Enhance detect singletons

This pull request addresses a bug in the _detect_singletons function and enhances its efficiency (see issue #229). The performance improvement is primarily due to the elimination of array copies, achieved through the use of explicit loops implemented with Numba. The function performs optimally when provided with a column-major order array, which avoids the need for additional copies of the input array. Additionally, this pull request introduces a small test suite to further validate the changes.
To facilitate a comparison between the old and new implementations, the following code can be executed. It's important to note that for this comparison, the bug in the old implementation has been corrected.

See comparison
from time import perf_counter

import numba as nb
import numpy as np
from numba.extending import overload

def _prepare_fixed_effects(ary):
    pass

@overload(_prepare_fixed_effects)
def _ol_preproc_fixed_effects(ary):
    # If array is already an F-array we tolerate
    # any dtype because it saves us a copy
    if ary.layout == "F":
        return lambda ary: ary

    if not isinstance(ary.dtype, nb.types.Integer):
        raise nb.TypingError("Fixed effects must be integers")

    max_nbits = 32
    nbits = min(max_nbits, ary.dtype.bitwidth)
    dtype = nb.types.Integer.from_bitwidth(nbits, signed=False)

    def impl(ary):
        n, m = ary.shape
        out = np.empty((m, n), dtype=dtype).T
        out[:] = ary[:]
        return out

    return impl

@nb.njit
def new_detect_singletons(ids):
    """
    Detect singleton fixed effects in a dataset.

    Args:
        ids (np.ndarray): A 2D numpy array representing fixed effects, with a
                          shape of (n_samples, n_features).
                          Elements should be non-negative integers representing
                          fixed effect identifiers.

    Returns:
        np.ndarray: A boolean array of shape (n_samples,), indicating which
                    observations have a singleton fixed effect.

    Note:
        The algorithm iterates over columns to identify fixed effects.
        After completing each column traversal, it updates the record of
        non-singleton rows. This approach is preferred as removing an
        observation in column 'i' may lead to the emergence of new singletons
        in subsequent columns (i.e., columns > i).

        Since we are operating on columns, we enforce column-major order for
        the input array. Working on a row-major array leads to considerable
        performance losses.
    """
    ids = _prepare_fixed_effects(ids)
    n_samples, n_features = ids.shape

    max_fixef = np.max(ids)
    counts = np.empty(max_fixef + 1, dtype=np.uint32)

    n_non_singletons = n_samples
    non_singletons = np.arange(n_non_singletons, dtype=np.uint32)

    while True:
        n_non_singletons_curr = n_non_singletons

        for j in range(n_features):
            col = ids[:, j]

            counts[:] = 0
            n_singletons = 0
            for i in range(n_non_singletons):
                e = col[non_singletons[i]]
                c = counts[e]
                # Branchless version of:
                #
                # if counts[e] == 1:
                #     n_singletons -= 1
                # elif counts[e] == 0:
                #     n_singletons += 1
                #
                n_singletons += (c == 0) - (c == 1)
                counts[e] += 1

            if not n_singletons:
                continue

            cnt = 0
            for i in range(n_non_singletons):
                e = col[non_singletons[i]]
                if counts[e] != 1:
                    non_singletons[cnt] = non_singletons[i]
                    cnt += 1

            n_non_singletons = cnt

        if n_non_singletons_curr == n_non_singletons:
            break

    is_singleton = np.ones(n_samples, dtype=np.bool_)
    for i in range(n_non_singletons):
        is_singleton[non_singletons[i]] = False

    return is_singleton

def old_detect_singletons(ids):
    """
    Detect singleton fixed effects
    Args:have a
        ids (np.ndarray): A numpy array of fixed effects.
    Returns:
        An array of booleans indicating which observations have a singleton fixed effect.
    """

    N, k = ids.shape

    singleton_idx = np.full(N, False, dtype=bool)
    singleton_idx_tmp = np.full(N, False, dtype=bool)
    singleton_idx_tmp_old = singleton_idx.copy()

    ids_tmp = ids.copy()

    while True:
        for x in range(k):
            col = ids[:, x]
            col_tmp = ids_tmp[:, x]

            # note that this only "works" as fixed effects are integers from 0, 1, ..., n_fixef -1
            # and np.bincount orders results in ascending (integer) order
            counts = np.bincount(col_tmp)

            if np.any(counts == 1):
                idx = np.where(counts == 1)

                singleton_idx[np.isin(col, idx)] = True
                singleton_idx_tmp[np.isin(col_tmp, idx)] = True

                ids_tmp = ids_tmp[~singleton_idx_tmp, :].astype(ids_tmp.dtype)
                singleton_idx_tmp = singleton_idx_tmp[~singleton_idx_tmp]

            # break

        if np.array_equal(singleton_idx_tmp, singleton_idx_tmp_old):
            break

        singleton_idx_tmp_old = singleton_idx_tmp.copy()

    return singleton_idx

@nb.njit
def make_deterministic(shape, n_singletons, dtype=np.int64):
    out = np.zeros(shape, dtype=dtype)
    assert n_singletons <= shape[0]
    for i in range(n_singletons):
        j = i % shape[1]
        out[i, j] = i + 1
    return out

class SimpleTimer:
    def __init__(self):
        self.tic = None
        self.toc = None

    def __enter__(self):
        self.tic = perf_counter()
        return self

    def __exit__(self, *args):
        self.toc = perf_counter()

    def __str__(self):
        return f"Elapsed [s]: {self.elapsed:.2f}"

    def __truediv__(self, other):
        return self.elapsed / other.elapsed

    @property
    def elapsed(self):
        return self.toc - self.tic

if __name__ == "__main__":
    # warmup
    new_detect_singletons(np.zeros((1, 1), dtype=np.int64))

    N, M = 100_000, 100

    for i, a in enumerate(
        (
            make_deterministic((N, M), n_singletons=0),
            make_deterministic((N, M), n_singletons=N // 100_000),
            make_deterministic((N, M), n_singletons=N // 10_000),
            make_deterministic((N, M), n_singletons=N // 1_000),
            make_deterministic((N, M), n_singletons=N // 100),
            make_deterministic((N, M), n_singletons=N // 10),
            make_deterministic((N, M), n_singletons=N),
        )
    ):
        print(f"\nRunning case {i+1}")

        with SimpleTimer() as t1:
            r1 = old_detect_singletons(a)

        with SimpleTimer() as t2:
            r2 = new_detect_singletons(a)

        assert np.array_equal(r1, r2)

        print(t1)
        print(t2)
        print(f"Speedup: {t1 / t2:.1f} (#singletons {r1.sum()}/{r1.shape[0]})")

Hi @styfenschaer, I finally managed to take a first look - sorry for the delay! Two questions:

are you not using the _ol_preproc_fixed_effects() function? If yes, can it be deleted?
what is the purpose of the _prepare_fixed_effects() function? It does not seem to do anything?

I will make some updates to where _detect_singletons() should be applied - I will move it from demean_model() to model_matrix_fixest(), which is a more natural place for it (I believe). On the fly I will also fix some other bugs in the code that relate to singleton fixed effects and will push them to this branch.
Also, once again, thanks so much for this!
Best, Alex

Btw these speedups are once again pretty amazing:
Running case 1
Elapsed [s]: 0.20
Elapsed [s]: 0.05
Speedup: 4.0 (#singletons 0/100000)

Running case 2
Elapsed [s]: 0.48
Elapsed [s]: 0.07
Speedup: 7.0 (#singletons 1/100000)

Running case 3
Elapsed [s]: 1.02
Elapsed [s]: 0.07
Speedup: 15.6 (#singletons 10/100000)

Running case 4
Elapsed [s]: 6.43
Elapsed [s]: 0.08
Speedup: 83.6 (#singletons 100/100000)

Running case 5
Elapsed [s]: 6.43
Elapsed [s]: 0.07
Speedup: 88.4 (#singletons 1000/100000)

Running case 6
Elapsed [s]: 5.91
Elapsed [s]: 0.08
Speedup: 77.1 (#singletons 10000/100000)

Running case 7
Elapsed [s]: 3.10
Elapsed [s]: 0.05
Speedup: 68.9 (#singletons 100000/100000)

Hello @s3alfisc
Don't worry, there is no deadline, so there is no delay.
These functions are both needed. _prepare_fixed_effects is just a dummy python function. When Numba encounters this function, it will call _ol_preproc_fixed_effects with the types of the arguments and _ol_preproc_fixed_effects must return the appropriate implementation. You can read about this here. I did it this way because Numba does not support the dtype argument to the numpy.asfortranarray function. And even then, I wanted a bit more control over the data type of the resulting array.
Sure, I was also wondering if this function should become public, which would mean that the leading underscore should be removed from the name.

Thanks for the explanation Styfen. As you can see, I've already merged it, added some simple tests against fixest and pur 'detect_singletons' into its own module & also made it public. I hope you'll have a great start into 2024 tonight!

@all-contributors please add @styfenschaer for code

@all-contributors please add @styfenschaer for code

@all-contributors please add @styfenschaer for code

@all-contributors please add @NKeleher for code and infra

@all-contributors please add @Wenzhi-Ding for code

@all-contributors please add @apoorvalal for code

@all-contributors please add @juanitorduz for infra, code

@all-contributors please add @juanitorduz for infra, code


style: update eslint dependencies

Update ESLint dependencies.
Fixed some ESLint errors.

@joeyparrish @johnjbarton do you think it is ok if I merge this PR? Thank you for your time! 😅


Use the Ollama chat API instead of the generate API

It currently uses the /api/generate endpoint to generate one-off responses. The /api/chat endpoint fits this use case better, and is better for integrating history/context

I'd recommend making a class to contain the conversation history, and instantiating it for each context environment you want (I did per channel, but IIRC you wanted to do per Server).
https://github.com/joshbuker/discord-bot/blob/main/lib/discord_bot/llm/conversation.rb
https://github.com/joshbuker/discord-bot/blob/main/lib/discord_bot/bot.rb#L197
https://github.com/joshbuker/discord-bot/blob/main/lib/discord_bot/bot.rb#L253
I'd also recommend abstracting the API calls into a class that can handle the implementation details:
https://github.com/joshbuker/discord-bot/blob/main/lib/discord_bot/llm/api_request.rb
Usage example:
https://github.com/joshbuker/discord-bot/blob/main/lib/discord_bot/llm/response.rb


When I uesd TAGADA, the task of my test data can not continue which show sleeping

Dear authors,
When I used this pipeline for improving annotation by RNA-seq data, the project can not continue. The task showed termination continuously. The problem displayed below. I am looking forward to your replay at your earliest convenience.
Thank you again.
My command line is :
nextflow run FAANG/analysis-TAGADA -profile docker --output output  --reads data/reads.txt  -revision 2.1.2  --genome data/genome.fasta --annotation data/genome
My problem is :
Launching https://github.com/FAANG/analysis-TAGADA [scruffy_poitras] DSL2 - revision: 07805fdca8 [2.1.2]
executor >  local (3)
executor >  local (3)
[-        ] process > SAMTOOLS_sort_reads                                 -
[0c/4c4431] process > TRIMGALORE_trim_adapters (1)                        [  0%] 0 of 1
[36/bec934] process > FASTQC_control_reads (2)                            [  0%] 0 of 2
[-        ] process > STAR_index_genome                                   -
[-        ] process > STAR_align_reads                                    -
[-        ] process > SAMTOOLS_control_flags                              -
[-        ] process > SAMTOOLS_control_alignments                         -
[-        ] process > SAMTOOLS_control_contigs                            -
[-        ] process > TAGADA_estimate_reads                               -
[-        ] process > BEDTOOLS_compute_coverage                           -
[-        ] process > MERGE_READS:SAMTOOLS_merge_reads_for_assembly       -
[-        ] process > MERGE_READS:SAMTOOLS_merge_reads_for_quantification -
[-        ] process > STRINGTIE_assemble_transcripts                      -
[-        ] process > TAGADA_filter_transcripts                           -
[-        ] process > TMERGE_coalesce_transcripts                         -
[-        ] process > FEELNC_classify_transcripts                         -
[-        ] process > STRINGTIE_quantify_expression                       -
[-        ] process > TAGADA_format_quantifications                       -
[-        ] process > TAGADA_cluster_expression                           -
[-        ] process > TAGADA_control_expression                           -
[-        ] process > TAGADA_control_annotation                           -
[-        ] process > FEATURECOUNTS_control_exons                         -
[-        ] process > MULTIQC_generate_report                             -
the output folder was not updated.

Hello and thank you for using Tagada.
Could you please supply the cotent of the .nextflow.log file? I don't see anything here indicating an error.
Are you using the pipeline on a single machine or on a cluster? If it is the latter you should set up -profile accordingly.
Best,
Cervin

Thank you for your reply, Tagada is quite convenient for using. My task required the docker according to the recommended installation manner. Maybe I think there were some configuration settings not applied well in my computer. The .nextflow.log file is listed below.
Thank you again.
Yours sincerely,
Liu

(base) ➜  my_tagada cat .nextflow.log
Jan-07 15:09:38.338 [main] DEBUG nextflow.cli.Launcher - Setting http proxy: ProxyConfig[protocol=http; host=<IP_ADDRESS>; port=20172]
Jan-07 15:09:38.351 [main] DEBUG nextflow.cli.Launcher - Setting https proxy: ProxyConfig[protocol=https; host=<IP_ADDRESS>; port=20172]
Jan-07 15:09:38.351 [main] DEBUG nextflow.cli.Launcher - $> nextflow run FAANG/analysis-TAGADA -revision 2.1.2 --output output/ --reads data/reads.txt --annotation data/Wm82_T2T.gtf --genome data/Wm82_T2T.genome.fasta --index data/Wm82_T2T.genome.fasta.fai --max-cpus 22 -profile docker
Jan-07 15:09:38.379 [main] INFO  nextflow.cli.CmdRun - N E X T F L O W  ~  version 23.10.0
Jan-07 15:09:38.387 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/home/tester/.nextflow/plugins; core-plugins: nf-amazon@2.1.4,nf-azure@1.3.2,nf-cloudcache@0.3.0,nf-codecommit@0.1.5,nf-console@1.0.6,nf-ga4gh@1.1.0,nf-google@1.8.3,nf-tower<EMAIL_ADDRESS>Jan-07 15:09:38.392 [main] INFO  o.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Jan-07 15:09:38.392 [main] INFO  o.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Jan-07 15:09:38.394 [main] INFO  org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode
Jan-07 15:09:38.398 [main] INFO  org.pf4j.AbstractPluginManager - No plugins
Jan-07 15:09:38.403 [main] DEBUG nextflow.scm.ProviderConfig - Using SCM config path: /home/tester/.nextflow/scm
Jan-07 15:09:38.654 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/tester/.nextflow/assets/FAANG/analysis-TAGADA/.git/config; branch: master; remote: origin; url: https://github.com/FAANG/analysis-TAGADA.git
Jan-07 15:09:38.662 [main] DEBUG nextflow.scm.RepositoryFactory - Found Git repository result: [RepositoryFactory]
Jan-07 15:09:38.666 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/tester/.nextflow/assets/FAANG/analysis-TAGADA/.git/config; branch: master; remote: origin; url: https://github.com/FAANG/analysis-TAGADA.git
Jan-07 15:09:39.665 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /home/tester/.nextflow/assets/FAANG/analysis-TAGADA/nextflow.config
Jan-07 15:09:39.665 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/tester/.nextflow/assets/FAANG/analysis-TAGADA/nextflow.config
Jan-07 15:09:39.669 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: docker
Jan-07 15:09:39.836 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [slurm, kubernetes, test, singularity, docker]
Jan-07 15:09:39.847 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declararion
Jan-07 15:09:39.847 [main] INFO  nextflow.cli.CmdRun - Launching https://github.com/FAANG/analysis-TAGADA [silly_rutherford] DSL2 - revision: 07805fdca8 [2.1.2]
Jan-07 15:09:39.848 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
Jan-07 15:09:39.848 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[]
Jan-07 15:09:39.849 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /home/tester/.nextflow/secrets/store.json
Jan-07 15:09:39.850 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@4a70d302] - activable => nextflow.secret.LocalSecretsProvider@4a70d302
Jan-07 15:09:39.872 [main] DEBUG nextflow.Session - Session UUID: 93c6a190-a3fa-4453-80d0-f22f46f45bef
Jan-07 15:09:39.872 [main] DEBUG nextflow.Session - Run name: silly_rutherford
Jan-07 15:09:39.873 [main] DEBUG nextflow.Session - Executor pool size: 32
Jan-07 15:09:39.875 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null
Jan-07 15:09:39.877 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=96; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
Jan-07 15:09:39.887 [main] DEBUG nextflow.cli.CmdRun -
Version: 23.10.0 build 5889
Created: 15-10-2023 15:07 UTC (23:07 CDT)
System: Linux 6.6.10-arch1-1
Runtime: Groovy 3.0.19 on OpenJDK 64-Bit Server VM 17.0.6+10
Encoding: UTF-8 (UTF-8)
Process: 121419@malab13 [<IP_ADDRESS>]
CPUs: 32 - Mem: 124.9 GB (101.9 GB) - Swap: 0 (0)
Jan-07 15:09:39.893 [main] DEBUG nextflow.Session - Work-dir: /home/tester/my_tagada/work [ext2/ext3]
Jan-07 15:09:39.899 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
Jan-07 15:09:39.904 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Jan-07 15:09:39.922 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
Jan-07 15:09:39.926 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 33; maxThreads: 1000
Jan-07 15:09:39.958 [main] DEBUG nextflow.Session - Session start
Jan-07 15:09:40.225 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Jan-07 15:09:41.063 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:SAMTOOLS_sort_reads matches process SAMTOOLS_sort_reads
Jan-07 15:09:41.067 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-07 15:09:41.067 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-07 15:09:41.070 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local
Jan-07 15:09:41.072 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=22; memory=64 GB; capacity=32; pollInterval=100ms; dumpInterval=5m
Jan-07 15:09:41.073 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: local)
Jan-07 15:09:41.096 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:TRIMGALORE_trim_adapters matches process TRIMGALORE_trim_adapters
Jan-07 15:09:41.097 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-07 15:09:41.097 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-07 15:09:41.102 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:FASTQC_control_reads matches process FASTQC_control_reads
Jan-07 15:09:41.102 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-07 15:09:41.102 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-07 15:09:41.108 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:STAR_align_reads matches process STAR_align_reads
Jan-07 15:09:41.108 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-07 15:09:41.108 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-07 15:09:41.111 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-07 15:09:41.111 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-07 15:09:41.113 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-07 15:09:41.113 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-07 15:09:41.115 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-07 15:09:41.115 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-07 15:09:41.119 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-07 15:09:41.119 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-07 15:09:41.122 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:BEDTOOLS_compute_coverage matches process BEDTOOLS_compute_coverage
Jan-07 15:09:41.123 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-07 15:09:41.123 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-07 15:09:41.128 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:SAMTOOLS_merge_reads matches process MERGE_READS:SAMTOOLS_merge_reads_for_assembly
Jan-07 15:09:41.129 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-07 15:09:41.129 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-07 15:09:41.135 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:SAMTOOLS_merge_reads matches process MERGE_READS:SAMTOOLS_merge_reads_for_quantification
Jan-07 15:09:41.136 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-07 15:09:41.136 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-07 15:09:41.139 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-07 15:09:41.139 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-07 15:09:41.143 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:TAGADA_filter_transcripts matches process TAGADA_filter_transcripts
Jan-07 15:09:41.143 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-07 15:09:41.143 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-07 15:09:41.145 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:TMERGE_coalesce_transcripts matches process TMERGE_coalesce_transcripts
Jan-07 15:09:41.145 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-07 15:09:41.145 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-07 15:09:41.147 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:FEELNC_classify_transcripts matches process FEELNC_classify_transcripts
Jan-07 15:09:41.147 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-07 15:09:41.147 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-07 15:09:41.153 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:STRINGTIE_quantify_expression matches process STRINGTIE_quantify_expression
Jan-07 15:09:41.153 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-07 15:09:41.153 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-07 15:09:41.158 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:TAGADA_format_quantifications matches process TAGADA_format_quantifications
Jan-07 15:09:41.158 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-07 15:09:41.158 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-07 15:09:41.160 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:TAGADA_cluster_expression matches process TAGADA_cluster_expression
Jan-07 15:09:41.160 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-07 15:09:41.160 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-07 15:09:41.162 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:TAGADA_control_expression matches process TAGADA_control_expression
Jan-07 15:09:41.162 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-07 15:09:41.162 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-07 15:09:41.164 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:TAGADA_control_annotation matches process TAGADA_control_annotation
Jan-07 15:09:41.164 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-07 15:09:41.164 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-07 15:09:41.167 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:FEATURECOUNTS_control_exons matches process FEATURECOUNTS_control_exons
Jan-07 15:09:41.168 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-07 15:09:41.168 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-07 15:09:41.171 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:MULTIQC_generate_report matches process MULTIQC_generate_report
Jan-07 15:09:41.172 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-07 15:09:41.172 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-07 15:09:41.173 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: FEATURECOUNTS_control_exons, MERGE_READS:SAMTOOLS_merge_reads_for_quantification, GZIP_decompress_index, TAGADA_cluster_expression, SAMTOOLS_control_alignments, TAGADA_format_quantifications, SAMTOOLS_merge_reads_for_assembly, TMERGE_coalesce_transcripts, GZIP_decompress_genome, FASTQC_control_reads, TAGADA_estimate_reads, SAMTOOLS_merge_reads, BEDTOOLS_compute_coverage, TAGADA_filter_transcripts, FEELNC_classify_transcripts, TRIMGALORE_trim_adapters, SAMTOOLS_control_flags, GZIP_decompress, TAGADA_control_expression, STRINGTIE_quantify_expression, GZIP_decompress_annotation, SAMTOOLS_sort_reads, TAGADA_control_annotation, SAMTOOLS_control_contigs, STRINGTIE_assemble_transcripts, STRINGTIE_coalesce_transcripts, MERGE_READS:SAMTOOLS_merge_reads_for_assembly, STAR_index_genome, SAMTOOLS_merge_reads_for_quantification, STAR_align_reads, MULTIQC_generate_report
Jan-07 15:09:41.175 [main] DEBUG nextflow.Session - Igniting dataflow network (38)
Jan-07 15:09:41.179 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > SAMTOOLS_sort_reads
Jan-07 15:09:41.179 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > TRIMGALORE_trim_adapters
Jan-07 15:09:41.179 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > FASTQC_control_reads
Jan-07 15:09:41.179 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > STAR_align_reads
Jan-07 15:09:41.179 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > SAMTOOLS_control_flags
Jan-07 15:09:41.179 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > SAMTOOLS_control_alignments
Jan-07 15:09:41.179 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > SAMTOOLS_control_contigs
Jan-07 15:09:41.180 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > TAGADA_estimate_reads
Jan-07 15:09:41.180 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > BEDTOOLS_compute_coverage
Jan-07 15:09:41.180 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > MERGE_READS:SAMTOOLS_merge_reads_for_assembly
Jan-07 15:09:41.180 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > MERGE_READS:SAMTOOLS_merge_reads_for_quantification
Jan-07 15:09:41.180 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > STRINGTIE_assemble_transcripts
Jan-07 15:09:41.180 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > TAGADA_filter_transcripts
Jan-07 15:09:41.180 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > TMERGE_coalesce_transcripts
Jan-07 15:09:41.180 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > FEELNC_classify_transcripts
Jan-07 15:09:41.180 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > STRINGTIE_quantify_expression
Jan-07 15:09:41.180 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > TAGADA_format_quantifications
Jan-07 15:09:41.180 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > TAGADA_cluster_expression
Jan-07 15:09:41.180 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > TAGADA_control_expression
Jan-07 15:09:41.180 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > TAGADA_control_annotation
Jan-07 15:09:41.180 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > FEATURECOUNTS_control_exons
Jan-07 15:09:41.181 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > MULTIQC_generate_report
Jan-07 15:09:41.181 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files:
Script_6b782a5d3ba84bd9: /home/tester/.nextflow/assets/FAANG/analysis-TAGADA/./modules/star.nf
Script_776698b8a57aed54: /home/tester/.nextflow/assets/FAANG/analysis-TAGADA/./modules/stringtie.nf
Script_9c77b63b98fad9c9: /home/tester/.nextflow/assets/FAANG/analysis-TAGADA/./modules/feelnc.nf
Script_55d169c54079398a: /home/tester/.nextflow/assets/FAANG/analysis-TAGADA/main.nf
Script_cb50db554a3e78b5: /home/tester/.nextflow/assets/FAANG/analysis-TAGADA/./workflows/merge_reads.nf
Script_b2f83e6560de6350: /home/tester/.nextflow/assets/FAANG/analysis-TAGADA/./modules/trimgalore.nf
Script_059ac6d7f486e8a9: /home/tester/.nextflow/assets/FAANG/analysis-TAGADA/./modules/multiqc.nf
Script_057d9d22364b0562: /home/tester/.nextflow/assets/FAANG/analysis-TAGADA/./modules/tagada.nf
Script_7ffb9822b7d287bd: /home/tester/.nextflow/assets/FAANG/analysis-TAGADA/./modules/featurecounts.nf
Script_a5e120c8c14bcfd1: /home/tester/.nextflow/assets/FAANG/analysis-TAGADA/./modules/bedtools.nf
Script_f923a991cbf4118d: /home/tester/.nextflow/assets/FAANG/analysis-TAGADA/./modules/tmerge.nf
Script_6575875e64aa914a: /home/tester/.nextflow/assets/FAANG/analysis-TAGADA/./workflows/../modules/samtools.nf
Script_5ae96960b3a3f95b: /home/tester/.nextflow/assets/FAANG/analysis-TAGADA/./modules/fastqc.nf
Script_a67f658c3cf24f8b: /home/tester/.nextflow/assets/FAANG/analysis-TAGADA/./workflows/../modules/gzip.nf
Script_045e1e437dec0e19: /home/tester/.nextflow/assets/FAANG/analysis-TAGADA/./workflows/create_channels.nf
Jan-07 15:09:41.181 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination
Jan-07 15:09:41.181 [main] DEBUG nextflow.Session - Session await
Jan-07 15:09:41.264 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-07 15:09:41.265 [Task submitter] INFO  nextflow.Session - [7c/f0e0ec] Submitted process > FASTQC_control_reads (2)
Jan-07 15:09:41.267 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-07 15:09:41.268 [Task submitter] INFO  nextflow.Session - [af/cbd71d] Submitted process > FASTQC_control_reads (1)
Jan-07 15:09:41.270 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-07 15:09:41.270 [Task submitter] INFO  nextflow.Session - [48/79c6d1] Submitted process > TRIMGALORE_trim_adapters (1)
Jan-07 15:14:41.221 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 3 -- submitted tasks are shown below
~> TaskHandler[id: 3; name: FASTQC_control_reads (2); status: RUNNING; exit: -; error: -; workDir: /home/tester/my_tagada/work/7c/f0e0ec241a8748180490f5f100f768]
~> TaskHandler[id: 2; name: FASTQC_control_reads (1); status: RUNNING; exit: -; error: -; workDir: /home/tester/my_tagada/work/af/cbd71d70e13732418eba76b54a7e5b]
~> TaskHandler[id: 1; name: TRIMGALORE_trim_adapters (1); status: RUNNING; exit: -; error: -; workDir: /home/tester/my_tagada/work/48/79c6d1b9f2917169ccc6d7404b5908]
Jan-07 15:19:41.270 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 3 -- submitted tasks are shown below
~> TaskHandler[id: 3; name: FASTQC_control_reads (2); status: RUNNING; exit: -; error: -; workDir: /home/tester/my_tagada/work/7c/f0e0ec241a8748180490f5f100f768]
~> TaskHandler[id: 2; name: FASTQC_control_reads (1); status: RUNNING; exit: -; error: -; workDir: /home/tester/my_tagada/work/af/cbd71d70e13732418eba76b54a7e5b]
~> TaskHandler[id: 1; name: TRIMGALORE_trim_adapters (1); status: RUNNING; exit: -; error: -; workDir: /home/tester/my_tagada/work/48/79c6d1b9f2917169ccc6d7404b5908]
Jan-07 15:24:41.303 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 3 -- submitted tasks are shown below
~> TaskHandler[id: 3; name: FASTQC_control_reads (2); status: RUNNING; exit: -; error: -; workDir: /home/tester/my_tagada/work/7c/f0e0ec241a8748180490f5f100f768]
~> TaskHandler[id: 2; name: FASTQC_control_reads (1); status: RUNNING; exit: -; error: -; workDir: /home/tester/my_tagada/work/af/cbd71d70e13732418eba76b54a7e5b]
~> TaskHandler[id: 1; name: TRIMGALORE_trim_adapters (1); status: RUNNING; exit: -; error: -; workDir: /home/tester/my_tagada/work/48/79c6d1b9f2917169ccc6d7404b5908]
Jan-07 15:29:41.321 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 3 -- submitted tasks are shown below
~> TaskHandler[id: 3; name: FASTQC_control_reads (2); status: RUNNING; exit: -; error: -; workDir: /home/tester/my_tagada/work/7c/f0e0ec241a8748180490f5f100f768]
~> TaskHandler[id: 2; name: FASTQC_control_reads (1); status: RUNNING; exit: -; error: -; workDir: /home/tester/my_tagada/work/af/cbd71d70e13732418eba76b54a7e5b]
~> TaskHandler[id: 1; name: TRIMGALORE_trim_adapters (1); status: RUNNING; exit: -; error: -; workDir: /home/tester/my_tagada/work/48/79c6d1b9f2917169ccc6d7404b5908]
Jan-07 15:34:32.116 [SIGHUP handler] DEBUG nextflow.Session - Session aborted -- Cause: SIGHUP
Jan-07 15:34:32.116 [SIGHUP handler] DEBUG nextflow.Session - Session aborted -- Cause: SIGHUP
Jan-07 15:34:32.123 [SIGHUP handler] DEBUG nextflow.Session - The following nodes are still active:
[process] FASTQC_control_reads
status=ACTIVE
port 0: (queue) OPEN  ; channel: -
port 1: (cntrl) -     ; channel: $
[process] STAR_align_reads
status=ACTIVE
port 0: (queue) OPEN  ; channel: -
port 1: (cntrl) -     ; channel: $
[process] SAMTOOLS_control_flags
status=ACTIVE
port 0: (queue) OPEN  ; channel: -
port 1: (cntrl) -     ; channel: $
[process] SAMTOOLS_control_alignments
status=ACTIVE
port 0: (queue) OPEN  ; channel: -
port 1: (cntrl) -     ; channel: $
[process] SAMTOOLS_control_contigs
status=ACTIVE
port 0: (queue) OPEN  ; channel: -
port 1: (cntrl) -     ; channel: $
[process] TAGADA_estimate_reads
status=ACTIVE
port 0: (queue) OPEN  ; channel: -
port 1: (cntrl) -     ; channel: $
[process] BEDTOOLS_compute_coverage
status=ACTIVE
port 0: (queue) OPEN  ; channel: -
port 1: (cntrl) -     ; channel: $
[process] MERGE_READS:SAMTOOLS_merge_reads_for_assembly
status=ACTIVE
port 0: (queue) OPEN  ; channel: -
port 1: (cntrl) -     ; channel: $
[process] MERGE_READS:SAMTOOLS_merge_reads_for_quantification
status=ACTIVE
port 0: (queue) OPEN  ; channel: -
port 1: (cntrl) -     ; channel: $
[process] STRINGTIE_assemble_transcripts
status=ACTIVE
port 0: (queue) OPEN  ; channel: -
port 1: (cntrl) -     ; channel: $
[process] TAGADA_filter_transcripts
status=ACTIVE
port 0: (value) OPEN  ; channel: assemblies
port 1: (cntrl) -     ; channel: $
[process] TMERGE_coalesce_transcripts
status=ACTIVE
port 0: (value) OPEN  ; channel: assemblies
port 1: (queue) OPEN  ; channel: annotation
port 2: (cntrl) -     ; channel: $
[process] FEELNC_classify_transcripts
status=ACTIVE
port 0: (queue) OPEN  ; channel: genome
port 1: (queue) OPEN  ; channel: reference_annotation
port 2: (queue) OPEN  ; channel: novel_annotation
port 3: (cntrl) -     ; channel: $
[process] STRINGTIE_quantify_expression
status=ACTIVE
port 0: (queue) OPEN  ; channel: -
port 1: (cntrl) -     ; channel: $
[process] TAGADA_format_quantifications
status=ACTIVE
port 0: (queue) OPEN  ; channel: quantifications
port 1: (cntrl) -     ; channel: $
[process] TAGADA_cluster_expression
status=ACTIVE
port 0: (queue) OPEN  ; channel: genes_tpm_quantification
port 1: (value) bound ; channel: quantification_metadata
port 2: (cntrl) -     ; channel: $
[process] TAGADA_control_expression
status=ACTIVE
port 0: (queue) OPEN  ; channel: genes_tpm_quantification
port 1: (queue) OPEN  ; channel: genes_counts_quantification
port 2: (cntrl) -     ; channel: $
[process] TAGADA_control_annotation
status=ACTIVE
port 0: (queue) OPEN  ; channel: reference_annotation
port 1: (queue) OPEN  ; channel: novel_annotation
port 2: (queue) OPEN  ; channel: transcripts_tpm_quantification
port 3: (queue) OPEN  ; channel: genes_tpm_quantification
port 4: (cntrl) -     ; channel: $
[process] FEATURECOUNTS_control_exons
status=ACTIVE
port 0: (value) OPEN  ; channel: bams
port 1: (queue) OPEN  ; channel: -
port 2: (cntrl) -     ; channel: $
[process] MULTIQC_generate_report
status=ACTIVE
port 0: (value) OPEN  ; channel: reports
port 1: (queue) OPEN  ; channel: config
port 2: (queue) OPEN  ; channel: images
port 3: (value) bound ; channel: metadata
port 4: (cntrl) -     ; channel: $
Jan-07 15:34:32.123 [SIGHUP handler] DEBUG nextflow.Session - The following nodes are still active:
[process] FASTQC_control_reads
status=ACTIVE
port 0: (queue) OPEN  ; channel: -
port 1: (cntrl) -     ; channel: $
[process] STAR_align_reads
status=ACTIVE
port 0: (queue) OPEN  ; channel: -
port 1: (cntrl) -     ; channel: $
[process] SAMTOOLS_control_flags
status=ACTIVE
port 0: (queue) OPEN  ; channel: -
port 1: (cntrl) -     ; channel: $
[process] SAMTOOLS_control_alignments
status=ACTIVE
port 0: (queue) OPEN  ; channel: -
port 1: (cntrl) -     ; channel: $
[process] SAMTOOLS_control_contigs
status=ACTIVE
port 0: (queue) OPEN  ; channel: -
port 1: (cntrl) -     ; channel: $
[process] TAGADA_estimate_reads
status=ACTIVE
port 0: (queue) OPEN  ; channel: -
port 1: (cntrl) -     ; channel: $
[process] BEDTOOLS_compute_coverage
status=ACTIVE
port 0: (queue) OPEN  ; channel: -
port 1: (cntrl) -     ; channel: $
[process] MERGE_READS:SAMTOOLS_merge_reads_for_assembly
status=ACTIVE
port 0: (queue) OPEN  ; channel: -
port 1: (cntrl) -     ; channel: $
[process] MERGE_READS:SAMTOOLS_merge_reads_for_quantification
status=ACTIVE
port 0: (queue) OPEN  ; channel: -
port 1: (cntrl) -     ; channel: $
[process] STRINGTIE_assemble_transcripts
status=ACTIVE
port 0: (queue) OPEN  ; channel: -
port 1: (cntrl) -     ; channel: $
[process] TAGADA_filter_transcripts
status=ACTIVE
port 0: (value) OPEN  ; channel: assemblies
port 1: (cntrl) -     ; channel: $
[process] TMERGE_coalesce_transcripts
status=ACTIVE
port 0: (value) OPEN  ; channel: assemblies
port 1: (queue) OPEN  ; channel: annotation
port 2: (cntrl) -     ; channel: $
[process] FEELNC_classify_transcripts
status=ACTIVE
port 0: (queue) OPEN  ; channel: genome
port 1: (queue) OPEN  ; channel: reference_annotation
port 2: (queue) OPEN  ; channel: novel_annotation
port 3: (cntrl) -     ; channel: $
[process] STRINGTIE_quantify_expression
status=ACTIVE
port 0: (queue) OPEN  ; channel: -
port 1: (cntrl) -     ; channel: $
[process] TAGADA_format_quantifications
status=ACTIVE
port 0: (queue) OPEN  ; channel: quantifications
port 1: (cntrl) -     ; channel: $
[process] TAGADA_cluster_expression
status=ACTIVE
port 0: (queue) OPEN  ; channel: genes_tpm_quantification
port 1: (value) bound ; channel: quantification_metadata
port 2: (cntrl) -     ; channel: $
[process] TAGADA_control_expression
status=ACTIVE
port 0: (queue) OPEN  ; channel: genes_tpm_quantification
port 1: (queue) OPEN  ; channel: genes_counts_quantification
port 2: (cntrl) -     ; channel: $
[process] TAGADA_control_annotation
status=ACTIVE
port 0: (queue) OPEN  ; channel: reference_annotation
port 1: (queue) OPEN  ; channel: novel_annotation
port 2: (queue) OPEN  ; channel: transcripts_tpm_quantification
port 3: (queue) OPEN  ; channel: genes_tpm_quantification
port 4: (cntrl) -     ; channel: $
[process] FEATURECOUNTS_control_exons
status=ACTIVE
port 0: (value) OPEN  ; channel: bams
port 1: (queue) OPEN  ; channel: -
port 2: (cntrl) -     ; channel: $
[process] MULTIQC_generate_report
status=ACTIVE
port 0: (value) OPEN  ; channel: reports
port 1: (queue) OPEN  ; channel: config
port 2: (queue) OPEN  ; channel: images
port 3: (value) bound ; channel: metadata
port 4: (cntrl) -     ; channel: $
Jan-07 15:34:32.123 [main] DEBUG nextflow.Session - Session await > all processes finished
Jan-07 15:34:32.123 [main] DEBUG nextflow.Session - Session await > all barriers passed
Jan-07 15:34:32.124 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 3; name: FASTQC_control_reads (2); status: COMPLETED; exit: 129; error: -; workDir: /home/tester/my_tagada/work/7c/f0e0ec241a8748180490f5f100f768]
Jan-07 15:34:32.125 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=FASTQC_control_reads (2); work-dir=/home/tester/my_tagada/work/7c/f0e0ec241a8748180490f5f100f768
error [nextflow.exception.ProcessFailedException]: Process FASTQC_control_reads (2) terminated with an error exit status (129)
Jan-07 15:34:32.126 [main] WARN  n.processor.TaskPollingMonitor - Killing running tasks (2)
Jan-07 15:34:32.128 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 2; name: FASTQC_control_reads (1); status: COMPLETED; exit: 129; error: -; workDir: /home/tester/my_tagada/work/af/cbd71d70e13732418eba76b54a7e5b]
Jan-07 15:34:32.128 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=FASTQC_control_reads (1); work-dir=/home/tester/my_tagada/work/af/cbd71d70e13732418eba76b54a7e5b
error [nextflow.exception.ProcessFailedException]: Process FASTQC_control_reads (1) terminated with an error exit status (129)
Jan-07 15:34:32.129 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 1; name: TRIMGALORE_trim_adapters (1); status: COMPLETED; exit: 129; error: -; workDir: /home/tester/my_tagada/work/48/79c6d1b9f2917169ccc6d7404b5908]
Jan-07 15:34:32.129 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=TRIMGALORE_trim_adapters (1); work-dir=/home/tester/my_tagada/work/48/79c6d1b9f2917169ccc6d7404b5908
error [nextflow.exception.ProcessFailedException]: Process TRIMGALORE_trim_adapters (1) terminated with an error exit status (129)
Jan-07 15:34:32.129 [Task monitor] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: local) - terminating tasks monitor poll loop
Jan-07 15:34:32.130 [main] DEBUG n.executor.local.LocalTaskHandler - Unable to kill FASTQC_control_reads (1) -- command: kill -TERM 121590; exit: 1
bash: line 1: kill: (121590) - No such process
Jan-07 15:34:32.131 [main] DEBUG n.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=0; failedCount=4; ignoredCount=0; cachedCount=0; pendingCount=0; submittedCount=0; runningCount=-1; retriesCount=0; abortedCount=0; succeedDuration=0ms; failedDuration=7h 52m 6s; cachedDuration=0ms;loadCpus=-1; loadMemory=0; peakRunning=3; peakCpus=18; peakMemory=20 GB; ]
Jan-07 15:34:32.159 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done
Jan-07 15:34:32.165 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye

So this in run on a single machine?
Only thing I see is a SIGHUP error indicative of some sort of connexion loss. Are you working locally on the machine?
Did you manage to run the test command (  nextflow run FAANG/analysis-TAGADA -profile test,docker -revision 2.1.2 --output directory ) ?

Thank you. The previous attempt was made through SSH. Today, I try my own data again in my local computer. But the status of process shows RUNNING while the 'work' folder was not changed.

Thank you. I have solved this problem. Best wishes.


Handle BucketAlreadyOwnedByYou s3 error

As per https://docs.aws.amazon.com/AmazonS3/latest/API/ErrorResponses.html,
in case a user tries to create a bucket which already exists
and owned by it, 'BucketAlreadyOwnedByYou' error should be returned
instead of 'BucketAlreadyExists'.
This patch is to address the same.
Signed-off-by: Soumya Koduri<EMAIL_ADDRESS>Explain the changes
While validating bucket during creation, match the owner too
Issues: Fixed #xxx / Gap #xxx
Fixed #5980
Testing Instructions:

Create a user with RW permissions to the noobaa end point or user admin user itself
Create a bucket via that user
Now try to create the bucket with same name.

if its the same user, "BucketAlreadyOwnedByYou" error should be returned and
if it is different user, "BucketAlreadyExists" error should be returned.

@soumyakoduri we better also add a small regression test for this case in here -
https://github.com/noobaa/noobaa-core/blob/c6e33a8aef9f547151ed8dae8e9008451be2216f/src/test/unit_tests/test_s3_ops.js#L47
If you need assistance to add it feel free to let us know.
@nimrod-becker can assign someone to suggest that test code.

@soumyakoduri we better also add a small regression test for this case in here -
https://github.com/noobaa/noobaa-core/blob/c6e33a8aef9f547151ed8dae8e9008451be2216f/src/test/unit_tests/test_s3_ops.js#L47
If you need assistance to add it feel free to let us know.
@nimrod-becker can assign someone to suggest that test code.

Okay.. I will take a look and let you know in case need help. Thanks!

@soumyakoduri we better also add a small regression test for this case in here -
https://github.com/noobaa/noobaa-core/blob/c6e33a8aef9f547151ed8dae8e9008451be2216f/src/test/unit_tests/test_s3_ops.js#L47
If you need assistance to add it feel free to let us know.
@nimrod-becker can assign someone to suggest that test code.
@nimrod-becker @guymguym
mocha.it('should not recreate bucket', async function() {
const res = await s3.createBucket({ Bucket: BKT1 }).promise();
assert(res.... == BucketAlreadyOwnedByYou);
});

Please let me know if above simple case is good enough and how to retrieve the error code from result 'res'?

mocha.it('should not recreate bucket', async function() {
const res = await s3.createBucket({ Bucket: BKT1 }).promise();
assert(res.... == BucketAlreadyOwnedByYou);
});
Please let me know if above simple case is good enough and how to retrieve the error code from result 'res'?

@soumyakoduri BTW this test uses the standard AWS JS SDK so online docs can help too.
In this case, after awaiting the promise, the error should be thrown as exception.
One way to assert for it is using https://nodejs.org/docs/latest-v12.x/api/assert.html#assert_assert_rejects_asyncfn_error_message.
So you can write something like this:
mocha.it('should not recreate bucket', async function() {
    const func = async () => s3.createBucket({ Bucket: BKT1 }).promise();
    const expected_err_props = {
        name: 'BucketAlreadyOwnedByYou',
        code: 'BucketAlreadyOwnedByYou',
        statusCode: 409,
    };
    await assert.rejects(func, expected_err_props);
});

@soumyakoduri You can run it manually with:
mocha src/test/unit_tests/test_s3_ops.js -g "should not recreate bucket"

But not sure if you have the repo setup for development.
In any case I'll approve once the test is pushed and passes the CI runs.
Thanks

@soumyakoduri In addition, can you remove that test case from the ceph/s3-tests blacklist to make the CI run the test_bucket_create_exists case too:
https://github.com/noobaa/noobaa-core/blob/c6e33a8aef9f547151ed8dae8e9008451be2216f/src/test/system_tests/test_ceph_s3.js#L242

@soumyakoduri BTW this test uses the standard AWS JS SDK so online docs can help too.
In this case, after awaiting the promise, the error should be thrown as exception.
One way to assert for it is using https://nodejs.org/docs/latest-v12.x/api/assert.html#assert_assert_rejects_asyncfn_error_message.
So you can write something like this:
mocha.it('should not recreate bucket', async function() {
    const func = async () => s3.createBucket({ Bucket: BKT1 }).promise();
    const expected_err_props = {
        name: 'BucketAlreadyOwnedByYou',
        code: 'BucketAlreadyOwnedByYou',
        statusCode: 409,
    };
    await assert.rejects(func, expected_err_props);
});

Thanks.. Added this case.

@soumyakoduri In addition, can you remove that test case from the ceph/s3-tests blacklist to make the CI run the test_bucket_create_exists case too:
https://github.com/noobaa/noobaa-core/blob/c6e33a8aef9f547151ed8dae8e9008451be2216f/src/test/system_tests/test_ceph_s3.js#L242

Done.

@soumyakoduri You can run it manually with:
mocha src/test/unit_tests/test_s3_ops.js -g "should not recreate bucket"

But not sure if you have the repo setup for development.
In any case I'll approve once the test is pushed and passes the CI runs.
Thanks

I do not have development environment installed as am still facing issues with 'npm install' errors. Right now I have been testing changes by building docker image and deploying it. I have uploaded the changes to check for CI runs

@soumyakoduri You can also run tests locally in docker simply with make test which will build a tested image with all the needed environment and run it.

@nimrod-becker @liranmauda Seems like CI completed in 19 minutes - is that about right?

@soumyakoduri You can also run tests locally in docker simply with make test which will build a tested image with all the needed environment and run it.

okay thanks.. I will try this out.

@guymguym yes we have issues running them on travis, merging


feat: add language picker

For now we're skipping the whole language lookup. This may be added later.

We can't go with just a input because we need the Q-ID of that language. :/
/Me starts codign

We can't use wikit, but I found another library with a working autocomplete. Let's have a look!

Reviewed with Itamar


ERROR: could not insert 'portalmem'

manish@manish:~/Desktop/Connectal/connectal$ sudo modprobe portalmem
[sudo] password for manish:
modprobe: ERROR: could not insert 'portalmem': Operation not permitted
In the step of installing drivers (Preparation for Kintex and Virtex boards), "sudo modprobe portalmem" command is giving the above error. Please help me resolve the error.

I think if you run dmesg you will find that your kernel has updated since you built portalmem.ko. If so, rebuild the module and you should be able to insmod / modprobe the module.

I think if you run dmesg you will find that your kernel has updated since you built portalmem.ko. If so, rebuild the module and you should be able to insmod / modprobe the module.

I disabled the "Secure Boot" in BIOS setting, now I am not getting any error but there is not output also.


WiKi - Sample code wrong function name?

In 'Getting Started' section:
Username-Password Authentication Flow
var auth = new AuthenticationClient(); await auth.UsernamePassword("YOURCONSUMERKEY", "YOURCONSUMERSECRET", "YOURUSERNAME", "YOURPASSWORD");
UsernamePassword should be UsernamePasswordAsync. Shouldn't it?

If this is still an issue (see latest updates to code) please re-open with more specifics.


Added Google Search Bar

Fixes Issue🛠

Closes #597
Description👨💻

Added google search bar in search bar components.
Type of change📄

[x] New feature (non-breaking change which adds functionality)

How this has been tested✅

This has been tested on local machine and works good.
Checklist✅

[X] My code follows the style guidelines of this project
[X] I have performed a self-review of my own code
[X] I have commented my code, particularly in hard-to-understand areas
[X] I have added demonstration in the form of GIF/video file
[X] I am an Open Source Contributor

Screenshots/GIF📷
https://github.com/Rakesh9100/Beautiify/assets/116893970/b429a950-0cbe-4d19-90dc-9d1173b4d0da

@Rakesh9100 Please review this PR

Merged ✨ @Abidsyed25


can i use this to manually draw rectangles over pdf?

I mean, can i open some PDF file and draw some line/rectangles/circles/arrow head over the pdf and save it?

You certainly can. Here are some examples of PDF modification:

https://github.com/Hopding/pdf-lib#document-modification
https://github.com/Hopding/pdf-lib/tree/master/examples/document_modification/node

Let me know if you run into any trouble and I can provide more assistance 👍


fix(module:style): added rtl support to input

PR Checklist
Please check if your PR fulfills the following requirements:

[x] The commit message follows our guidelines: https://github.com/NG-ZORRO/ng-zorro-antd/blob/master/CONTRIBUTING.md#commit
[ ] Tests for the changes have been added (for bug fixes / features)
[ ] Docs have been added / updated (for bug fixes / features)

PR Type
What kind of change does this PR introduce?
RTL support for input component
this is the first component if you like my work i can change the other components also

[ ] Bugfix
[ ] Feature
[ ] Code style update (formatting, local variables)
[ ] Refactoring (no functional changes, no api changes)
[ ] Build related changes
[ ] CI related changes
[ ] Documentation content changes
[ ] Application (the showcase website) / infrastructure changes
[x] Other... Please describe:

changes to support RTL
What is the current behavior?

Issue Number: N/A
What is the new behavior?
Does this PR introduce a breaking change?
[ ] Yes
[x] No

Other information

Hi @Abdullah700
Thanks a lot to your contribution, all styles in ng-zorro-antd are synced from antd react version via robot, you can submit the style pull request to https://github.com/ant-design/ant-design


config: Update to the latest CI payloads

Let's bump to the latest CI payloads and make sure those are and will continue to be passing the CI till we release the Operator at some point soon.

/test

/test

/test
/test-tdx

/test

Some of the tests timed out at scenario 15?

That's a test to uninstall the operator, and yep, I've noticed that's hanging even before the updates we've done.
See: https://github.com/confidential-containers/operator/pull/160, for instance.

Test 15 is failing, because post-install-daemon fails:
confidential-containers-system   cc-operator-post-uninstall-daemon-vf96h           0/1     CrashLoopBackOff   11 (4m4s ago)   35m

Log output is short and ends after "Restarting contianerd".

The failure is caused by an orphaned /opt/confidential-containers/runtime-rs, fix here: https://github.com/kata-containers/kata-containers/pull/6397. The rmdir in post-uninstall.sh is failing because coreutils logic is weird in v8.22: https://github.com/coreutils/coreutils/blob/v8.22/src/rmdir.c#L101-L107

/test

/test-tdx

@UnmeshDeodhar, @ryansavino, @fitzthum, mind to take a look at the failures we're having on SEV?

/test-kata-qemu-tdx

/test-kata-clh-tdx

I think we might need https://github.com/confidential-containers/operator/pull/159
@ryansavino @UnmeshDeodhar wdyt?

/test

/test

/test

/test

I am really not sure what's going on with Jenkins, as it's not being triggered for any job here.
/cc @wainersm

/test

I am really not sure what's going on with Jenkins, as it's not being triggered for any job here. /cc @wainersm

It usually happens when the queue is too big, but it seems not the case. I noticed a bunch of bare-metal machines are offline, something seems wrong with Jenkins.

/test

I'm seeing this in buildlogs (http://jenkins.katacontainers.io/view/all/job/confidential-containers-operator-main-ubuntu-20.04_sev-x86_64-containerd_kata-qemu-sev-PR/187/console)
org.kohsuke.github.HttpException: {"message":"`confidential-containers` forbids access via a personal access token (classic). Please use a GitHub App, OAuth App, or a personal access token with fine-grained permissions.","documentation_url":"https://docs.github.com/rest/commits/statuses#create-a-commit-status"}

Oh, I did adjust the org settings for classic personal access tokens yesterday. I don't think I changed anything there, but let me double check.


Upgrade Swinsian.app to v1.11.7

Closes https://github.com/caskroom/homebrew-cask/issues/17878.

Merged as c75289e66c8d397ed2ba1a2f0bb13fdc46f7f399.


pypr throws error

I wanted to setup some scratchpads, and i followed the guide on their github page. I had to install it from the AUR, because pip kept complaining about externally managed packages. I also tried using pipx for that matter, but it doesn't seem to work.
Traceback (most recent call last):
  File "/usr/bin/pypr", line 8, in <module>
    sys.exit(main())
             ^^^^^^
  File "/usr/lib/python3.11/site-packages/pyprland/command.py", line 171, in main
    asyncio.run(run_daemon() if len(sys.argv) <= 1 else run_client())
  File "/usr/lib/python3.11/asyncio/runners.py", line 190, in run
    return runner.run(main)
           ^^^^^^^^^^^^^^^^
  File "/usr/lib/python3.11/asyncio/runners.py", line 118, in run
    return self._loop.run_until_complete(task)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/lib/python3.11/asyncio/base_events.py", line 653, in run_until_complete
    return future.result()
           ^^^^^^^^^^^^^^^
  File "/usr/lib/python3.11/site-packages/pyprland/command.py", line 162, in run_client
    _, writer = await asyncio.open_unix_connection(CONTROL)
                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/lib/python3.11/asyncio/streams.py", line 98, in open_unix_connection
    transport, _ = await loop.create_unix_connection(
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/lib/python3.11/asyncio/unix_events.py", line 259, in create_unix_connection
    await self.sock_connect(sock, path)
  File "/usr/lib/python3.11/asyncio/selector_events.py", line 634, in sock_connect
    return await fut
           ^^^^^^^^^
  File "/usr/lib/python3.11/asyncio/selector_events.py", line 642, in _sock_connect
    sock.connect(address)

I get this error when I manually try to run pypr toggle term. This is also the case with hpr-scratcher. I can see that processes are spawned, but i just can't seem to access the scratchpads.
I also don't see pypr in btop after restarting. I do have the exec-once line in hyprland.conf

I have same issue.

Just for clarification, what do you mean remove all pip-installed packages? I have quite a few packages, here is the out put for pip list: https://pastebin.com/QZc5J4cs
I did try installing it from AUR, in fact, that's how I did it at first. It didn't work either.

By the way, I digressed with the pip problem.
Here pypr didn't start, you can remove everything from the hyprland config, and run manually in a terminal:
DEBUG=1 pypr
You'll have traces and pypr will run in the foreground in this window. I bet it's not starting, you'll see why (you can paste the content here).

I have the same problem, if i run pypr on a terminal, and use the keyboard shortcuts (i.e. term scratchpad), it works fine, of course this means i must have the terminal open with pypr running, which defeats the purpose.
Still havent tried reinstalling the python packages, although i installed this with yay.

you can make a script which will log the error, I hope it will provide more useful information:
#!/bin/bash
DEBUG=1 pypr > /tmp/pypr.log

I changed something in the master branch, fixing a race condition - it's also a possibility for this bug.
You might be interested in upgrading to the git version to test it in case you suffer from this problem.

I added better error handling in master.
You can also log to a file using --debug path_to_some_file.txt.
On startup, run pypr with this flag so we can fetch the output easily.
When failing, I hope you'll get more comprehensible error message.

Released version 1.4.0,  hoping you'll get better debug output helping you understand this problem.
Error handling can still be improved, please share your feedback.
I'll close this bug until more details are provided, discarding an environment anomaly.

I wanted to setup some scratchpads, and i followed the guide on their github page. I had to install it from the AUR, because pip kept complaining about externally managed packages. I also tried using pipx for that matter, but it doesn't seem to work.
Traceback (most recent call last):
  File "/usr/bin/pypr", line 8, in <module>
    sys.exit(main())
             ^^^^^^
  File "/usr/lib/python3.11/site-packages/pyprland/command.py", line 171, in main
    asyncio.run(run_daemon() if len(sys.argv) <= 1 else run_client())
  File "/usr/lib/python3.11/asyncio/runners.py", line 190, in run
    return runner.run(main)
           ^^^^^^^^^^^^^^^^
  File "/usr/lib/python3.11/asyncio/runners.py", line 118, in run
    return self._loop.run_until_complete(task)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/lib/python3.11/asyncio/base_events.py", line 653, in run_until_complete
    return future.result()
           ^^^^^^^^^^^^^^^
  File "/usr/lib/python3.11/site-packages/pyprland/command.py", line 162, in run_client
    _, writer = await asyncio.open_unix_connection(CONTROL)
                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/lib/python3.11/asyncio/streams.py", line 98, in open_unix_connection
    transport, _ = await loop.create_unix_connection(
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/lib/python3.11/asyncio/unix_events.py", line 259, in create_unix_connection
    await self.sock_connect(sock, path)
  File "/usr/lib/python3.11/asyncio/selector_events.py", line 634, in sock_connect
    return await fut
           ^^^^^^^^^
  File "/usr/lib/python3.11/asyncio/selector_events.py", line 642, in _sock_connect
    sock.connect(address)

I get this error when I manually try to run pypr toggle term. This is also the case with hpr-scratcher. I can see that processes are spawned, but i just can't seem to access the scratchpads. I also don't see pypr in btop after restarting. I do have the exec-once line in hyprland.conf

Use pip check to identify any missing or broken dependencies. I had to downgrade some packages.

I wanted to setup some scratchpads, and i followed the guide on their github page. I had to install it from the AUR, because pip kept complaining about externally managed packages. I also tried using pipx for that matter, but it doesn't seem to work.
Traceback (most recent call last):
  File "/usr/bin/pypr", line 8, in <module>
    sys.exit(main())
             ^^^^^^
  File "/usr/lib/python3.11/site-packages/pyprland/command.py", line 171, in main
    asyncio.run(run_daemon() if len(sys.argv) <= 1 else run_client())
  File "/usr/lib/python3.11/asyncio/runners.py", line 190, in run
    return runner.run(main)
           ^^^^^^^^^^^^^^^^
  File "/usr/lib/python3.11/asyncio/runners.py", line 118, in run
    return self._loop.run_until_complete(task)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/lib/python3.11/asyncio/base_events.py", line 653, in run_until_complete
    return future.result()
           ^^^^^^^^^^^^^^^
  File "/usr/lib/python3.11/site-packages/pyprland/command.py", line 162, in run_client
    _, writer = await asyncio.open_unix_connection(CONTROL)
                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/lib/python3.11/asyncio/streams.py", line 98, in open_unix_connection
    transport, _ = await loop.create_unix_connection(
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/lib/python3.11/asyncio/unix_events.py", line 259, in create_unix_connection
    await self.sock_connect(sock, path)
  File "/usr/lib/python3.11/asyncio/selector_events.py", line 634, in sock_connect
    return await fut
           ^^^^^^^^^
  File "/usr/lib/python3.11/asyncio/selector_events.py", line 642, in _sock_connect
    sock.connect(address)

I get this error when I manually try to run pypr toggle term. This is also the case with hpr-scratcher. I can see that processes are spawned, but i just can't seem to access the scratchpads. I also don't see pypr in btop after restarting. I do have the exec-once line in hyprland.conf

same issue. solved.
you should run pypr as server first, then when you run pypr you may get some error, for me it's "placement ...", then you should add "monitors" option in your pyprland.json file
like this
"monitors": {
    "placement": {
      "BenQ PJ": {
        "topOf": "VGA-1"
      }
    },
    "unknown": "wlrlui"
}


feat: Don't set feature gate TopologyManager and CustomCPUCFSQuotaPeriod, Get them from kubelet configs

What type of PR is this?
/kind feature

What this PR does / why we need it:
Currently, if TopologyManagerPolicy and CPUCFSQuotaPeriod are set in CustomKubeletConfigs, agent baker set feature gates "TopologyManager=true" and "CustomCPUCFSQuotaPeriod =true".
This PR remove the logic above because we set it in RP: https://dev.azure.com/msazure/CloudNativeCompute/_git/aks-rp/pullrequest/9808037
Which issue(s) this PR fixes:

Fixes #
Requirements:

[ ] uses conventional commit messages

[ ] includes documentation
[ ] adds unit tests
[ ] tested upgrade from previous version

Special notes for your reviewer:
Release note:
none

Pull Request Test Coverage Report for Build<PHONE_NUMBER>
Details

0 of 0   changed or added relevant lines in 0 files are covered.
No unchanged relevant lines lost coverage.
Overall coverage increased (+0.2%) to 80.494%

Totals

Change from base Build<PHONE_NUMBER>:
0.2%

Covered Lines:
2377

Relevant Lines:
2953

💛  - Coveralls

we should probably wait on merging on this until the RP change has rolled out to all regions, otherwise we'll risk those feature gates not getting properly set

also we don't generally link to ADO PRs and things of that nature here since this is OSS :)

Yes this one should wait for the RP change.

The RP change has already rolled out to all regions, now we can merge this,  @cameronmeissner  could you help to review again?

The RP change has already rolled out to all regions, now we can merge this, @cameronmeissner could you help to review again?

do we still want/need to merge this?

Hi @cameronmeissner  yes it's still needed.


Konami Code

Konami Code - by Tommaso "Giampiero" Bresciani
Allows to input the classic Konami Code ("Up, Up, Down, Down, Left, Right, Left, Right, B, A") into a scene for cheats and easter eggs.
To use it, simply attach the behavior to any object in a scene and use the Konami Code condition in the editor to trigger your desired effects with events.
Checklist

[ 🆗 ] Extension has a proper name and description.
[ 🆗  ] Extension has tags (for example: "platform, brick, breakable").
[ 🆗  ] All behaviors have a description.
[ 🆗  ] All functions (actions, conditions, expressions) have descriptions.
[ 🆗 ] I confirm that this extension can be intergrated to this GitHub repository, distributed and MIT licensed.

Extension file
KonamiCodeExtension.zip
🙌

Haha that's a great idea! Seems to be well done, easy to use and well explained - great job 👍
Added!


Dependency-check is failing on CircleCi for multiple projects - started today

Dependency-check is executed for several of my projects on CircleCi using following command:
docker run -v /src:/src:z   owasp/dependency-check  --scan /src --format "ALL" --project na-leaveplanner --out /report
It has been failing for all projects with different errors during each attempt, some referring to connectivity issues, while others to DB-related errors.
See two sample logs attached.
Please assist in getting this issue resolved.
dc1.log
dc2.log

That's something to address with your CircleCI maintainers as they are clearly networking-issues.

It's also possible the NVD was down temporarily.


Examples in codesandbox load without view

In the docs examples are loaded in codesandbox, but codesandbox initialises without a view. The reason for this is the query param &view=split. Removing the query param will fix it and load codesandbox in split view.
Example in docs:
https://react-table.js.org/#/story/server-side-data
Loads this in iframe (not working):
https://codesandbox.io/embed/wjrn8wy3R?autoresize=1&hidenavigation=1&view=split
Should load without view param:
https://codesandbox.io/embed/wjrn8wy3R?autoresize=1&hidenavigation=1
That's all.

Closing.  This seems as though it may have been related to breaking changes in codesandbox that seem to be resolved.  If the problem still exists, please open another issue.
NOTE: Ives is in a fairly quick release cycle for changes and there are no resources available for ReactTable to keep pace


Catalog Refactoring (Hierarchically Cached Catalog Objects)

(At this point, we are still cleaning up our code. We will update when we think it is ready.)
We have added DatabaseCatalogObject, TableCatalogObject, IndexCatalogObject, and ColumnCatalogObject.

Each catalog object contains the most up-to-date metadata information within the transaction for the corresponding object.
Catalog objects are cached within the transaction handler. But it should not be directly accessible to other parts of the database, i.e., it is self-maintained by the catalog. Thus, we will not discuss the implementation detail.
Catalog objects follow a hierarchical structure: DatabaseCatalogObject contains TableCatalogObjects; TableCatalogObject contains IndexCatalogObjects and ColumnCatalogObjects.
Access interface:

auto database_object = catalog::DatabaseCatalog::GetInstance()->
                       GetDatabaseObject(database_name or database_oid, txn);
auto table_object = database_object->GetTableObject(table_name or table oid);
auto index_object = table_object->GetIndexObject(index_name or index_oid);
auto column_object = table_object->GetColumnObject(column_name or column_id);

TODOs:

Evict index & column
Lookup index by name
Hide catalog internal API using private and friend
Use access function
Use catalog object in optimizer and plan

Coverage increased (+0.2%) to 73.117% when pulling 7308d75afefcd16ca3e1d8097c3a5f9ab2995bed on AngLi-Leon:catalog_manager into 0ad47758afb0cc397acadfc1efbe4b1aee906979 on cmu-db:master.

Coverage increased (+0.2%) to 73.121% when pulling d5c60e2781b0add690f11ba27e8e3c304bad1a8f on AngLi-Leon:catalog_manager into 0ad47758afb0cc397acadfc1efbe4b1aee906979 on cmu-db:master.

Coverage increased (+0.2%) to 73.087% when pulling 4308bed521417aa3158cd6c2d09cc27d76c8e998 on AngLi-Leon:catalog_manager into 0ad47758afb0cc397acadfc1efbe4b1aee906979 on cmu-db:master.

Coverage increased (+0.2%) to 73.091% when pulling 79dfa356910dbe3d9fc62b7e56d7994f5bca4925 on AngLi-Leon:catalog_manager into 0ad47758afb0cc397acadfc1efbe4b1aee906979 on cmu-db:master.

Coverage increased (+0.2%) to 73.091% when pulling 79dfa356910dbe3d9fc62b7e56d7994f5bca4925 on AngLi-Leon:catalog_manager into 0ad47758afb0cc397acadfc1efbe4b1aee906979 on cmu-db:master.

Coverage increased (+0.2%) to 73.133% when pulling e66a047713cf205292f5f6c8b3ec6dcc178f10e1 on AngLi-Leon:catalog_manager into 0ad47758afb0cc397acadfc1efbe4b1aee906979 on cmu-db:master.

Coverage increased (+0.3%) to 73.257% when pulling 8de97dd542d5a8083c00a1e4244b44f21284f321 on AngLi-Leon:catalog_manager into 0ad47758afb0cc397acadfc1efbe4b1aee906979 on cmu-db:master.

Coverage decreased (-72.9%) to 0.0% when pulling 1f0b21e9bbb71c55d5836830efd6bc65275b0c1f on AngLi-Leon:catalog_manager into 0ad47758afb0cc397acadfc1efbe4b1aee906979 on cmu-db:master.

Coverage decreased (-72.9%) to 0.0% when pulling 123f054acfda9636b450ef95da7cf3bd13007a90 on AngLi-Leon:catalog_manager into 0ad47758afb0cc397acadfc1efbe4b1aee906979 on cmu-db:master.

Coverage decreased (-72.9%) to 0.0% when pulling 123f054acfda9636b450ef95da7cf3bd13007a90 on AngLi-Leon:catalog_manager into 0ad47758afb0cc397acadfc1efbe4b1aee906979 on cmu-db:master.

Coverage decreased (-72.9%) to 0.0% when pulling 9f6989e4dddbafbea500864b3592b24eb20800ce on AngLi-Leon:catalog_manager into 0ad47758afb0cc397acadfc1efbe4b1aee906979 on cmu-db:master.

Coverage decreased (-72.9%) to 0.0% when pulling 393b787f5cdaf1dc189762d60a7f044b3c504c9b on AngLi-Leon:catalog_manager into 0ad47758afb0cc397acadfc1efbe4b1aee906979 on cmu-db:master.

Coverage increased (+0.3%) to 73.172% when pulling 03b4fbb3e537d0912aef57f1304e4e205f80b539 on AngLi-Leon:catalog_manager into 0ad47758afb0cc397acadfc1efbe4b1aee906979 on cmu-db:master.

Coverage increased (+0.2%) to 73.164% when pulling ce330d2796b74365815bdede60b95de3ee91bede on AngLi-Leon:catalog_manager into 0ad47758afb0cc397acadfc1efbe4b1aee906979 on cmu-db:master.

Coverage decreased (-5.4%) to 67.54% when pulling 06fef79775dc8d28442a8d34e04e4f46be71b514 on AngLi-Leon:catalog_manager into 0ad47758afb0cc397acadfc1efbe4b1aee906979 on cmu-db:master.

Coverage decreased (-72.9%) to 0.0% when pulling 06fef79775dc8d28442a8d34e04e4f46be71b514 on AngLi-Leon:catalog_manager into 0ad47758afb0cc397acadfc1efbe4b1aee906979 on cmu-db:master.

Coverage decreased (-72.9%) to 0.0% when pulling 06fef79775dc8d28442a8d34e04e4f46be71b514 on AngLi-Leon:catalog_manager into 0ad47758afb0cc397acadfc1efbe4b1aee906979 on cmu-db:master.

Coverage decreased (-72.9%) to 0.0% when pulling 7ce616e10d6b07bdf414dc7f3460c0795487ed2b on AngLi-Leon:catalog_manager into 0ad47758afb0cc397acadfc1efbe4b1aee906979 on cmu-db:master.

Coverage increased (+0.02%) to 72.937% when pulling 7ce616e10d6b07bdf414dc7f3460c0795487ed2b on AngLi-Leon:catalog_manager into 0ad47758afb0cc397acadfc1efbe4b1aee906979 on cmu-db:master.

Coverage increased (+0.01%) to 72.932% when pulling 9e62c0cf04724b4590833f4e6113fe47fbf72afc on AngLi-Leon:catalog_manager into 0ad47758afb0cc397acadfc1efbe4b1aee906979 on cmu-db:master.

Coverage increased (+0.2%) to 73.144% when pulling 9e62c0cf04724b4590833f4e6113fe47fbf72afc on AngLi-Leon:catalog_manager into 0ad47758afb0cc397acadfc1efbe4b1aee906979 on cmu-db:master.

Coverage increased (+0.2%) to 73.144% when pulling 9e62c0cf04724b4590833f4e6113fe47fbf72afc on AngLi-Leon:catalog_manager into 0ad47758afb0cc397acadfc1efbe4b1aee906979 on cmu-db:master.

Coverage increased (+0.2%) to 73.095% when pulling 6365b25ac08bf24a812b4eaf87fd31a19f6398ae on AngLi-Leon:catalog_manager into 0ad47758afb0cc397acadfc1efbe4b1aee906979 on cmu-db:master.

Coverage increased (+0.2%) to 73.144% when pulling 6365b25ac08bf24a812b4eaf87fd31a19f6398ae on AngLi-Leon:catalog_manager into 0ad47758afb0cc397acadfc1efbe4b1aee906979 on cmu-db:master.

Coverage decreased (-0.3%) to 72.636% when pulling e2e7cc92d69ee08623ebfaa2286911db0d852f7b on AngLi-Leon:catalog_manager into 0ad47758afb0cc397acadfc1efbe4b1aee906979 on cmu-db:master.

Coverage decreased (-0.3%) to 72.655% when pulling ba86e00598655e0f81a6714562fa22e3ca3d528e on AngLi-Leon:catalog_manager into 0ad47758afb0cc397acadfc1efbe4b1aee906979 on cmu-db:master.

Coverage decreased (-72.9%) to 0.0% when pulling 2d13ae11ded2f6d8ff79d3a17947300599a48be3 on AngLi-Leon:catalog_manager into 0ad47758afb0cc397acadfc1efbe4b1aee906979 on cmu-db:master.

Coverage decreased (-0.4%) to 72.543% when pulling 0f3101a8458ca67b40c5770dd9d44ded28ae1b4a on AngLi-Leon:catalog_manager into 0ad47758afb0cc397acadfc1efbe4b1aee906979 on cmu-db:master.

Coverage decreased (-0.2%) to 72.672% when pulling a8cbc598d83e92b1424b30b1fe2987aab4453ecf on AngLi-Leon:catalog_manager into 0ad47758afb0cc397acadfc1efbe4b1aee906979 on cmu-db:master.

Coverage decreased (-11.3%) to 61.656% when pulling 09ef4bef656d93ef65c7304188ec8910e1d34cfd on AngLi-Leon:catalog_manager into 0ad47758afb0cc397acadfc1efbe4b1aee906979 on cmu-db:master.

Coverage increased (+0.1%) to 73.052% when pulling 0f3101a8458ca67b40c5770dd9d44ded28ae1b4a on AngLi-Leon:catalog_manager into 0ad47758afb0cc397acadfc1efbe4b1aee906979 on cmu-db:master.

Coverage increased (+0.09%) to 73.011% when pulling 0f3101a8458ca67b40c5770dd9d44ded28ae1b4a on AngLi-Leon:catalog_manager into 0ad47758afb0cc397acadfc1efbe4b1aee906979 on cmu-db:master.

Coverage increased (+0.1%) to 73.023% when pulling 0f3101a8458ca67b40c5770dd9d44ded28ae1b4a on AngLi-Leon:catalog_manager into 0ad47758afb0cc397acadfc1efbe4b1aee906979 on cmu-db:master.

Coverage increased (+0.1%) to 73.023% when pulling 0f3101a8458ca67b40c5770dd9d44ded28ae1b4a on AngLi-Leon:catalog_manager into 0ad47758afb0cc397acadfc1efbe4b1aee906979 on cmu-db:master.

Coverage increased (+0.09%) to 73.015% when pulling 0f3101a8458ca67b40c5770dd9d44ded28ae1b4a on AngLi-Leon:catalog_manager into 0ad47758afb0cc397acadfc1efbe4b1aee906979 on cmu-db:master.

Coverage increased (+0.09%) to 73.011% when pulling 0f3101a8458ca67b40c5770dd9d44ded28ae1b4a on AngLi-Leon:catalog_manager into 0ad47758afb0cc397acadfc1efbe4b1aee906979 on cmu-db:master.

Coverage increased (+0.1%) to 73.023% when pulling 0f3101a8458ca67b40c5770dd9d44ded28ae1b4a on AngLi-Leon:catalog_manager into 0ad47758afb0cc397acadfc1efbe4b1aee906979 on cmu-db:master.

Coverage increased (+0.1%) to 73.048% when pulling 3c80a06873c8afdd93944ce9e4d51bbd9e2f7737 on AngLi-Leon:catalog_manager into 0ad47758afb0cc397acadfc1efbe4b1aee906979 on cmu-db:master.

Coverage increased (+0.1%) to 73.023% when pulling 0f3101a8458ca67b40c5770dd9d44ded28ae1b4a on AngLi-Leon:catalog_manager into 0ad47758afb0cc397acadfc1efbe4b1aee906979 on cmu-db:master.

Coverage increased (+0.08%) to 72.999% when pulling e91d345c04da9b92b1f06b1cf81931a375466501 on AngLi-Leon:catalog_manager into 0ad47758afb0cc397acadfc1efbe4b1aee906979 on cmu-db:master.

Coverage increased (+0.08%) to 73.003% when pulling e91d345c04da9b92b1f06b1cf81931a375466501 on AngLi-Leon:catalog_manager into 0ad47758afb0cc397acadfc1efbe4b1aee906979 on cmu-db:master.

Coverage increased (+0.1%) to 73.018% when pulling caa9fd3a8639f42bb27550e00f305322ef25f09d on AngLi-Leon:catalog_manager into 0ad47758afb0cc397acadfc1efbe4b1aee906979 on cmu-db:master.

Coverage increased (+0.05%) to 72.972% when pulling d50e1b5df20aa99882898bd75ca7a96020b50221 on AngLi-Leon:catalog_manager into 0ad47758afb0cc397acadfc1efbe4b1aee906979 on cmu-db:master.

Coverage increased (+0.09%) to 73.012% when pulling 1ab7677fede70cdb9bfa22dab830571602cda61a on AngLi-Leon:catalog_manager into 0ad47758afb0cc397acadfc1efbe4b1aee906979 on cmu-db:master.

Coverage increased (+0.09%) to 73.007% when pulling 1ab7677fede70cdb9bfa22dab830571602cda61a on AngLi-Leon:catalog_manager into 0ad47758afb0cc397acadfc1efbe4b1aee906979 on cmu-db:master.

Coverage increased (+0.07%) to 72.995% when pulling 6f07d2bc53fa433c32b73b32a45d4415c0384f6e on AngLi-Leon:catalog_manager into 0ad47758afb0cc397acadfc1efbe4b1aee906979 on cmu-db:master.

@camellyx Is this branch ready to be reviewed?

@apavlo Yes, this PR is ready for review.

@rohit-cmu Can you review this?

@apavlo Sure. Ill review this.

Coverage decreased (-73.2%) to 0.0% when pulling d4baad905ac1f804d9f526e49ef5839c57df2345 on AngLi-Leon:catalog_manager into d9c9e1d20d24fabbe8e8afb0c740cc3ad42085d1 on cmu-db:master.

Coverage decreased (-72.9%) to 0.0% when pulling e9004bb9b0f36250d13e78901484468b5592e588 on AngLi-Leon:catalog_manager into e4023183d26117f2ef77d7ede3ea2dc6803e5d8a on cmu-db:master.

Coverage decreased (-0.05%) to 72.88% when pulling 44e0a1f52ffd9e704fc845f8261c1dc9e5ec9d6b on AngLi-Leon:catalog_manager into e4023183d26117f2ef77d7ede3ea2dc6803e5d8a on cmu-db:master.

Coverage decreased (-0.04%) to 72.899% when pulling 1863d34d1a62f6b43f5f14a0d4b42c39eb9f2e5b on AngLi-Leon:catalog_manager into 4cb8d7499f5e5da6f387f9304dc6e72cb28b5a96 on cmu-db:master.


generated Spring Boot Quickstarter code does not compile locally

The documentation states that one have to manually create an gradle.properties to define nexus related properties.
If those properties are not defined (Eighter by enviroment variables or properties), the  build does not succed:
FAILURE: Build failed with an exception.
* What went wrong:
Execution failed for task ':compileJava'.
> Failed to notify dependency resolution listener.
   > Could not resolve all dependencies for configuration ':detachedConfiguration1'.
      > Authentication scheme 'all'(Authentication) is not supported by protocol 'file'
   > Could not resolve all dependencies for configuration ':detachedConfiguration2'.
      > Authentication scheme 'all'(Authentication) is not supported by protocol 'file'

The specificatin of those properties is fine if nexus is needed. If not needed, the build should compile without any further action. Specification of gradle.properties should be optional in this case. Dependencies can be downloaded from jcenter and mavenCentral.

Can we handle it in the quickstarter, the same way it works for the provisioning app (no_nexus property)?

Yes, but we do not need to specify no_nexus property at all:
buildscript {
    ext
            {
                nexus_url = "${project.findProperty('nexus_url') ?: System.getenv('NEXUS_HOST')}"
                nexus_user = "${project.findProperty('nexus_user') ?: System.getenv('NEXUS_USERNAME')}"
                nexus_pw = "${project.findProperty('nexus_pw') ?: System.getenv('NEXUS_PASSWORD')}"
                nexus_folder = "${project.findProperty('nexus_folder') ?: System.getenv('NEXUS_FOLDER')}"
                nexus_folder = nexus_folder == "null" ? "candidates" : nexus_folder
                no_nexus = nexus_url == "null" || nexus_user == "null" || nexus_pw == "null"
                if (no_nexus) {
                    println("Do not use nexus, since at least one of properties nexus_url, nexus_user or nexus_pw is not configured")
                }
                snippetsDir = file('build/generated-snippets')
            }
}
repositories {
    if (no_nexus) {
        jcenter()
        mavenCentral()
    } else {
//...
}

Hi @stefanlack, I´m not really convinced about not failing the build if any nexus property is missing is a good idea. One reason why companies uses an artifcat repository like Nexus is reproducibility. This guarantees that software can be build even in case an artifact can´t be located in internet.

I close this issue. The build should realy fail if nexus properties are not defined correctly.
However, in this case the build should print some helpfull error messages. I will implement better error messages in the PR for #330


some wrong i don't know

please help me.
when i go run with  steps,but something is wrong
i do pip install opencv-python,tqdm sh make.sh,and put the pth into the file "weights",then I run the py python demo.py -c=configs/m2det512_vgg.py -m=weights/m2det512_vgg.pth --show, I fund the wrong.
(pytorch0.4.1) csy@csy:~/M2Det$ python demo.py -c=configs/m2det512_vgg.py -m=weights/m2det512_vgg.pth --show

M2Det Demo Program

The Anchor info:

{'clip': True, 'variance': [0.1, 0.2], 'steps': [8, 16, 32, 64, 128, 256], 'min_dim': 512, 'min_sizes': [30.72, 76.8, 168.96, 261.12, 353.28, 445.44], 'aspect_ratios': [[2, 3], [2, 3], [2, 3], [2, 3], [2, 3], [2, 3]], 'feature_maps': [64, 32, 16, 8, 4, 2], 'max_sizes': [76.8, 168.96, 261.12, 353.28, 445.44, 537.6]}

===> Constructing M2Det model

Loading resume network...

===> Finished constructing and loading model

<class 'm2det.M2Det'>

THCudaCheck FAIL file=/pytorch/aten/src/THC/THCGeneral.cpp line=663 error=11 : invalid argument

Traceback (most recent call last):

File "demo.py", line 113, in

out = net(img)

File "/home/csy/anaconda3/envs/pytorch0.4.1/lib/python3.5/site-packages/torch/nn/modules/module.py", line 477, in call
result = self.forward(*input, **kwargs)
File "/home/csy/M2Det/m2det.py", line 106, in forward
x = self.basek
File "/home/csy/anaconda3/envs/pytorch0.4.1/lib/python3.5/site-packages/torch/nn/modules/module.py", line 477, in call
result = self.forward(*input, **kwargs)
File "/home/csy/anaconda3/envs/pytorch0.4.1/lib/python3.5/site-packages/torch/nn/modules/conv.py", line 301, in forward
self.padding, self.dilation, self.groups)
RuntimeError: cuda runtime error (11) : invalid argument at /pytorch/aten/src/THC/THCGeneral.cpp:663
whether i forgot  to modify something in others? I am puzzled or not,please help me

I sugest check cuda  and pytorch version.....May be  they are not match ....

我sugest检查cuda和pytorch版本.....可能是他们不匹配....
you are right .something is wrong in my torch


Please fix it

The way you made the number display in the hotbar is just awful. My inner perfectionist is terrified. Please do this that according to the standard, the numbers start "in the upper left corner" and then, when increased, they are added from the right side, BUT did not shift. It's so logical, but for some reason you didn't do it. Setting up in your mod is useless in this regard, from the word "absolutely".

@BlazingTwist  I would like it to be something like this.

read the wiki, it's not that hard. https://github.com/BlazingTwist/ItemCounts/wiki/Configuring-an-Overlay
(if you wanted a nicer response, you should work on your ticketing.)

read the wiki, it's not that hard. https://github.com/BlazingTwist/ItemCounts/wiki/Configuring-an-Overlay
(if you wanted a nicer response, you should work on your ticketing.)

I sincerely apologize to you.  There is one wish for the future update of your mod, the ability to change the color of the numbers.

Alright, I'm assuming you figured out how the anchor works.

change the color of the numbers

Sure, I can do that. One question though: what about items with durability? (Since these go from green to red text color) I can think of 3 ways to handle those:

Add an option to toggle between durability-color and custom-color.
Add 3 configurable colors, for 'normal items', 'low durability' and 'high durability'
Apply some kind of blending between the custom color and the durability color (e.g. multiplying) - I think this option would just look bad in most cases.

To be honest, I do not know, since I do not use the "show durability" option. I have a mod "Simple Durability Tooltip" it shows me the durability on objects.

Added. Uploaded to curseforge for mc 1.18.0 - 1.19.4.
These files should become visible in a few hours or so.


ManagedMqttClient / WithWillDelayInterval not working

With the latest NuGet version of MQTTnet and the ManagedClient (<IP_ADDRESS>) the WillMessage is not working as expected. I tried to test it with the following code:
// Creates a new client
var builder = new MqttClientOptionsBuilder()
                    .WithClientId(this.config.MqttIdentity)
                    .WithTcpServer(this.config.MqttServer, this.config.MqttPort)
                    .WithWillDelayInterval(15000)
                    .WithWillTopic("info/connection")
                    .WithWillPayload("false");

// Create client options objects
var options = new ManagedMqttClientOptionsBuilder()
                    .WithAutoReconnectDelay(TimeSpan.FromSeconds(10))
                    .WithClientOptions(builder.Build())
                    .Build();

// Creates the client object
this.mqttClient = new MqttFactory().CreateManagedMqttClient();

// Starts a connection with the Broker
this.mqttClient.StartAsync(options).GetAwaiter().GetResult();

The will-message is executed immediately after disconnecting. The delay time is not regarded / the WithWillDelayInterval settings has no effect.
As server I use the MQTT broker integrated in ioBroker.

With v5 I have connection (authentication) problems. I think the problem is the broker with lacking v5 support. I didn't know that "will interval" is an v5 feature. Thank you very much for the tip.
So I close this bug report because it's probably not an client issue.


Add Hamburger Icon for Mobile Navbar

Description:
Enhance mobile user experience by adding a hamburger icon to the navbar. Clicking the icon should reveal the navigation menu for easy access on smaller screens.
Note:
I'd like to take on this task. Please assign it to me.

Thats good issue.
Go for it @ayushichoudhary-19 🚀

Pls raise the PR ASAP.

@ayushichoudhary-19 ??

Hello @abhay-raj19 I'm currently in the midst of some exams, which are demanding my full attention until the 26th. I apologize for any inconvenience this may cause regarding the issue. I can work on this after 26th but if someone else wants to work on it in the mean time, I'm absolutely fine with it. Please consider marking this issue with 'up-for-grabs' if the feature needs an urgent addressing. Sorry for the delay though. Thankyou.

Can i do this?? @abhay-raj19


Autocomplete no longer puts exact match at top

It should do.

Scratch that.  It does.  I had a filter on!


fix(dhcpv6): fix panic when accessing a missing option

When trying to get a non-existent option code from the DhcpOptions struct, the code panics due to an underflowing substraction.

Actually I think dropping this manual binary search implementation altogether would be better. std provides partition_point since 1.52 and the library's MSRV is 1.53. This would reduce a great deal the amount of code of the library and remove index-based code that's error prone.
@leshow WDYT?

Assuming we can just replace the manual impl with the std-lib function, I'm on board of course. No need to maintain an implementation like this if we don't need to.

I'll merge this now, feel free to submit another PR if you want to replace the logic though.

Thanks!

No, thank you! The dhcpv6 decoder is not used as heavily at the moment so it's a big help to find these issues.

Sure! I will push a new release shortly.


Write batch number onto opps and payments inside a batch

Critical Changes
Changes

The autogenerated batch number for new donations will now be written to the opportunity and payment when the batch is processed.

Issues Closed
Community Ideas Delivered
New Metadata

Fields

Opportunity.Batch_Number__c
npe01__OppPayment__c.Batch_Number__c

Deleted Metadata

@melissabarber there are several scenarios to this that are outlined in the WI. Let me know how much detail for those scenarios we should put into the Changes section.

yeah that was the last piece I was going to add after addressing the other feedback

Have you considered adding a test method to cover this new code? I think it would be good to have for this sort of special handling of this field mapping.

@kenlewis-sfdo Yeah that was the last piece I was going to add after addressing the other review feedback

@dfuller114 & @ptewson-sfdo I added one more help text change suggestion. After that's implemented, I'm all good to go on this PR.


DwarfEH: 32 bit Linux support

This is a work in progress.

Requires https://github.com/D-Programming-Language/druntime/pull/1474

This is a bit frustrating. The test case druntime/test/shared/finalizer is seg faulting after main() returns, and it's failing in gc_term(). It only happens when linking to shared libraries in release build. Anyone have any ideas?

Pull #1482 fixed it. Ready to pull.

Auto-merge toggled on


Add textContent for cross-browser compatibility.

Fixes issue #96. The click handler fires fine, but the text doesn't update. Firefox doesn't appear to like innerText.

Oh, duh, I missed that!

Btw you could've just done a.innerText = a.textContent = b


ARXIVNG-897 added InvalidStack handling to verify_user controller, and tests

This also contributes to ARXIVNG-911 by changing the form request method on verify_user to POST.
The basic idea is that we are catching InvalidStack, and displaying the exception messages on its constituent InvalidEvents at the top of the page. Here's a mockup (not real exceptions):

In addition, we should leverage the event's own validation on the form. Will do this next.

Pull Request Test Coverage Report for Build 65

83 of 88 (94.32%)  changed or added relevant lines in 4 files are covered.
2 unchanged lines in 1 file lost coverage.
Overall coverage increased (+54.8%) to 56.325%

Changes Missing Coverage
Covered Lines
Changed/Added Lines
%

submit/controllers/util.py
4
5
80.0%

submit/routes/ui.py
0
4
0.0%

Files with Coverage Reduction
New Missed Lines
%

submit/routes/ui.py
2
0.0%

Totals

Change from base Build 57:
54.8%

Covered Lines:
187

Relevant Lines:
332

💛  - Coveralls

@eawoods Ok, made a few changes, and addressed the authorship controller. In the first two steps, we are now also pulling the current state of the submission and pre-populating the form on GET requests (so that the state is reflected in the form).

Maybe something to think about, can we dump the existing page and allow navigation if the option selected is something other than "Continue"? I think we had talked about saving the data on a page if the form validates, but otherwise allowing prev/exit navigation without saving if it doesn't validate.

Yes, I had similar thoughts. Let's discuss (add to sprint agenda?)

This actually delivers ARXIVNG-911 for all implemented controllers.

I noticed that the authorship page defaults to "I am an author of this paper" -- didn't see how that could be happening in code? Jim's point to not having defaults in order to force the user to think about the choice probably applies here.

This appears to be because a default is being set in the core events. Will address as: https://culibrary.atlassian.net/browse/ARXIVNG-917

I skimmed over the code and it looks good to me. Only comment I have is on validation of form. Sounds like there is a desire to dump what's there if the form does not validate then user clicks previous or save&exist. I thought we had discussed saving the data fields that validate. If a user enters a bunch of metadata and then clicks 'save&exit' I suspect they might be upset if we detect a validation error and dump all of their hard work (specially if they spent an hour entering individual authors). Maybe at least warn user? Data contains validation errors, fix or we save remaining valid fields? Likely only matters for pages with a significant amount of input data.

That's an excellent point. Let's revisit this when we do the metadata
controller, sinxe it will be especially relevant in that context
On Fri, Jun 15, 2018, 1:40 PM DavidLFielding<EMAIL_ADDRESS>wrote:

I skimmed over the code and it looks good to me. Only comment I have is on
validation of form. Sounds like there is a desire to dump what's there if
the form does not validate then user clicks previous or save&exist. I
thought we had discussed saving the data fields that validate. If a user
enters a bunch of metadata and then clicks 'save&exit' I suspect they might
be upset if we detect a validation error and dump all of their hard work
(specially if they spent an hour entering individual authors). Maybe at
least warn user? Data contains validation errors, fix or we save remaining
valid fields? Likely only matters for pages with a significant amount of
input data.
—
You are receiving this because you modified the open/close state.
Reply to this email directly, view it on GitHub
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or mute the thread
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.


Allows to select the back date as year “0000”

Submit an Issue or feature enhancement
Hi,
Using this control we want to restrict the user from selecting the past date less than the given date.
For example: I want to restrict the user from selecting the date before year 1970 but currently it is allowing user to select even "0000"
It might be a feature enhancement.

Support for min and max were added back in August, apologies for not updating this issue.