NET Framework release with MSMQ is 4.8. We can bump to this and then leave this as is for the forseeable.

Closing as we will leave the extension at 461 for compatibility.

repo: snowplow/snowplow-dotnet-tracker


text:
JOSS Review: Documentation

Originally from @jochym in openjournals/joss-reviews#440
There is only very limited API documentation for two functions. Judging from the simplest example, even this simplest usage requires calling additional API functions (multiphonon.sqe.interp). The only functional documentation is a tersely commented notebook which I was unable to run (see above).

Will add some more API documentation

List of functions to add API doc or to expose API doc:

https://github.com/sns-chops/multiphonon/blob/61dd792aa3695281240abf51e9151a308e86163c/multiphonon/redutils.py#L1
https://github.com/sns-chops/multiphonon/blob/61dd792aa3695281240abf51e9151a308e86163c/multiphonon/backward/singlephonon_sqe2dos.py#L10
Plotting methods in https://github.com/sns-chops/multiphonon/blob/61dd792aa3695281240abf51e9151a308e86163c/multiphonon/backward/plotutils.py
https://github.com/sns-chops/multiphonon/blob/61dd792aa3695281240abf51e9151a308e86163c/multiphonon/forward/__init__.py#L7
https://github.com/sns-chops/multiphonon/blob/61dd792aa3695281240abf51e9151a308e86163c/multiphonon/forward/phonon.py#L21
https://github.com/sns-chops/multiphonon/blob/61dd792aa3695281240abf51e9151a308e86163c/multiphonon/forward/phonon.py#L30
https://github.com/sns-chops/multiphonon/blob/61dd792aa3695281240abf51e9151a308e86163c/multiphonon/sqe/__init__.py#L27

API

Try to aim for the level of documentation used in scipy - such that users will have all necessary data to use your code.
Please add some overview paragraphs to the docs to help users orient themselves.

Functional docs
The notebook tutorial is a very good idea and it is mostly fine (except it did not run on my system). I have only one comment regarding the contents: please consider adding more narrative material, some overview and step by step explanation.  Remember you are writing for a novice user not an expert (they can figure out everything without your help).

@jochym Please check the new API doc at http://sns-chops.github.io/multiphonon/. We added API docs for  the methods intended for users. We also added a brief introduction.
We added comments to the jupyter notebook, and added one more example to show users how to work directly from numpy arrays of I(Q,E) spectrum.

authors: jochym lheagy yxqd

repo: sns-chops/multiphonon


text:
Adding log4j-detector

Detects vulnerable log4j versions on your file-system within any application. It is able to even find instances that are hidden several layers deep. Works on Linux, Windows, and Mac, and everywhere else Java runs, too!
Currently detects log4j-core versions 2.12.2 and 2.16.0 as SAFE, 2.15.0 as OKAY and all other versions as VULNERABLE (although it does report pre-2.0-beta9 as "POTENTIALLY_SAFE").
Can correctly detect log4j inside executable spring-boot jars/wars, dependencies blended into uber jars, shaded jars, and even exploded jar files just sitting uncompressed on the file-system (aka *.class).

thanks for the contribution !

authors: MarkvanOsch mattj-io


text:
chore: update copyright notice and cleanup warnings

Description
Update to copyright notice to use copyright symbol, cleaned up most warnings.
Checklist

[ ] Tests added and all succeed
[x] Linted
[ ] README.md updated, if user-facing
[ ] License file updated, if new 3rd-party dependency is introduced

Screenshots / GIFs
Visuals that may help the reviewer. Please add screenshots for any UI change. GIFs are most welcome!

There's some special character that got pulled in (Â). Also, can we make all the error-ignoring stuff 1 line instead of 3?

This is extremely weird. If you tell github to show the file, the Â character is not there. On my computer, I can't see it either - it seems to be a problem with the github diff view.

repo: snyk/snyk-ls


text:
🛑 Interseed (interseed.app) is down

In 23ab8d8, Interseed (interseed.app) (https://interseed.app) was down:

HTTP code: 404
Response time: 128 ms

Resolved: Interseed (interseed.app) is back up in 9d23977 after 11 minutes.

repo: so-more/proof-monitoring


text:
Location of ARSLineProgress view

Hi
You've made a super beautiful activity indicator!
I've been having some issues with its location, however.
To give some context:
Upon selection of a cell in a UITableViewController, we segue to a UIWebView taking up the entirety of the screen. All of my ViewControllers are embedded in a UINavigationController.
So if I type, for example:
ARSLineProgress.show()
two things occur:

It appears in the middle of the screen, but only in its initial orientation - changing orientation skews the location of the ARSLineProgress.
It blocks the UI; I cannot click the back button for example.

If I type:
ARSLineProgress.showOnView(showDoc) //showDoc is the name of the UIWebView
two things occur:

It no longer blocks the UI!
It also no longer appears in the centre of the screen :(

Have you encountered anything like this yet?
If you're able to offer any advice, it would be greatly appreciated.
Either way, I thought I would provide this feedback, as well as thank you for everything you've done on this project thus far - it's really wonderful :)
Cheers
Saf

This is scenario 1 (where it blocks the UI)
Here it is in the initial orientation:

Here it is once the orientation has been changed:

Hey!
Thank you :)
First of all - none of the methods block the UI as I intentionally leave it up to a developer to do it.
As for the positioning problem - I do remember that during development there was this issue but I fixed it, at least it worked fine on iOS9. Looks like behaviour changed in iOS10.
Anyways, I have fixed this issue, feel free to pull updates.

authors: sarfrazb soberman

repo: soberman/ARSLineProgress


text:
Add TweetNoteTweetObj to TweetObj

Add TweetNoteTweetObj to TweetObj

@yuyan7
下記で追加しましたので、お手すきでご確認よろしくお願いします！
76636238c7172436d1ff1fa8748db4d1cb904d2e


text:
Use prefix of this itself

It's better to use this.prefix than an upper scope's prefix.

I was thinking we could add a proto function that is the sole place responsible for generating a channel name, such as :
Redis.prototype.channelName = function(room){
  var channelName = this.prefix + '#' + this.nsp.name + '#';
  if ( room ) {
    channelName +=  room + '#';
  }
}

There are currently 5 or so places in the code that do string concatenation to form Redis channel names.

I think we can just append namespace to prefix in the first place like
this.prefix = prefix + '#' + this.nsp.name + '#';

@nkzawa Looks good :+1:

@Lellansin can you resolve the merge conflicts?

authors: Lellansin nkzawa objectiveSee


text:
leastActive worker is undefined when socket io worker servers are built with an express server

There is a problem with the function computeWorkerId when express is used to construct the socket io server. When all the socket worker servers have been closed, the following error appears:
/home/wvhulle/Documents/socket.io-fiddle/node_modules/@socket.io/sticky/index.js:58
        return leastActiveWorker.id;
                                 ^

TypeError: Cannot read properties of undefined (reading 'id')
    at computeWorkerId (/home/wvhulle/Documents/socket.io-fiddle/node_modules/@socket.io/sticky/index.js:58:34)
    at Socket.<anonymous> (/home/wvhulle/Documents/socket.io-fiddle/node_modules/@socket.io/sticky/index.js:80:18)
    at Socket.emit (node:events:525:35)
    at addChunk (node:internal/streams/readable:324:12)
    at readableAddChunk (node:internal/streams/readable:297:9)
    at Readable.push (node:internal/streams/readable:234:10)
    at TCP.onStreamRead (node:internal/stream_base_commons:190:23)

It seems like the function cannot deal with the case where there are no workers. When I remove express, the problem disappears.
The bug can be seen in https://github.com/wvhulle/socket.io-fiddle/tree/cluster-adapter, after running the client and the server, then waiting until the worker threads quit.

Adding app.close() in the workers does not seem to help.
But adding this in the primary
  cluster.on("exit", (worker) => {
    console.log(`Worker ${worker.process.pid} died`);
    if (Object.values(cluster.workers).length === 0) {
      httpServer.close()
    }
  });

solves the problem, but maybe this library should also have something opposite to setupMaster? Like closeMaster? Or otherwise be able to deal with data still coming in the primary server but no workers available.

  cluster.on("exit", (worker) => {
    console.log(`Worker ${worker.process.pid} died`);
    if (Object.values(cluster.workers).length === 0) {
      httpServer.prependListener("connection", (socket) => { socket.destroy() })
    }
  });

Also seems to work.

@wvhulle I could indeed reproduce, thanks. We should definitely handle the case where there are no available worker.

Shoul I open a merge request with one of my fixes?

That would be awesome 👍

For future readers:
This should be fixed by https://github.com/socketio/socket.io-sticky/commit/e8b4203d18fc9601e05af3457baba49fafdb15f0, included in version 1.0.3. Please reopen if needed!

Thanks a lot!

authors: darrachequesne wvhulle


text:
21BCAB20_GEETHA D

What type of PR is this?

Uncomment only one  /kind <> line, hit enter to put that in a new line, and remove leading whitespace from that line:
/kind new feature
/kind bug fix
/kind cleanup
/kind revert change
/kind design
/kind documentation
/kind enhancement

What this PR does / why we need it:
Which issue(s) this PR fixes:

Fixes #
Test Report Added?:

Uncomment only one  /kind <> line, hit enter to put that in a new line, and remove leading whitespace from that line:
/kind TESTED
/kind NOT-TESTED

Test Report:

Special notes for your reviewer:

@kalaiselvikks76


text:
支持sofa-serverless-adapter-logback

logback 的多模块化适配

这个PR我来试试 @lvjing2

这个PR我来试试 @lvjing2

好的，非常欢迎，下周二晚上也有双周会，想了解 sofaserverless 的迭代和规划也可以参加哈

repo: sofastack/sofa-serverless


text:
在springcloud应用中引入sofatrace仅仅想使用MDC功能如何实现

Your question
在springcloud应用中引入sofatrace仅仅想使用MDC功能，发现SofaBootstrapRunListener启动早于BootstrapApplicationListener，这样导致bootstrap无法获取相关的bootstrap.yml配置导致无法启动
Your scenes
旧工程改造，想快速增加应用日志链路（单个应用级别）
Your advice
describe the advice or solution you'd like
Environment

SOFATracer version:3.4.4
JVM version (e.g. java -version):1.8.0_231
OS version (e.g. uname -a):Linux x86_64 x86_64 x86_64 GNU/Linux
Maven version:Apache Maven 3.5.4
IDE version:2020.2

该问题通过增加Environment的aware解决配置加载问题

repo: sofastack/sofa-tracer


text:
Needs a LICENSE.md

Thank for all of the hard work. This looks great!
What license is this project under? Are you able to add the appropriate LICENSE.md?

Hey @dapperdandev , thanks for the info. It will be MIT license. Does that look alright or do I miss anything: https://github.com/softarc-consulting/sheriff/pull/65

@rainerhahnekamp lgtm. Thanks again!

Thanks for mentioning it!

authors: dapperdandev rainerhahnekamp

repo: softarc-consulting/sheriff


text:
installation instructions improvment

When i installed knife-soflayer i ran into those issues ( so i paln to create a PR for this soon)

The default location in which knife expects to find this file is ~/.chef/knife.rb

and if you run into installation error like these :-
"Building nokogiri using packaged libraries. checking for gzdopen() in -lz... no zlib is missing; necessary for building libxml2 *** extconf.rb failed ***"

then try :-
sudo apt-get install zlib1g-dev
gem install nokogiri
gem install knife-softlayer

I'd love to see a PR with updated documentation.
Your fix though is specific to the platform and version you're working from, and nokogiri causes problems on basically every platform somewhat regularly.
When you put up the PR let's do an alternative recommendation that should fix that problem across most common platforms?  Maybe something like this?
export NOKOGIRI_USE_SYSTEM_LIBRARIES=1
gem install knife-softlayer

Thx @Neetuj

yes .. http://www.nokogiri.org/tutorials/installing_nokogiri.html

authors: Neetuj cphrmky

repo: softlayer/knife-softlayer


text:
Simplify types around expect_events cheatcode

Just found an opportunity here to clean up things.

I'd rename EventExpectation* to ExpectedEvent*

@MaksymilianDemitraszek wdyt? We have alternatively thought about the name EventData

@kasperski95 @MaksymilianDemitraszek actually the name ExpectedEvent is already used by something else which is imported in this module... reverting some changes

@kasperski95 ping

repo: software-mansion/protostar


text:
Mask type does not work correctly on Android

Bug
Unexpected behavior
objects don't appear on Android when inside a mask which should show them. iOS shows them as expected.
code
/* eslint-disable i18next/no-literal-string */
import * as React from "react";
import Svg, { G, Mask, Path, SvgProps } from "react-native-svg";

export const SVGWithMask = (props: SvgProps): JSX.Element => (
  <Svg
    xmlns="http://www.w3.org/2000/svg"
    width={304}
    height={271}
    fill="none"
    {...props}
  >
    <Mask
      id="e"
      width={28}
      height={28}
      x={240}
      y={108}
    >
      <Path fill="#fff" d="M267.568 108.903h-26.867v26.867h26.867v-26.867Z" />
    </Mask>
    <G mask="url(#e)"> // <---- removing this, makes the element appear as expected
      <Path
        fill="#2D3142"
        d="M250.321 116.318c2.337 1.713 4.455 5.751 5.502 6.48 1.041.722 7.913 3.053 7.913 3.053s3.309 1.021 3.477 1.321c.168.299-.187.51-.187.51l-10.86-2.729a10.21 10.21 0 0 0-.075.879.68.68 0 0 1-.137.461.648.648 0 0 1-.399.262s1.221 1.788 1.408 2.043c.181.256.106 1.166.106 1.166l-3.956-2.916-.897.442-1.976 3.894c.424 0 .835.025 1.259.075.611.068.287.324.33.542.038.218-.648-.106-.648-.106s-.685-.075-1.227-.075c0 .156-.019.318-.038.474 0 0 .904-.038 1.44-.112a1.106 1.106 0 0 1 1.084.548c.181.293-.686-.106-.686-.106s-.317.15-.392.293c-.075.149-.904.218-1.115.181-.218-.038-.979 0-1.259 0-.511.149-1.016.33-1.514.548-.287.075-1.221.037-1.184-.112.037-.15.897-.287.897-.287l-.791-.181-1.146.038s-.256-.218-.219-.324c.038-.106 1.153-.075 1.153-.075l.791-.075s.106-.143.219-.068c.461.118.947.106 1.401-.038.462-.187.505-.479.505-.479a8.47 8.47 0 0 0-.791.037c-.611.025-1.221.012-1.832-.037a.805.805 0 0 1-.573-.362c-.038-.106-.287-.037-.611-.324a1.583 1.583 0 0 1 1.115.144c.387.074.792.074 1.184 0 .262-.019.524-.094.754-.219a19.388 19.388 0 0 0 2.449-3.638c-8.2.511-9.384-5.639-9.558-7.602-.175-1.963.872-4.037.872-4.037s.324-1.097-.106-1.564c-.43-.468-1.308-.549-1.258-.692.043-.149.972-.33 1.302-.368 0 0 .866-2.436 2.879-2.199 2.006.237 3.669.903 5.427 5.352h-.013l-.019-.018Z"
      />
    </G>
  </Svg>
);

Environment info
expo 48

Library version: 13.4.0
Steps To Reproduce
Describe what you expected to happen:

copy the above code
view on android and ios. you'll see a bird appear on ios but not on android
remove the G tag and both platforms show the same content.

Hello @MorganDavid,
I tried to reproduce that issue, but couldn't.

Android
IOS

Let me know if you still have that issue. Try to update react-native-svg library.
Thank you

authors: MorganDavid bohdanprog

repo: software-mansion/react-native-svg


text:
Add to github repos from

Add github repos
from
https://github.com/softwareunderground/awesome-open-geoscience
to
https://github.com/softwareunderground/open_geosciene_code_projects_viz/blob/main/_explore/input_lists.json
As a first pass, do this manually.
Steps:

Fork this repo.
Add repos to the _explore/input_lists.json file in your fork.
Submit back pull request with explaination of your change.
Justin will merge the pull request
Justin will rerun the scripts that generate the metadata for all the repos and then push those changes into main branch and redeploy as Github Pages page.

Right- so other useful ones not there?

Are all the org ones listed there covered already?

This file has all the orgs & repos in the current data visualizations  @RichardScottOZ
https://github.com/softwareunderground/open_geosciene_code_projects_viz/blob/main/_explore/input_lists.json
I've only got the first 3 sections included so far. It was just a quick test. Now more are needed.
Ideally, there would be a script to do this instead of doing it by hand. But by hand is okay for now.

Thanks to the 2 pull requests on this issue #14 and #4 keep them coming!

Just FYI that capitalization needs to be exact or it won't work.

authors: JustinGOSSES RichardScottOZ


text:
/tmp-Verzeichnis aufräumen

Die iox-Geschichten ebenfalls nach gewisser Zeit löschen.

ioxtmp-Dateien werden durch ilivalidator selber gelöscht.
Das temporäre lokale Verzeichnis (falls S3 verwendet wird) wird geleert (durch Service-Klasse) aber nicht gelöscht. -> https://github.com/sogis/ilivalidatorws/commit/ee750b25fff23bb3cad629dbfbee5adbb5e59722 plus zwei Folge-Commits wegen Fehler in Test.

repo: sogis/ilivalidatorws


text:
Feature/support web

Add a focus trap only web platform to make it easier to build accessible modals on Web

Opened PR to wrong repo. Closing.

repo: sohobloo/react-native-modal-dropdown


text:
Governance: Use separate thresholds to create proposals for council and community tokens

Summary

This change introduces min_council_tokens_to_create_proposal and min_community_tokens_to_create_proposal instead of a single min_tokens_to_create_proposal threshold to make it possible to use different thresholds for council and community tokens. A single threshold min_tokens_to_create_proposal is not sufficient for scenarios when the Council and Community mints supplies are significantly different (the most common case) and have different decimal places.

This change also makes it possible for community token holders to create proposals voted on by the council and council token holders can now create proposals voted on by the community.
This restriction existed in previous versions but it was a side effect of the implementation and not by design.

Sorry for the slowness on this, but it looks great! The test cases covered all the best conditions I could think of

thank you

repo: solana-labs/solana-program-library


text:
Manual Merge

I'm submitting a ...
[X] bug report
[X] feature request
[ ] question about the decisions made in the repository
[ ] question about how to use this project

Summary

Other information (Add Official Website DroidBits Token, and some bug i added decimal 6 but showing 9 on solscan.)
-New PR Fix https://github.com/solana-labs/token-list/pull/26910

@keone could you please merge this PR? thanks :)

hello , can you help me @mercs-shashank

What happened ?

i need to update our website please approve manual merge thank a lot

i need to update our website please approve manual merge thank a lot

i dont have authority to merge

authors: droidbitnft mercs-shashank

repo: solana-labs/token-list


text:
update token symbol

Please note: This repository is being rebuilt to accept the new volume of token additions and modifications. PR merges will be delayed.

I agree to not ping anybody on Discord/Twitter/email about this pull request. Instead I will inquire by posting a new comment in the pull request if needed.

PRs are reviewed in bulk and and can take up to two weeks to be merged.
This repository is managed using an auto merge action. Please ensure your PR has no deleted lines, and it will be merged.
Please provide the following information for your token.
Please include change to the src/tokens/solana.tokenlist.json file in the PR.
DON'T modify any other token on the list.
At minimum each entry should have

Token Address:
Token Name:
Token Symbol:
Logo: (logo should be uploaded under assets/mainnet//*.<png/svg>)
Link to the official homepage of token:
Coingecko ID if available (https://www.coingecko.com/api/documentations/v3#/coins/get_coins__id_):

Auto merge requirements
Your pull request will be automatically merged if the following conditions are met:

Your pull request only adds new tokens to the list. Any modification to existing
tokens will require manual review to prevent unwanted modifications.

Your pull request does not touch unrelated code. In particular, reformatting changes to unrelated
code will cause the auto merge to reject your PR.

Any asset files added correspond to the token address you are adding. Asset files
must be PNG, JPG or SVG files.

Your change is valid JSON and conforms to the schema. If your change failed validation,
read the error message carefully and update your PR accordingly.

No other tokens shares the same name, symbol or address.

For example, this change would be rejected due to unrelated changes:

The bot runs every 60 minutes and bulk-merges all open pull requests to prevent conflicts.
This means that you need to wait up to 60 minutes for your pull request to be merged or reprocessed.

https://github.com/solana-labs/token-list/commit/8c395200922fe8e01d41c49d32215c1abff9e8bd

authors: keone yongbeam


text:
consul_acl makes api call before ACL api is available

I get connection refused when trying to create/modify an acl policy via the consul_acl type.  I was able to create one by hacking in a wait, showing it to be a timing issue:
  exec { 'wait_a_damn_minute' :
    command => "echo 'Waiting...' && sleep 30",
    path  => "/usr/bin:/bin",
  }

  consul_acl { 'anonymous':
    ensure        => 'present',
    name          => 'Anonymous Token',
    acl_api_token => 'S3Cr3tStuFFs',
    rules => {
      'key' => {
        "" => {'policy'    => 'read'},
        '_rexec' => {'policy' => 'write'},
      }
    },
    type    => 'client',
    require => Exec['wait_a_damn_minute'],
  }

@reppard quick question, when you mean the API call is made before ACL api is available...is this happening right after consul has recently restarted? I can't imagine the API not being available during normal usage.

Yes this is on a new node.  The service is started and the acl policy apply
is attempted directly after.  The failing request is /v1/acl/list I believe.
On Oct 14, 2015 5:08 PM, "AJ" notifications@github.com wrote:

@reppard https://github.com/reppard quick question, when you mean the
API call is made before ACL api is available...is this happening right
after consul has recently restarted? I can't imagine the API not being
available during normal usage.
—
Reply to this email directly or view it on GitHub
https://github.com/solarkennedy/puppet-consul/issues/193#issuecomment-148201057
.

You need to have a leader elected before you can use the rest API. This is how we implemented bootstrapping a cluster with ACLS in an idempotent way.
exec { 'leader_elected':
  command     => "/usr/bin/test \"$(curl -s http://localhost:6500/v1/status/leader)\" != '\"\"'",
  tries       => 5,
  try_sleep   => 1,
  unless      => "/usr/bin/test \"$(curl -s http://localhost:6500/v1/status/leader)\" != '\"\"'",
}

Consul_acl <||> { require => Exec['leader_elected'] }

authors: aj-jester reppard sigerber

repo: solarkennedy/puppet-consul


text:
scripts/gen-html: escape double quotes on default values

Otherwise it may break the generated page.
Signed-off-by: Bruno Dilly bruno.dilly@intel.com

merged after an ack of @cabelitos on irc

repo: solettaproject/soletta


text:
Parent folder .acl is not consulted, even if local .acl does not specify permissions

Given a folder contains a .acl file specifying permissions to a file inside that folder, but does not say something about permissions to the folder itself:
<#owner>
    a acl:Authorization;
    acl:agent <https://angelo.veltens.org/profile/card#me>;
    acl:accessTo <./file.ttl>;
    acl:mode acl:Read, acl:Write, acl:Control.

The parent folder grants all access for the same agent as default (acl:default)
Actual behaviour:
Both, the folder and the file.ttl are unreachable for the agent (403 Forbidden).
Expected behaviour:
Since the .acl does not specify access control for the folder, the parent folder .acl should be checked and access granted to the folder (granted by parent .acl) and to the file.ttl (granted by the folder's .acl).

Yes, this has been discussed in the specification, and it is actually the intended behaviour. Here is the spec issue, pointing to timbl's comment on this:
https://github.com/solid/specification/issues/55#issuecomment-536092174

Should'nt at least file.ttl be accessible, since permission is excplicitly granted? Do you know about any specification or NSS improvments, so that ACLs that do not mention the container itself are prevented?

It sounds like it could be enforced by a shape to not get into that kind of situation, but other than that, I'm not aware of that.
But please mention the problem in solid/specification#55 so we can look into it in that context.

authors: angelo-v kjetilk

repo: solid/acl-check


text:
Configs for initialization with custom non-root PODs

Feature description:
I noticed that there is now a ConfigPodInitializer so in my understanding it should now be possible to define some configs that create a few sample users on startup (for example for a test environment).
Are there sample configs on how to do this for non-root users - (I can only see ones for root users in the initializers configs). I made the following attempt of my own, but was not sure how to correctly configure the WebID - nor what the appropriate values for storageKey were.
{
  "@context": "https://linkedsoftwaredependencies.org/bundles/npm/@solid/community-server/^2.0.0/components/context.jsonld",
  "@graph": [
    {
      "comment": "Makes sure the root container exists and contains the necessary resources.",
      "@id": "urn:solid-server:default:PodInitializer",
      "@type": "ConditionalHandler",
      "storageKey": "foo",
      "storageValue": true,
      "storage": { "@id": "urn:solid-server:default:SetupStorage" },
      "source": {
        "@type": "ContainerInitializer",
        "args_baseUrl": { "@id": "urn:solid-server:default:variable:baseUrl" },
        "args_path": "/wright",
        "args_store": { "@id": "urn:solid-server:default:ResourceStore" },
        "args_generator": {
          "@type": "TemplatedResourcesGenerator",
          "templateFolder": "@css:templates/pod",
          "factory": { "@type": "ExtensionBasedMapperFactory" },
          "templateEngine": { "@type": "HandlebarsTemplateEngine" }
        },
        "args_storageKey": "foo",
        "args_storage": { "@id": "urn:solid-server:default:SetupStorage" }
      }
    }
  ]
}

Happy to create a couple of such configs for others to use in dev environments if I can be pointed in the right direction for solving these problems.

I noticed that there is now a ConfigPodInitializer so in my understanding it should now be possible to define some configs that create a few sample users on startup (for example for a test environment).

This is actually an "old" feature that was added before the first release of CSS, but not iterated upon afterwards due to shifting priorities. It's not exactly what you think it is though so I'll cover what it does here.
ConfigPodInitializer is part of the dynamic pod creation feature, which is enabled by the imports in the dynamic.json config. The idea behind dynamic pod creation is that every individual pod could have its own custom Components.js configuration. This would allow one user to have a file backend for their pod, and another user to have a SPARQL backend or even a composite backend where part of it is used for their hue lights. Registering a pod in such a server takes an extra template parameter, as seen in the corresponding integration test. This string refers to one of the stored templates on the server. The server then uses a router store to the correct instantiated mini-store based on the podname found in each URL.
One issue is that if the server restarts it needs to instantiate all these pods again. That is where the ConfigPodInitializer comes in. Every time a new pod is created on such a dynamic server, its settings (owner, template, name, etc.) are writting to a JSON config. When starting the ConfigPodInitializer it then reads that config file and calls Components.js for each entry.
What the ConfigPodInitializer does NOT do is:

Create files in those pods, since those would have been stored in whatever backend.
Register those pods in the IdP, since that would have already have happened during registration.

So i don't think the initializer would fit for your use case. If you want to quickly set up a bunch of pods your best bet is to have a JSON list where each entry is a set of parameters that can be sent to the registration endpoint and then a small script that iterates over them and does the POST requests.

authors: jeswr joachimvh

repo: solid/community-server


text:
Latest IDP changes break conformance test harness run

Description
As the title says. This is not unexpected, should have seen this coming actually.
There are 2 issues with the current implementations. Both could be fixed in CSS itself.
1. The test harness can't find the HTML POST form
Relevant failed run: https://github.com/solid/community-server/runs/5180518302?check_suite_focus=true#step:9:164
During the login procedure the CTH does a GET to /idp/login/ and tries to find the form. The issue here is that the CTH does not send an Accept header requesting HTML and since the latest changes, we return JSON instead of HTML if there are no preferences. Easiest solution here is to add a line changing the preferences to HTML in case there is no accept header.
Note that it actually is not really necessary for the CTH to find the form, it can just post to the same URL and the JSON we return when doing the GET there is
{
  "required": {
    "email": "string",
    "password": "string",
    "remember": "boolean"
  },
  "controls": {
    "register": "http://localhost:3000/idp/register/",
    "index": "http://localhost:3000/idp/",
    "prompt": "http://localhost:3000/idp/prompt/",
    "login": "http://localhost:3000/idp/login/",
    "forgotPassword": "http://localhost:3000/idp/forgotpassword/"
  },
  "apiVersion": "0.3"
}

But perhaps it is easier for the CTH to check for a form to have a consistent solution for all servers. Although it would be nice to send a Accept: text/html header along in that case.
2. We no longer send the location headers the CTH expects
Relevant failed run: https://github.com/solid/community-server/runs/5180809325?check_suite_focus=true#step:9:267
This is completely caused by the server. The IDP API was changed to no longer do redirects but instead return JSON objects containing a location field to make it easier to handle the server output on a dynamic HTML page. But of course this breaks systems that did the call directly and did not depend on the HTML behaviour. The easy fix here is to simply also send a location here together with the JSON object. Fortunately CTH does not check the status code, only if the header is there so this actually solves the problem.
This is not completely correct from an HTTP point of view though, so we probably want a more decent solution (although the previous could be used in the meantime). I was thinking of either doing the redirect as usual again, unless a client sends along a specific HTTP header indicating they do not want to do redirects (a different accept header? application/no-redirect+json? 😄), or set up a server specifically that does normal redirect behaviour by removing the class that does this change from the config. Personally I prefer the first solution so we don't need a specific config for the CTH.

I was thinking of either doing the redirect as usual again, unless a client sends along a specific HTTP header indicating they do not want to do redirects

I do like that direction; and we should still set up a meeting where you walk me through the need of the non-redirect version.

Tested also with the changes from #1166 and PKCE had to be disabled. After that everything works though. This does seem an issue as the Solid OIDC spec states:

... this specification assumes the use of the Authorization Code Flow with PKCE

So this seems to be an issue with the CTH. Can disable this on the server in the meantime though.
Relevant failed run: https://github.com/solid/community-server/runs/5216797899?check_suite_focus=true#step:9:159
/cc @edwardsph

That's great Pete, thanks! ^^
Going to leave this issue open for now since we might still want to look at what we do with the redirects.

Going to leave this issue open for now since we might still want to look at what we do with the redirects.

We have decided to keep this behaviour for now.

authors: RubenVerborgh joachimvh


text:
container start fails if DB_PASSWORD is changed from secret to something else

When changing the database password used in the docker-compose.yml (lines 6, 9, 21) the container won't start up (only the mysql container starts). Looking into the logs for the bookstack container shows the following error:
Starting Migration...

   Illuminate\Database\QueryException  : SQLSTATE[HY000] [1045] Access denied for user 'bookstack'@'172.21.0.3' (using password: YES) (SQL: select * from information_schema.tables where table_schema = bookstack and table_name = migrations and table_type = 'BASE TABLE')

  at /var/www/bookstack/vendor/laravel/framework/src/Illuminate/Database/Connection.php:669
    665|         // If an exception occurs when attempting to run a query, we'll format the error
    666|         // message to include the bindings with SQL, which will make this exception a
    667|         // lot more helpful to the developer instead of just the database's errors.
    668|         catch (Exception $e) {
  > 669|             throw new QueryException(
    670|                 $query, $this->prepareBindings($bindings), $e
    671|             );
    672|         }
    673|

  Exception trace:

  1   Doctrine\DBAL\Driver\PDOException::("SQLSTATE[HY000] [1045] Access denied for user 'bookstack'@'172.21.0.3' (using password: YES)")
      /var/www/bookstack/vendor/doctrine/dbal/lib/Doctrine/DBAL/Driver/PDOConnection.php:31

  2   PDOException::("SQLSTATE[HY000] [1045] Access denied for user 'bookstack'@'172.21.0.3' (using password: YES)")
      /var/www/bookstack/vendor/doctrine/dbal/lib/Doctrine/DBAL/Driver/PDOConnection.php:27

When changing the MYSQL_ROOT_PASSWORD (line 6), MYSQL_PASSWORD (line 9) and DB_PASSWORD (line 21) back to secret everything works fine again. However, I would like to change the default password for obvious reasons. Did I miss anything to be done in advance to changing this password?
BTW: i'm starting the containers using docker-compose up -d

When you launched docker-compose the first time, you created a new database naked bookstack with a user and root passwords "secret". If you then change the passwords in the docker-compose file, it is too late, the database is already created and you need the "secret" password to access it.
Assuming you have not put any content in bookstack, here is how to fix this:

Delete the database folder and its content.
Put the desired password in docker-compose.yml.
Relaunch using docker-compose.

When you launched docker-compose the first time, you created a new database naked bookstack with a user and root passwords "secret". If you then change the passwords in the docker-compose file, it is too late, the database is already created and you need the "secret" password to access it.
Assuming you have not put any content in bookstack, here is how to fix this:

Delete the database folder and its content.
Put the desired password in docker-compose.yml.
Relaunch using docker-compose.

Thanks for your answer and proposal. I deleted the database folder and its content from /var/lib/mysql/. I also removed any related docker container via docker rm. Still I get the same issue when launching via docker-compose up -d. The error is exactly the same like mentioned above.
Did I miss deleting anything else? Is it sufficient to delete the related folder under /var/lib/mysql/?

Hey @johannes-gilbert,
for a secure delete use docker-compose down -v. This will also delete all volumes. I think this could solve your problem.

Hey @johannes-gilbert,
for a secure delete use docker-compose down -v. This will also delete all volumes. I think this could solve your problem.

Thanks. I just was on my way to describe that deleting the corresponding volume is necessary. Looking into the docker-compose.yml shows that no host-mounted volume is used but a named volume.
Hence I looked up all bookstack related volumes via docker volume ls. There are three volumes which I deleted by using docker volume rm <name>. That solved my issue.
Thanks for the quick support and help!

I faced the same problem. Strangely enough docker volume prune didn't work out.
However, the following snippet removed the volumes thanks to this SO reply!
docker-compose down --volumes

authors: johannes-gilbert ptoulouse s-gbz solidnerd

repo: solidnerd/docker-bookstack


text:
Required attribute

Hi guys
I was wondering if there is an ability to mark attribute as required. So if attribute is not passed in this case, it should raise some error. I found required option for attribute, but not sure how to use it.
So, is it possible to require mandatory attribute?
Thanks for help!

---
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I will specify question a bit. It's actually working with build in types, just haven't tried that (with String for example). But is doesn't work with my models (for example User).
With build in type:
attribute :city, String
=> Virtus::CoercionError: Failed to coerce attribute city from nil into String
With my mode:
attribute :user, User
=> no failure error

repo: solnic/virtus


text:
🛑 agropump.com is down

In 174e3ab, agropump.com (https://agropump.com/) was down:

HTTP code: 500
Response time: 1301 ms

Resolved: agropump.com is back up in 78177b9.


text:
🛑 server.h-24871.kz is down

In e7ce22a, server.h-24871.kz (185.121.81.43) was down:

HTTP code: 0
Response time: 0 ms

Resolved: server.h-24871.kz is back up in b2aef89.