text:
Upgrade to bdg-formats:0.6.0, add Fragment datatype converters

Resolves #779, #788. This is a fairly big PR and could use some close review. I'm CCing @arahuja to review the modifications to the VariantContextConverter, and @laserson and @ilveroluca to review the Fragment additions.
There are a few things in specific that I think could use a closer look. I'll comment on these inline.

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Test FAILed.

Jenkins, test this please.

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Jenkins, test this please.

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Test FAILed.

Seems like a git force-push test failure, Jenkins retest this please

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Test FAILed.

oops

[ERROR] Failed to execute goal on project adam-core_2.10: Could not resolve dependencies for project org.bdgenomics.adam:adam-core_2.10:jar:0.17.2-SNAPSHOT: Could not find artifact org.bdgenomics.bdg-formats:bdg-formats:jar:e1ca0a3 in central (http://repo.maven.apache.org/maven2) -> [Help 1]

https://github.com/fnothaft/adam/pull/7 was merged in here but was still pointing to a custom build of bdg-formats later than 0.6.0
Let me push my change to bdg-formats, we can release a 0.6.1 or 0.7.0, then depend on that here.

Proposed https://github.com/bigdatagenomics/bdg-formats/pull/63 with the change that https://github.com/fnothaft/adam/pull/7 (and now this PR) needs

This is up to date with @ryan-williams's fixes (that upgrade us to bdg-formats/0.6.1). I think this resolves all outstanding issues.

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Test FAILed.

Jenkins, test this please.

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Test FAILed.

missing unordered.sam, maybe I forgot to git add it?

or it's in adam-core test/resources and is being referenced from adam-cli and the letter's not being found

Ah, let me fix that.

weirdly, it passes for me locally.
should we make adam-cli tests include the adam-core test/resources in their resources path?

we already do a somewhat silly thing and have the same bqsr1.sam file in adam-cli and adam-core

Yeah, I've just symlinked them from adam-core to adam-cli.

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Test FAILed.

Jenkins, retest this please

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Could we get merge/additional review by the end of the week? This has been open more than a month.

This LGTM @fnothaft. A couple of observations:

Sorry that my PR on this PR has cluttered up the review here! I think that leaving that one hanging until we got this one in might have been a better course of action, I'll try to be more clear about that in the future.
This seems similar to the last time I looked at it but with the simplification that you took out the Sequence stuff and just have ARs in the Fragment, right?

Fixed the oops @ryan-williams and rebased.

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Test FAILed.

Jenkins, test this please.

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@massie @laserson @ryan-williams if I don't get any further comments on this, I will merge it myself on Monday.

I just reviewed this again and I didn't see any outstanding issues by @laserson or @ryan-williams, so I'm going to merge it now.

authors: AmplabJenkins fnothaft massie ryan-williams

repo: bigdatagenomics/adam


text:
Change Expandable State at real time

Is it possible when populating the recycleView onBind period or anywhere else to change the default expandable state given by the interface ParentListItem -> isInitiallyExpanded by default all of my header items are false (closed) but I want when entering data to the field to decide wheter or not should expand or not.
Is that possible and If so how can I achieve it because I tried to do it on bind but I get the error Cannot call this method while RecyclerView is computing a layout or scrolling

Hi @mitko9000 do you maybe mean to have the ability to expand/collapse the parent items programmatically? If so, take a look at https://github.com/bignerdranch/expandable-recycler-view/blob/master/expandablerecyclerview/src/main/java/com/bignerdranch/expandablerecyclerview/Adapter/ExpandableRecyclerAdapter.java#L317-L424
That has expand/collapse methods on the adapter that you can use to trigger a change after the initialization.

Hi @paul-turner  I have seen those methods but every time I invoke them I get recycleView is not ready crash when its the best time to expand the items I want programmatically ?

Do you have a snippet showing when and what you are currently doing? Also maybe a copy of the exception to see. Version information would also help, what version of the support library, and what version of ExpandableRecyclerView.

For example:
@Override
    public void onBindParentViewHolder(HistoryParentViewHolder hisotryParentViewHolder, int i, ParentListItem parentListItem) {

        History history = (History) parentListItem;

        if(currentDate.equals("TODAY") || currentDate.equals("YESTERDAY"))
        {
          expandParent(0);
}

}

I see, seems like dataSetChanges should not be triggered during onBind but I'm not familiar with that error.
Why not have the logic of if(currentDate.equals("TODAY") || currentDate.equals("YESTERDAY")) inside your isInitiallyExpanded() method? seems like you are trying to have them expand based on that logic. Otherwise, I'd say call for your item to expand in onCreateView after you set the adapter on the recyclerView.
For the call to expandParent(0) are you sure the parent has child items? seems odd for it to not expand at all. (for example, if you remove this expansion code and just click on the item, does it expand?)

@paul-turner Hi paul I cant use that logic inside the ParentViewholder because there I dont have access to the data that its going to be displayed I will try with the onCreateView, the whole Idea is when the adapter loads the items needed I need to parse the headers and everywhere on those headers where the date equals TODAY or YESTERDAY to expand that item I will try some solutions next week and keep you updated when I find a solution about that.
Yeah expandParent(0) do nothing because at this state the internal list is with item count of zero.
Regards,
Mitko

OK, seems there are two tweaks that need to be made. One, the data should be available inside the ParentListItem (Not the ParentViewHolder), and you can hold that logic of initial expansion in isInitiallyExpanded(). Two, you'll need to have children already or else there is nothing that will change when you call for expandParent() (also if you have it initiallyExpand to true, you will need to have the children there).  If there are changes to the data you will need to call the corresponding notifyParent or notifyChild methods, and it seems those cannot be called while binding.
Unfortunately it does not seem at this time that there is something wrong with the library, just need some small changes on your data side. Best of luck finding a solution, let me know if you run into any issues with the library.

@paul-turner I changed my logic so I can input as parameter weather or not I want this item to be expanded and it worked like charm

source: gharchive/issue

repo: bignerdranch/expandable-recycler-view

license: mit

license_type: permissive

license_source: bigquery


text:
Create dataset bangla_sentiment_classification_datasets

uid: bangla_sentiment_classification_datasets
type: processed
description:

name: Bangla Sentiment Classification Datasets

description: Multiple sentiment classification datasets for Bengali, which can also be used for training LMs. The Datasets are the following:
ABSA_datasets -- This dataset has developed to perform aspect based sentiment analysis task in Bangla.
License: CC BY 4.0
SAIL_data -- This dataset, consists of tweet posts, has developed in the Shared task on Sentiment Analysis in Indian Languages (SAIL) 2015. [2]
License: Non-profit
multichannel_bsentiment -- This data was collected from several newspapers, TV news, books, blogs, and social media.
License: NA (N.B.: We have the permission to share this dataset.)
youtube_sentiment -- This dataset was developed by extracting comments from various YouTube videos.
License: NA

homepage: https://github.com/banglanlp/bnlp-resources/tree/main/sentiment

validated: True

languages:

language_names:

Indic
Bengali

language_comments:
language_locations:

Southern Asia
Bangladesh

validated: False

custodian:

name:
in_catalogue:
type:
location:
contact_name:
contact_email:
contact_submitter: False
additional:
validated: False

availability:

procurement:

for_download: Yes - it has a direct download link or links
download_url: https://github.com/banglanlp/bnlp-resources/tree/main/sentiment
download_email:

licensing:

has_licenses: Yes
license_text: The work is licensed under https://creativecommons.org/licenses/by-nc/4.0/. However, for each dataset, please see the license information associated with it. Any private dataset can be accessed by contacting with the respective authors.
license_properties:

research use

license_list:

cc-by-4.0: Creative Commons Attribution 4.0 International

pii:

has_pii: Unclear
generic_pii_likely:
generic_pii_list:
numeric_pii_likely:
numeric_pii_list:
sensitive_pii_likely:
sensitive_pii_list:
no_pii_justification_class: general knowledge not written by or referring to private persons
no_pii_justification_text:

validated: False

processed_from_primary:

from_primary: Taken from primary source
primary_availability: No - the dataset curators describe the primary sources but they are fully private
primary_license:
primary_types:
validated: False
from_primary_entries:

media:

category:

text

text_format:

other
.TSV

audiovisual_format:
image_format:
database_format:

.ZIP

text_is_transcribed: No
instance_type: post
instance_count: 10K<n<100K
instance_size: 100<n<10,000
validated: False

fname: bangla_sentiment_classification_datasets.json

DONE: https://huggingface.co/datasets/bigscience-catalogue-data/bangla_sentiment_classification_datasets
ds = load_dataset("bigscience-catalogue-data/bangla_sentiment_classification_datasets", split="train", streaming=True, use_auth_token=True)
item = next(iter(ds))
item

Outputs:
{'text': 'আফতাব আপনি ভালো আছেন?'}

https://huggingface.co/datasets/bigscience-catalogue-lm-data/lm_indic-bn_bangla_sentiment_classification_datasets

The repo at https://huggingface.co/datasets/bigscience-catalogue-lm-data/lm_indic-bn_bangla_sentiment_classification_datasets/tree/main is empty @albertvillanova
let me copy the script from https://huggingface.co/datasets/bigscience-catalogue-data/bangla_sentiment_classification_datasets/blob/main/bangla_sentiment_classification_datasets.py

Sorry, I forgot to push the commit.

authors: albertvillanova lhoestq

license_source: github-api


text:
🛑 Jefferson Real is down

In 66bcef4, Jefferson Real (https://jeffersonreal.uk) was down:

HTTP code: 0
Response time: 0 ms

Resolved: Jefferson Real is back up in 3ea6d07.

repo: bigupjeff/my-site-uptime-monitor

license: MIT


text:
Make bike router ignore ferries, configurably

Fixes an issue where we get recommended a ferry with very specific hours.

We can get ferries to show up in the public transit routing instead, so ignore ferries at the bike router level.

Also, since the ultimate problem we're trying to fix is a special event only ferry being used by default in bike directions, it seems bad that stock GraphHopper will continue to have that problem. Any thoughts on what a more targeted fix would look like? Maybe only use ferries that have at least X number of voyages per day? Not to obligate you to solve it, just thinking out loud.

I think the way to solve this properly is to parse opening_hours for the ferry, but that's very complicated and I don't want to be the one to do it. I expect this will come up for them tho.

This bug appears to be back?

source: gharchive/pull-request

authors: MingweiSamuel hcourt

repo: bikehopper/graphhopper


text:
启动项目报错：undefined: balancer.PickOptions

主要原因新生成的项目grpc版本太高了，降到v1.26.0即可，可以在go.mod文件里加一句：
replace google.golang.org/grpc v1.27.0 => google.golang.org/grpc v1.26.0

能否帮适配下新版本的grpc

#550

authors: ChouBaoDxs Terry-Mao tonyboxes

repo: bilibili/kratos


text:
How should Git extensions look?

Bin is intended to have extensions a la Go/Node.js, where build functionality can be imported directly from a script. However, these extensions are to be automatically obtained given their string - so, more like Go than Node.js in all honesty.
I also want to define a way for extensions to register themselves as handlers for specific things - i.e. compiling C++ on windows means the MSVC toolchain registers itself with the c++ handler, etc.
I want it to be as simple as
use('cpp')

-- or

use('cpp.msvc')
use('cpp.gcc')
use('cpp.clang')
use('./scripts/a-custom-compiler')

Each of the above registers itself with a global command, such as cpp_project(), that can be intelligently selected (automatic, or manual overrides).

The next question becomes how do we allow users to select these? How are they normally selected? In the C++ example, how can we allow the user to build more than one at a time if necessary (e.g. cross-compilers)? What about variants? (variants might be a completely different discussion)
This might be going off some sort of greater 'configuration' discussion that needs to happen.

Well it's a no brainer - using libgit2 for this.

There are a few things to mention; I'll break them into sections.
Lua exposed function
The Lua package has been specifically blocked from being loaded to prevent malicious code execution - as well, a few globals have been blacklisted.
Bin will expose the bin.use() function that will load modules. It's a bit of a magic method that accepts a few different format strings.

bin.use('./relative/path.lua') - effectively a remap of dofile() (anything that starts with a .)
bin.use('https://hostname.com/some/repo.git') - checks if a remote has a Bin.lua file and clones it into $BINPATH (defaults to ./bin/.ext)
bin.use('user/repo') - alias of bin.use('https://github.com/user/repo.git')
bin.use('modulename') - alias of bin.use('https://github.com/bin-build/ext-modulename')

Order of Operations (and getting to the first goal, a Ninja parser)
As mentioned in the self-hosted commit comments (cc295bb27da81eca77a5e8d302a9010037b89dd2) the next step after the graphing library architecture refactor (#6) is to flesh out the scripting environment.
Fleshing out that step looks like:

get libgit2 included and get the above described magic function declared (the plumbing will result in a new class, ExtensionManager, which is controlled by a Context).
figure out global helper function structure (#17)
create bin-build/ext-cpp, bin-build/ext-cpp-clang, bin-build/ext-cpp-gcc, and bin-build/ext-cpp-msvc
test the absolute shit out of those (i.e. make Bin itself use them) -- yes, even testing on windows with many versions of visual studio :dancer:
use a peg parser to create a build.ninja parser/visitor (ColinH/PEGTL looks promising) and a corresponding module that is linked against Bin (also, buildable by Bin - hence the c++ compiler step above) and call it bin-build/ext-ninja -- have it register itself with Context
implement automatic detection of build systems (with precedence) and allow modules to register themselves as potential build sub-systems (#18)
have bin-build/ext-ninja register itself as a subsystem to look for a build.ninja file

repo: bin-build/bin


text:
Mahdiyeh/Fix: compare_accounts_content_for_eu_conuntries

Changes:

...

Type of change

Bug fix
[ ] New feature
[ ] Update feature
[ ] Refactor code
[ ] Translation to code
[ ] Translation to crowdin
[ ] Script configuration
[ ] Improve performance
[ ] Style only
[ ] Dependency update
[ ] Documentation update
[ ] Release

Any text changes that require translations will need to be branched of Crowdin branch. You can rebase this branch to Crowdin.

authors: mahdiyeh-fs sean-binary

repo: binary-com/deriv-com


text:
Improved encoding and decoding speed of Vec

Running against the benchmarks in #618
bench v1                time:   [48.663 µs 49.119 µs 49.573 µs]
                        change: [-0.9286% +0.8850% +2.7884%] (p = 0.35 > 0.05)
                        No change in performance detected.
Found 4 outliers among 100 measurements (4.00%)
  1 (1.00%) low mild
  2 (2.00%) high mild
  1 (1.00%) high severe

bench v2 (standard)     time:   [642.39 µs 646.82 µs 651.41 µs]
                        change: [-71.758% -71.415% -71.093%] (p = 0.00 < 0.05)
                        Performance has improved.
Found 1 outliers among 100 measurements (1.00%)
  1 (1.00%) high mild

bench v2 (legacy)       time:   [650.62 µs 653.72 µs 656.93 µs]
                        change: [-71.322% -71.089% -70.844%] (p = 0.00 < 0.05)
                        Performance has improved.
Found 3 outliers among 100 measurements (3.00%)
  2 (2.00%) high mild
  1 (1.00%) high severe

bench v1 decode         time:   [301.58 µs 302.76 µs 303.97 µs]
                        change: [-42.809% -40.022% -36.789%] (p = 0.00 < 0.05)
                        Performance has improved.
Found 5 outliers among 100 measurements (5.00%)
  3 (3.00%) low mild
  1 (1.00%) high mild
  1 (1.00%) high severe

bench v2 decode (legacy)
                        time:   [326.89 µs 328.24 µs 329.63 µs]
                        change: [-81.836% -81.650% -81.457%] (p = 0.00 < 0.05)
                        Performance has improved.
Found 5 outliers among 100 measurements (5.00%)
  3 (3.00%) low mild
  2 (2.00%) high mild

decoding seems to be on-par with bincode 1 now. Encoding is down to being a factor 10 slower.

Pre-computing the size drops the execution speed down by another 50%
bench v1                time:   [51.224 µs 51.781 µs 52.294 µs]
                        change: [+5.4681% +7.4038% +9.4670%] (p = 0.00 < 0.05)
                        Performance has regressed.
Found 24 outliers among 100 measurements (24.00%)
  3 (3.00%) low severe
  10 (10.00%) low mild
  9 (9.00%) high mild
  2 (2.00%) high severe

bench v2 (standard)     time:   [363.31 µs 364.96 µs 366.79 µs]
                        change: [-83.761% -83.543% -83.335%] (p = 0.00 < 0.05)
                        Performance has improved.
Found 6 outliers among 100 measurements (6.00%)
  1 (1.00%) low mild
  4 (4.00%) high mild
  1 (1.00%) high severe

bench v2 (legacy)       time:   [326.16 µs 327.39 µs 328.81 µs]
                        change: [-85.568% -85.459% -85.338%] (p = 0.00 < 0.05)
                        Performance has improved.
Found 9 outliers among 100 measurements (9.00%)
  6 (6.00%) high mild
  3 (3.00%) high severe

bench v1 decode         time:   [339.01 µs 341.76 µs 344.70 µs]
                        change: [-34.888% -31.648% -27.911%] (p = 0.00 < 0.05)
                        Performance has improved.
Found 11 outliers among 100 measurements (11.00%)
  5 (5.00%) low mild
  4 (4.00%) high mild
  2 (2.00%) high severe

bench v2 decode (legacy)
                        time:   [351.59 µs 357.93 µs 364.61 µs]
                        change: [-80.044% -79.714% -79.330%] (p = 0.00 < 0.05)
                        Performance has improved.
Found 6 outliers among 100 measurements (6.00%)
  5 (5.00%) high mild
  1 (1.00%) high severe

I'm willing to call this good if this is okay with you @JojiiOfficial
Execution speeds in the order of 51.781 µs and 364.96 µs are essentially instant. We can probably optimize this further, but we're hunting very specific LLVM optimizations at this point. In a real world scenario we would almost certainly not notice a difference between the two.
I'd suggest we say that this is fast enough for now and if we find a real world example where bincode 2 is significantly slower than bincode 1 we can add more benchmarks.

If you have a benchmark with data that lasts a minute to encode/decode that would be very interesting to dive into

Change the parameter for build_data from 100 to 2500 and it'll take around a minute with this PR merged.

The following code improves the performance even more for Strings and [u8] arrays:
impl<T> Encode for [T]
where
    T: Encode + 'static,
{
    fn encode<E: Encoder>(&self, encoder: &mut E) -> Result<(), EncodeError> {
        super::encode_slice_len(encoder, self.len())?;

        if core::any::TypeId::of::<T>() == core::any::TypeId::of::<u8>() {
            let t: &[u8] = unsafe { transmute(self) };
            encoder.writer().write(t)?;
            return Ok(());
        }

        for item in self {
            item.encode(encoder)?;
        }
        Ok(())
    }
}

Added a couple of #[inline] and now the performance is almost identical
bench v1                time:   [58.788 µs 59.134 µs 59.497 µs]
bench v2 (standard)     time:   [61.595 µs 62.437 µs 63.531 µs]
bench v2 (legacy)       time:   [62.514 µs 63.413 µs 64.394 µs]

Indeed, very nice!

authors: JojiiOfficial VictorKoenders

repo: bincode-org/bincode


text:
Versioning?

Hi there,
I would like to create an aur package (arch linux users repo) for try but I saw that there is no version at all or any git tag.
Do you have in plan to release any version soon?
thanks
ps may I also suggest bats for the testing part?

Done! When the package exists, could you please send a PR to our README.md to mention it as an installation method?
And: thanks for the testing pointer!

Great!
done: https://github.com/binpash/try/pull/64
however I did not included the man page because pandoc will require too many packages as dependecies only for the build part of the package.
Could you consider to create the man page as part of the ci and store it in the repo? I can create a PR with a GH action for that if you want
Also if you need help with bats let me know :)

Is it easier for you if the manpage is stored as a GH action artifact or actually in the repo?
(I was planning on copying the prerelease logic from ffs and folding in the manpage generation there.)

Is it easier for you if the manpage is stored as a GH action artifact or actually in the repo?

It's the same, as artifact is good :)

(I was planning on copying the prerelease logic from ffs and folding in the manpage generation there.)

omg I love ffs now

(NB I have not forgotten this, but it likely won't happen until the weekend.)

Just kidding, found time this morning. @brokenpip3, please let me know if you want anything else: I'm happy to include the bash completions in the artifact/pre-release; I'm also happy to bump to v0.1.1 if you want a clean release with the right stuff in it.

hei @mgree it's the same for me, I can include temporary the man page from the latest version or from a new tag, I let you decide :)

Okay---let's do the temporary one from the prerelease/artifact for now. We'll cut a new release when a few of the more interesting WIP PRs land.

Fyi the latest version of the package contains the man page but it's taken from the latest one you created last time because the 0.2 tag does not contain the man page as asset: https://github.com/binpash/try/releases/tag/v0.2.0

Noted, thank you! I'll be sure to include versioned manpages in the next release.

repo: binpash/try


text:
each.attr.href issue

let`s say  I can get  a html just like from http://xxxxxxxxxxx?terms=A01&c=atc_number
xxxxxxxxxx
xxxxxxxxxx
xxxxxxxxxx

if I  want to escape scraping the original web and the parent one(http://xxxxxxxxxxx?terms=A&c=atc_number),how could I do this?

define "parent one"
write your rule down as script code

pls show me some pseudocode.
right now I just use a tricky way
    def third_category(self, response):
        for each in response.doc('a[href^="http://cheman.chemnet.com/atc/search.cgi?terms="]').items():
            if len(each.attr.href) < len(response.url):
                print "已经抓取过该页面"

            else:
                self.crawl(each.attr.href, callback=self.fourth_category)

define "parent one" first.

authors: binux wanghaisheng

repo: binux/pyspider


text:
Modifies panel styling to be responsive and more user friendly

Stylizes panels, adds responsive sizing, and makes graphs easier to interact with.

 Evo: Stylize config/status panel (add unsaved msg) and controls

 Evo: Responsive CSS

repo: bio-sims/evo


text:
ABC for scikit-bio classes

A user relies on a common, shared interface implemented in all scikit-bio classes to understand an object they've never seen before.
@wasade suggested in #465 that we add an abstract base class that all scikit-bio classes derive from. I think this is a fantastic idea as it would guarantee that all objects in skbio have a minimal, consistent API. If a user gets comfortable using object A, they'll likely find it easier to start using object B if there is a core set of methods that each object implements. As @ebolyen noted, this will also help with writing documentation (especially skbio intros/tutorials).
I think we should use the abc module for this, since it will force developers to override and implement all methods/properties defined in the ABC.
Here's a quick list that @ebolyen and I put together for ABC methods. Unless otherwise noted, these would only be interfaces (no implementation):

[ ] __eq__
[ ] __ne__
[ ] equals (see #465 for some discussion)
[ ] copy
[ ] __copy__ (implementation inheritance, calls copy)
[ ] __deepcopy__ (implementation inheritance, calls copy)
[ ] __repr__
[ ] __str__: #753
read (implementation inheritance)
write (implementation inheritance)
[ ] plot
[ ] IPython Notebook reprs (implementation inheritance)

What other methods/properties would be useful to have in the ABC?
Dependencies:

[ ] refactor TreeNode (#809)
[ ] refactor DistanceMatrix (#824)
[ ] refactor sequence objects (#826)
[ ] refactor alignment (#823)
[ ] refactor ordination (#825)

A .summary() method could be nice. This might be a little more in-depth than a __repr__() and will make more sense to a beginner than calling .__repr__() (not that we wouldn't have __repr__ also, but that could be reserved for situations like "%r some text" % object)

authors: ebolyen jairideout

repo: biocore/scikit-bio


text:
Within and between distance API methods for the DissimilarityMatrix object

This pull request adds in .within and .between methods to the DissimilarityMatrix object, and expressing the data as a pd.DataFrame. These methods provide a standard way for obtaining within and between group distances, a common operation for beta-diversity derived distance matrices.
Please complete the following checklist:

[x] I have read the guidelines in CONTRIBUTING.md.

[x] I have documented all public-facing changes in CHANGELOG.md.

[ ] This pull request includes code, documentation, or other content derived from external source(s). If this is the case, ensure the external source's license is compatible with scikit-bio's license. Include the license in the licenses directory and add a comment in the code giving proper attribution. Ensure any other requirements set forth by the license and/or author are satisfied. It is your responsibility to disclose code, documentation, or other content derived from external source(s). If you have questions about whether something can be included in the project or how to give proper attribution, include those questions in your pull request and a reviewer will assist you.

[x] This pull request does not include code, documentation, or other content derived from external source(s).

Note: REVIEWING.md may also be helpful to see some of the things code reviewers will be verifying when reviewing your pull request.

The test failures appear unrelated to this PR with the exception of a Sphinx warning that I don't understand. I took a look back at the code for instances of "from" in the between method (using from_ in code, and nothing obvious stood out.

I think this is good to merge?

Sorry for the delay in responding. Everything looks good to merge (IMO, at least).

authors: fedarko wasade


text:
Pileup regression

commit 6fb9bfbbeb1f83c030b224dbd2146f4a482e41df (HEAD -> master)
Merge: d7c369d 51dfcec
Author: Agnieszka Szmurło amszmurlo@gmail.com
Date:   Fri Oct 22 14:41:25 2021 +0200
Merge pull request #89 from biodatageeks/feature/piluep-perf

Pileup cleanup

Time taken: 528142 ms
commit 1a7cdfef26ca8310818dc86432ca13ee64db9fce (HEAD -> master, origin/master, origin/HEAD)
Author: Agnieszka Szmurło amszmurlo@gmail.com
Date:   Tue Nov 9 13:09:49 2021 +0100
Feature/quals buffer (#95)

Time taken: 611228 ms

Fixed.

repo: biodatageeks/sequila


text:
fix(cli): ignore files and directories from working directory

Summary
Closes https://github.com/biomejs/biome/issues/1465
I nuked globset; it doesn't have what we need. Luckily, ignore::gitignore does what we need. It correctly resolves the globs based on a specified path, which is our working directory.
This means I had to pass the working directory to all the functions that create a new Matcher.
Also, I had to remove a check on directories during the traversal because it was preveniently blocking the traversal of said directories, causing false positives.
I took the chance to update the documentation page with a better explanation of how the globs work inside Biome.

Test Plan

I tested it on an actual project that specifies src/**/*.js as including globs.
I updated one of the tests with an incorrect assertion. Even globs that start with / e.g. /src/**/*.js are resolved from the working directory.

I tried to test this on a local project: it seems that .gitignore is no longer taken into account.

I compared Biome v1.4.1 with the current branch using a dedicated reproduction: branches main, variant1, \variant2, and variant3`.
Biome v1.4.1 has the correct behavior ignoring both the .gitignore and formatter.ignore.
The current branches doesn't fix the issue for me and no longer take the .gitignore into account.

This PR fixes cases where specifying a file in globs works. I checked the reproduction repository, and the main branch doesn't cover what's addressed here.

@Conaclos the latest commit should address your repository case

@Conaclos the latest commit should address your repository case

.gitignore is now taken int oaccount :)
However, it is still not working for formatter.ignore. Should I open another issue?

What's the expected behaviour? You could create an issue that explains what we should expect.
I'll use this PR to fix it

What's the expected behaviour?

The tests folder is listed in formatter.ignore in biome.json. Each branch uses a different syntax:

main: tests
variant1: ./tests
variant2: .tests/*
variant3: .tests/**/*

I expect that running biom format . results in ignoring the tests folder.

authors: Conaclos ematipico

repo: biomejs/biome